[1] "ofn"        "-oTSTAD-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/STAD-TP/22507291/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/22815770/transformed.cor.cli.txt"

nPatients in clinical file=443, in cluster file=393, common to both=393
[1] "Reduce the number of clustering variables from 1195 to 1193."
[1] 1193  393
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           188            205 
  TP53 MUTATED TP53 WILD-TYPE 
           188            205 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              99              294 
  ARID1A MUTATED ARID1A WILD-TYPE 
              99              294 
[1] "RNF43 MUTATION ANALYSIS"
[1] 3
  RNF43 MUTATED RNF43 WILD-TYPE 
             45             348 
  RNF43 MUTATED RNF43 WILD-TYPE 
             45             348 
[1] "XYLT2 MUTATION ANALYSIS"
[1] 3
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             38             355 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             38             355 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            37            356 
  KRAS MUTATED KRAS WILD-TYPE 
            37            356 
[1] "LARP4B MUTATION ANALYSIS"
[1] 3
  LARP4B MUTATED LARP4B WILD-TYPE 
              30              363 
  LARP4B MUTATED LARP4B WILD-TYPE 
              30              363 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
             28             365 
  HLA-B MUTATED HLA-B WILD-TYPE 
             28             365 
[1] "RHOA MUTATION ANALYSIS"
[1] 3
  RHOA MUTATED RHOA WILD-TYPE 
            19            374 
  RHOA MUTATED RHOA WILD-TYPE 
            19            374 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             28             365 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             28             365 
[1] "B2M MUTATION ANALYSIS"
[1] 3
  B2M MUTATED B2M WILD-TYPE 
           18           375 
  B2M MUTATED B2M WILD-TYPE 
           18           375 
[1] "C7ORF50 MUTATION ANALYSIS"
[1] 3
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
               12               381 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
               12               381 
[1] "MLL4 MUTATION ANALYSIS"
[1] 3
  MLL4 MUTATED MLL4 WILD-TYPE 
            45            348 
  MLL4 MUTATED MLL4 WILD-TYPE 
            45            348 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            30            363 
  PTEN MUTATED PTEN WILD-TYPE 
            30            363 
[1] "CDH1 MUTATION ANALYSIS"
[1] 3
  CDH1 MUTATED CDH1 WILD-TYPE 
            32            361 
  CDH1 MUTATED CDH1 WILD-TYPE 
            32            361 
[1] "GNG12 MUTATION ANALYSIS"
[1] 3
  GNG12 MUTATED GNG12 WILD-TYPE 
             12             381 
  GNG12 MUTATED GNG12 WILD-TYPE 
             12             381 
[1] "PGM5 MUTATION ANALYSIS"
[1] 3
  PGM5 MUTATED PGM5 WILD-TYPE 
            39            354 
  PGM5 MUTATED PGM5 WILD-TYPE 
            39            354 
[1] "CBWD1 MUTATION ANALYSIS"
[1] 3
  CBWD1 MUTATED CBWD1 WILD-TYPE 
             21             372 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
             21             372 
[1] "ZBTB20 MUTATION ANALYSIS"
[1] 3
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              37              356 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              37              356 
[1] "ARID4A MUTATION ANALYSIS"
[1] 3
  ARID4A MUTATED ARID4A WILD-TYPE 
              22              371 
  ARID4A MUTATED ARID4A WILD-TYPE 
              22              371 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            67            326 
  MLL2 MUTATED MLL2 WILD-TYPE 
            67            326 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             32             361 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             32             361 
[1] "MBD6 MUTATION ANALYSIS"
[1] 3
  MBD6 MUTATED MBD6 WILD-TYPE 
            24            369 
  MBD6 MUTATED MBD6 WILD-TYPE 
            24            369 
[1] "MUC6 MUTATION ANALYSIS"
[1] 3
  MUC6 MUTATED MUC6 WILD-TYPE 
            46            347 
  MUC6 MUTATED MUC6 WILD-TYPE 
            46            347 
[1] "DDX17 MUTATION ANALYSIS"
[1] 3
  DDX17 MUTATED DDX17 WILD-TYPE 
             15             378 
  DDX17 MUTATED DDX17 WILD-TYPE 
             15             378 
[1] "HOXD8 MUTATION ANALYSIS"
[1] 3
  HOXD8 MUTATED HOXD8 WILD-TYPE 
             13             380 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
             13             380 
[1] "ZBTB7C MUTATION ANALYSIS"
[1] 3
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              17              376 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              17              376 
[1] "KLF3 MUTATION ANALYSIS"
[1] 3
  KLF3 MUTATED KLF3 WILD-TYPE 
            19            374 
  KLF3 MUTATED KLF3 WILD-TYPE 
            19            374 
[1] "TENC1 MUTATION ANALYSIS"
[1] 3
  TENC1 MUTATED TENC1 WILD-TYPE 
             20             373 
  TENC1 MUTATED TENC1 WILD-TYPE 
             20             373 
[1] "MTG1 MUTATION ANALYSIS"
[1] 3
  MTG1 MUTATED MTG1 WILD-TYPE 
             9            384 
  MTG1 MUTATED MTG1 WILD-TYPE 
             9            384 
[1] "LARP7 MUTATION ANALYSIS"
[1] 3
  LARP7 MUTATED LARP7 WILD-TYPE 
             18             375 
  LARP7 MUTATED LARP7 WILD-TYPE 
             18             375 
[1] "MVK MUTATION ANALYSIS"
[1] 3
  MVK MUTATED MVK WILD-TYPE 
           15           378 
  MVK MUTATED MVK WILD-TYPE 
           15           378 
[1] "KIAA0406 MUTATION ANALYSIS"
[1] 3
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                23                370 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                23                370 
[1] "FRMD4A MUTATION ANALYSIS"
[1] 3
  FRMD4A MUTATED FRMD4A WILD-TYPE 
              21              372 
  FRMD4A MUTATED FRMD4A WILD-TYPE 
              21              372 
[1] "MCM8 MUTATION ANALYSIS"
[1] 3
  MCM8 MUTATED MCM8 WILD-TYPE 
            25            368 
  MCM8 MUTATED MCM8 WILD-TYPE 
            25            368 
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
           48           345 
  APC MUTATED APC WILD-TYPE 
           48           345 
[1] "TRIP4 MUTATION ANALYSIS"
[1] 3
  TRIP4 MUTATED TRIP4 WILD-TYPE 
             12             381 
  TRIP4 MUTATED TRIP4 WILD-TYPE 
             12             381 
[1] "CTNND1 MUTATION ANALYSIS"
[1] 3
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              24              369 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              24              369 
[1] "FAM9A MUTATION ANALYSIS"
[1] 3
  FAM9A MUTATED FAM9A WILD-TYPE 
             12             381 
  FAM9A MUTATED FAM9A WILD-TYPE 
             12             381 
[1] "SLC27A3 MUTATION ANALYSIS"
[1] 3
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                9               384 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                9               384 
[1] "PAX6 MUTATION ANALYSIS"
[1] 3
  PAX6 MUTATED PAX6 WILD-TYPE 
            20            373 
  PAX6 MUTATED PAX6 WILD-TYPE 
            20            373 
[1] "KRT75 MUTATION ANALYSIS"
[1] 3
  KRT75 MUTATED KRT75 WILD-TYPE 
             37             356 
  KRT75 MUTATED KRT75 WILD-TYPE 
             37             356 
[1] "P4HTM MUTATION ANALYSIS"
[1] 3
  P4HTM MUTATED P4HTM WILD-TYPE 
             26             367 
  P4HTM MUTATED P4HTM WILD-TYPE 
             26             367 
[1] "DSTN MUTATION ANALYSIS"
[1] 3
  DSTN MUTATED DSTN WILD-TYPE 
             7            386 
  DSTN MUTATED DSTN WILD-TYPE 
             7            386 
[1] "CIC MUTATION ANALYSIS"
[1] 3
  CIC MUTATED CIC WILD-TYPE 
           47           346 
  CIC MUTATED CIC WILD-TYPE 
           47           346 
[1] "OSBP2 MUTATION ANALYSIS"
[1] 3
  OSBP2 MUTATED OSBP2 WILD-TYPE 
             15             378 
  OSBP2 MUTATED OSBP2 WILD-TYPE 
             15             378 
[1] "CEP57 MUTATION ANALYSIS"
[1] 3
  CEP57 MUTATED CEP57 WILD-TYPE 
             13             380 
  CEP57 MUTATED CEP57 WILD-TYPE 
             13             380 
[1] "PRRG1 MUTATION ANALYSIS"
[1] 3
  PRRG1 MUTATED PRRG1 WILD-TYPE 
             10             383 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
             10             383 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
            28            365 
  BCOR MUTATED BCOR WILD-TYPE 
            28            365 
[1] "KIAA1967 MUTATION ANALYSIS"
[1] 3
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                22                371 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                22                371 
[1] "KIAA1267 MUTATION ANALYSIS"
[1] 3
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                19                374 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                19                374 
[1] "ZNF48 MUTATION ANALYSIS"
[1] 3
  ZNF48 MUTATED ZNF48 WILD-TYPE 
             13             380 
  ZNF48 MUTATED ZNF48 WILD-TYPE 
             13             380 
[1] "WASF3 MUTATION ANALYSIS"
[1] 3
  WASF3 MUTATED WASF3 WILD-TYPE 
             19             374 
  WASF3 MUTATED WASF3 WILD-TYPE 
             19             374 
[1] "NLK MUTATION ANALYSIS"
[1] 3
  NLK MUTATED NLK WILD-TYPE 
           14           379 
  NLK MUTATED NLK WILD-TYPE 
           14           379 
[1] "CYP27B1 MUTATION ANALYSIS"
[1] 3
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                9               384 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                9               384 
[1] "C14ORF43 MUTATION ANALYSIS"
[1] 3
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                26                367 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                26                367 
[1] "PRSS36 MUTATION ANALYSIS"
[1] 3
  PRSS36 MUTATED PRSS36 WILD-TYPE 
              16              377 
  PRSS36 MUTATED PRSS36 WILD-TYPE 
              16              377 
[1] "FZD3 MUTATION ANALYSIS"
[1] 3
  FZD3 MUTATED FZD3 WILD-TYPE 
            11            382 
  FZD3 MUTATED FZD3 WILD-TYPE 
            11            382 
[1] "NFASC MUTATION ANALYSIS"
[1] 3
  NFASC MUTATED NFASC WILD-TYPE 
             31             362 
  NFASC MUTATED NFASC WILD-TYPE 
             31             362 
[1] "GRK4 MUTATION ANALYSIS"
[1] 3
  GRK4 MUTATED GRK4 WILD-TYPE 
            11            382 
  GRK4 MUTATED GRK4 WILD-TYPE 
            11            382 
[1] "ATXN2L MUTATION ANALYSIS"
[1] 3
  ATXN2L MUTATED ATXN2L WILD-TYPE 
              23              370 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
              23              370 
[1] "GLI1 MUTATION ANALYSIS"
[1] 3
  GLI1 MUTATED GLI1 WILD-TYPE 
            20            373 
  GLI1 MUTATED GLI1 WILD-TYPE 
            20            373 
[1] "INPPL1 MUTATION ANALYSIS"
[1] 3
  INPPL1 MUTATED INPPL1 WILD-TYPE 
              24              369 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
              24              369 
[1] "SOX7 MUTATION ANALYSIS"
[1] 3
  SOX7 MUTATED SOX7 WILD-TYPE 
            19            374 
  SOX7 MUTATED SOX7 WILD-TYPE 
            19            374 
[1] "FHOD3 MUTATION ANALYSIS"
[1] 3
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             30             363 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             30             363 
[1] "RNF128 MUTATION ANALYSIS"
[1] 3
  RNF128 MUTATED RNF128 WILD-TYPE 
              14              379 
  RNF128 MUTATED RNF128 WILD-TYPE 
              14              379 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
             19             374 
  HLA-A MUTATED HLA-A WILD-TYPE 
             19             374 
[1] "MFRP MUTATION ANALYSIS"
[1] 3
  MFRP MUTATED MFRP WILD-TYPE 
            15            378 
  MFRP MUTATED MFRP WILD-TYPE 
            15            378 
[1] "EIF5B MUTATION ANALYSIS"
[1] 3
  EIF5B MUTATED EIF5B WILD-TYPE 
             25             368 
  EIF5B MUTATED EIF5B WILD-TYPE 
             25             368 
[1] "C9ORF131 MUTATION ANALYSIS"
[1] 3
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                19                374 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                19                374 
[1] "BCORL1 MUTATION ANALYSIS"
[1] 3
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              26              367 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              26              367 
[1] "PAFAH1B1 MUTATION ANALYSIS"
[1] 3
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
                15                378 
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
                15                378 
[1] "EPB49 MUTATION ANALYSIS"
[1] 3
  EPB49 MUTATED EPB49 WILD-TYPE 
             13             380 
  EPB49 MUTATED EPB49 WILD-TYPE 
             13             380 
[1] "DDC MUTATION ANALYSIS"
[1] 3
  DDC MUTATED DDC WILD-TYPE 
           10           383 
  DDC MUTATED DDC WILD-TYPE 
           10           383 
[1] "IWS1 MUTATION ANALYSIS"
[1] 3
  IWS1 MUTATED IWS1 WILD-TYPE 
            14            379 
  IWS1 MUTATED IWS1 WILD-TYPE 
            14            379 
[1] "LMAN1 MUTATION ANALYSIS"
[1] 3
  LMAN1 MUTATED LMAN1 WILD-TYPE 
             13             380 
  LMAN1 MUTATED LMAN1 WILD-TYPE 
             13             380 
[1] "FAM116A MUTATION ANALYSIS"
[1] 3
  FAM116A MUTATED FAM116A WILD-TYPE 
                9               384 
  FAM116A MUTATED FAM116A WILD-TYPE 
                9               384 
[1] "KIAA0664 MUTATION ANALYSIS"
[1] 3
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                23                370 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                23                370 
[1] "JARID2 MUTATION ANALYSIS"
[1] 3
  JARID2 MUTATED JARID2 WILD-TYPE 
              36              357 
  JARID2 MUTATED JARID2 WILD-TYPE 
              36              357 
[1] "SLC9A10 MUTATION ANALYSIS"
[1] 3
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               13               380 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               13               380 
[1] "ZFP36L2 MUTATION ANALYSIS"
[1] 3
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               14               379 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               14               379 
[1] "CTCF MUTATION ANALYSIS"
[1] 3
  CTCF MUTATED CTCF WILD-TYPE 
            16            377 
  CTCF MUTATED CTCF WILD-TYPE 
            16            377 
[1] "HDAC4 MUTATION ANALYSIS"
[1] 3
  HDAC4 MUTATED HDAC4 WILD-TYPE 
             26             367 
  HDAC4 MUTATED HDAC4 WILD-TYPE 
             26             367 
[1] "NAPEPLD MUTATION ANALYSIS"
[1] 3
  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
               10               383 
  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
               10               383 
[1] "RASA1 MUTATION ANALYSIS"
[1] 3
  RASA1 MUTATED RASA1 WILD-TYPE 
             19             374 
  RASA1 MUTATED RASA1 WILD-TYPE 
             19             374 
[1] "RHOQ MUTATION ANALYSIS"
[1] 3
  RHOQ MUTATED RHOQ WILD-TYPE 
             5            388 
  RHOQ MUTATED RHOQ WILD-TYPE 
             5            388 
[1] "NT5M MUTATION ANALYSIS"
[1] 3
  NT5M MUTATED NT5M WILD-TYPE 
             6            387 
  NT5M MUTATED NT5M WILD-TYPE 
             6            387 
[1] "CELSR1 MUTATION ANALYSIS"
[1] 3
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              37              356 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              37              356 
[1] "YIPF2 MUTATION ANALYSIS"
[1] 3
  YIPF2 MUTATED YIPF2 WILD-TYPE 
              7             386 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
              7             386 
[1] "CR1 MUTATION ANALYSIS"
[1] 3
  CR1 MUTATED CR1 WILD-TYPE 
           30           363 
  CR1 MUTATED CR1 WILD-TYPE 
           30           363 
[1] "C19ORF40 MUTATION ANALYSIS"
[1] 3
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
                 7                386 
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
                 7                386 
[1] "WNT1 MUTATION ANALYSIS"
[1] 3
  WNT1 MUTATED WNT1 WILD-TYPE 
            10            383 
  WNT1 MUTATED WNT1 WILD-TYPE 
            10            383 
[1] "IRF2 MUTATION ANALYSIS"
[1] 3
  IRF2 MUTATED IRF2 WILD-TYPE 
            19            374 
  IRF2 MUTATED IRF2 WILD-TYPE 
            19            374 
[1] "CR2 MUTATION ANALYSIS"
[1] 3
  CR2 MUTATED CR2 WILD-TYPE 
           23           370 
  CR2 MUTATED CR2 WILD-TYPE 
           23           370 
[1] "LEMD1 MUTATION ANALYSIS"
[1] 3
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              4             389 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              4             389 
[1] "INF2 MUTATION ANALYSIS"
[1] 3
  INF2 MUTATED INF2 WILD-TYPE 
            19            374 
  INF2 MUTATED INF2 WILD-TYPE 
            19            374 
[1] "CR1L MUTATION ANALYSIS"
[1] 3
  CR1L MUTATED CR1L WILD-TYPE 
            16            377 
  CR1L MUTATED CR1L WILD-TYPE 
            16            377 
[1] "NPHP1 MUTATION ANALYSIS"
[1] 3
  NPHP1 MUTATED NPHP1 WILD-TYPE 
             10             383 
  NPHP1 MUTATED NPHP1 WILD-TYPE 
             10             383 
[1] "ADAMDEC1 MUTATION ANALYSIS"
[1] 3
  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
                12                381 
  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
                12                381 
[1] "GXYLT1 MUTATION ANALYSIS"
[1] 3
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
              14              379 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
              14              379 
[1] "ENTPD2 MUTATION ANALYSIS"
[1] 3
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               6              387 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               6              387 
[1] "EIF4G3 MUTATION ANALYSIS"
[1] 3
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
              20              373 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
              20              373 
[1] "PIGT MUTATION ANALYSIS"
[1] 3
  PIGT MUTATED PIGT WILD-TYPE 
            11            382 
  PIGT MUTATED PIGT WILD-TYPE 
            11            382 
[1] "POLM MUTATION ANALYSIS"
[1] 3
  POLM MUTATED POLM WILD-TYPE 
            13            380 
  POLM MUTATED POLM WILD-TYPE 
            13            380 
[1] "CCDC108 MUTATION ANALYSIS"
[1] 3
  CCDC108 MUTATED CCDC108 WILD-TYPE 
               26               367 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
               26               367 
[1] "KIAA0195 MUTATION ANALYSIS"
[1] 3
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                20                373 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                20                373 
[1] "CDH16 MUTATION ANALYSIS"
[1] 3
  CDH16 MUTATED CDH16 WILD-TYPE 
             16             377 
  CDH16 MUTATED CDH16 WILD-TYPE 
             16             377 
[1] "ARHGAP5 MUTATION ANALYSIS"
[1] 3
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               22               371 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               22               371 
[1] "STK38 MUTATION ANALYSIS"
[1] 3
  STK38 MUTATED STK38 WILD-TYPE 
              6             387 
  STK38 MUTATED STK38 WILD-TYPE 
              6             387 
[1] "CST1 MUTATION ANALYSIS"
[1] 3
  CST1 MUTATED CST1 WILD-TYPE 
             7            386 
  CST1 MUTATED CST1 WILD-TYPE 
             7            386 
[1] "PTCHD3 MUTATION ANALYSIS"
[1] 3
  PTCHD3 MUTATED PTCHD3 WILD-TYPE 
              19              374 
  PTCHD3 MUTATED PTCHD3 WILD-TYPE 
              19              374 
[1] "TBX4 MUTATION ANALYSIS"
[1] 3
  TBX4 MUTATED TBX4 WILD-TYPE 
            14            379 
  TBX4 MUTATED TBX4 WILD-TYPE 
            14            379 
[1] "ZMYM4 MUTATION ANALYSIS"
[1] 3
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
             19             374 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
             19             374 
[1] "SPTY2D1 MUTATION ANALYSIS"
[1] 3
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
               19               374 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
               19               374 
[1] "SLC12A9 MUTATION ANALYSIS"
[1] 3
  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
               20               373 
  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
               20               373 
[1] "ALPK2 MUTATION ANALYSIS"
[1] 3
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             24             369 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             24             369 
[1] "CABP5 MUTATION ANALYSIS"
[1] 3
  CABP5 MUTATED CABP5 WILD-TYPE 
              6             387 
  CABP5 MUTATED CABP5 WILD-TYPE 
              6             387 
[1] "MED15 MUTATION ANALYSIS"
[1] 3
  MED15 MUTATED MED15 WILD-TYPE 
             18             375 
  MED15 MUTATED MED15 WILD-TYPE 
             18             375 
[1] "GYLTL1B MUTATION ANALYSIS"
[1] 3
  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
               17               376 
  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
               17               376 
[1] "IL2RG MUTATION ANALYSIS"
[1] 3
  IL2RG MUTATED IL2RG WILD-TYPE 
             10             383 
  IL2RG MUTATED IL2RG WILD-TYPE 
             10             383 
[1] "CCDC88A MUTATION ANALYSIS"
[1] 3
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               22               371 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               22               371 
[1] "PIGB MUTATION ANALYSIS"
[1] 3
  PIGB MUTATED PIGB WILD-TYPE 
            10            383 
  PIGB MUTATED PIGB WILD-TYPE 
            10            383 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              65              328 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              65              328 
[1] "PPIG MUTATION ANALYSIS"
[1] 3
  PPIG MUTATED PPIG WILD-TYPE 
            18            375 
  PPIG MUTATED PPIG WILD-TYPE 
            18            375 
[1] "ATP6V1B1 MUTATION ANALYSIS"
[1] 3
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                21                372 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                21                372 
[1] "PLEKHA6 MUTATION ANALYSIS"
[1] 3
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               23               370 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               23               370 
[1] "PLA2G1B MUTATION ANALYSIS"
[1] 3
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
                6               387 
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
                6               387 
[1] "RTKN2 MUTATION ANALYSIS"
[1] 3
  RTKN2 MUTATED RTKN2 WILD-TYPE 
             11             382 
  RTKN2 MUTATED RTKN2 WILD-TYPE 
             11             382 
[1] "PAX2 MUTATION ANALYSIS"
[1] 3
  PAX2 MUTATED PAX2 WILD-TYPE 
            12            381 
  PAX2 MUTATED PAX2 WILD-TYPE 
            12            381 
[1] "SERPINI1 MUTATION ANALYSIS"
[1] 3
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
                 9                384 
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
                 9                384 
[1] "TMEM41A MUTATION ANALYSIS"
[1] 3
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                9               384 
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                9               384 
[1] "ADAM30 MUTATION ANALYSIS"
[1] 3
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              16              377 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              16              377 
[1] "B3GNT5 MUTATION ANALYSIS"
[1] 3
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
              11              382 
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
              11              382 
[1] "PAPD4 MUTATION ANALYSIS"
[1] 3
  PAPD4 MUTATED PAPD4 WILD-TYPE 
             11             382 
  PAPD4 MUTATED PAPD4 WILD-TYPE 
             11             382 
[1] "DTX3 MUTATION ANALYSIS"
[1] 3
  DTX3 MUTATED DTX3 WILD-TYPE 
             7            386 
  DTX3 MUTATED DTX3 WILD-TYPE 
             7            386 
[1] "BTBD11 MUTATION ANALYSIS"
[1] 3
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              26              367 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              26              367 
[1] "ART1 MUTATION ANALYSIS"
[1] 3
  ART1 MUTATED ART1 WILD-TYPE 
             8            385 
  ART1 MUTATED ART1 WILD-TYPE 
             8            385 
[1] "BRD8 MUTATION ANALYSIS"
[1] 3
  BRD8 MUTATED BRD8 WILD-TYPE 
            32            361 
  BRD8 MUTATED BRD8 WILD-TYPE 
            32            361 
[1] "FOXN3 MUTATION ANALYSIS"
[1] 3
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             13             380 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             13             380 
[1] "SPG20 MUTATION ANALYSIS"
[1] 3
  SPG20 MUTATED SPG20 WILD-TYPE 
             22             371 
  SPG20 MUTATED SPG20 WILD-TYPE 
             22             371 
[1] "WNK4 MUTATION ANALYSIS"
[1] 3
  WNK4 MUTATED WNK4 WILD-TYPE 
            24            369 
  WNK4 MUTATED WNK4 WILD-TYPE 
            24            369 
[1] "CBLL1 MUTATION ANALYSIS"
[1] 3
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              8             385 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              8             385 
[1] "TTF1 MUTATION ANALYSIS"
[1] 3
  TTF1 MUTATED TTF1 WILD-TYPE 
            16            377 
  TTF1 MUTATED TTF1 WILD-TYPE 
            16            377 
[1] "SCLT1 MUTATION ANALYSIS"
[1] 3
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             17             376 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             17             376 
[1] "PALB2 MUTATION ANALYSIS"
[1] 3
  PALB2 MUTATED PALB2 WILD-TYPE 
             11             382 
  PALB2 MUTATED PALB2 WILD-TYPE 
             11             382 
[1] "ABCC4 MUTATION ANALYSIS"
[1] 3
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             19             374 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             19             374 
[1] "EAF2 MUTATION ANALYSIS"
[1] 3
  EAF2 MUTATED EAF2 WILD-TYPE 
             9            384 
  EAF2 MUTATED EAF2 WILD-TYPE 
             9            384 
[1] "FAAH MUTATION ANALYSIS"
[1] 3
  FAAH MUTATED FAAH WILD-TYPE 
             5            388 
  FAAH MUTATED FAAH WILD-TYPE 
             5            388 
[1] "BTBD7 MUTATION ANALYSIS"
[1] 3
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             20             373 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             20             373 
[1] "MAGEE2 MUTATION ANALYSIS"
[1] 3
  MAGEE2 MUTATED MAGEE2 WILD-TYPE 
              11              382 
  MAGEE2 MUTATED MAGEE2 WILD-TYPE 
              11              382 
[1] "DOCK5 MUTATION ANALYSIS"
[1] 3
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             25             368 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             25             368 
[1] "ZFHX4 MUTATION ANALYSIS"
[1] 3
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
             68             325 
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
             68             325 
[1] "FHDC1 MUTATION ANALYSIS"
[1] 3
  FHDC1 MUTATED FHDC1 WILD-TYPE 
             17             376 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
             17             376 
[1] "RB1CC1 MUTATION ANALYSIS"
[1] 3
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
              15              378 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
              15              378 
[1] "PRRG3 MUTATION ANALYSIS"
[1] 3
  PRRG3 MUTATED PRRG3 WILD-TYPE 
              8             385 
  PRRG3 MUTATED PRRG3 WILD-TYPE 
              8             385 
[1] "KIAA1462 MUTATION ANALYSIS"
[1] 3
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
                24                369 
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
                24                369 
[1] "KCNJ10 MUTATION ANALYSIS"
[1] 3
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
              14              379 
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
              14              379 
[1] "GANAB MUTATION ANALYSIS"
[1] 3
  GANAB MUTATED GANAB WILD-TYPE 
             18             375 
  GANAB MUTATED GANAB WILD-TYPE 
             18             375 
[1] "GPSM3 MUTATION ANALYSIS"
[1] 3
  GPSM3 MUTATED GPSM3 WILD-TYPE 
             12             381 
  GPSM3 MUTATED GPSM3 WILD-TYPE 
             12             381 
[1] "WNT16 MUTATION ANALYSIS"
[1] 3
  WNT16 MUTATED WNT16 WILD-TYPE 
             12             381 
  WNT16 MUTATED WNT16 WILD-TYPE 
             12             381 
[1] "KIRREL MUTATION ANALYSIS"
[1] 3
  KIRREL MUTATED KIRREL WILD-TYPE 
              20              373 
  KIRREL MUTATED KIRREL WILD-TYPE 
              20              373 
[1] "MTMR9 MUTATION ANALYSIS"
[1] 3
  MTMR9 MUTATED MTMR9 WILD-TYPE 
             13             380 
  MTMR9 MUTATED MTMR9 WILD-TYPE 
             13             380 
[1] "FAHD2B MUTATION ANALYSIS"
[1] 3
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               9              384 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               9              384 
[1] "KLRK1 MUTATION ANALYSIS"
[1] 3
  KLRK1 MUTATED KLRK1 WILD-TYPE 
              5             388 
  KLRK1 MUTATED KLRK1 WILD-TYPE 
              5             388 
[1] "KLC2 MUTATION ANALYSIS"
[1] 3
  KLC2 MUTATED KLC2 WILD-TYPE 
            14            379 
  KLC2 MUTATED KLC2 WILD-TYPE 
            14            379 
[1] "WDR7 MUTATION ANALYSIS"
[1] 3
  WDR7 MUTATED WDR7 WILD-TYPE 
            22            371 
  WDR7 MUTATED WDR7 WILD-TYPE 
            22            371 
[1] "TCHP MUTATION ANALYSIS"
[1] 3
  TCHP MUTATED TCHP WILD-TYPE 
            12            381 
  TCHP MUTATED TCHP WILD-TYPE 
            12            381 
[1] "SNRK MUTATION ANALYSIS"
[1] 3
  SNRK MUTATED SNRK WILD-TYPE 
            16            377 
  SNRK MUTATED SNRK WILD-TYPE 
            16            377 
[1] "SNAPC1 MUTATION ANALYSIS"
[1] 3
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               8              385 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               8              385 
[1] "ALG10 MUTATION ANALYSIS"
[1] 3
  ALG10 MUTATED ALG10 WILD-TYPE 
             14             379 
  ALG10 MUTATED ALG10 WILD-TYPE 
             14             379 
[1] "HDLBP MUTATION ANALYSIS"
[1] 3
  HDLBP MUTATED HDLBP WILD-TYPE 
             31             362 
  HDLBP MUTATED HDLBP WILD-TYPE 
             31             362 
[1] "GRINA MUTATION ANALYSIS"
[1] 3
  GRINA MUTATED GRINA WILD-TYPE 
              9             384 
  GRINA MUTATED GRINA WILD-TYPE 
              9             384 
[1] "RAB42 MUTATION ANALYSIS"
[1] 3
  RAB42 MUTATED RAB42 WILD-TYPE 
              5             388 
  RAB42 MUTATED RAB42 WILD-TYPE 
              5             388 
[1] "SAMD9L MUTATION ANALYSIS"
[1] 3
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              22              371 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              22              371 
[1] "GLT6D1 MUTATION ANALYSIS"
[1] 3
  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
              14              379 
  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
              14              379 
[1] "SLC22A6 MUTATION ANALYSIS"
[1] 3
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
               14               379 
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
               14               379 
[1] "SVIL MUTATION ANALYSIS"
[1] 3
  SVIL MUTATED SVIL WILD-TYPE 
            30            363 
  SVIL MUTATED SVIL WILD-TYPE 
            30            363 
[1] "CCDC148 MUTATION ANALYSIS"
[1] 3
  CCDC148 MUTATED CCDC148 WILD-TYPE 
                8               385 
  CCDC148 MUTATED CCDC148 WILD-TYPE 
                8               385 
[1] "MOBKL1A MUTATION ANALYSIS"
[1] 3
  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
                6               387 
  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
                6               387 
[1] "SETDB2 MUTATION ANALYSIS"
[1] 3
  SETDB2 MUTATED SETDB2 WILD-TYPE 
              12              381 
  SETDB2 MUTATED SETDB2 WILD-TYPE 
              12              381 
[1] "ZNF43 MUTATION ANALYSIS"
[1] 3
  ZNF43 MUTATED ZNF43 WILD-TYPE 
             25             368 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
             25             368 
[1] "NOX5 MUTATION ANALYSIS"
[1] 3
  NOX5 MUTATED NOX5 WILD-TYPE 
            17            376 
  NOX5 MUTATED NOX5 WILD-TYPE 
            17            376 
[1] "ANKRD34A MUTATION ANALYSIS"
[1] 3
  ANKRD34A MUTATED ANKRD34A WILD-TYPE 
                11                382 
  ANKRD34A MUTATED ANKRD34A WILD-TYPE 
                11                382 
[1] "PHACTR4 MUTATION ANALYSIS"
[1] 3
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
               10               383 
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
               10               383 
[1] "RAD50 MUTATION ANALYSIS"
[1] 3
  RAD50 MUTATED RAD50 WILD-TYPE 
             12             381 
  RAD50 MUTATED RAD50 WILD-TYPE 
             12             381 
[1] "JAK1 MUTATION ANALYSIS"
[1] 3
  JAK1 MUTATED JAK1 WILD-TYPE 
            17            376 
  JAK1 MUTATED JAK1 WILD-TYPE 
            17            376 
[1] "FAM155B MUTATION ANALYSIS"
[1] 3
  FAM155B MUTATED FAM155B WILD-TYPE 
               13               380 
  FAM155B MUTATED FAM155B WILD-TYPE 
               13               380 
[1] "DIDO1 MUTATION ANALYSIS"
[1] 3
  DIDO1 MUTATED DIDO1 WILD-TYPE 
             38             355 
  DIDO1 MUTATED DIDO1 WILD-TYPE 
             38             355 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             18             375 
  CASP8 MUTATED CASP8 WILD-TYPE 
             18             375 
[1] "NWD1 MUTATION ANALYSIS"
[1] 3
  NWD1 MUTATED NWD1 WILD-TYPE 
            32            361 
  NWD1 MUTATED NWD1 WILD-TYPE 
            32            361 
[1] "RBM6 MUTATION ANALYSIS"
[1] 3
  RBM6 MUTATED RBM6 WILD-TYPE 
            23            370 
  RBM6 MUTATED RBM6 WILD-TYPE 
            23            370 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             26             367 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             26             367 
[1] "TOP2A MUTATION ANALYSIS"
[1] 3
  TOP2A MUTATED TOP2A WILD-TYPE 
             14             379 
  TOP2A MUTATED TOP2A WILD-TYPE 
             14             379 
[1] "KIF21A MUTATION ANALYSIS"
[1] 3
  KIF21A MUTATED KIF21A WILD-TYPE 
              18              375 
  KIF21A MUTATED KIF21A WILD-TYPE 
              18              375 
[1] "LTBP3 MUTATION ANALYSIS"
[1] 3
  LTBP3 MUTATED LTBP3 WILD-TYPE 
             17             376 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
             17             376 
[1] "ZC3H4 MUTATION ANALYSIS"
[1] 3
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
             20             373 
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
             20             373 
[1] "TATDN1 MUTATION ANALYSIS"
[1] 3
  TATDN1 MUTATED TATDN1 WILD-TYPE 
               6              387 
  TATDN1 MUTATED TATDN1 WILD-TYPE 
               6              387 
[1] "PPIP5K2 MUTATION ANALYSIS"
[1] 3
  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE 
               14               379 
  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE 
               14               379 
[1] "C5ORF42 MUTATION ANALYSIS"
[1] 3
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               31               362 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               31               362 
[1] "C13ORF33 MUTATION ANALYSIS"
[1] 3
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 7                386 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 7                386 
[1] "COIL MUTATION ANALYSIS"
[1] 3
  COIL MUTATED COIL WILD-TYPE 
            10            383 
  COIL MUTATED COIL WILD-TYPE 
            10            383 
[1] "TP53BP2 MUTATION ANALYSIS"
[1] 3
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
               14               379 
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
               14               379 
[1] "TGFBR2 MUTATION ANALYSIS"
[1] 3
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              16              377 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              16              377 
[1] "FBXO21 MUTATION ANALYSIS"
[1] 3
  FBXO21 MUTATED FBXO21 WILD-TYPE 
              15              378 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
              15              378 
[1] "CASP7 MUTATION ANALYSIS"
[1] 3
  CASP7 MUTATED CASP7 WILD-TYPE 
              4             389 
  CASP7 MUTATED CASP7 WILD-TYPE 
              4             389 
[1] "TMEM41B MUTATION ANALYSIS"
[1] 3
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                5               388 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                5               388 
[1] "ORC3L MUTATION ANALYSIS"
[1] 3
  ORC3L MUTATED ORC3L WILD-TYPE 
             12             381 
  ORC3L MUTATED ORC3L WILD-TYPE 
             12             381 
[1] "CBWD6 MUTATION ANALYSIS"
[1] 3
  CBWD6 MUTATED CBWD6 WILD-TYPE 
              7             386 
  CBWD6 MUTATED CBWD6 WILD-TYPE 
              7             386 
[1] "PRKAB1 MUTATION ANALYSIS"
[1] 3
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
              10              383 
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
              10              383 
[1] "RABGAP1 MUTATION ANALYSIS"
[1] 3
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
               22               371 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
               22               371 
[1] "SRCIN1 MUTATION ANALYSIS"
[1] 3
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
              14              379 
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
              14              379 
[1] "NIN MUTATION ANALYSIS"
[1] 3
  NIN MUTATED NIN WILD-TYPE 
           23           370 
  NIN MUTATED NIN WILD-TYPE 
           23           370 
[1] "PET112L MUTATION ANALYSIS"
[1] 3
  PET112L MUTATED PET112L WILD-TYPE 
                8               385 
  PET112L MUTATED PET112L WILD-TYPE 
                8               385 
[1] "ZKSCAN5 MUTATION ANALYSIS"
[1] 3
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
               11               382 
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
               11               382 
[1] "CTSC MUTATION ANALYSIS"
[1] 3
  CTSC MUTATED CTSC WILD-TYPE 
            11            382 
  CTSC MUTATED CTSC WILD-TYPE 
            11            382 
[1] "AQP8 MUTATION ANALYSIS"
[1] 3
  AQP8 MUTATED AQP8 WILD-TYPE 
            13            380 
  AQP8 MUTATED AQP8 WILD-TYPE 
            13            380 
[1] "KANK4 MUTATION ANALYSIS"
[1] 3
  KANK4 MUTATED KANK4 WILD-TYPE 
             15             378 
  KANK4 MUTATED KANK4 WILD-TYPE 
             15             378 
[1] "ACVR1B MUTATION ANALYSIS"
[1] 3
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              13              380 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              13              380 
[1] "STAT6 MUTATION ANALYSIS"
[1] 3
  STAT6 MUTATED STAT6 WILD-TYPE 
              6             387 
  STAT6 MUTATED STAT6 WILD-TYPE 
              6             387 
[1] "PUS7L MUTATION ANALYSIS"
[1] 3
  PUS7L MUTATED PUS7L WILD-TYPE 
              9             384 
  PUS7L MUTATED PUS7L WILD-TYPE 
              9             384 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
             29             364 
  ARID2 MUTATED ARID2 WILD-TYPE 
             29             364 
[1] "ZMYM3 MUTATION ANALYSIS"
[1] 3
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
             15             378 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
             15             378 
[1] "EOMES MUTATION ANALYSIS"
[1] 3
  EOMES MUTATED EOMES WILD-TYPE 
              9             384 
  EOMES MUTATED EOMES WILD-TYPE 
              9             384 
[1] "BPTF MUTATION ANALYSIS"
[1] 3
  BPTF MUTATED BPTF WILD-TYPE 
            30            363 
  BPTF MUTATED BPTF WILD-TYPE 
            30            363 
[1] "MTIF2 MUTATION ANALYSIS"
[1] 3
  MTIF2 MUTATED MTIF2 WILD-TYPE 
             18             375 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
             18             375 
[1] "ARHGAP18 MUTATION ANALYSIS"
[1] 3
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                 9                384 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                 9                384 
[1] "EFNB3 MUTATION ANALYSIS"
[1] 3
  EFNB3 MUTATED EFNB3 WILD-TYPE 
             13             380 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
             13             380 
[1] "NDST2 MUTATION ANALYSIS"
[1] 3
  NDST2 MUTATED NDST2 WILD-TYPE 
             11             382 
  NDST2 MUTATED NDST2 WILD-TYPE 
             11             382 
[1] "MICALCL MUTATION ANALYSIS"
[1] 3
  MICALCL MUTATED MICALCL WILD-TYPE 
               15               378 
  MICALCL MUTATED MICALCL WILD-TYPE 
               15               378 
[1] "MMP3 MUTATION ANALYSIS"
[1] 3
  MMP3 MUTATED MMP3 WILD-TYPE 
            12            381 
  MMP3 MUTATED MMP3 WILD-TYPE 
            12            381 
[1] "OPTN MUTATION ANALYSIS"
[1] 3
  OPTN MUTATED OPTN WILD-TYPE 
            12            381 
  OPTN MUTATED OPTN WILD-TYPE 
            12            381 
[1] "ZFHX3 MUTATION ANALYSIS"
[1] 3
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             38             355 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             38             355 
[1] "ACP1 MUTATION ANALYSIS"
[1] 3
  ACP1 MUTATED ACP1 WILD-TYPE 
             9            384 
  ACP1 MUTATED ACP1 WILD-TYPE 
             9            384 
[1] "YY1 MUTATION ANALYSIS"
[1] 3
  YY1 MUTATED YY1 WILD-TYPE 
            8           385 
  YY1 MUTATED YY1 WILD-TYPE 
            8           385 
[1] "CUL2 MUTATION ANALYSIS"
[1] 3
  CUL2 MUTATED CUL2 WILD-TYPE 
             9            384 
  CUL2 MUTATED CUL2 WILD-TYPE 
             9            384 
[1] "DAO MUTATION ANALYSIS"
[1] 3
  DAO MUTATED DAO WILD-TYPE 
           14           379 
  DAO MUTATED DAO WILD-TYPE 
           14           379 
[1] "TRUB1 MUTATION ANALYSIS"
[1] 3
  TRUB1 MUTATED TRUB1 WILD-TYPE 
             11             382 
  TRUB1 MUTATED TRUB1 WILD-TYPE 
             11             382 
[1] "PKN2 MUTATION ANALYSIS"
[1] 3
  PKN2 MUTATED PKN2 WILD-TYPE 
            16            377 
  PKN2 MUTATED PKN2 WILD-TYPE 
            16            377 
[1] "KLHDC5 MUTATION ANALYSIS"
[1] 3
  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
              10              383 
  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
              10              383 
[1] "TFE3 MUTATION ANALYSIS"
[1] 3
  TFE3 MUTATED TFE3 WILD-TYPE 
             9            384 
  TFE3 MUTATED TFE3 WILD-TYPE 
             9            384 
[1] "GCC2 MUTATION ANALYSIS"
[1] 3
  GCC2 MUTATED GCC2 WILD-TYPE 
            14            379 
  GCC2 MUTATED GCC2 WILD-TYPE 
            14            379 
[1] "ARAF MUTATION ANALYSIS"
[1] 3
  ARAF MUTATED ARAF WILD-TYPE 
            12            381 
  ARAF MUTATED ARAF WILD-TYPE 
            12            381 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              16              377 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              16              377 
[1] "MDM2 MUTATION ANALYSIS"
[1] 3
  MDM2 MUTATED MDM2 WILD-TYPE 
             7            386 
  MDM2 MUTATED MDM2 WILD-TYPE 
             7            386 
[1] "C4ORF6 MUTATION ANALYSIS"
[1] 3
  C4ORF6 MUTATED C4ORF6 WILD-TYPE 
              12              381 
  C4ORF6 MUTATED C4ORF6 WILD-TYPE 
              12              381 
[1] "CASC3 MUTATION ANALYSIS"
[1] 3
  CASC3 MUTATED CASC3 WILD-TYPE 
             11             382 
  CASC3 MUTATED CASC3 WILD-TYPE 
             11             382 
[1] "CCDC153 MUTATION ANALYSIS"
[1] 3
  CCDC153 MUTATED CCDC153 WILD-TYPE 
                7               386 
  CCDC153 MUTATED CCDC153 WILD-TYPE 
                7               386 
[1] "SF3B3 MUTATION ANALYSIS"
[1] 3
  SF3B3 MUTATED SF3B3 WILD-TYPE 
             20             373 
  SF3B3 MUTATED SF3B3 WILD-TYPE 
             20             373 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
            52            341 
  MLL3 MUTATED MLL3 WILD-TYPE 
            52            341 
[1] "CA2 MUTATION ANALYSIS"
[1] 3
  CA2 MUTATED CA2 WILD-TYPE 
            7           386 
  CA2 MUTATED CA2 WILD-TYPE 
            7           386 
[1] "CNBD1 MUTATION ANALYSIS"
[1] 3
  CNBD1 MUTATED CNBD1 WILD-TYPE 
             18             375 
  CNBD1 MUTATED CNBD1 WILD-TYPE 
             18             375 
[1] "DNAH7 MUTATION ANALYSIS"
[1] 3
  DNAH7 MUTATED DNAH7 WILD-TYPE 
             52             341 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
             52             341 
[1] "ASB11 MUTATION ANALYSIS"
[1] 3
  ASB11 MUTATED ASB11 WILD-TYPE 
             10             383 
  ASB11 MUTATED ASB11 WILD-TYPE 
             10             383 
[1] "CDC14A MUTATION ANALYSIS"
[1] 3
  CDC14A MUTATED CDC14A WILD-TYPE 
              15              378 
  CDC14A MUTATED CDC14A WILD-TYPE 
              15              378 
[1] "NHLRC1 MUTATION ANALYSIS"
[1] 3
  NHLRC1 MUTATED NHLRC1 WILD-TYPE 
              12              381 
  NHLRC1 MUTATED NHLRC1 WILD-TYPE 
              12              381 
[1] "ZC3H18 MUTATION ANALYSIS"
[1] 3
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
              20              373 
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
              20              373 
[1] "RGS9BP MUTATION ANALYSIS"
[1] 3
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               8              385 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               8              385 
[1] "GLYR1 MUTATION ANALYSIS"
[1] 3
  GLYR1 MUTATED GLYR1 WILD-TYPE 
             15             378 
  GLYR1 MUTATED GLYR1 WILD-TYPE 
             15             378 
[1] "FILIP1L MUTATION ANALYSIS"
[1] 3
  FILIP1L MUTATED FILIP1L WILD-TYPE 
               21               372 
  FILIP1L MUTATED FILIP1L WILD-TYPE 
               21               372 
[1] "USP26 MUTATION ANALYSIS"
[1] 3
  USP26 MUTATED USP26 WILD-TYPE 
             22             371 
  USP26 MUTATED USP26 WILD-TYPE 
             22             371 
[1] "VPS13B MUTATION ANALYSIS"
[1] 3
  VPS13B MUTATED VPS13B WILD-TYPE 
              49              344 
  VPS13B MUTATED VPS13B WILD-TYPE 
              49              344 
[1] "RCOR3 MUTATION ANALYSIS"
[1] 3
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             14             379 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             14             379 
[1] "CASD1 MUTATION ANALYSIS"
[1] 3
  CASD1 MUTATED CASD1 WILD-TYPE 
             12             381 
  CASD1 MUTATED CASD1 WILD-TYPE 
             12             381 
[1] "CDC25C MUTATION ANALYSIS"
[1] 3
  CDC25C MUTATED CDC25C WILD-TYPE 
              11              382 
  CDC25C MUTATED CDC25C WILD-TYPE 
              11              382 
[1] "BCL9L MUTATION ANALYSIS"
[1] 3
  BCL9L MUTATED BCL9L WILD-TYPE 
             26             367 
  BCL9L MUTATED BCL9L WILD-TYPE 
             26             367 
[1] "TNFSF10 MUTATION ANALYSIS"
[1] 3
  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
                8               385 
  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
                8               385 
[1] "PIK3R3 MUTATION ANALYSIS"
[1] 3
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
               8              385 
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
               8              385 
[1] "ZNF124 MUTATION ANALYSIS"
[1] 3
  ZNF124 MUTATED ZNF124 WILD-TYPE 
              10              383 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
              10              383 
[1] "KNTC1 MUTATION ANALYSIS"
[1] 3
  KNTC1 MUTATED KNTC1 WILD-TYPE 
             20             373 
  KNTC1 MUTATED KNTC1 WILD-TYPE 
             20             373 
[1] "GAS6 MUTATION ANALYSIS"
[1] 3
  GAS6 MUTATED GAS6 WILD-TYPE 
            16            377 
  GAS6 MUTATED GAS6 WILD-TYPE 
            16            377 
[1] "HCFC1R1 MUTATION ANALYSIS"
[1] 3
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                6               387 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                6               387 
[1] "NCAPD3 MUTATION ANALYSIS"
[1] 3
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              19              374 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              19              374 
[1] "TAF1L MUTATION ANALYSIS"
[1] 3
  TAF1L MUTATED TAF1L WILD-TYPE 
             31             362 
  TAF1L MUTATED TAF1L WILD-TYPE 
             31             362 
[1] "LRRN2 MUTATION ANALYSIS"
[1] 3
  LRRN2 MUTATED LRRN2 WILD-TYPE 
             34             359 
  LRRN2 MUTATED LRRN2 WILD-TYPE 
             34             359 
[1] "C17ORF57 MUTATION ANALYSIS"
[1] 3
  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
                12                381 
  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
                12                381 
[1] "BEND3 MUTATION ANALYSIS"
[1] 3
  BEND3 MUTATED BEND3 WILD-TYPE 
             12             381 
  BEND3 MUTATED BEND3 WILD-TYPE 
             12             381 
[1] "FAM98C MUTATION ANALYSIS"
[1] 3
  FAM98C MUTATED FAM98C WILD-TYPE 
               8              385 
  FAM98C MUTATED FAM98C WILD-TYPE 
               8              385 
[1] "KIAA0100 MUTATION ANALYSIS"
[1] 3
  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
                26                367 
  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
                26                367 
[1] "MYLK3 MUTATION ANALYSIS"
[1] 3
  MYLK3 MUTATED MYLK3 WILD-TYPE 
              9             384 
  MYLK3 MUTATED MYLK3 WILD-TYPE 
              9             384 
[1] "PLOD3 MUTATION ANALYSIS"
[1] 3
  PLOD3 MUTATED PLOD3 WILD-TYPE 
             16             377 
  PLOD3 MUTATED PLOD3 WILD-TYPE 
             16             377 
[1] "RAD51AP2 MUTATION ANALYSIS"
[1] 3
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                16                377 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                16                377 
[1] "U2AF2 MUTATION ANALYSIS"
[1] 3
  U2AF2 MUTATED U2AF2 WILD-TYPE 
             14             379 
  U2AF2 MUTATED U2AF2 WILD-TYPE 
             14             379 
[1] "MFN1 MUTATION ANALYSIS"
[1] 3
  MFN1 MUTATED MFN1 WILD-TYPE 
             9            384 
  MFN1 MUTATED MFN1 WILD-TYPE 
             9            384 
[1] "ATP6V1C2 MUTATION ANALYSIS"
[1] 3
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                15                378 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                15                378 
[1] "NFE2L1 MUTATION ANALYSIS"
[1] 3
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
              11              382 
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
              11              382 
[1] "ERF MUTATION ANALYSIS"
[1] 3
  ERF MUTATED ERF WILD-TYPE 
           16           377 
  ERF MUTATED ERF WILD-TYPE 
           16           377 
[1] "TAS2R10 MUTATION ANALYSIS"
[1] 3
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
                4               389 
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
                4               389 
[1] "FAM82A1 MUTATION ANALYSIS"
[1] 3
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
                5               388 
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
                5               388 
[1] "DYRK4 MUTATION ANALYSIS"
[1] 3
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              8             385 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              8             385 
[1] "BTNL3 MUTATION ANALYSIS"
[1] 3
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              6             387 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              6             387 
[1] "ADNP MUTATION ANALYSIS"
[1] 3
  ADNP MUTATED ADNP WILD-TYPE 
            18            375 
  ADNP MUTATED ADNP WILD-TYPE 
            18            375 
[1] "ELF3 MUTATION ANALYSIS"
[1] 3
  ELF3 MUTATED ELF3 WILD-TYPE 
            13            380 
  ELF3 MUTATED ELF3 WILD-TYPE 
            13            380 
[1] "NID2 MUTATION ANALYSIS"
[1] 3
  NID2 MUTATED NID2 WILD-TYPE 
            19            374 
  NID2 MUTATED NID2 WILD-TYPE 
            19            374 
[1] "FBN3 MUTATION ANALYSIS"
[1] 3
  FBN3 MUTATED FBN3 WILD-TYPE 
            33            360 
  FBN3 MUTATED FBN3 WILD-TYPE 
            33            360 
[1] "ABCA6 MUTATION ANALYSIS"
[1] 3
  ABCA6 MUTATED ABCA6 WILD-TYPE 
             15             378 
  ABCA6 MUTATED ABCA6 WILD-TYPE 
             15             378 
[1] "IDE MUTATION ANALYSIS"
[1] 3
  IDE MUTATED IDE WILD-TYPE 
           11           382 
  IDE MUTATED IDE WILD-TYPE 
           11           382 
[1] "BCLAF1 MUTATION ANALYSIS"
[1] 3
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              30              363 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              30              363 
[1] "DLGAP3 MUTATION ANALYSIS"
[1] 3
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              20              373 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              20              373 
[1] "ZC3H13 MUTATION ANALYSIS"
[1] 3
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              31              362 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              31              362 
[1] "RTN2 MUTATION ANALYSIS"
[1] 3
  RTN2 MUTATED RTN2 WILD-TYPE 
            15            378 
  RTN2 MUTATED RTN2 WILD-TYPE 
            15            378 
[1] "RAI1 MUTATION ANALYSIS"
[1] 3
  RAI1 MUTATED RAI1 WILD-TYPE 
            29            364 
  RAI1 MUTATED RAI1 WILD-TYPE 
            29            364 
[1] "C6ORF165 MUTATION ANALYSIS"
[1] 3
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                16                377 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                16                377 
[1] "HIAT1 MUTATION ANALYSIS"
[1] 3
  HIAT1 MUTATED HIAT1 WILD-TYPE 
              9             384 
  HIAT1 MUTATED HIAT1 WILD-TYPE 
              9             384 
[1] "HSPG2 MUTATION ANALYSIS"
[1] 3
  HSPG2 MUTATED HSPG2 WILD-TYPE 
             62             331 
  HSPG2 MUTATED HSPG2 WILD-TYPE 
             62             331 
[1] "NBN MUTATION ANALYSIS"
[1] 3
  NBN MUTATED NBN WILD-TYPE 
           15           378 
  NBN MUTATED NBN WILD-TYPE 
           15           378 
[1] "ERBB3 MUTATION ANALYSIS"
[1] 3
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             35             358 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             35             358 
[1] "IPO5 MUTATION ANALYSIS"
[1] 3
  IPO5 MUTATED IPO5 WILD-TYPE 
            21            372 
  IPO5 MUTATED IPO5 WILD-TYPE 
            21            372 
[1] "MARVELD3 MUTATION ANALYSIS"
[1] 3
  MARVELD3 MUTATED MARVELD3 WILD-TYPE 
                12                381 
  MARVELD3 MUTATED MARVELD3 WILD-TYPE 
                12                381 
[1] "NOS3 MUTATION ANALYSIS"
[1] 3
  NOS3 MUTATED NOS3 WILD-TYPE 
            15            378 
  NOS3 MUTATED NOS3 WILD-TYPE 
            15            378 
[1] "TAS2R42 MUTATION ANALYSIS"
[1] 3
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
                6               387 
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
                6               387 
[1] "ANKRD20A4 MUTATION ANALYSIS"
[1] 3
  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
                  7                 386 
  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
                  7                 386 
[1] "UGP2 MUTATION ANALYSIS"
[1] 3
  UGP2 MUTATED UGP2 WILD-TYPE 
             9            384 
  UGP2 MUTATED UGP2 WILD-TYPE 
             9            384 
[1] "KLHDC8B MUTATION ANALYSIS"
[1] 3
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
               10               383 
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
               10               383 
[1] "ABCB6 MUTATION ANALYSIS"
[1] 3
  ABCB6 MUTATED ABCB6 WILD-TYPE 
             12             381 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
             12             381 
[1] "TMC4 MUTATION ANALYSIS"
[1] 3
  TMC4 MUTATED TMC4 WILD-TYPE 
            15            378 
  TMC4 MUTATED TMC4 WILD-TYPE 
            15            378 
[1] "TM6SF1 MUTATION ANALYSIS"
[1] 3
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
               8              385 
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
               8              385 
[1] "ARID1B MUTATION ANALYSIS"
[1] 3
  ARID1B MUTATED ARID1B WILD-TYPE 
              26              367 
  ARID1B MUTATED ARID1B WILD-TYPE 
              26              367 
[1] "TNKS1BP1 MUTATION ANALYSIS"
[1] 3
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
                27                366 
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
                27                366 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             19             374 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             19             374 
[1] "FAM70B MUTATION ANALYSIS"
[1] 3
  FAM70B MUTATED FAM70B WILD-TYPE 
              13              380 
  FAM70B MUTATED FAM70B WILD-TYPE 
              13              380 
[1] "MYEOV MUTATION ANALYSIS"
[1] 3
  MYEOV MUTATED MYEOV WILD-TYPE 
              9             384 
  MYEOV MUTATED MYEOV WILD-TYPE 
              9             384 
[1] "IRS1 MUTATION ANALYSIS"
[1] 3
  IRS1 MUTATED IRS1 WILD-TYPE 
            21            372 
  IRS1 MUTATED IRS1 WILD-TYPE 
            21            372 
[1] "WDR5 MUTATION ANALYSIS"
[1] 3
  WDR5 MUTATED WDR5 WILD-TYPE 
             5            388 
  WDR5 MUTATED WDR5 WILD-TYPE 
             5            388 
[1] "RPL22 MUTATION ANALYSIS"
[1] 3
  RPL22 MUTATED RPL22 WILD-TYPE 
              9             384 
  RPL22 MUTATED RPL22 WILD-TYPE 
              9             384 
[1] "DDX26B MUTATION ANALYSIS"
[1] 3
  DDX26B MUTATED DDX26B WILD-TYPE 
              12              381 
  DDX26B MUTATED DDX26B WILD-TYPE 
              12              381 
[1] "EPHX1 MUTATION ANALYSIS"
[1] 3
  EPHX1 MUTATED EPHX1 WILD-TYPE 
             10             383 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
             10             383 
[1] "CLMN MUTATION ANALYSIS"
[1] 3
  CLMN MUTATED CLMN WILD-TYPE 
            14            379 
  CLMN MUTATED CLMN WILD-TYPE 
            14            379 
[1] "TRAM1L1 MUTATION ANALYSIS"
[1] 3
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
               15               378 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
               15               378 
[1] "EHMT2 MUTATION ANALYSIS"
[1] 3
  EHMT2 MUTATED EHMT2 WILD-TYPE 
             19             374 
  EHMT2 MUTATED EHMT2 WILD-TYPE 
             19             374 
[1] "GALNTL1 MUTATION ANALYSIS"
[1] 3
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
               10               383 
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
               10               383 
[1] "DMXL2 MUTATION ANALYSIS"
[1] 3
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             41             352 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             41             352 
[1] "MIA2 MUTATION ANALYSIS"
[1] 3
  MIA2 MUTATED MIA2 WILD-TYPE 
            10            383 
  MIA2 MUTATED MIA2 WILD-TYPE 
            10            383 
[1] "NT5DC1 MUTATION ANALYSIS"
[1] 3
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
               8              385 
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
               8              385 
[1] "SYCP1 MUTATION ANALYSIS"
[1] 3
  SYCP1 MUTATED SYCP1 WILD-TYPE 
             23             370 
  SYCP1 MUTATED SYCP1 WILD-TYPE 
             23             370 
[1] "ZNF878 MUTATION ANALYSIS"
[1] 3
  ZNF878 MUTATED ZNF878 WILD-TYPE 
              13              380 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
              13              380 
[1] "KIAA1009 MUTATION ANALYSIS"
[1] 3
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
                16                377 
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
                16                377 
[1] "SENP3 MUTATION ANALYSIS"
[1] 3
  SENP3 MUTATED SENP3 WILD-TYPE 
             13             380 
  SENP3 MUTATED SENP3 WILD-TYPE 
             13             380 
[1] "ERBB4 MUTATION ANALYSIS"
[1] 3
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             49             344 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             49             344 
[1] "COL12A1 MUTATION ANALYSIS"
[1] 3
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               53               340 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               53               340 
[1] "PANK1 MUTATION ANALYSIS"
[1] 3
  PANK1 MUTATED PANK1 WILD-TYPE 
             10             383 
  PANK1 MUTATED PANK1 WILD-TYPE 
             10             383 
[1] "SNRNP35 MUTATION ANALYSIS"
[1] 3
  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
                6               387 
  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
                6               387 
[1] "PTPN4 MUTATION ANALYSIS"
[1] 3
  PTPN4 MUTATED PTPN4 WILD-TYPE 
             12             381 
  PTPN4 MUTATED PTPN4 WILD-TYPE 
             12             381 
[1] "TNFRSF9 MUTATION ANALYSIS"
[1] 3
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
               10               383 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
               10               383 
[1] "SIGLEC10 MUTATION ANALYSIS"
[1] 3
  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
                13                380 
  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
                13                380 
[1] "HTR7 MUTATION ANALYSIS"
[1] 3
  HTR7 MUTATED HTR7 WILD-TYPE 
            14            379 
  HTR7 MUTATED HTR7 WILD-TYPE 
            14            379 
[1] "OBSCN MUTATION ANALYSIS"
[1] 3
  OBSCN MUTATED OBSCN WILD-TYPE 
             90             303 
  OBSCN MUTATED OBSCN WILD-TYPE 
             90             303 
[1] "GAB2 MUTATION ANALYSIS"
[1] 3
  GAB2 MUTATED GAB2 WILD-TYPE 
            11            382 
  GAB2 MUTATED GAB2 WILD-TYPE 
            11            382 
[1] "SLC12A7 MUTATION ANALYSIS"
[1] 3
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
               24               369 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
               24               369 
[1] "KIAA1522 MUTATION ANALYSIS"
[1] 3
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
                12                381 
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
                12                381 
[1] "FERMT2 MUTATION ANALYSIS"
[1] 3
  FERMT2 MUTATED FERMT2 WILD-TYPE 
              12              381 
  FERMT2 MUTATED FERMT2 WILD-TYPE 
              12              381 
[1] "PPP1R13B MUTATION ANALYSIS"
[1] 3
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
                14                379 
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
                14                379 
[1] "KIAA0240 MUTATION ANALYSIS"
[1] 3
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                13                380 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                13                380 
[1] "TP53BP1 MUTATION ANALYSIS"
[1] 3
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
               22               371 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
               22               371 
[1] "CHPF2 MUTATION ANALYSIS"
[1] 3
  CHPF2 MUTATED CHPF2 WILD-TYPE 
             16             377 
  CHPF2 MUTATED CHPF2 WILD-TYPE 
             16             377 
[1] "GPR141 MUTATION ANALYSIS"
[1] 3
  GPR141 MUTATED GPR141 WILD-TYPE 
              11              382 
  GPR141 MUTATED GPR141 WILD-TYPE 
              11              382 
[1] "PPP1R15A MUTATION ANALYSIS"
[1] 3
  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
                 5                388 
  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
                 5                388 
[1] "KYNU MUTATION ANALYSIS"
[1] 3
  KYNU MUTATED KYNU WILD-TYPE 
            12            381 
  KYNU MUTATED KYNU WILD-TYPE 
            12            381 
[1] "RIF1 MUTATION ANALYSIS"
[1] 3
  RIF1 MUTATED RIF1 WILD-TYPE 
            24            369 
  RIF1 MUTATED RIF1 WILD-TYPE 
            24            369 
[1] "TBC1D10C MUTATION ANALYSIS"
[1] 3
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 9                384 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 9                384 
[1] "UHRF1BP1 MUTATION ANALYSIS"
[1] 3
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                19                374 
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                19                374 
[1] "DLAT MUTATION ANALYSIS"
[1] 3
  DLAT MUTATED DLAT WILD-TYPE 
             8            385 
  DLAT MUTATED DLAT WILD-TYPE 
             8            385 
[1] "CD93 MUTATION ANALYSIS"
[1] 3
  CD93 MUTATED CD93 WILD-TYPE 
            18            375 
  CD93 MUTATED CD93 WILD-TYPE 
            18            375 
[1] "SGOL2 MUTATION ANALYSIS"
[1] 3
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             13             380 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             13             380 
[1] "ADNP2 MUTATION ANALYSIS"
[1] 3
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             19             374 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             19             374 
[1] "DPP7 MUTATION ANALYSIS"
[1] 3
  DPP7 MUTATED DPP7 WILD-TYPE 
             9            384 
  DPP7 MUTATED DPP7 WILD-TYPE 
             9            384 
[1] "CSGALNACT1 MUTATION ANALYSIS"
[1] 3
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                  19                  374 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                  19                  374 
[1] "CNNM1 MUTATION ANALYSIS"
[1] 3
  CNNM1 MUTATED CNNM1 WILD-TYPE 
             12             381 
  CNNM1 MUTATED CNNM1 WILD-TYPE 
             12             381 
[1] "IFRD1 MUTATION ANALYSIS"
[1] 3
  IFRD1 MUTATED IFRD1 WILD-TYPE 
             10             383 
  IFRD1 MUTATED IFRD1 WILD-TYPE 
             10             383 
[1] "IGFBP1 MUTATION ANALYSIS"
[1] 3
  IGFBP1 MUTATED IGFBP1 WILD-TYPE 
              11              382 
  IGFBP1 MUTATED IGFBP1 WILD-TYPE 
              11              382 
[1] "SH3KBP1 MUTATION ANALYSIS"
[1] 3
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
               15               378 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
               15               378 
[1] "HIST1H1A MUTATION ANALYSIS"
[1] 3
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 9                384 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 9                384 
[1] "TUBE1 MUTATION ANALYSIS"
[1] 3
  TUBE1 MUTATED TUBE1 WILD-TYPE 
              9             384 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
              9             384 
[1] "IPO11 MUTATION ANALYSIS"
[1] 3
  IPO11 MUTATED IPO11 WILD-TYPE 
             11             382 
  IPO11 MUTATED IPO11 WILD-TYPE 
             11             382 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
             4            389 
  IDH2 MUTATED IDH2 WILD-TYPE 
             4            389 
[1] "ZCCHC11 MUTATION ANALYSIS"
[1] 3
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
               18               375 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
               18               375 
[1] "SYNCRIP MUTATION ANALYSIS"
[1] 3
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               15               378 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               15               378 
[1] "BAT3 MUTATION ANALYSIS"
[1] 3
  BAT3 MUTATED BAT3 WILD-TYPE 
            13            380 
  BAT3 MUTATED BAT3 WILD-TYPE 
            13            380 
[1] "PRPF40B MUTATION ANALYSIS"
[1] 3
  PRPF40B MUTATED PRPF40B WILD-TYPE 
               17               376 
  PRPF40B MUTATED PRPF40B WILD-TYPE 
               17               376 
[1] "OXNAD1 MUTATION ANALYSIS"
[1] 3
  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
               6              387 
  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
               6              387 
[1] "YLPM1 MUTATION ANALYSIS"
[1] 3
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             24             369 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             24             369 
[1] "PLEKHA5 MUTATION ANALYSIS"
[1] 3
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
               19               374 
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
               19               374 
[1] "TM7SF4 MUTATION ANALYSIS"
[1] 3
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
              19              374 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
              19              374 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              24              369 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              24              369 
[1] "SNAPC2 MUTATION ANALYSIS"
[1] 3
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               9              384 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               9              384 
[1] "MAP2K7 MUTATION ANALYSIS"
[1] 3
  MAP2K7 MUTATED MAP2K7 WILD-TYPE 
              27              366 
  MAP2K7 MUTATED MAP2K7 WILD-TYPE 
              27              366 
[1] "CETN3 MUTATION ANALYSIS"
[1] 3
  CETN3 MUTATED CETN3 WILD-TYPE 
              9             384 
  CETN3 MUTATED CETN3 WILD-TYPE 
              9             384 
[1] "CUBN MUTATION ANALYSIS"
[1] 3
  CUBN MUTATED CUBN WILD-TYPE 
            58            335 
  CUBN MUTATED CUBN WILD-TYPE 
            58            335 
[1] "TRMT6 MUTATION ANALYSIS"
[1] 3
  TRMT6 MUTATED TRMT6 WILD-TYPE 
              7             386 
  TRMT6 MUTATED TRMT6 WILD-TYPE 
              7             386 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           38           355 
  ATM MUTATED ATM WILD-TYPE 
           38           355 
[1] "PMEPA1 MUTATION ANALYSIS"
[1] 3
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
               6              387 
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
               6              387 
[1] "POP1 MUTATION ANALYSIS"
[1] 3
  POP1 MUTATED POP1 WILD-TYPE 
            19            374 
  POP1 MUTATED POP1 WILD-TYPE 
            19            374 
[1] "EPHA2 MUTATION ANALYSIS"
[1] 3
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             27             366 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             27             366 
[1] "MPRIP MUTATION ANALYSIS"
[1] 3
  MPRIP MUTATED MPRIP WILD-TYPE 
             17             376 
  MPRIP MUTATED MPRIP WILD-TYPE 
             17             376 
[1] "LARP1B MUTATION ANALYSIS"
[1] 3
  LARP1B MUTATED LARP1B WILD-TYPE 
              12              381 
  LARP1B MUTATED LARP1B WILD-TYPE 
              12              381 
[1] "EIF5A2 MUTATION ANALYSIS"
[1] 3
  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
               5              388 
  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
               5              388 
[1] "RING1 MUTATION ANALYSIS"
[1] 3
  RING1 MUTATED RING1 WILD-TYPE 
              8             385 
  RING1 MUTATED RING1 WILD-TYPE 
              8             385 
[1] "FAM83E MUTATION ANALYSIS"
[1] 3
  FAM83E MUTATED FAM83E WILD-TYPE 
              13              380 
  FAM83E MUTATED FAM83E WILD-TYPE 
              13              380 
[1] "CLDN6 MUTATION ANALYSIS"
[1] 3
  CLDN6 MUTATED CLDN6 WILD-TYPE 
              9             384 
  CLDN6 MUTATED CLDN6 WILD-TYPE 
              9             384 
[1] "SULF1 MUTATION ANALYSIS"
[1] 3
  SULF1 MUTATED SULF1 WILD-TYPE 
             24             369 
  SULF1 MUTATED SULF1 WILD-TYPE 
             24             369 
[1] "PCGF3 MUTATION ANALYSIS"
[1] 3
  PCGF3 MUTATED PCGF3 WILD-TYPE 
              7             386 
  PCGF3 MUTATED PCGF3 WILD-TYPE 
              7             386 
[1] "SF3B2 MUTATION ANALYSIS"
[1] 3
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             16             377 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             16             377 
[1] "C19ORF70 MUTATION ANALYSIS"
[1] 3
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
                 6                387 
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
                 6                387 
[1] "RNASEH2B MUTATION ANALYSIS"
[1] 3
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 4                389 
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 4                389 
[1] "GPR161 MUTATION ANALYSIS"
[1] 3
  GPR161 MUTATED GPR161 WILD-TYPE 
              12              381 
  GPR161 MUTATED GPR161 WILD-TYPE 
              12              381 
[1] "RRS1 MUTATION ANALYSIS"
[1] 3
  RRS1 MUTATED RRS1 WILD-TYPE 
             7            386 
  RRS1 MUTATED RRS1 WILD-TYPE 
             7            386 
[1] "ZCRB1 MUTATION ANALYSIS"
[1] 3
  ZCRB1 MUTATED ZCRB1 WILD-TYPE 
              6             387 
  ZCRB1 MUTATED ZCRB1 WILD-TYPE 
              6             387 
[1] "LINGO4 MUTATION ANALYSIS"
[1] 3
  LINGO4 MUTATED LINGO4 WILD-TYPE 
              11              382 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
              11              382 
[1] "MAP9 MUTATION ANALYSIS"
[1] 3
  MAP9 MUTATED MAP9 WILD-TYPE 
            13            380 
  MAP9 MUTATED MAP9 WILD-TYPE 
            13            380 
[1] "CCDC27 MUTATION ANALYSIS"
[1] 3
  CCDC27 MUTATED CCDC27 WILD-TYPE 
               8              385 
  CCDC27 MUTATED CCDC27 WILD-TYPE 
               8              385 
[1] "DDX60 MUTATION ANALYSIS"
[1] 3
  DDX60 MUTATED DDX60 WILD-TYPE 
             15             378 
  DDX60 MUTATED DDX60 WILD-TYPE 
             15             378 
[1] "ACTL6A MUTATION ANALYSIS"
[1] 3
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               8              385 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               8              385 
[1] "PFKP MUTATION ANALYSIS"
[1] 3
  PFKP MUTATED PFKP WILD-TYPE 
            18            375 
  PFKP MUTATED PFKP WILD-TYPE 
            18            375 
[1] "OR2J3 MUTATION ANALYSIS"
[1] 3
  OR2J3 MUTATED OR2J3 WILD-TYPE 
              9             384 
  OR2J3 MUTATED OR2J3 WILD-TYPE 
              9             384 
[1] "C20ORF160 MUTATION ANALYSIS"
[1] 3
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
                  7                 386 
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
                  7                 386 
[1] "SGK3 MUTATION ANALYSIS"
[1] 3
  SGK3 MUTATED SGK3 WILD-TYPE 
             7            386 
  SGK3 MUTATED SGK3 WILD-TYPE 
             7            386 
[1] "SMTN MUTATION ANALYSIS"
[1] 3
  SMTN MUTATED SMTN WILD-TYPE 
            20            373 
  SMTN MUTATED SMTN WILD-TYPE 
            20            373 
[1] "SLC9A11 MUTATION ANALYSIS"
[1] 3
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               24               369 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               24               369 
[1] "JHDM1D MUTATION ANALYSIS"
[1] 3
  JHDM1D MUTATED JHDM1D WILD-TYPE 
              10              383 
  JHDM1D MUTATED JHDM1D WILD-TYPE 
              10              383 
[1] "GLT8D1 MUTATION ANALYSIS"
[1] 3
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               7              386 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               7              386 
[1] "DAPK1 MUTATION ANALYSIS"
[1] 3
  DAPK1 MUTATED DAPK1 WILD-TYPE 
             22             371 
  DAPK1 MUTATED DAPK1 WILD-TYPE 
             22             371 
[1] "EDNRB MUTATION ANALYSIS"
[1] 3
  EDNRB MUTATED EDNRB WILD-TYPE 
             28             365 
  EDNRB MUTATED EDNRB WILD-TYPE 
             28             365 
[1] "C16ORF70 MUTATION ANALYSIS"
[1] 3
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
                 6                387 
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
                 6                387 
[1] "SLC10A6 MUTATION ANALYSIS"
[1] 3
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
                8               385 
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
                8               385 
[1] "CCDC80 MUTATION ANALYSIS"
[1] 3
  CCDC80 MUTATED CCDC80 WILD-TYPE 
              19              374 
  CCDC80 MUTATED CCDC80 WILD-TYPE 
              19              374 
[1] "DNAJC1 MUTATION ANALYSIS"
[1] 3
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
              11              382 
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
              11              382 
[1] "CADPS2 MUTATION ANALYSIS"
[1] 3
  CADPS2 MUTATED CADPS2 WILD-TYPE 
              10              383 
  CADPS2 MUTATED CADPS2 WILD-TYPE 
              10              383 
[1] "ART5 MUTATION ANALYSIS"
[1] 3
  ART5 MUTATED ART5 WILD-TYPE 
             5            388 
  ART5 MUTATED ART5 WILD-TYPE 
             5            388 
[1] "PLAGL2 MUTATION ANALYSIS"
[1] 3
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               7              386 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               7              386 
[1] "C16ORF63 MUTATION ANALYSIS"
[1] 3
  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
                 8                385 
  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
                 8                385 
[1] "GCDH MUTATION ANALYSIS"
[1] 3
  GCDH MUTATED GCDH WILD-TYPE 
             7            386 
  GCDH MUTATED GCDH WILD-TYPE 
             7            386 
[1] "FBXO34 MUTATION ANALYSIS"
[1] 3
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               9              384 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               9              384 
[1] "SERPINA1 MUTATION ANALYSIS"
[1] 3
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
                 7                386 
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
                 7                386 
[1] "KIAA1632 MUTATION ANALYSIS"
[1] 3
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                27                366 
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                27                366 
[1] "CCDC138 MUTATION ANALYSIS"
[1] 3
  CCDC138 MUTATED CCDC138 WILD-TYPE 
               10               383 
  CCDC138 MUTATED CCDC138 WILD-TYPE 
               10               383 
[1] "ALDH3A1 MUTATION ANALYSIS"
[1] 3
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
               12               381 
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
               12               381 
[1] "PAMR1 MUTATION ANALYSIS"
[1] 3
  PAMR1 MUTATED PAMR1 WILD-TYPE 
             15             378 
  PAMR1 MUTATED PAMR1 WILD-TYPE 
             15             378 
[1] "ZNF776 MUTATION ANALYSIS"
[1] 3
  ZNF776 MUTATED ZNF776 WILD-TYPE 
               8              385 
  ZNF776 MUTATED ZNF776 WILD-TYPE 
               8              385 
[1] "SH2B1 MUTATION ANALYSIS"
[1] 3
  SH2B1 MUTATED SH2B1 WILD-TYPE 
             11             382 
  SH2B1 MUTATED SH2B1 WILD-TYPE 
             11             382 
[1] "GPR82 MUTATION ANALYSIS"
[1] 3
  GPR82 MUTATED GPR82 WILD-TYPE 
              9             384 
  GPR82 MUTATED GPR82 WILD-TYPE 
              9             384 
[1] "ANK3 MUTATION ANALYSIS"
[1] 3
  ANK3 MUTATED ANK3 WILD-TYPE 
            47            346 
  ANK3 MUTATED ANK3 WILD-TYPE 
            47            346 
[1] "MLH1 MUTATION ANALYSIS"
[1] 3
  MLH1 MUTATED MLH1 WILD-TYPE 
             8            385 
  MLH1 MUTATED MLH1 WILD-TYPE 
             8            385 
[1] "BCKDHA MUTATION ANALYSIS"
[1] 3
  BCKDHA MUTATED BCKDHA WILD-TYPE 
              10              383 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
              10              383 
[1] "MMP10 MUTATION ANALYSIS"
[1] 3
  MMP10 MUTATED MMP10 WILD-TYPE 
              9             384 
  MMP10 MUTATED MMP10 WILD-TYPE 
              9             384 
[1] "HAX1 MUTATION ANALYSIS"
[1] 3
  HAX1 MUTATED HAX1 WILD-TYPE 
             5            388 
  HAX1 MUTATED HAX1 WILD-TYPE 
             5            388 
[1] "ULK2 MUTATION ANALYSIS"
[1] 3
  ULK2 MUTATED ULK2 WILD-TYPE 
            11            382 
  ULK2 MUTATED ULK2 WILD-TYPE 
            11            382 
[1] "C11ORF70 MUTATION ANALYSIS"
[1] 3
  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
                 4                389 
  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
                 4                389 
[1] "AKAP11 MUTATION ANALYSIS"
[1] 3
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              15              378 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              15              378 
[1] "MAN1C1 MUTATION ANALYSIS"
[1] 3
  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
              10              383 
  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
              10              383 
[1] "KCTD3 MUTATION ANALYSIS"
[1] 3
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             14             379 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             14             379 
[1] "RALGAPB MUTATION ANALYSIS"
[1] 3
  RALGAPB MUTATED RALGAPB WILD-TYPE 
               17               376 
  RALGAPB MUTATED RALGAPB WILD-TYPE 
               17               376 
[1] "CRYGA MUTATION ANALYSIS"
[1] 3
  CRYGA MUTATED CRYGA WILD-TYPE 
             11             382 
  CRYGA MUTATED CRYGA WILD-TYPE 
             11             382 
[1] "CROT MUTATION ANALYSIS"
[1] 3
  CROT MUTATED CROT WILD-TYPE 
            15            378 
  CROT MUTATED CROT WILD-TYPE 
            15            378 
[1] "MAP7D3 MUTATION ANALYSIS"
[1] 3
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              18              375 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              18              375 
[1] "ZFC3H1 MUTATION ANALYSIS"
[1] 3
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              16              377 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              16              377 
[1] "NCOA7 MUTATION ANALYSIS"
[1] 3
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             16             377 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             16             377 
[1] "USP13 MUTATION ANALYSIS"
[1] 3
  USP13 MUTATED USP13 WILD-TYPE 
             12             381 
  USP13 MUTATED USP13 WILD-TYPE 
             12             381 
[1] "ICAM4 MUTATION ANALYSIS"
[1] 3
  ICAM4 MUTATED ICAM4 WILD-TYPE 
              8             385 
  ICAM4 MUTATED ICAM4 WILD-TYPE 
              8             385 
[1] "USP15 MUTATION ANALYSIS"
[1] 3
  USP15 MUTATED USP15 WILD-TYPE 
              7             386 
  USP15 MUTATED USP15 WILD-TYPE 
              7             386 
[1] "FAM113B MUTATION ANALYSIS"
[1] 3
  FAM113B MUTATED FAM113B WILD-TYPE 
               15               378 
  FAM113B MUTATED FAM113B WILD-TYPE 
               15               378 
[1] "PCCA MUTATION ANALYSIS"
[1] 3
  PCCA MUTATED PCCA WILD-TYPE 
            12            381 
  PCCA MUTATED PCCA WILD-TYPE 
            12            381 
[1] "P2RX1 MUTATION ANALYSIS"
[1] 3
  P2RX1 MUTATED P2RX1 WILD-TYPE 
              4             389 
  P2RX1 MUTATED P2RX1 WILD-TYPE 
              4             389 
[1] "KIAA0649 MUTATION ANALYSIS"
[1] 3
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                18                375 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                18                375 
[1] "CD79A MUTATION ANALYSIS"
[1] 3
  CD79A MUTATED CD79A WILD-TYPE 
              7             386 
  CD79A MUTATED CD79A WILD-TYPE 
              7             386 
[1] "C22ORF30 MUTATION ANALYSIS"
[1] 3
  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
                 6                387 
  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
                 6                387 
[1] "SRP72 MUTATION ANALYSIS"
[1] 3
  SRP72 MUTATED SRP72 WILD-TYPE 
             14             379 
  SRP72 MUTATED SRP72 WILD-TYPE 
             14             379 
[1] "PLAG1 MUTATION ANALYSIS"
[1] 3
  PLAG1 MUTATED PLAG1 WILD-TYPE 
             12             381 
  PLAG1 MUTATED PLAG1 WILD-TYPE 
             12             381 
[1] "HSPA14 MUTATION ANALYSIS"
[1] 3
  HSPA14 MUTATED HSPA14 WILD-TYPE 
               6              387 
  HSPA14 MUTATED HSPA14 WILD-TYPE 
               6              387 
[1] "CYP7B1 MUTATION ANALYSIS"
[1] 3
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
              20              373 
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
              20              373 
[1] "SLC7A10 MUTATION ANALYSIS"
[1] 3
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                6               387 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                6               387 
[1] "FASTKD1 MUTATION ANALYSIS"
[1] 3
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
               12               381 
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
               12               381 
[1] "NEUROD6 MUTATION ANALYSIS"
[1] 3
  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
                6               387 
  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
                6               387 
[1] "KRTAP10-9 MUTATION ANALYSIS"
[1] 3
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  8                 385 
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  8                 385 
[1] "RBMX MUTATION ANALYSIS"
[1] 3
  RBMX MUTATED RBMX WILD-TYPE 
            10            383 
  RBMX MUTATED RBMX WILD-TYPE 
            10            383 
[1] "C10ORF71 MUTATION ANALYSIS"
[1] 3
  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
                12                381 
  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
                12                381 
[1] "MRE11A MUTATION ANALYSIS"
[1] 3
  MRE11A MUTATED MRE11A WILD-TYPE 
               7              386 
  MRE11A MUTATED MRE11A WILD-TYPE 
               7              386 
[1] "MAP2K1 MUTATION ANALYSIS"
[1] 3
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               7              386 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               7              386 
[1] "C1ORF177 MUTATION ANALYSIS"
[1] 3
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
                12                381 
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
                12                381 
[1] "IGF2BP3 MUTATION ANALYSIS"
[1] 3
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
                7               386 
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
                7               386 
[1] "AKAP13 MUTATION ANALYSIS"
[1] 3
  AKAP13 MUTATED AKAP13 WILD-TYPE 
              32              361 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
              32              361 
[1] "ABCE1 MUTATION ANALYSIS"
[1] 3
  ABCE1 MUTATED ABCE1 WILD-TYPE 
             10             383 
  ABCE1 MUTATED ABCE1 WILD-TYPE 
             10             383 
[1] "KLHL14 MUTATION ANALYSIS"
[1] 3
  KLHL14 MUTATED KLHL14 WILD-TYPE 
              19              374 
  KLHL14 MUTATED KLHL14 WILD-TYPE 
              19              374 
[1] "H2AFY MUTATION ANALYSIS"
[1] 3
  H2AFY MUTATED H2AFY WILD-TYPE 
              7             386 
  H2AFY MUTATED H2AFY WILD-TYPE 
              7             386 
[1] "USP35 MUTATION ANALYSIS"
[1] 3
  USP35 MUTATED USP35 WILD-TYPE 
              8             385 
  USP35 MUTATED USP35 WILD-TYPE 
              8             385 
[1] "ZFP36L1 MUTATION ANALYSIS"
[1] 3
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
                5               388 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
                5               388 
[1] "RASAL2 MUTATION ANALYSIS"
[1] 3
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              19              374 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              19              374 
[1] "GTF3C1 MUTATION ANALYSIS"
[1] 3
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
              35              358 
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
              35              358 
[1] "RPS20 MUTATION ANALYSIS"
[1] 3
  RPS20 MUTATED RPS20 WILD-TYPE 
              4             389 
  RPS20 MUTATED RPS20 WILD-TYPE 
              4             389 
[1] "KIAA0748 MUTATION ANALYSIS"
[1] 3
  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
                16                377 
  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
                16                377 
[1] "USP1 MUTATION ANALYSIS"
[1] 3
  USP1 MUTATED USP1 WILD-TYPE 
             5            388 
  USP1 MUTATED USP1 WILD-TYPE 
             5            388 
[1] "BRMS1 MUTATION ANALYSIS"
[1] 3
  BRMS1 MUTATED BRMS1 WILD-TYPE 
              6             387 
  BRMS1 MUTATED BRMS1 WILD-TYPE 
              6             387 
[1] "RNASEL MUTATION ANALYSIS"
[1] 3
  RNASEL MUTATED RNASEL WILD-TYPE 
               6              387 
  RNASEL MUTATED RNASEL WILD-TYPE 
               6              387 
[1] "TIMP3 MUTATION ANALYSIS"
[1] 3
  TIMP3 MUTATED TIMP3 WILD-TYPE 
              9             384 
  TIMP3 MUTATED TIMP3 WILD-TYPE 
              9             384 
[1] "RELT MUTATION ANALYSIS"
[1] 3
  RELT MUTATED RELT WILD-TYPE 
             7            386 
  RELT MUTATED RELT WILD-TYPE 
             7            386 
[1] "HAUS3 MUTATION ANALYSIS"
[1] 3
  HAUS3 MUTATED HAUS3 WILD-TYPE 
             11             382 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
             11             382 
[1] "CCDC150 MUTATION ANALYSIS"
[1] 3
  CCDC150 MUTATED CCDC150 WILD-TYPE 
               10               383 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
               10               383 
[1] "GLIPR1L2 MUTATION ANALYSIS"
[1] 3
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
                13                380 
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
                13                380 
[1] "ZNF23 MUTATION ANALYSIS"
[1] 3
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              3             390 
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              3             390 
[1] "OSGEPL1 MUTATION ANALYSIS"
[1] 3
  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE 
                4               389 
  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE 
                4               389 
[1] "EFHA2 MUTATION ANALYSIS"
[1] 3
  EFHA2 MUTATED EFHA2 WILD-TYPE 
             14             379 
  EFHA2 MUTATED EFHA2 WILD-TYPE 
             14             379 
[1] "CDH24 MUTATION ANALYSIS"
[1] 3
  CDH24 MUTATED CDH24 WILD-TYPE 
             14             379 
  CDH24 MUTATED CDH24 WILD-TYPE 
             14             379 
[1] "C6ORF150 MUTATION ANALYSIS"
[1] 3
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 8                385 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 8                385 
[1] "MGA MUTATION ANALYSIS"
[1] 3
  MGA MUTATED MGA WILD-TYPE 
           28           365 
  MGA MUTATED MGA WILD-TYPE 
           28           365 
[1] "SH3RF1 MUTATION ANALYSIS"
[1] 3
  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
              12              381 
  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
              12              381 
[1] "HTR1E MUTATION ANALYSIS"
[1] 3
  HTR1E MUTATED HTR1E WILD-TYPE 
             12             381 
  HTR1E MUTATED HTR1E WILD-TYPE 
             12             381 
[1] "FLNB MUTATION ANALYSIS"
[1] 3
  FLNB MUTATED FLNB WILD-TYPE 
            28            365 
  FLNB MUTATED FLNB WILD-TYPE 
            28            365 
[1] "NCAPH MUTATION ANALYSIS"
[1] 3
  NCAPH MUTATED NCAPH WILD-TYPE 
             12             381 
  NCAPH MUTATED NCAPH WILD-TYPE 
             12             381 
[1] "SLFN13 MUTATION ANALYSIS"
[1] 3
  SLFN13 MUTATED SLFN13 WILD-TYPE 
               9              384 
  SLFN13 MUTATED SLFN13 WILD-TYPE 
               9              384 
[1] "GATA3 MUTATION ANALYSIS"
[1] 3
  GATA3 MUTATED GATA3 WILD-TYPE 
             18             375 
  GATA3 MUTATED GATA3 WILD-TYPE 
             18             375 
[1] "RDBP MUTATION ANALYSIS"
[1] 3
  RDBP MUTATED RDBP WILD-TYPE 
            10            383 
  RDBP MUTATED RDBP WILD-TYPE 
            10            383 
[1] "TNRC6C MUTATION ANALYSIS"
[1] 3
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              15              378 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              15              378 
[1] "ZNF292 MUTATION ANALYSIS"
[1] 3
  ZNF292 MUTATED ZNF292 WILD-TYPE 
              29              364 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
              29              364 
[1] "TPTE2 MUTATION ANALYSIS"
[1] 3
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             17             376 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             17             376 
[1] "FBXO48 MUTATION ANALYSIS"
[1] 3
  FBXO48 MUTATED FBXO48 WILD-TYPE 
               5              388 
  FBXO48 MUTATED FBXO48 WILD-TYPE 
               5              388 
[1] "KRTAP5-5 MUTATION ANALYSIS"
[1] 3
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 6                387 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 6                387 
[1] "SERPINB12 MUTATION ANALYSIS"
[1] 3
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
                  6                 387 
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
                  6                 387 
[1] "TAF7L MUTATION ANALYSIS"
[1] 3
  TAF7L MUTATED TAF7L WILD-TYPE 
              9             384 
  TAF7L MUTATED TAF7L WILD-TYPE 
              9             384 
[1] "INTS12 MUTATION ANALYSIS"
[1] 3
  INTS12 MUTATED INTS12 WILD-TYPE 
               6              387 
  INTS12 MUTATED INTS12 WILD-TYPE 
               6              387 
[1] "CTSA MUTATION ANALYSIS"
[1] 3
  CTSA MUTATED CTSA WILD-TYPE 
             5            388 
  CTSA MUTATED CTSA WILD-TYPE 
             5            388 
[1] "C1QA MUTATION ANALYSIS"
[1] 3
  C1QA MUTATED C1QA WILD-TYPE 
             5            388 
  C1QA MUTATED C1QA WILD-TYPE 
             5            388 
[1] "KCNN3 MUTATION ANALYSIS"
[1] 3
  KCNN3 MUTATED KCNN3 WILD-TYPE 
             10             383 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
             10             383 
[1] "NPHS1 MUTATION ANALYSIS"
[1] 3
  NPHS1 MUTATED NPHS1 WILD-TYPE 
             16             377 
  NPHS1 MUTATED NPHS1 WILD-TYPE 
             16             377 
[1] "HSP90B1 MUTATION ANALYSIS"
[1] 3
  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
                9               384 
  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
                9               384 
[1] "P2RY4 MUTATION ANALYSIS"
[1] 3
  P2RY4 MUTATED P2RY4 WILD-TYPE 
             12             381 
  P2RY4 MUTATED P2RY4 WILD-TYPE 
             12             381 
[1] "LRFN3 MUTATION ANALYSIS"
[1] 3
  LRFN3 MUTATED LRFN3 WILD-TYPE 
             22             371 
  LRFN3 MUTATED LRFN3 WILD-TYPE 
             22             371 
[1] "SMARCB1 MUTATION ANALYSIS"
[1] 3
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               13               380 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               13               380 
[1] "ITGA6 MUTATION ANALYSIS"
[1] 3
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              9             384 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              9             384 
[1] "TRIP11 MUTATION ANALYSIS"
[1] 3
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              13              380 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              13              380 
[1] "PNPLA7 MUTATION ANALYSIS"
[1] 3
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
              23              370 
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
              23              370 
[1] "C7ORF49 MUTATION ANALYSIS"
[1] 3
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
                7               386 
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
                7               386 
[1] "C14ORF50 MUTATION ANALYSIS"
[1] 3
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 8                385 
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 8                385 
[1] "PKN1 MUTATION ANALYSIS"
[1] 3
  PKN1 MUTATED PKN1 WILD-TYPE 
            10            383 
  PKN1 MUTATED PKN1 WILD-TYPE 
            10            383 
[1] "ASAP2 MUTATION ANALYSIS"
[1] 3
  ASAP2 MUTATED ASAP2 WILD-TYPE 
             16             377 
  ASAP2 MUTATED ASAP2 WILD-TYPE 
             16             377 
[1] "FAM133A MUTATION ANALYSIS"
[1] 3
  FAM133A MUTATED FAM133A WILD-TYPE 
                9               384 
  FAM133A MUTATED FAM133A WILD-TYPE 
                9               384 
[1] "METTL6 MUTATION ANALYSIS"
[1] 3
  METTL6 MUTATED METTL6 WILD-TYPE 
               5              388 
  METTL6 MUTATED METTL6 WILD-TYPE 
               5              388 
[1] "EFHD1 MUTATION ANALYSIS"
[1] 3
  EFHD1 MUTATED EFHD1 WILD-TYPE 
              6             387 
  EFHD1 MUTATED EFHD1 WILD-TYPE 
              6             387 
[1] "VPS13A MUTATION ANALYSIS"
[1] 3
  VPS13A MUTATED VPS13A WILD-TYPE 
              38              355 
  VPS13A MUTATED VPS13A WILD-TYPE 
              38              355 
[1] "ANKRD28 MUTATION ANALYSIS"
[1] 3
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
               13               380 
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
               13               380 
[1] "OR5M3 MUTATION ANALYSIS"
[1] 3
  OR5M3 MUTATED OR5M3 WILD-TYPE 
             19             374 
  OR5M3 MUTATED OR5M3 WILD-TYPE 
             19             374 
[1] "EXPH5 MUTATION ANALYSIS"
[1] 3
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             15             378 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             15             378 
[1] "ABCB4 MUTATION ANALYSIS"
[1] 3
  ABCB4 MUTATED ABCB4 WILD-TYPE 
             26             367 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
             26             367 
[1] "HRNR MUTATION ANALYSIS"
[1] 3
  HRNR MUTATED HRNR WILD-TYPE 
            42            351 
  HRNR MUTATED HRNR WILD-TYPE 
            42            351 
[1] "BAHCC1 MUTATION ANALYSIS"
[1] 3
  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
              12              381 
  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
              12              381 
[1] "C1RL MUTATION ANALYSIS"
[1] 3
  C1RL MUTATED C1RL WILD-TYPE 
             6            387 
  C1RL MUTATED C1RL WILD-TYPE 
             6            387 
[1] "USP21 MUTATION ANALYSIS"
[1] 3
  USP21 MUTATED USP21 WILD-TYPE 
             13             380 
  USP21 MUTATED USP21 WILD-TYPE 
             13             380 
[1] "ZBTB38 MUTATION ANALYSIS"
[1] 3
  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
              20              373 
  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
              20              373 
[1] "CBLN3 MUTATION ANALYSIS"
[1] 3
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              7             386 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              7             386 
[1] "AXIN2 MUTATION ANALYSIS"
[1] 3
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             20             373 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             20             373 
[1] "CFI MUTATION ANALYSIS"
[1] 3
  CFI MUTATED CFI WILD-TYPE 
           13           380 
  CFI MUTATED CFI WILD-TYPE 
           13           380 
[1] "UNC50 MUTATION ANALYSIS"
[1] 3
  UNC50 MUTATED UNC50 WILD-TYPE 
              4             389 
  UNC50 MUTATED UNC50 WILD-TYPE 
              4             389 
[1] "TH1L MUTATION ANALYSIS"
[1] 3
  TH1L MUTATED TH1L WILD-TYPE 
            11            382 
  TH1L MUTATED TH1L WILD-TYPE 
            11            382 
[1] "HEXDC MUTATION ANALYSIS"
[1] 3
  HEXDC MUTATED HEXDC WILD-TYPE 
              8             385 
  HEXDC MUTATED HEXDC WILD-TYPE 
              8             385 
[1] "SOS2 MUTATION ANALYSIS"
[1] 3
  SOS2 MUTATED SOS2 WILD-TYPE 
            18            375 
  SOS2 MUTATED SOS2 WILD-TYPE 
            18            375 
[1] "SPOCD1 MUTATION ANALYSIS"
[1] 3
  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
              13              380 
  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
              13              380 
[1] "STX2 MUTATION ANALYSIS"
[1] 3
  STX2 MUTATED STX2 WILD-TYPE 
             6            387 
  STX2 MUTATED STX2 WILD-TYPE 
             6            387 
[1] "SMAD7 MUTATION ANALYSIS"
[1] 3
  SMAD7 MUTATED SMAD7 WILD-TYPE 
              7             386 
  SMAD7 MUTATED SMAD7 WILD-TYPE 
              7             386 
[1] "GNPNAT1 MUTATION ANALYSIS"
[1] 3
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
                6               387 
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
                6               387 
[1] "ALDH2 MUTATION ANALYSIS"
[1] 3
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             13             380 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             13             380 
[1] "TMEM55A MUTATION ANALYSIS"
[1] 3
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                3               390 
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                3               390 
[1] "SPATA5L1 MUTATION ANALYSIS"
[1] 3
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
                 6                387 
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
                 6                387 
[1] "CDC42EP1 MUTATION ANALYSIS"
[1] 3
  CDC42EP1 MUTATED CDC42EP1 WILD-TYPE 
                 4                389 
  CDC42EP1 MUTATED CDC42EP1 WILD-TYPE 
                 4                389 
[1] "SPATA20 MUTATION ANALYSIS"
[1] 3
  SPATA20 MUTATED SPATA20 WILD-TYPE 
               17               376 
  SPATA20 MUTATED SPATA20 WILD-TYPE 
               17               376 
[1] "KIN MUTATION ANALYSIS"
[1] 3
  KIN MUTATED KIN WILD-TYPE 
            7           386 
  KIN MUTATED KIN WILD-TYPE 
            7           386 
[1] "TMEM87B MUTATION ANALYSIS"
[1] 3
  TMEM87B MUTATED TMEM87B WILD-TYPE 
                5               388 
  TMEM87B MUTATED TMEM87B WILD-TYPE 
                5               388 
[1] "SP100 MUTATION ANALYSIS"
[1] 3
  SP100 MUTATED SP100 WILD-TYPE 
             18             375 
  SP100 MUTATED SP100 WILD-TYPE 
             18             375 
[1] "SOAT1 MUTATION ANALYSIS"
[1] 3
  SOAT1 MUTATED SOAT1 WILD-TYPE 
             10             383 
  SOAT1 MUTATED SOAT1 WILD-TYPE 
             10             383 
[1] "IL7R MUTATION ANALYSIS"
[1] 3
  IL7R MUTATED IL7R WILD-TYPE 
            14            379 
  IL7R MUTATED IL7R WILD-TYPE 
            14            379 
[1] "KRT222 MUTATION ANALYSIS"
[1] 3
  KRT222 MUTATED KRT222 WILD-TYPE 
               8              385 
  KRT222 MUTATED KRT222 WILD-TYPE 
               8              385 
[1] "AP2A2 MUTATION ANALYSIS"
[1] 3
  AP2A2 MUTATED AP2A2 WILD-TYPE 
             14             379 
  AP2A2 MUTATED AP2A2 WILD-TYPE 
             14             379 
[1] "RUSC2 MUTATION ANALYSIS"
[1] 3
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             20             373 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             20             373 
[1] "FAM186B MUTATION ANALYSIS"
[1] 3
  FAM186B MUTATED FAM186B WILD-TYPE 
               13               380 
  FAM186B MUTATED FAM186B WILD-TYPE 
               13               380 
[1] "MEGF8 MUTATION ANALYSIS"
[1] 3
  MEGF8 MUTATED MEGF8 WILD-TYPE 
             30             363 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
             30             363 
[1] "CTSD MUTATION ANALYSIS"
[1] 3
  CTSD MUTATED CTSD WILD-TYPE 
             8            385 
  CTSD MUTATED CTSD WILD-TYPE 
             8            385 
[1] "UBQLN2 MUTATION ANALYSIS"
[1] 3
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               7              386 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               7              386 
[1] "FNDC4 MUTATION ANALYSIS"
[1] 3
  FNDC4 MUTATED FNDC4 WILD-TYPE 
              6             387 
  FNDC4 MUTATED FNDC4 WILD-TYPE 
              6             387 
[1] "LIPH MUTATION ANALYSIS"
[1] 3
  LIPH MUTATED LIPH WILD-TYPE 
             7            386 
  LIPH MUTATED LIPH WILD-TYPE 
             7            386 
[1] "FBXO43 MUTATION ANALYSIS"
[1] 3
  FBXO43 MUTATED FBXO43 WILD-TYPE 
              10              383 
  FBXO43 MUTATED FBXO43 WILD-TYPE 
              10              383 
[1] "HOXB7 MUTATION ANALYSIS"
[1] 3
  HOXB7 MUTATED HOXB7 WILD-TYPE 
              6             387 
  HOXB7 MUTATED HOXB7 WILD-TYPE 
              6             387 
[1] "AGAP6 MUTATION ANALYSIS"
[1] 3
  AGAP6 MUTATED AGAP6 WILD-TYPE 
             10             383 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
             10             383 
[1] "GPR160 MUTATION ANALYSIS"
[1] 3
  GPR160 MUTATED GPR160 WILD-TYPE 
               8              385 
  GPR160 MUTATED GPR160 WILD-TYPE 
               8              385 
[1] "FAM46D MUTATION ANALYSIS"
[1] 3
  FAM46D MUTATED FAM46D WILD-TYPE 
              10              383 
  FAM46D MUTATED FAM46D WILD-TYPE 
              10              383 
[1] "CSF3R MUTATION ANALYSIS"
[1] 3
  CSF3R MUTATED CSF3R WILD-TYPE 
             12             381 
  CSF3R MUTATED CSF3R WILD-TYPE 
             12             381 
[1] "PRMT3 MUTATION ANALYSIS"
[1] 3
  PRMT3 MUTATED PRMT3 WILD-TYPE 
              9             384 
  PRMT3 MUTATED PRMT3 WILD-TYPE 
              9             384 
[1] "FGF7 MUTATION ANALYSIS"
[1] 3
  FGF7 MUTATED FGF7 WILD-TYPE 
             5            388 
  FGF7 MUTATED FGF7 WILD-TYPE 
             5            388 
[1] "AGAP5 MUTATION ANALYSIS"
[1] 3
  AGAP5 MUTATED AGAP5 WILD-TYPE 
              8             385 
  AGAP5 MUTATED AGAP5 WILD-TYPE 
              8             385 
[1] "STEAP2 MUTATION ANALYSIS"
[1] 3
  STEAP2 MUTATED STEAP2 WILD-TYPE 
               6              387 
  STEAP2 MUTATED STEAP2 WILD-TYPE 
               6              387 
[1] "CDKL3 MUTATION ANALYSIS"
[1] 3
  CDKL3 MUTATED CDKL3 WILD-TYPE 
              7             386 
  CDKL3 MUTATED CDKL3 WILD-TYPE 
              7             386 
[1] "FAM113A MUTATION ANALYSIS"
[1] 3
  FAM113A MUTATED FAM113A WILD-TYPE 
                9               384 
  FAM113A MUTATED FAM113A WILD-TYPE 
                9               384 
[1] "ZNF207 MUTATION ANALYSIS"
[1] 3
  ZNF207 MUTATED ZNF207 WILD-TYPE 
               8              385 
  ZNF207 MUTATED ZNF207 WILD-TYPE 
               8              385 
[1] "ICAM3 MUTATION ANALYSIS"
[1] 3
  ICAM3 MUTATED ICAM3 WILD-TYPE 
              4             389 
  ICAM3 MUTATED ICAM3 WILD-TYPE 
              4             389 
[1] "MKL1 MUTATION ANALYSIS"
[1] 3
  MKL1 MUTATED MKL1 WILD-TYPE 
            15            378 
  MKL1 MUTATED MKL1 WILD-TYPE 
            15            378 
[1] "HSP90AA1 MUTATION ANALYSIS"
[1] 3
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                12                381 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                12                381 
[1] "PRPF4B MUTATION ANALYSIS"
[1] 3
  PRPF4B MUTATED PRPF4B WILD-TYPE 
              10              383 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
              10              383 
[1] "BRCA2 MUTATION ANALYSIS"
[1] 3
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             33             360 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             33             360 
[1] "MAP3K1 MUTATION ANALYSIS"
[1] 3
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
              15              378 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
              15              378 
[1] "ASPN MUTATION ANALYSIS"
[1] 3
  ASPN MUTATED ASPN WILD-TYPE 
             6            387 
  ASPN MUTATED ASPN WILD-TYPE 
             6            387 
[1] "PHACTR1 MUTATION ANALYSIS"
[1] 3
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
               10               383 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
               10               383 
[1] "DNAJB13 MUTATION ANALYSIS"
[1] 3
  DNAJB13 MUTATED DNAJB13 WILD-TYPE 
                6               387 
  DNAJB13 MUTATED DNAJB13 WILD-TYPE 
                6               387 
[1] "KDM3B MUTATION ANALYSIS"
[1] 3
  KDM3B MUTATED KDM3B WILD-TYPE 
             20             373 
  KDM3B MUTATED KDM3B WILD-TYPE 
             20             373 
[1] "PDCD1 MUTATION ANALYSIS"
[1] 3
  PDCD1 MUTATED PDCD1 WILD-TYPE 
              5             388 
  PDCD1 MUTATED PDCD1 WILD-TYPE 
              5             388 
[1] "SYCP2L MUTATION ANALYSIS"
[1] 3
  SYCP2L MUTATED SYCP2L WILD-TYPE 
              13              380 
  SYCP2L MUTATED SYCP2L WILD-TYPE 
              13              380 
[1] "RNF111 MUTATION ANALYSIS"
[1] 3
  RNF111 MUTATED RNF111 WILD-TYPE 
              11              382 
  RNF111 MUTATED RNF111 WILD-TYPE 
              11              382 
[1] "OPLAH MUTATION ANALYSIS"
[1] 3
  OPLAH MUTATED OPLAH WILD-TYPE 
             23             370 
  OPLAH MUTATED OPLAH WILD-TYPE 
             23             370 
[1] "DYX1C1 MUTATION ANALYSIS"
[1] 3
  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
              12              381 
  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
              12              381 
[1] "RSF1 MUTATION ANALYSIS"
[1] 3
  RSF1 MUTATED RSF1 WILD-TYPE 
            15            378 
  RSF1 MUTATED RSF1 WILD-TYPE 
            15            378 
[1] "PRICKLE4 MUTATION ANALYSIS"
[1] 3
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
                 6                387 
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
                 6                387 
[1] "ANTXR1 MUTATION ANALYSIS"
[1] 3
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              10              383 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              10              383 
[1] "DNAJA1 MUTATION ANALYSIS"
[1] 3
  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
               9              384 
  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
               9              384 
[1] "C11ORF80 MUTATION ANALYSIS"
[1] 3
  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
                 6                387 
  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
                 6                387 
[1] "CLCA4 MUTATION ANALYSIS"
[1] 3
  CLCA4 MUTATED CLCA4 WILD-TYPE 
             17             376 
  CLCA4 MUTATED CLCA4 WILD-TYPE 
             17             376 
[1] "ANAPC1 MUTATION ANALYSIS"
[1] 3
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
              16              377 
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
              16              377 
[1] "SYT4 MUTATION ANALYSIS"
[1] 3
  SYT4 MUTATED SYT4 WILD-TYPE 
            14            379 
  SYT4 MUTATED SYT4 WILD-TYPE 
            14            379 
[1] "TAF6 MUTATION ANALYSIS"
[1] 3
  TAF6 MUTATED TAF6 WILD-TYPE 
            14            379 
  TAF6 MUTATED TAF6 WILD-TYPE 
            14            379 
[1] "C9ORF41 MUTATION ANALYSIS"
[1] 3
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
                5               388 
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
                5               388 
[1] "MARCH7 MUTATION ANALYSIS"
[1] 3
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               6              387 
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               6              387 
[1] "TAPT1 MUTATION ANALYSIS"
[1] 3
  TAPT1 MUTATED TAPT1 WILD-TYPE 
              6             387 
  TAPT1 MUTATED TAPT1 WILD-TYPE 
              6             387 
[1] "SDAD1 MUTATION ANALYSIS"
[1] 3
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              8             385 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              8             385 
[1] "PPIAL4A MUTATION ANALYSIS"
[1] 3
  PPIAL4A MUTATED PPIAL4A WILD-TYPE 
                3               390 
  PPIAL4A MUTATED PPIAL4A WILD-TYPE 
                3               390 
[1] "SCN10A MUTATION ANALYSIS"
[1] 3
  SCN10A MUTATED SCN10A WILD-TYPE 
              39              354 
  SCN10A MUTATED SCN10A WILD-TYPE 
              39              354 
[1] "PSD MUTATION ANALYSIS"
[1] 3
  PSD MUTATED PSD WILD-TYPE 
           18           375 
  PSD MUTATED PSD WILD-TYPE 
           18           375 
[1] "PODN MUTATION ANALYSIS"
[1] 3
  PODN MUTATED PODN WILD-TYPE 
            12            381 
  PODN MUTATED PODN WILD-TYPE 
            12            381 
[1] "NUFIP2 MUTATION ANALYSIS"
[1] 3
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
               8              385 
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
               8              385 
[1] "FRYL MUTATION ANALYSIS"
[1] 3
  FRYL MUTATED FRYL WILD-TYPE 
            24            369 
  FRYL MUTATED FRYL WILD-TYPE 
            24            369 
[1] "MYCN MUTATION ANALYSIS"
[1] 3
  MYCN MUTATED MYCN WILD-TYPE 
             7            386 
  MYCN MUTATED MYCN WILD-TYPE 
             7            386 
[1] "TNK2 MUTATION ANALYSIS"
[1] 3
  TNK2 MUTATED TNK2 WILD-TYPE 
            18            375 
  TNK2 MUTATED TNK2 WILD-TYPE 
            18            375 
[1] "C2ORF42 MUTATION ANALYSIS"
[1] 3
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
               12               381 
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
               12               381 
[1] "ADCY10 MUTATION ANALYSIS"
[1] 3
  ADCY10 MUTATED ADCY10 WILD-TYPE 
              20              373 
  ADCY10 MUTATED ADCY10 WILD-TYPE 
              20              373 
[1] "QRFPR MUTATION ANALYSIS"
[1] 3
  QRFPR MUTATED QRFPR WILD-TYPE 
             12             381 
  QRFPR MUTATED QRFPR WILD-TYPE 
             12             381 
[1] "C19ORF26 MUTATION ANALYSIS"
[1] 3
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
                10                383 
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
                10                383 
[1] "SPANXC MUTATION ANALYSIS"
[1] 3
  SPANXC MUTATED SPANXC WILD-TYPE 
               8              385 
  SPANXC MUTATED SPANXC WILD-TYPE 
               8              385 
[1] "XRN1 MUTATION ANALYSIS"
[1] 3
  XRN1 MUTATED XRN1 WILD-TYPE 
            24            369 
  XRN1 MUTATED XRN1 WILD-TYPE 
            24            369 
[1] "SORBS2 MUTATION ANALYSIS"
[1] 3
  SORBS2 MUTATED SORBS2 WILD-TYPE 
              21              372 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
              21              372 
[1] "LRP12 MUTATION ANALYSIS"
[1] 3
  LRP12 MUTATED LRP12 WILD-TYPE 
             30             363 
  LRP12 MUTATED LRP12 WILD-TYPE 
             30             363 
[1] "KIF13A MUTATION ANALYSIS"
[1] 3
  KIF13A MUTATED KIF13A WILD-TYPE 
              19              374 
  KIF13A MUTATED KIF13A WILD-TYPE 
              19              374 
[1] "C6 MUTATION ANALYSIS"
[1] 3
  C6 MUTATED C6 WILD-TYPE 
          11          382 
  C6 MUTATED C6 WILD-TYPE 
          11          382 
[1] "HIVEP3 MUTATION ANALYSIS"
[1] 3
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
              30              363 
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
              30              363 
[1] "FAM123C MUTATION ANALYSIS"
[1] 3
  FAM123C MUTATED FAM123C WILD-TYPE 
               13               380 
  FAM123C MUTATED FAM123C WILD-TYPE 
               13               380 
[1] "EPHB6 MUTATION ANALYSIS"
[1] 3
  EPHB6 MUTATED EPHB6 WILD-TYPE 
             17             376 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
             17             376 
[1] "PTPN13 MUTATION ANALYSIS"
[1] 3
  PTPN13 MUTATED PTPN13 WILD-TYPE 
              29              364 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
              29              364 
[1] "CALCRL MUTATION ANALYSIS"
[1] 3
  CALCRL MUTATED CALCRL WILD-TYPE 
              10              383 
  CALCRL MUTATED CALCRL WILD-TYPE 
              10              383 
[1] "AZGP1 MUTATION ANALYSIS"
[1] 3
  AZGP1 MUTATED AZGP1 WILD-TYPE 
              4             389 
  AZGP1 MUTATED AZGP1 WILD-TYPE 
              4             389 
[1] "DOK1 MUTATION ANALYSIS"
[1] 3
  DOK1 MUTATED DOK1 WILD-TYPE 
             5            388 
  DOK1 MUTATED DOK1 WILD-TYPE 
             5            388 
[1] "CDC5L MUTATION ANALYSIS"
[1] 3
  CDC5L MUTATED CDC5L WILD-TYPE 
             16             377 
  CDC5L MUTATED CDC5L WILD-TYPE 
             16             377 
[1] "KIF2B MUTATION ANALYSIS"
[1] 3
  KIF2B MUTATED KIF2B WILD-TYPE 
             32             361 
  KIF2B MUTATED KIF2B WILD-TYPE 
             32             361 
[1] "NOBOX MUTATION ANALYSIS"
[1] 3
  NOBOX MUTATED NOBOX WILD-TYPE 
             10             383 
  NOBOX MUTATED NOBOX WILD-TYPE 
             10             383 
[1] "GPR45 MUTATION ANALYSIS"
[1] 3
  GPR45 MUTATED GPR45 WILD-TYPE 
             16             377 
  GPR45 MUTATED GPR45 WILD-TYPE 
             16             377 
[1] "ACTR8 MUTATION ANALYSIS"
[1] 3
  ACTR8 MUTATED ACTR8 WILD-TYPE 
             11             382 
  ACTR8 MUTATED ACTR8 WILD-TYPE 
             11             382 
[1] "SCAMP2 MUTATION ANALYSIS"
[1] 3
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
               7              386 
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
               7              386 
[1] "HMGCLL1 MUTATION ANALYSIS"
[1] 3
  HMGCLL1 MUTATED HMGCLL1 WILD-TYPE 
               10               383 
  HMGCLL1 MUTATED HMGCLL1 WILD-TYPE 
               10               383 
[1] "COL11A1 MUTATION ANALYSIS"
[1] 3
  COL11A1 MUTATED COL11A1 WILD-TYPE 
               41               352 
  COL11A1 MUTATED COL11A1 WILD-TYPE 
               41               352 
[1] "BIN3 MUTATION ANALYSIS"
[1] 3
  BIN3 MUTATED BIN3 WILD-TYPE 
             4            389 
  BIN3 MUTATED BIN3 WILD-TYPE 
             4            389 
[1] "SLC25A17 MUTATION ANALYSIS"
[1] 3
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 4                389 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 4                389 
[1] "CTSO MUTATION ANALYSIS"
[1] 3
  CTSO MUTATED CTSO WILD-TYPE 
             6            387 
  CTSO MUTATED CTSO WILD-TYPE 
             6            387 
[1] "PAM MUTATION ANALYSIS"
[1] 3
  PAM MUTATED PAM WILD-TYPE 
            9           384 
  PAM MUTATED PAM WILD-TYPE 
            9           384 
[1] "TLE1 MUTATION ANALYSIS"
[1] 3
  TLE1 MUTATED TLE1 WILD-TYPE 
            12            381 
  TLE1 MUTATED TLE1 WILD-TYPE 
            12            381 
[1] "ZNF285 MUTATION ANALYSIS"
[1] 3
  ZNF285 MUTATED ZNF285 WILD-TYPE 
               9              384 
  ZNF285 MUTATED ZNF285 WILD-TYPE 
               9              384 
[1] "PTOV1 MUTATION ANALYSIS"
[1] 3
  PTOV1 MUTATED PTOV1 WILD-TYPE 
             11             382 
  PTOV1 MUTATED PTOV1 WILD-TYPE 
             11             382 
[1] "SLC6A11 MUTATION ANALYSIS"
[1] 3
  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
               10               383 
  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
               10               383 
[1] "BRCA1 MUTATION ANALYSIS"
[1] 3
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             15             378 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             15             378 
[1] "HAUS6 MUTATION ANALYSIS"
[1] 3
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             13             380 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             13             380 
[1] "ARHGEF11 MUTATION ANALYSIS"
[1] 3
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
                21                372 
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
                21                372 
[1] "MGST2 MUTATION ANALYSIS"
[1] 3
  MGST2 MUTATED MGST2 WILD-TYPE 
              3             390 
  MGST2 MUTATED MGST2 WILD-TYPE 
              3             390 
[1] "CD4 MUTATION ANALYSIS"
[1] 3
  CD4 MUTATED CD4 WILD-TYPE 
           11           382 
  CD4 MUTATED CD4 WILD-TYPE 
           11           382 
[1] "RP1L1 MUTATION ANALYSIS"
[1] 3
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             31             362 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             31             362 
[1] "UVRAG MUTATION ANALYSIS"
[1] 3
  UVRAG MUTATED UVRAG WILD-TYPE 
             12             381 
  UVRAG MUTATED UVRAG WILD-TYPE 
             12             381 
[1] "CHD1 MUTATION ANALYSIS"
[1] 3
  CHD1 MUTATED CHD1 WILD-TYPE 
            13            380 
  CHD1 MUTATED CHD1 WILD-TYPE 
            13            380 
[1] "ZMYND8 MUTATION ANALYSIS"
[1] 3
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
              19              374 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
              19              374 
[1] "GPATCH4 MUTATION ANALYSIS"
[1] 3
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                9               384 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                9               384 
[1] "MASTL MUTATION ANALYSIS"
[1] 3
  MASTL MUTATED MASTL WILD-TYPE 
             13             380 
  MASTL MUTATED MASTL WILD-TYPE 
             13             380 
[1] "KIRREL2 MUTATION ANALYSIS"
[1] 3
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               16               377 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               16               377 
[1] "HSPB8 MUTATION ANALYSIS"
[1] 3
  HSPB8 MUTATED HSPB8 WILD-TYPE 
              6             387 
  HSPB8 MUTATED HSPB8 WILD-TYPE 
              6             387 
[1] "GTF3C4 MUTATION ANALYSIS"
[1] 3
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
              13              380 
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
              13              380 
[1] "PPP3CA MUTATION ANALYSIS"
[1] 3
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              12              381 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              12              381 
[1] "NOB1 MUTATION ANALYSIS"
[1] 3
  NOB1 MUTATED NOB1 WILD-TYPE 
             7            386 
  NOB1 MUTATED NOB1 WILD-TYPE 
             7            386 
[1] "C15ORF52 MUTATION ANALYSIS"
[1] 3
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 6                387 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 6                387 
[1] "MEN1 MUTATION ANALYSIS"
[1] 3
  MEN1 MUTATED MEN1 WILD-TYPE 
            10            383 
  MEN1 MUTATED MEN1 WILD-TYPE 
            10            383 
[1] "MAPK15 MUTATION ANALYSIS"
[1] 3
  MAPK15 MUTATED MAPK15 WILD-TYPE 
               8              385 
  MAPK15 MUTATED MAPK15 WILD-TYPE 
               8              385 
[1] "DDX50 MUTATION ANALYSIS"
[1] 3
  DDX50 MUTATED DDX50 WILD-TYPE 
             12             381 
  DDX50 MUTATED DDX50 WILD-TYPE 
             12             381 
[1] "ATP6V1H MUTATION ANALYSIS"
[1] 3
  ATP6V1H MUTATED ATP6V1H WILD-TYPE 
               13               380 
  ATP6V1H MUTATED ATP6V1H WILD-TYPE 
               13               380 
[1] "KIAA1609 MUTATION ANALYSIS"
[1] 3
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
                 8                385 
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
                 8                385 
[1] "ITPR2 MUTATION ANALYSIS"
[1] 3
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             27             366 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             27             366 
[1] "NUP35 MUTATION ANALYSIS"
[1] 3
  NUP35 MUTATED NUP35 WILD-TYPE 
              6             387 
  NUP35 MUTATED NUP35 WILD-TYPE 
              6             387 
[1] "LIMCH1 MUTATION ANALYSIS"
[1] 3
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              12              381 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              12              381 
[1] "NAGPA MUTATION ANALYSIS"
[1] 3
  NAGPA MUTATED NAGPA WILD-TYPE 
              7             386 
  NAGPA MUTATED NAGPA WILD-TYPE 
              7             386 
[1] "PDS5A MUTATION ANALYSIS"
[1] 3
  PDS5A MUTATED PDS5A WILD-TYPE 
             17             376 
  PDS5A MUTATED PDS5A WILD-TYPE 
             17             376 
[1] "CEP110 MUTATION ANALYSIS"
[1] 3
  CEP110 MUTATED CEP110 WILD-TYPE 
              15              378 
  CEP110 MUTATED CEP110 WILD-TYPE 
              15              378 
[1] "DPAGT1 MUTATION ANALYSIS"
[1] 3
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
               6              387 
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
               6              387 
[1] "KCNH4 MUTATION ANALYSIS"
[1] 3
  KCNH4 MUTATED KCNH4 WILD-TYPE 
             11             382 
  KCNH4 MUTATED KCNH4 WILD-TYPE 
             11             382 
[1] "TCF20 MUTATION ANALYSIS"
[1] 3
  TCF20 MUTATED TCF20 WILD-TYPE 
             17             376 
  TCF20 MUTATED TCF20 WILD-TYPE 
             17             376 
[1] "EPB41 MUTATION ANALYSIS"
[1] 3
  EPB41 MUTATED EPB41 WILD-TYPE 
             13             380 
  EPB41 MUTATED EPB41 WILD-TYPE 
             13             380 
[1] "ARSJ MUTATION ANALYSIS"
[1] 3
  ARSJ MUTATED ARSJ WILD-TYPE 
             6            387 
  ARSJ MUTATED ARSJ WILD-TYPE 
             6            387 
[1] "PNMT MUTATION ANALYSIS"
[1] 3
  PNMT MUTATED PNMT WILD-TYPE 
            11            382 
  PNMT MUTATED PNMT WILD-TYPE 
            11            382 
[1] "AP3M2 MUTATION ANALYSIS"
[1] 3
  AP3M2 MUTATED AP3M2 WILD-TYPE 
             12             381 
  AP3M2 MUTATED AP3M2 WILD-TYPE 
             12             381 
[1] "EHBP1 MUTATION ANALYSIS"
[1] 3
  EHBP1 MUTATED EHBP1 WILD-TYPE 
             14             379 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
             14             379 
[1] "CRAT MUTATION ANALYSIS"
[1] 3
  CRAT MUTATED CRAT WILD-TYPE 
            12            381 
  CRAT MUTATED CRAT WILD-TYPE 
            12            381 
[1] "SMAP2 MUTATION ANALYSIS"
[1] 3
  SMAP2 MUTATED SMAP2 WILD-TYPE 
              5             388 
  SMAP2 MUTATED SMAP2 WILD-TYPE 
              5             388 
[1] "APITD1 MUTATION ANALYSIS"
[1] 3
  APITD1 MUTATED APITD1 WILD-TYPE 
               5              388 
  APITD1 MUTATED APITD1 WILD-TYPE 
               5              388 
[1] "KIFAP3 MUTATION ANALYSIS"
[1] 3
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
              14              379 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
              14              379 
[1] "ELL2 MUTATION ANALYSIS"
[1] 3
  ELL2 MUTATED ELL2 WILD-TYPE 
            15            378 
  ELL2 MUTATED ELL2 WILD-TYPE 
            15            378 
[1] "CEP290 MUTATION ANALYSIS"
[1] 3
  CEP290 MUTATED CEP290 WILD-TYPE 
              14              379 
  CEP290 MUTATED CEP290 WILD-TYPE 
              14              379 
[1] "MBD2 MUTATION ANALYSIS"
[1] 3
  MBD2 MUTATED MBD2 WILD-TYPE 
             9            384 
  MBD2 MUTATED MBD2 WILD-TYPE 
             9            384 
[1] "DDX43 MUTATION ANALYSIS"
[1] 3
  DDX43 MUTATED DDX43 WILD-TYPE 
             13             380 
  DDX43 MUTATED DDX43 WILD-TYPE 
             13             380 
[1] "DDHD1 MUTATION ANALYSIS"
[1] 3
  DDHD1 MUTATED DDHD1 WILD-TYPE 
             13             380 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
             13             380 
[1] "TMEM64 MUTATION ANALYSIS"
[1] 3
  TMEM64 MUTATED TMEM64 WILD-TYPE 
               7              386 
  TMEM64 MUTATED TMEM64 WILD-TYPE 
               7              386 
[1] "ECSIT MUTATION ANALYSIS"
[1] 3
  ECSIT MUTATED ECSIT WILD-TYPE 
              6             387 
  ECSIT MUTATED ECSIT WILD-TYPE 
              6             387 
[1] "KIAA1543 MUTATION ANALYSIS"
[1] 3
  KIAA1543 MUTATED KIAA1543 WILD-TYPE 
                17                376 
  KIAA1543 MUTATED KIAA1543 WILD-TYPE 
                17                376 
[1] "UPK2 MUTATION ANALYSIS"
[1] 3
  UPK2 MUTATED UPK2 WILD-TYPE 
             4            389 
  UPK2 MUTATED UPK2 WILD-TYPE 
             4            389 
[1] "IGFBP7 MUTATION ANALYSIS"
[1] 3
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               4              389 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               4              389 
[1] "ARPC5L MUTATION ANALYSIS"
[1] 3
  ARPC5L MUTATED ARPC5L WILD-TYPE 
               3              390 
  ARPC5L MUTATED ARPC5L WILD-TYPE 
               3              390 
[1] "TEX13A MUTATION ANALYSIS"
[1] 3
  TEX13A MUTATED TEX13A WILD-TYPE 
               5              388 
  TEX13A MUTATED TEX13A WILD-TYPE 
               5              388 
[1] "KCNQ1 MUTATION ANALYSIS"
[1] 3
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
              6             387 
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
              6             387 
[1] "HAPLN1 MUTATION ANALYSIS"
[1] 3
  HAPLN1 MUTATED HAPLN1 WILD-TYPE 
               9              384 
  HAPLN1 MUTATED HAPLN1 WILD-TYPE 
               9              384 
[1] "AXIN1 MUTATION ANALYSIS"
[1] 3
  AXIN1 MUTATED AXIN1 WILD-TYPE 
             14             379 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
             14             379 
[1] "AOC3 MUTATION ANALYSIS"
[1] 3
  AOC3 MUTATED AOC3 WILD-TYPE 
            11            382 
  AOC3 MUTATED AOC3 WILD-TYPE 
            11            382 
[1] "ANKRD23 MUTATION ANALYSIS"
[1] 3
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                6               387 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                6               387 
[1] "SOHLH2 MUTATION ANALYSIS"
[1] 3
  SOHLH2 MUTATED SOHLH2 WILD-TYPE 
              17              376 
  SOHLH2 MUTATED SOHLH2 WILD-TYPE 
              17              376 
[1] "SLC26A7 MUTATION ANALYSIS"
[1] 3
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               15               378 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               15               378 
[1] "RHOBTB2 MUTATION ANALYSIS"
[1] 3
  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE 
               20               373 
  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE 
               20               373 
[1] "DGKA MUTATION ANALYSIS"
[1] 3
  DGKA MUTATED DGKA WILD-TYPE 
             9            384 
  DGKA MUTATED DGKA WILD-TYPE 
             9            384 
[1] "KIAA1797 MUTATION ANALYSIS"
[1] 3
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                19                374 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                19                374 
[1] "SERPINB10 MUTATION ANALYSIS"
[1] 3
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                  8                 385 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                  8                 385 
[1] "SMCHD1 MUTATION ANALYSIS"
[1] 3
  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
              14              379 
  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
              14              379 
[1] "MOCS2 MUTATION ANALYSIS"
[1] 3
  MOCS2 MUTATED MOCS2 WILD-TYPE 
              5             388 
  MOCS2 MUTATED MOCS2 WILD-TYPE 
              5             388 
[1] "DGKD MUTATION ANALYSIS"
[1] 3
  DGKD MUTATED DGKD WILD-TYPE 
             6            387 
  DGKD MUTATED DGKD WILD-TYPE 
             6            387 
[1] "THEMIS MUTATION ANALYSIS"
[1] 3
  THEMIS MUTATED THEMIS WILD-TYPE 
              11              382 
  THEMIS MUTATED THEMIS WILD-TYPE 
              11              382 
[1] "BMPR2 MUTATION ANALYSIS"
[1] 3
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             19             374 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             19             374 
[1] "R3HDM2 MUTATION ANALYSIS"
[1] 3
  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
               9              384 
  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
               9              384 
[1] "BLMH MUTATION ANALYSIS"
[1] 3
  BLMH MUTATED BLMH WILD-TYPE 
             5            388 
  BLMH MUTATED BLMH WILD-TYPE 
             5            388 
[1] "PLEKHO1 MUTATION ANALYSIS"
[1] 3
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
                7               386 
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
                7               386 
[1] "INPP5F MUTATION ANALYSIS"
[1] 3
  INPP5F MUTATED INPP5F WILD-TYPE 
              15              378 
  INPP5F MUTATED INPP5F WILD-TYPE 
              15              378 
[1] "NLRC5 MUTATION ANALYSIS"
[1] 3
  NLRC5 MUTATED NLRC5 WILD-TYPE 
             23             370 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
             23             370 
[1] "MYCT1 MUTATION ANALYSIS"
[1] 3
  MYCT1 MUTATED MYCT1 WILD-TYPE 
              8             385 
  MYCT1 MUTATED MYCT1 WILD-TYPE 
              8             385 
[1] "CDC6 MUTATION ANALYSIS"
[1] 3
  CDC6 MUTATED CDC6 WILD-TYPE 
             8            385 
  CDC6 MUTATED CDC6 WILD-TYPE 
             8            385 
[1] "CDX2 MUTATION ANALYSIS"
[1] 3
  CDX2 MUTATED CDX2 WILD-TYPE 
             4            389 
  CDX2 MUTATED CDX2 WILD-TYPE 
             4            389 
[1] "EFHA1 MUTATION ANALYSIS"
[1] 3
  EFHA1 MUTATED EFHA1 WILD-TYPE 
             14             379 
  EFHA1 MUTATED EFHA1 WILD-TYPE 
             14             379 
[1] "GPR124 MUTATION ANALYSIS"
[1] 3
  GPR124 MUTATED GPR124 WILD-TYPE 
              17              376 
  GPR124 MUTATED GPR124 WILD-TYPE 
              17              376 
[1] "TEX15 MUTATION ANALYSIS"
[1] 3
  TEX15 MUTATED TEX15 WILD-TYPE 
             27             366 
  TEX15 MUTATED TEX15 WILD-TYPE 
             27             366 
[1] "CD33 MUTATION ANALYSIS"
[1] 3
  CD33 MUTATED CD33 WILD-TYPE 
             9            384 
  CD33 MUTATED CD33 WILD-TYPE 
             9            384 
[1] "GIPC3 MUTATION ANALYSIS"
[1] 3
  GIPC3 MUTATED GIPC3 WILD-TYPE 
              7             386 
  GIPC3 MUTATED GIPC3 WILD-TYPE 
              7             386 
[1] "PRAMEF14 MUTATION ANALYSIS"
[1] 3
  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
                 5                388 
  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
                 5                388 
[1] "PYGO2 MUTATION ANALYSIS"
[1] 3
  PYGO2 MUTATED PYGO2 WILD-TYPE 
              8             385 
  PYGO2 MUTATED PYGO2 WILD-TYPE 
              8             385 
[1] "AVEN MUTATION ANALYSIS"
[1] 3
  AVEN MUTATED AVEN WILD-TYPE 
             7            386 
  AVEN MUTATED AVEN WILD-TYPE 
             7            386 
[1] "BAT4 MUTATION ANALYSIS"
[1] 3
  BAT4 MUTATED BAT4 WILD-TYPE 
             5            388 
  BAT4 MUTATED BAT4 WILD-TYPE 
             5            388 
[1] "GPR1 MUTATION ANALYSIS"
[1] 3
  GPR1 MUTATED GPR1 WILD-TYPE 
             6            387 
  GPR1 MUTATED GPR1 WILD-TYPE 
             6            387 
[1] "KCTD9 MUTATION ANALYSIS"
[1] 3
  KCTD9 MUTATED KCTD9 WILD-TYPE 
             11             382 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
             11             382 
[1] "ZNF514 MUTATION ANALYSIS"
[1] 3
  ZNF514 MUTATED ZNF514 WILD-TYPE 
               9              384 
  ZNF514 MUTATED ZNF514 WILD-TYPE 
               9              384 
[1] "AFP MUTATION ANALYSIS"
[1] 3
  AFP MUTATED AFP WILD-TYPE 
            4           389 
  AFP MUTATED AFP WILD-TYPE 
            4           389 
[1] "TRIOBP MUTATION ANALYSIS"
[1] 3
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              30              363 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              30              363 
[1] "CCAR1 MUTATION ANALYSIS"
[1] 3
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             19             374 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             19             374 
[1] "TMEM127 MUTATION ANALYSIS"
[1] 3
  TMEM127 MUTATED TMEM127 WILD-TYPE 
                5               388 
  TMEM127 MUTATED TMEM127 WILD-TYPE 
                5               388 
[1] "ZNF142 MUTATION ANALYSIS"
[1] 3
  ZNF142 MUTATED ZNF142 WILD-TYPE 
              19              374 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
              19              374 
[1] "MRPS5 MUTATION ANALYSIS"
[1] 3
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              7             386 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              7             386 
[1] "CEP250 MUTATION ANALYSIS"
[1] 3
  CEP250 MUTATED CEP250 WILD-TYPE 
              21              372 
  CEP250 MUTATED CEP250 WILD-TYPE 
              21              372 
[1] "ARMC4 MUTATION ANALYSIS"
[1] 3
  ARMC4 MUTATED ARMC4 WILD-TYPE 
             18             375 
  ARMC4 MUTATED ARMC4 WILD-TYPE 
             18             375 
[1] "PCF11 MUTATION ANALYSIS"
[1] 3
  PCF11 MUTATED PCF11 WILD-TYPE 
             22             371 
  PCF11 MUTATED PCF11 WILD-TYPE 
             22             371 
[1] "C2ORF76 MUTATION ANALYSIS"
[1] 3
  C2ORF76 MUTATED C2ORF76 WILD-TYPE 
                4               389 
  C2ORF76 MUTATED C2ORF76 WILD-TYPE 
                4               389 
[1] "MBNL2 MUTATION ANALYSIS"
[1] 3
  MBNL2 MUTATED MBNL2 WILD-TYPE 
             11             382 
  MBNL2 MUTATED MBNL2 WILD-TYPE 
             11             382 
[1] "ITGAE MUTATION ANALYSIS"
[1] 3
  ITGAE MUTATED ITGAE WILD-TYPE 
             15             378 
  ITGAE MUTATED ITGAE WILD-TYPE 
             15             378 
[1] "KIF6 MUTATION ANALYSIS"
[1] 3
  KIF6 MUTATED KIF6 WILD-TYPE 
            12            381 
  KIF6 MUTATED KIF6 WILD-TYPE 
            12            381 
[1] "TNFSF13 MUTATION ANALYSIS"
[1] 3
  TNFSF13 MUTATED TNFSF13 WILD-TYPE 
                3               390 
  TNFSF13 MUTATED TNFSF13 WILD-TYPE 
                3               390 
[1] "CASKIN2 MUTATION ANALYSIS"
[1] 3
  CASKIN2 MUTATED CASKIN2 WILD-TYPE 
               15               378 
  CASKIN2 MUTATED CASKIN2 WILD-TYPE 
               15               378 
[1] "ALPK1 MUTATION ANALYSIS"
[1] 3
  ALPK1 MUTATED ALPK1 WILD-TYPE 
             19             374 
  ALPK1 MUTATED ALPK1 WILD-TYPE 
             19             374 
[1] "SUCLG2 MUTATION ANALYSIS"
[1] 3
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
               7              386 
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
               7              386 
[1] "NOS1 MUTATION ANALYSIS"
[1] 3
  NOS1 MUTATED NOS1 WILD-TYPE 
            31            362 
  NOS1 MUTATED NOS1 WILD-TYPE 
            31            362 
[1] "SLA MUTATION ANALYSIS"
[1] 3
  SLA MUTATED SLA WILD-TYPE 
            6           387 
  SLA MUTATED SLA WILD-TYPE 
            6           387 
[1] "C9ORF98 MUTATION ANALYSIS"
[1] 3
  C9ORF98 MUTATED C9ORF98 WILD-TYPE 
               10               383 
  C9ORF98 MUTATED C9ORF98 WILD-TYPE 
               10               383 
[1] "TOPBP1 MUTATION ANALYSIS"
[1] 3
  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
              16              377 
  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
              16              377 
[1] "KCNH2 MUTATION ANALYSIS"
[1] 3
  KCNH2 MUTATED KCNH2 WILD-TYPE 
             14             379 
  KCNH2 MUTATED KCNH2 WILD-TYPE 
             14             379 
[1] "FAHD2A MUTATION ANALYSIS"
[1] 3
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               8              385 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               8              385 
[1] "PTPN3 MUTATION ANALYSIS"
[1] 3
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             15             378 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             15             378 
[1] "E2F5 MUTATION ANALYSIS"
[1] 3
  E2F5 MUTATED E2F5 WILD-TYPE 
             4            389 
  E2F5 MUTATED E2F5 WILD-TYPE 
             4            389 
[1] "PABPC4 MUTATION ANALYSIS"
[1] 3
  PABPC4 MUTATED PABPC4 WILD-TYPE 
               9              384 
  PABPC4 MUTATED PABPC4 WILD-TYPE 
               9              384 
[1] "ERV3 MUTATION ANALYSIS"
[1] 3
  ERV3 MUTATED ERV3 WILD-TYPE 
             5            388 
  ERV3 MUTATED ERV3 WILD-TYPE 
             5            388 
[1] "SLC39A8 MUTATION ANALYSIS"
[1] 3
  SLC39A8 MUTATED SLC39A8 WILD-TYPE 
                7               386 
  SLC39A8 MUTATED SLC39A8 WILD-TYPE 
                7               386 
[1] "RIMKLB MUTATION ANALYSIS"
[1] 3
  RIMKLB MUTATED RIMKLB WILD-TYPE 
              11              382 
  RIMKLB MUTATED RIMKLB WILD-TYPE 
              11              382 
[1] "UGT1A4 MUTATION ANALYSIS"
[1] 3
  UGT1A4 MUTATED UGT1A4 WILD-TYPE 
              10              383 
  UGT1A4 MUTATED UGT1A4 WILD-TYPE 
              10              383 
[1] "PLA2G15 MUTATION ANALYSIS"
[1] 3
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
               10               383 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
               10               383 
[1] "MNS1 MUTATION ANALYSIS"
[1] 3
  MNS1 MUTATED MNS1 WILD-TYPE 
             8            385 
  MNS1 MUTATED MNS1 WILD-TYPE 
             8            385 
[1] "ZNF800 MUTATION ANALYSIS"
[1] 3
  ZNF800 MUTATED ZNF800 WILD-TYPE 
              12              381 
  ZNF800 MUTATED ZNF800 WILD-TYPE 
              12              381 
[1] "PHACTR2 MUTATION ANALYSIS"
[1] 3
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
               15               378 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
               15               378 
[1] "PLK2 MUTATION ANALYSIS"
[1] 3
  PLK2 MUTATED PLK2 WILD-TYPE 
             8            385 
  PLK2 MUTATED PLK2 WILD-TYPE 
             8            385 
[1] "SERPINB7 MUTATION ANALYSIS"
[1] 3
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 6                387 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 6                387 
[1] "ZNF295 MUTATION ANALYSIS"
[1] 3
  ZNF295 MUTATED ZNF295 WILD-TYPE 
              18              375 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
              18              375 
[1] "RINT1 MUTATION ANALYSIS"
[1] 3
  RINT1 MUTATED RINT1 WILD-TYPE 
              7             386 
  RINT1 MUTATED RINT1 WILD-TYPE 
              7             386 
[1] "PDS5B MUTATION ANALYSIS"
[1] 3
  PDS5B MUTATED PDS5B WILD-TYPE 
             19             374 
  PDS5B MUTATED PDS5B WILD-TYPE 
             19             374 
[1] "YBX2 MUTATION ANALYSIS"
[1] 3
  YBX2 MUTATED YBX2 WILD-TYPE 
             6            387 
  YBX2 MUTATED YBX2 WILD-TYPE 
             6            387 
[1] "CNOT6 MUTATION ANALYSIS"
[1] 3
  CNOT6 MUTATED CNOT6 WILD-TYPE 
              8             385 
  CNOT6 MUTATED CNOT6 WILD-TYPE 
              8             385 
[1] "ESRP1 MUTATION ANALYSIS"
[1] 3
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              9             384 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              9             384 
[1] "LCE1A MUTATION ANALYSIS"
[1] 3
  LCE1A MUTATED LCE1A WILD-TYPE 
              4             389 
  LCE1A MUTATED LCE1A WILD-TYPE 
              4             389 
[1] "PPARGC1B MUTATION ANALYSIS"
[1] 3
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                10                383 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                10                383 
[1] "MRPL24 MUTATION ANALYSIS"
[1] 3
  MRPL24 MUTATED MRPL24 WILD-TYPE 
               6              387 
  MRPL24 MUTATED MRPL24 WILD-TYPE 
               6              387 
[1] "F8 MUTATION ANALYSIS"
[1] 3
  F8 MUTATED F8 WILD-TYPE 
          30          363 
  F8 MUTATED F8 WILD-TYPE 
          30          363 
[1] "GOLT1B MUTATION ANALYSIS"
[1] 3
  GOLT1B MUTATED GOLT1B WILD-TYPE 
               5              388 
  GOLT1B MUTATED GOLT1B WILD-TYPE 
               5              388 
[1] "HOOK1 MUTATION ANALYSIS"
[1] 3
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              7             386 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              7             386 
[1] "ARHGEF5 MUTATION ANALYSIS"
[1] 3
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                7               386 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                7               386 
[1] "CIB3 MUTATION ANALYSIS"
[1] 3
  CIB3 MUTATED CIB3 WILD-TYPE 
             5            388 
  CIB3 MUTATED CIB3 WILD-TYPE 
             5            388 
[1] "TBL1XR1 MUTATION ANALYSIS"
[1] 3
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                8               385 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                8               385 
[1] "WHSC1L1 MUTATION ANALYSIS"
[1] 3
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
               18               375 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
               18               375 
[1] "C1ORF14 MUTATION ANALYSIS"
[1] 3
  C1ORF14 MUTATED C1ORF14 WILD-TYPE 
               14               379 
  C1ORF14 MUTATED C1ORF14 WILD-TYPE 
               14               379 
[1] "CUL1 MUTATION ANALYSIS"
[1] 3
  CUL1 MUTATED CUL1 WILD-TYPE 
            20            373 
  CUL1 MUTATED CUL1 WILD-TYPE 
            20            373 
[1] "C9ORF46 MUTATION ANALYSIS"
[1] 3
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
                4               389 
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
                4               389 
[1] "VPRBP MUTATION ANALYSIS"
[1] 3
  VPRBP MUTATED VPRBP WILD-TYPE 
              8             385 
  VPRBP MUTATED VPRBP WILD-TYPE 
              8             385 
[1] "INO80D MUTATION ANALYSIS"
[1] 3
  INO80D MUTATED INO80D WILD-TYPE 
              16              377 
  INO80D MUTATED INO80D WILD-TYPE 
              16              377 
[1] "B4GALNT4 MUTATION ANALYSIS"
[1] 3
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                18                375 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                18                375 
[1] "PTX4 MUTATION ANALYSIS"
[1] 3
  PTX4 MUTATED PTX4 WILD-TYPE 
            12            381 
  PTX4 MUTATED PTX4 WILD-TYPE 
            12            381 
[1] "ARHGEF17 MUTATION ANALYSIS"
[1] 3
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
                22                371 
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
                22                371 
[1] "GPR137B MUTATION ANALYSIS"
[1] 3
  GPR137B MUTATED GPR137B WILD-TYPE 
                6               387 
  GPR137B MUTATED GPR137B WILD-TYPE 
                6               387 
[1] "FAM109B MUTATION ANALYSIS"
[1] 3
  FAM109B MUTATED FAM109B WILD-TYPE 
                7               386 
  FAM109B MUTATED FAM109B WILD-TYPE 
                7               386 
[1] "HGF MUTATION ANALYSIS"
[1] 3
  HGF MUTATED HGF WILD-TYPE 
           18           375 
  HGF MUTATED HGF WILD-TYPE 
           18           375 
[1] "GPR114 MUTATION ANALYSIS"
[1] 3
  GPR114 MUTATED GPR114 WILD-TYPE 
               9              384 
  GPR114 MUTATED GPR114 WILD-TYPE 
               9              384 
[1] "DHRS9 MUTATION ANALYSIS"
[1] 3
  DHRS9 MUTATED DHRS9 WILD-TYPE 
              9             384 
  DHRS9 MUTATED DHRS9 WILD-TYPE 
              9             384 
[1] "RGS12 MUTATION ANALYSIS"
[1] 3
  RGS12 MUTATED RGS12 WILD-TYPE 
             30             363 
  RGS12 MUTATED RGS12 WILD-TYPE 
             30             363 
[1] "TRIP10 MUTATION ANALYSIS"
[1] 3
  TRIP10 MUTATED TRIP10 WILD-TYPE 
               9              384 
  TRIP10 MUTATED TRIP10 WILD-TYPE 
               9              384 
[1] "BTBD12 MUTATION ANALYSIS"
[1] 3
  BTBD12 MUTATED BTBD12 WILD-TYPE 
              25              368 
  BTBD12 MUTATED BTBD12 WILD-TYPE 
              25              368 
[1] "WAPAL MUTATION ANALYSIS"
[1] 3
  WAPAL MUTATED WAPAL WILD-TYPE 
             16             377 
  WAPAL MUTATED WAPAL WILD-TYPE 
             16             377 
[1] "CAB39L MUTATION ANALYSIS"
[1] 3
  CAB39L MUTATED CAB39L WILD-TYPE 
               7              386 
  CAB39L MUTATED CAB39L WILD-TYPE 
               7              386 
[1] "ZCCHC2 MUTATION ANALYSIS"
[1] 3
  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
               6              387 
  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
               6              387 
[1] "WDR90 MUTATION ANALYSIS"
[1] 3
  WDR90 MUTATED WDR90 WILD-TYPE 
             20             373 
  WDR90 MUTATED WDR90 WILD-TYPE 
             20             373 
[1] "UGT2A3 MUTATION ANALYSIS"
[1] 3
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
               7              386 
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
               7              386 
[1] "BRF1 MUTATION ANALYSIS"
[1] 3
  BRF1 MUTATED BRF1 WILD-TYPE 
            11            382 
  BRF1 MUTATED BRF1 WILD-TYPE 
            11            382 
[1] "PLK1 MUTATION ANALYSIS"
[1] 3
  PLK1 MUTATED PLK1 WILD-TYPE 
            16            377 
  PLK1 MUTATED PLK1 WILD-TYPE 
            16            377 
[1] "DUSP9 MUTATION ANALYSIS"
[1] 3
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              8             385 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              8             385 
[1] "KIAA0427 MUTATION ANALYSIS"
[1] 3
  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
                16                377 
  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
                16                377 
[1] "UBXN6 MUTATION ANALYSIS"
[1] 3
  UBXN6 MUTATED UBXN6 WILD-TYPE 
             12             381 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
             12             381 
[1] "EEF2K MUTATION ANALYSIS"
[1] 3
  EEF2K MUTATED EEF2K WILD-TYPE 
             10             383 
  EEF2K MUTATED EEF2K WILD-TYPE 
             10             383 
[1] "PYHIN1 MUTATION ANALYSIS"
[1] 3
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
              11              382 
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
              11              382 
[1] "C9ORF25 MUTATION ANALYSIS"
[1] 3
  C9ORF25 MUTATED C9ORF25 WILD-TYPE 
                5               388 
  C9ORF25 MUTATED C9ORF25 WILD-TYPE 
                5               388 
[1] "CD58 MUTATION ANALYSIS"
[1] 3
  CD58 MUTATED CD58 WILD-TYPE 
             7            386 
  CD58 MUTATED CD58 WILD-TYPE 
             7            386 
[1] "C20ORF7 MUTATION ANALYSIS"
[1] 3
  C20ORF7 MUTATED C20ORF7 WILD-TYPE 
                6               387 
  C20ORF7 MUTATED C20ORF7 WILD-TYPE 
                6               387 
[1] "POLE3 MUTATION ANALYSIS"
[1] 3
  POLE3 MUTATED POLE3 WILD-TYPE 
              3             390 
  POLE3 MUTATED POLE3 WILD-TYPE 
              3             390 
[1] "CHMP7 MUTATION ANALYSIS"
[1] 3
  CHMP7 MUTATED CHMP7 WILD-TYPE 
              5             388 
  CHMP7 MUTATED CHMP7 WILD-TYPE 
              5             388 
[1] "AMELX MUTATION ANALYSIS"
[1] 3
  AMELX MUTATED AMELX WILD-TYPE 
              5             388 
  AMELX MUTATED AMELX WILD-TYPE 
              5             388 
[1] "NEK8 MUTATION ANALYSIS"
[1] 3
  NEK8 MUTATED NEK8 WILD-TYPE 
            11            382 
  NEK8 MUTATED NEK8 WILD-TYPE 
            11            382 
[1] "POMGNT1 MUTATION ANALYSIS"
[1] 3
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
               10               383 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
               10               383 
[1] "ATP2B4 MUTATION ANALYSIS"
[1] 3
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
              15              378 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
              15              378 
[1] "KIAA1539 MUTATION ANALYSIS"
[1] 3
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
                10                383 
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
                10                383 
[1] "SEZ6 MUTATION ANALYSIS"
[1] 3
  SEZ6 MUTATED SEZ6 WILD-TYPE 
            13            380 
  SEZ6 MUTATED SEZ6 WILD-TYPE 
            13            380 
[1] "NARG2 MUTATION ANALYSIS"
[1] 3
  NARG2 MUTATED NARG2 WILD-TYPE 
             13             380 
  NARG2 MUTATED NARG2 WILD-TYPE 
             13             380 
[1] "CHD3 MUTATION ANALYSIS"
[1] 3
  CHD3 MUTATED CHD3 WILD-TYPE 
            28            365 
  CHD3 MUTATED CHD3 WILD-TYPE 
            28            365 
[1] "THSD1 MUTATION ANALYSIS"
[1] 3
  THSD1 MUTATED THSD1 WILD-TYPE 
             22             371 
  THSD1 MUTATED THSD1 WILD-TYPE 
             22             371 
[1] "CTNNA1 MUTATION ANALYSIS"
[1] 3
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
              15              378 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
              15              378 
[1] "BANK1 MUTATION ANALYSIS"
[1] 3
  BANK1 MUTATED BANK1 WILD-TYPE 
             11             382 
  BANK1 MUTATED BANK1 WILD-TYPE 
             11             382 
[1] "ZNF441 MUTATION ANALYSIS"
[1] 3
  ZNF441 MUTATED ZNF441 WILD-TYPE 
               9              384 
  ZNF441 MUTATED ZNF441 WILD-TYPE 
               9              384 
[1] "TBC1D8B MUTATION ANALYSIS"
[1] 3
  TBC1D8B MUTATED TBC1D8B WILD-TYPE 
                9               384 
  TBC1D8B MUTATED TBC1D8B WILD-TYPE 
                9               384 
[1] "CD3EAP MUTATION ANALYSIS"
[1] 3
  CD3EAP MUTATED CD3EAP WILD-TYPE 
              10              383 
  CD3EAP MUTATED CD3EAP WILD-TYPE 
              10              383 
[1] "EFNA4 MUTATION ANALYSIS"
[1] 3
  EFNA4 MUTATED EFNA4 WILD-TYPE 
              5             388 
  EFNA4 MUTATED EFNA4 WILD-TYPE 
              5             388 
[1] "COL20A1 MUTATION ANALYSIS"
[1] 3
  COL20A1 MUTATED COL20A1 WILD-TYPE 
               20               373 
  COL20A1 MUTATED COL20A1 WILD-TYPE 
               20               373 
[1] "SEC16B MUTATION ANALYSIS"
[1] 3
  SEC16B MUTATED SEC16B WILD-TYPE 
               7              386 
  SEC16B MUTATED SEC16B WILD-TYPE 
               7              386 
[1] "SIX3 MUTATION ANALYSIS"
[1] 3
  SIX3 MUTATED SIX3 WILD-TYPE 
            10            383 
  SIX3 MUTATED SIX3 WILD-TYPE 
            10            383 
[1] "SLC7A13 MUTATION ANALYSIS"
[1] 3
  SLC7A13 MUTATED SLC7A13 WILD-TYPE 
               11               382 
  SLC7A13 MUTATED SLC7A13 WILD-TYPE 
               11               382 
[1] "EMILIN3 MUTATION ANALYSIS"
[1] 3
  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
               14               379 
  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
               14               379 
[1] "EPB41L5 MUTATION ANALYSIS"
[1] 3
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
               10               383 
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
               10               383 
[1] "UTY MUTATION ANALYSIS"
[1] 3
  UTY MUTATED UTY WILD-TYPE 
            3           390 
  UTY MUTATED UTY WILD-TYPE 
            3           390 
[1] "CCT6A MUTATION ANALYSIS"
[1] 3
  CCT6A MUTATED CCT6A WILD-TYPE 
              8             385 
  CCT6A MUTATED CCT6A WILD-TYPE 
              8             385 
[1] "DGAT1 MUTATION ANALYSIS"
[1] 3
  DGAT1 MUTATED DGAT1 WILD-TYPE 
              9             384 
  DGAT1 MUTATED DGAT1 WILD-TYPE 
              9             384 
[1] "VWA1 MUTATION ANALYSIS"
[1] 3
  VWA1 MUTATED VWA1 WILD-TYPE 
             7            386 
  VWA1 MUTATED VWA1 WILD-TYPE 
             7            386 
[1] "ABCA5 MUTATION ANALYSIS"
[1] 3
  ABCA5 MUTATED ABCA5 WILD-TYPE 
             21             372 
  ABCA5 MUTATED ABCA5 WILD-TYPE 
             21             372 
[1] "LONRF1 MUTATION ANALYSIS"
[1] 3
  LONRF1 MUTATED LONRF1 WILD-TYPE 
               6              387 
  LONRF1 MUTATED LONRF1 WILD-TYPE 
               6              387 
[1] "PHF10 MUTATION ANALYSIS"
[1] 3
  PHF10 MUTATED PHF10 WILD-TYPE 
              4             389 
  PHF10 MUTATED PHF10 WILD-TYPE 
              4             389 
[1] "CYP4B1 MUTATION ANALYSIS"
[1] 3
  CYP4B1 MUTATED CYP4B1 WILD-TYPE 
              10              383 
  CYP4B1 MUTATED CYP4B1 WILD-TYPE 
              10              383 
[1] "EXO1 MUTATION ANALYSIS"
[1] 3
  EXO1 MUTATED EXO1 WILD-TYPE 
            17            376 
  EXO1 MUTATED EXO1 WILD-TYPE 
            17            376 
[1] "THYN1 MUTATION ANALYSIS"
[1] 3
  THYN1 MUTATED THYN1 WILD-TYPE 
              8             385 
  THYN1 MUTATED THYN1 WILD-TYPE 
              8             385 
[1] "FOXQ1 MUTATION ANALYSIS"
[1] 3
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              3             390 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              3             390 
[1] "HIVEP1 MUTATION ANALYSIS"
[1] 3
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
              24              369 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
              24              369 
[1] "ZNF687 MUTATION ANALYSIS"
[1] 3
  ZNF687 MUTATED ZNF687 WILD-TYPE 
              11              382 
  ZNF687 MUTATED ZNF687 WILD-TYPE 
              11              382 
[1] "PTPN23 MUTATION ANALYSIS"
[1] 3
  PTPN23 MUTATED PTPN23 WILD-TYPE 
              21              372 
  PTPN23 MUTATED PTPN23 WILD-TYPE 
              21              372 
[1] "ADAM7 MUTATION ANALYSIS"
[1] 3
  ADAM7 MUTATED ADAM7 WILD-TYPE 
             16             377 
  ADAM7 MUTATED ADAM7 WILD-TYPE 
             16             377 
[1] "NOP2 MUTATION ANALYSIS"
[1] 3
  NOP2 MUTATED NOP2 WILD-TYPE 
             8            385 
  NOP2 MUTATED NOP2 WILD-TYPE 
             8            385 
[1] "FAM26E MUTATION ANALYSIS"
[1] 3
  FAM26E MUTATED FAM26E WILD-TYPE 
               3              390 
  FAM26E MUTATED FAM26E WILD-TYPE 
               3              390 
[1] "OTX2 MUTATION ANALYSIS"
[1] 3
  OTX2 MUTATED OTX2 WILD-TYPE 
             9            384 
  OTX2 MUTATED OTX2 WILD-TYPE 
             9            384 
[1] "TMEM116 MUTATION ANALYSIS"
[1] 3
  TMEM116 MUTATED TMEM116 WILD-TYPE 
                3               390 
  TMEM116 MUTATED TMEM116 WILD-TYPE 
                3               390 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
            24            369 
  IRS4 MUTATED IRS4 WILD-TYPE 
            24            369 
[1] "C9ORF152 MUTATION ANALYSIS"
[1] 3
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
                 3                390 
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
                 3                390 
[1] "YIF1A MUTATION ANALYSIS"
[1] 3
  YIF1A MUTATED YIF1A WILD-TYPE 
              5             388 
  YIF1A MUTATED YIF1A WILD-TYPE 
              5             388 
[1] "RUSC1 MUTATION ANALYSIS"
[1] 3
  RUSC1 MUTATED RUSC1 WILD-TYPE 
             19             374 
  RUSC1 MUTATED RUSC1 WILD-TYPE 
             19             374 
[1] "CNTLN MUTATION ANALYSIS"
[1] 3
  CNTLN MUTATED CNTLN WILD-TYPE 
             36             357 
  CNTLN MUTATED CNTLN WILD-TYPE 
             36             357 
[1] "NUAK1 MUTATION ANALYSIS"
[1] 3
  NUAK1 MUTATED NUAK1 WILD-TYPE 
             18             375 
  NUAK1 MUTATED NUAK1 WILD-TYPE 
             18             375 
[1] "GCG MUTATION ANALYSIS"
[1] 3
  GCG MUTATED GCG WILD-TYPE 
            7           386 
  GCG MUTATED GCG WILD-TYPE 
            7           386 
[1] "VPS4B MUTATION ANALYSIS"
[1] 3
  VPS4B MUTATED VPS4B WILD-TYPE 
              8             385 
  VPS4B MUTATED VPS4B WILD-TYPE 
              8             385 
[1] "C12ORF40 MUTATION ANALYSIS"
[1] 3
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                 7                386 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                 7                386 
[1] "NHSL2 MUTATION ANALYSIS"
[1] 3
  NHSL2 MUTATED NHSL2 WILD-TYPE 
              6             387 
  NHSL2 MUTATED NHSL2 WILD-TYPE 
              6             387 
[1] "MYO9B MUTATION ANALYSIS"
[1] 3
  MYO9B MUTATED MYO9B WILD-TYPE 
             20             373 
  MYO9B MUTATED MYO9B WILD-TYPE 
             20             373 
[1] "PCLO MUTATION ANALYSIS"
[1] 3
  PCLO MUTATED PCLO WILD-TYPE 
            80            313 
  PCLO MUTATED PCLO WILD-TYPE 
            80            313 
[1] "KCNK13 MUTATION ANALYSIS"
[1] 3
  KCNK13 MUTATED KCNK13 WILD-TYPE 
              11              382 
  KCNK13 MUTATED KCNK13 WILD-TYPE 
              11              382 
[1] "SHMT2 MUTATION ANALYSIS"
[1] 3
  SHMT2 MUTATED SHMT2 WILD-TYPE 
             10             383 
  SHMT2 MUTATED SHMT2 WILD-TYPE 
             10             383 
[1] "TBC1D22B MUTATION ANALYSIS"
[1] 3
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
                 7                386 
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
                 7                386 
[1] "TACC2 MUTATION ANALYSIS"
[1] 3
  TACC2 MUTATED TACC2 WILD-TYPE 
             33             360 
  TACC2 MUTATED TACC2 WILD-TYPE 
             33             360 
[1] "EXOC3L2 MUTATION ANALYSIS"
[1] 3
  EXOC3L2 MUTATED EXOC3L2 WILD-TYPE 
                3               390 
  EXOC3L2 MUTATED EXOC3L2 WILD-TYPE 
                3               390 
[1] "BAG4 MUTATION ANALYSIS"
[1] 3
  BAG4 MUTATED BAG4 WILD-TYPE 
             5            388 
  BAG4 MUTATED BAG4 WILD-TYPE 
             5            388 
[1] "SLC26A8 MUTATION ANALYSIS"
[1] 3
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               10               383 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               10               383 
[1] "MBOAT2 MUTATION ANALYSIS"
[1] 3
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               3              390 
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               3              390 
[1] "GIMAP7 MUTATION ANALYSIS"
[1] 3
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
               5              388 
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
               5              388 
[1] "C2CD3 MUTATION ANALYSIS"
[1] 3
  C2CD3 MUTATED C2CD3 WILD-TYPE 
             23             370 
  C2CD3 MUTATED C2CD3 WILD-TYPE 
             23             370 
[1] "TAF1D MUTATION ANALYSIS"
[1] 3
  TAF1D MUTATED TAF1D WILD-TYPE 
              7             386 
  TAF1D MUTATED TAF1D WILD-TYPE 
              7             386 
[1] "CEP120 MUTATION ANALYSIS"
[1] 3
  CEP120 MUTATED CEP120 WILD-TYPE 
              12              381 
  CEP120 MUTATED CEP120 WILD-TYPE 
              12              381 
[1] "OR2M5 MUTATION ANALYSIS"
[1] 3
  OR2M5 MUTATED OR2M5 WILD-TYPE 
             15             378 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
             15             378 
[1] "ANKMY2 MUTATION ANALYSIS"
[1] 3
  ANKMY2 MUTATED ANKMY2 WILD-TYPE 
               4              389 
  ANKMY2 MUTATED ANKMY2 WILD-TYPE 
               4              389 
[1] "TYRO3 MUTATION ANALYSIS"
[1] 3
  TYRO3 MUTATED TYRO3 WILD-TYPE 
             11             382 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
             11             382 
[1] "VASH1 MUTATION ANALYSIS"
[1] 3
  VASH1 MUTATED VASH1 WILD-TYPE 
              7             386 
  VASH1 MUTATED VASH1 WILD-TYPE 
              7             386 
[1] "MCM4 MUTATION ANALYSIS"
[1] 3
  MCM4 MUTATED MCM4 WILD-TYPE 
            15            378 
  MCM4 MUTATED MCM4 WILD-TYPE 
            15            378 
[1] "PPP1R12C MUTATION ANALYSIS"
[1] 3
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 9                384 
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 9                384 
[1] "PRB1 MUTATION ANALYSIS"
[1] 3
  PRB1 MUTATED PRB1 WILD-TYPE 
             3            390 
  PRB1 MUTATED PRB1 WILD-TYPE 
             3            390 
[1] "TPD52L1 MUTATION ANALYSIS"
[1] 3
  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
               10               383 
  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
               10               383 
[1] "IGFALS MUTATION ANALYSIS"
[1] 3
  IGFALS MUTATED IGFALS WILD-TYPE 
               9              384 
  IGFALS MUTATED IGFALS WILD-TYPE 
               9              384 
[1] "PAPOLB MUTATION ANALYSIS"
[1] 3
  PAPOLB MUTATED PAPOLB WILD-TYPE 
              14              379 
  PAPOLB MUTATED PAPOLB WILD-TYPE 
              14              379 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              9             384 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              9             384 
[1] "ZMYND19 MUTATION ANALYSIS"
[1] 3
  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
                8               385 
  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
                8               385 
[1] "UBE2Q1 MUTATION ANALYSIS"
[1] 3
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
               7              386 
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
               7              386 
[1] "RYR2 MUTATION ANALYSIS"
[1] 3
  RYR2 MUTATED RYR2 WILD-TYPE 
            77            316 
  RYR2 MUTATED RYR2 WILD-TYPE 
            77            316 
[1] "STAU1 MUTATION ANALYSIS"
[1] 3
  STAU1 MUTATED STAU1 WILD-TYPE 
             10             383 
  STAU1 MUTATED STAU1 WILD-TYPE 
             10             383 
[1] "DLL1 MUTATION ANALYSIS"
[1] 3
  DLL1 MUTATED DLL1 WILD-TYPE 
            15            378 
  DLL1 MUTATED DLL1 WILD-TYPE 
            15            378 
[1] "E2F7 MUTATION ANALYSIS"
[1] 3
  E2F7 MUTATED E2F7 WILD-TYPE 
            20            373 
  E2F7 MUTATED E2F7 WILD-TYPE 
            20            373 
[1] "MYOCD MUTATION ANALYSIS"
[1] 3
  MYOCD MUTATED MYOCD WILD-TYPE 
             17             376 
  MYOCD MUTATED MYOCD WILD-TYPE 
             17             376 
[1] "EVI2B MUTATION ANALYSIS"
[1] 3
  EVI2B MUTATED EVI2B WILD-TYPE 
              9             384 
  EVI2B MUTATED EVI2B WILD-TYPE 
              9             384 
[1] "NRIP3 MUTATION ANALYSIS"
[1] 3
  NRIP3 MUTATED NRIP3 WILD-TYPE 
              7             386 
  NRIP3 MUTATED NRIP3 WILD-TYPE 
              7             386 
[1] "ABCA7 MUTATION ANALYSIS"
[1] 3
  ABCA7 MUTATED ABCA7 WILD-TYPE 
             20             373 
  ABCA7 MUTATED ABCA7 WILD-TYPE 
             20             373 
[1] "CWF19L2 MUTATION ANALYSIS"
[1] 3
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               14               379 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               14               379 
[1] "FIBP MUTATION ANALYSIS"
[1] 3
  FIBP MUTATED FIBP WILD-TYPE 
            11            382 
  FIBP MUTATED FIBP WILD-TYPE 
            11            382 
[1] "PLEKHH3 MUTATION ANALYSIS"
[1] 3
  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE 
               10               383 
  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE 
               10               383 
[1] "MAP7D2 MUTATION ANALYSIS"
[1] 3
  MAP7D2 MUTATED MAP7D2 WILD-TYPE 
               5              388 
  MAP7D2 MUTATED MAP7D2 WILD-TYPE 
               5              388 
[1] "ZDHHC7 MUTATION ANALYSIS"
[1] 3
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               7              386 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               7              386 
[1] "HTRA2 MUTATION ANALYSIS"
[1] 3
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              7             386 
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              7             386 
[1] "INSIG2 MUTATION ANALYSIS"
[1] 3
  INSIG2 MUTATED INSIG2 WILD-TYPE 
               7              386 
  INSIG2 MUTATED INSIG2 WILD-TYPE 
               7              386 
[1] "CLSTN1 MUTATION ANALYSIS"
[1] 3
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
              10              383 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
              10              383 
[1] "HNF1B MUTATION ANALYSIS"
[1] 3
  HNF1B MUTATED HNF1B WILD-TYPE 
              5             388 
  HNF1B MUTATED HNF1B WILD-TYPE 
              5             388 
[1] "IBTK MUTATION ANALYSIS"
[1] 3
  IBTK MUTATED IBTK WILD-TYPE 
            19            374 
  IBTK MUTATED IBTK WILD-TYPE 
            19            374 
[1] "SALL2 MUTATION ANALYSIS"
[1] 3
  SALL2 MUTATED SALL2 WILD-TYPE 
             14             379 
  SALL2 MUTATED SALL2 WILD-TYPE 
             14             379 
[1] "ELMO1 MUTATION ANALYSIS"
[1] 3
  ELMO1 MUTATED ELMO1 WILD-TYPE 
             23             370 
  ELMO1 MUTATED ELMO1 WILD-TYPE 
             23             370 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            18            375 
  BRAF MUTATED BRAF WILD-TYPE 
            18            375 
[1] "NFAT5 MUTATION ANALYSIS"
[1] 3
  NFAT5 MUTATED NFAT5 WILD-TYPE 
             12             381 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
             12             381 
[1] "ESRP2 MUTATION ANALYSIS"
[1] 3
  ESRP2 MUTATED ESRP2 WILD-TYPE 
              8             385 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
              8             385 
[1] "DHX36 MUTATION ANALYSIS"
[1] 3
  DHX36 MUTATED DHX36 WILD-TYPE 
             20             373 
  DHX36 MUTATED DHX36 WILD-TYPE 
             20             373 
[1] "ZCCHC6 MUTATION ANALYSIS"
[1] 3
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
              12              381 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
              12              381 
[1] "C8ORF38 MUTATION ANALYSIS"
[1] 3
  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
                8               385 
  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
                8               385 
[1] "NTAN1 MUTATION ANALYSIS"
[1] 3
  NTAN1 MUTATED NTAN1 WILD-TYPE 
              5             388 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
              5             388 
[1] "MLXIPL MUTATION ANALYSIS"
[1] 3
  MLXIPL MUTATED MLXIPL WILD-TYPE 
              13              380 
  MLXIPL MUTATED MLXIPL WILD-TYPE 
              13              380 
[1] "SFRS18 MUTATION ANALYSIS"
[1] 3
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              15              378 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              15              378 
[1] "PADI3 MUTATION ANALYSIS"
[1] 3
  PADI3 MUTATED PADI3 WILD-TYPE 
             13             380 
  PADI3 MUTATED PADI3 WILD-TYPE 
             13             380 
[1] "SLC38A6 MUTATION ANALYSIS"
[1] 3
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
                8               385 
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
                8               385 
[1] "RGS22 MUTATION ANALYSIS"
[1] 3
  RGS22 MUTATED RGS22 WILD-TYPE 
             21             372 
  RGS22 MUTATED RGS22 WILD-TYPE 
             21             372 
[1] "EVI5 MUTATION ANALYSIS"
[1] 3
  EVI5 MUTATED EVI5 WILD-TYPE 
            10            383 
  EVI5 MUTATED EVI5 WILD-TYPE 
            10            383 
[1] "POU5F1B MUTATION ANALYSIS"
[1] 3
  POU5F1B MUTATED POU5F1B WILD-TYPE 
                8               385 
  POU5F1B MUTATED POU5F1B WILD-TYPE 
                8               385 
[1] "NEIL1 MUTATION ANALYSIS"
[1] 3
  NEIL1 MUTATED NEIL1 WILD-TYPE 
              7             386 
  NEIL1 MUTATED NEIL1 WILD-TYPE 
              7             386 
[1] "LRRFIP2 MUTATION ANALYSIS"
[1] 3
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
                8               385 
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
                8               385 
[1] "IGDCC4 MUTATION ANALYSIS"
[1] 3
  IGDCC4 MUTATED IGDCC4 WILD-TYPE 
              13              380 
  IGDCC4 MUTATED IGDCC4 WILD-TYPE 
              13              380 
[1] "TRPM6 MUTATION ANALYSIS"
[1] 3
  TRPM6 MUTATED TRPM6 WILD-TYPE 
             22             371 
  TRPM6 MUTATED TRPM6 WILD-TYPE 
             22             371 
[1] "IL1F7 MUTATION ANALYSIS"
[1] 3
  IL1F7 MUTATED IL1F7 WILD-TYPE 
              3             390 
  IL1F7 MUTATED IL1F7 WILD-TYPE 
              3             390 
[1] "BRPF3 MUTATION ANALYSIS"
[1] 3
  BRPF3 MUTATED BRPF3 WILD-TYPE 
             11             382 
  BRPF3 MUTATED BRPF3 WILD-TYPE 
             11             382 
[1] "ACACB MUTATION ANALYSIS"
[1] 3
  ACACB MUTATED ACACB WILD-TYPE 
             32             361 
  ACACB MUTATED ACACB WILD-TYPE 
             32             361 
[1] "PIGZ MUTATION ANALYSIS"
[1] 3
  PIGZ MUTATED PIGZ WILD-TYPE 
             9            384 
  PIGZ MUTATED PIGZ WILD-TYPE 
             9            384 
[1] "SPATA2L MUTATION ANALYSIS"
[1] 3
  SPATA2L MUTATED SPATA2L WILD-TYPE 
                6               387 
  SPATA2L MUTATED SPATA2L WILD-TYPE 
                6               387 
[1] "SLC9A1 MUTATION ANALYSIS"
[1] 3
  SLC9A1 MUTATED SLC9A1 WILD-TYPE 
              12              381 
  SLC9A1 MUTATED SLC9A1 WILD-TYPE 
              12              381 
[1] "PAQR9 MUTATION ANALYSIS"
[1] 3
  PAQR9 MUTATED PAQR9 WILD-TYPE 
             16             377 
  PAQR9 MUTATED PAQR9 WILD-TYPE 
             16             377 
[1] "BTBD10 MUTATION ANALYSIS"
[1] 3
  BTBD10 MUTATED BTBD10 WILD-TYPE 
               5              388 
  BTBD10 MUTATED BTBD10 WILD-TYPE 
               5              388 
[1] "RAB40B MUTATION ANALYSIS"
[1] 3
  RAB40B MUTATED RAB40B WILD-TYPE 
               8              385 
  RAB40B MUTATED RAB40B WILD-TYPE 
               8              385 
[1] "CSNK1G3 MUTATION ANALYSIS"
[1] 3
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                9               384 
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                9               384 
[1] "ITGB8 MUTATION ANALYSIS"
[1] 3
  ITGB8 MUTATED ITGB8 WILD-TYPE 
             15             378 
  ITGB8 MUTATED ITGB8 WILD-TYPE 
             15             378 
[1] "ADAMTS18 MUTATION ANALYSIS"
[1] 3
  ADAMTS18 MUTATED ADAMTS18 WILD-TYPE 
                29                364 
  ADAMTS18 MUTATED ADAMTS18 WILD-TYPE 
                29                364 
[1] "NPR3 MUTATION ANALYSIS"
[1] 3
  NPR3 MUTATED NPR3 WILD-TYPE 
            10            383 
  NPR3 MUTATED NPR3 WILD-TYPE 
            10            383 
[1] "MTSS1L MUTATION ANALYSIS"
[1] 3
  MTSS1L MUTATED MTSS1L WILD-TYPE 
              10              383 
  MTSS1L MUTATED MTSS1L WILD-TYPE 
              10              383 
[1] "MINA MUTATION ANALYSIS"
[1] 3
  MINA MUTATED MINA WILD-TYPE 
             8            385 
  MINA MUTATED MINA WILD-TYPE 
             8            385 
[1] "CYTH3 MUTATION ANALYSIS"
[1] 3
  CYTH3 MUTATED CYTH3 WILD-TYPE 
              6             387 
  CYTH3 MUTATED CYTH3 WILD-TYPE 
              6             387 
[1] "PCDH19 MUTATION ANALYSIS"
[1] 3
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              26              367 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              26              367 
[1] "C11ORF88 MUTATION ANALYSIS"
[1] 3
  C11ORF88 MUTATED C11ORF88 WILD-TYPE 
                 7                386 
  C11ORF88 MUTATED C11ORF88 WILD-TYPE 
                 7                386 
[1] "MON2 MUTATION ANALYSIS"
[1] 3
  MON2 MUTATED MON2 WILD-TYPE 
            16            377 
  MON2 MUTATED MON2 WILD-TYPE 
            16            377 
[1] "AKD1 MUTATION ANALYSIS"
[1] 3
  AKD1 MUTATED AKD1 WILD-TYPE 
            15            378 
  AKD1 MUTATED AKD1 WILD-TYPE 
            15            378 
[1] "EXOSC8 MUTATION ANALYSIS"
[1] 3
  EXOSC8 MUTATED EXOSC8 WILD-TYPE 
               6              387 
  EXOSC8 MUTATED EXOSC8 WILD-TYPE 
               6              387 
[1] "CDH11 MUTATION ANALYSIS"
[1] 3
  CDH11 MUTATED CDH11 WILD-TYPE 
             32             361 
  CDH11 MUTATED CDH11 WILD-TYPE 
             32             361 
[1] "HCRTR1 MUTATION ANALYSIS"
[1] 3
  HCRTR1 MUTATED HCRTR1 WILD-TYPE 
               6              387 
  HCRTR1 MUTATED HCRTR1 WILD-TYPE 
               6              387 
[1] "ANKRD12 MUTATION ANALYSIS"
[1] 3
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
               20               373 
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
               20               373 
[1] "BMPR1B MUTATION ANALYSIS"
[1] 3
  BMPR1B MUTATED BMPR1B WILD-TYPE 
               9              384 
  BMPR1B MUTATED BMPR1B WILD-TYPE 
               9              384 
[1] "CRYBG3 MUTATION ANALYSIS"
[1] 3
  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
              14              379 
  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
              14              379 
[1] "KIDINS220 MUTATION ANALYSIS"
[1] 3
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
                 18                 375 
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
                 18                 375 
[1] "INSM2 MUTATION ANALYSIS"
[1] 3
  INSM2 MUTATED INSM2 WILD-TYPE 
             12             381 
  INSM2 MUTATED INSM2 WILD-TYPE 
             12             381 
[1] "ELOVL2 MUTATION ANALYSIS"
[1] 3
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
               7              386 
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
               7              386 
[1] "GON4L MUTATION ANALYSIS"
[1] 3
  GON4L MUTATED GON4L WILD-TYPE 
             12             381 
  GON4L MUTATED GON4L WILD-TYPE 
             12             381 
[1] "MSL3 MUTATION ANALYSIS"
[1] 3
  MSL3 MUTATED MSL3 WILD-TYPE 
             9            384 
  MSL3 MUTATED MSL3 WILD-TYPE 
             9            384 
[1] "FANCA MUTATION ANALYSIS"
[1] 3
  FANCA MUTATED FANCA WILD-TYPE 
             12             381 
  FANCA MUTATED FANCA WILD-TYPE 
             12             381 
[1] "SMPD1 MUTATION ANALYSIS"
[1] 3
  SMPD1 MUTATED SMPD1 WILD-TYPE 
              6             387 
  SMPD1 MUTATED SMPD1 WILD-TYPE 
              6             387 
[1] "IKBIP MUTATION ANALYSIS"
[1] 3
  IKBIP MUTATED IKBIP WILD-TYPE 
              3             390 
  IKBIP MUTATED IKBIP WILD-TYPE 
              3             390 
[1] "LEFTY1 MUTATION ANALYSIS"
[1] 3
  LEFTY1 MUTATED LEFTY1 WILD-TYPE 
               3              390 
  LEFTY1 MUTATED LEFTY1 WILD-TYPE 
               3              390 
[1] "PIWIL2 MUTATION ANALYSIS"
[1] 3
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
               9              384 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
               9              384 
[1] "ZNF7 MUTATION ANALYSIS"
[1] 3
  ZNF7 MUTATED ZNF7 WILD-TYPE 
             9            384 
  ZNF7 MUTATED ZNF7 WILD-TYPE 
             9            384 
[1] "CHST4 MUTATION ANALYSIS"
[1] 3
  CHST4 MUTATED CHST4 WILD-TYPE 
              7             386 
  CHST4 MUTATED CHST4 WILD-TYPE 
              7             386 
[1] "SCGB1A1 MUTATION ANALYSIS"
[1] 3
  SCGB1A1 MUTATED SCGB1A1 WILD-TYPE 
                3               390 
  SCGB1A1 MUTATED SCGB1A1 WILD-TYPE 
                3               390 
[1] "ZIM3 MUTATION ANALYSIS"
[1] 3
  ZIM3 MUTATED ZIM3 WILD-TYPE 
            11            382 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
            11            382 
[1] "ACTG2 MUTATION ANALYSIS"
[1] 3
  ACTG2 MUTATED ACTG2 WILD-TYPE 
             10             383 
  ACTG2 MUTATED ACTG2 WILD-TYPE 
             10             383 
[1] "PIK3CB MUTATION ANALYSIS"
[1] 3
  PIK3CB MUTATED PIK3CB WILD-TYPE 
              11              382 
  PIK3CB MUTATED PIK3CB WILD-TYPE 
              11              382 
[1] "LAT2 MUTATION ANALYSIS"
[1] 3
  LAT2 MUTATED LAT2 WILD-TYPE 
             8            385 
  LAT2 MUTATED LAT2 WILD-TYPE 
             8            385 
[1] "ZBTB40 MUTATION ANALYSIS"
[1] 3
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
              11              382 
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
              11              382 
[1] "PIGO MUTATION ANALYSIS"
[1] 3
  PIGO MUTATED PIGO WILD-TYPE 
             9            384 
  PIGO MUTATED PIGO WILD-TYPE 
             9            384 
[1] "NAA16 MUTATION ANALYSIS"
[1] 3
  NAA16 MUTATED NAA16 WILD-TYPE 
              9             384 
  NAA16 MUTATED NAA16 WILD-TYPE 
              9             384 
[1] "NRN1 MUTATION ANALYSIS"
[1] 3
  NRN1 MUTATED NRN1 WILD-TYPE 
             3            390 
  NRN1 MUTATED NRN1 WILD-TYPE 
             3            390 
[1] "EPN1 MUTATION ANALYSIS"
[1] 3
  EPN1 MUTATED EPN1 WILD-TYPE 
             8            385 
  EPN1 MUTATED EPN1 WILD-TYPE 
             8            385 
[1] "PPARG MUTATION ANALYSIS"
[1] 3
  PPARG MUTATED PPARG WILD-TYPE 
              4             389 
  PPARG MUTATED PPARG WILD-TYPE 
              4             389 
[1] "C1ORF141 MUTATION ANALYSIS"
[1] 3
  C1ORF141 MUTATED C1ORF141 WILD-TYPE 
                12                381 
  C1ORF141 MUTATED C1ORF141 WILD-TYPE 
                12                381 
[1] "EXOSC10 MUTATION ANALYSIS"
[1] 3
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
               12               381 
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
               12               381 
[1] "ARID3A MUTATION ANALYSIS"
[1] 3
  ARID3A MUTATED ARID3A WILD-TYPE 
               6              387 
  ARID3A MUTATED ARID3A WILD-TYPE 
               6              387 
[1] "RAB14 MUTATION ANALYSIS"
[1] 3
  RAB14 MUTATED RAB14 WILD-TYPE 
              6             387 
  RAB14 MUTATED RAB14 WILD-TYPE 
              6             387 
[1] "IGSF9B MUTATION ANALYSIS"
[1] 3
  IGSF9B MUTATED IGSF9B WILD-TYPE 
              20              373 
  IGSF9B MUTATED IGSF9B WILD-TYPE 
              20              373 
[1] "ARNT MUTATION ANALYSIS"
[1] 3
  ARNT MUTATED ARNT WILD-TYPE 
             8            385 
  ARNT MUTATED ARNT WILD-TYPE 
             8            385 
[1] "CSNK2A2 MUTATION ANALYSIS"
[1] 3
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                8               385 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                8               385 
[1] "HOXA1 MUTATION ANALYSIS"
[1] 3
  HOXA1 MUTATED HOXA1 WILD-TYPE 
             10             383 
  HOXA1 MUTATED HOXA1 WILD-TYPE 
             10             383 
[1] "SYNJ1 MUTATION ANALYSIS"
[1] 3
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
             11             382 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
             11             382 
[1] "ABCC2 MUTATION ANALYSIS"
[1] 3
  ABCC2 MUTATED ABCC2 WILD-TYPE 
             16             377 
  ABCC2 MUTATED ABCC2 WILD-TYPE 
             16             377 
[1] "HEPACAM2 MUTATION ANALYSIS"
[1] 3
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                 8                385 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                 8                385 
[1] "MAP4K4 MUTATION ANALYSIS"
[1] 3
  MAP4K4 MUTATED MAP4K4 WILD-TYPE 
              13              380 
  MAP4K4 MUTATED MAP4K4 WILD-TYPE 
              13              380 
[1] "B4GALT6 MUTATION ANALYSIS"
[1] 3
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
                6               387 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
                6               387 
[1] "NAA25 MUTATION ANALYSIS"
[1] 3
  NAA25 MUTATED NAA25 WILD-TYPE 
             15             378 
  NAA25 MUTATED NAA25 WILD-TYPE 
             15             378 
[1] "SAFB MUTATION ANALYSIS"
[1] 3
  SAFB MUTATED SAFB WILD-TYPE 
             8            385 
  SAFB MUTATED SAFB WILD-TYPE 
             8            385 
[1] "ABLIM2 MUTATION ANALYSIS"
[1] 3
  ABLIM2 MUTATED ABLIM2 WILD-TYPE 
              14              379 
  ABLIM2 MUTATED ABLIM2 WILD-TYPE 
              14              379 
[1] "CEL MUTATION ANALYSIS"
[1] 3
  CEL MUTATED CEL WILD-TYPE 
           15           378 
  CEL MUTATED CEL WILD-TYPE 
           15           378 
[1] "FAM178A MUTATION ANALYSIS"
[1] 3
  FAM178A MUTATED FAM178A WILD-TYPE 
               11               382 
  FAM178A MUTATED FAM178A WILD-TYPE 
               11               382 
[1] "BUB1B MUTATION ANALYSIS"
[1] 3
  BUB1B MUTATED BUB1B WILD-TYPE 
             12             381 
  BUB1B MUTATED BUB1B WILD-TYPE 
             12             381 
[1] "EEA1 MUTATION ANALYSIS"
[1] 3
  EEA1 MUTATED EEA1 WILD-TYPE 
            14            379 
  EEA1 MUTATED EEA1 WILD-TYPE 
            14            379 
[1] "KCNH3 MUTATION ANALYSIS"
[1] 3
  KCNH3 MUTATED KCNH3 WILD-TYPE 
             17             376 
  KCNH3 MUTATED KCNH3 WILD-TYPE 
             17             376 
[1] "DIP2C MUTATION ANALYSIS"
[1] 3
  DIP2C MUTATED DIP2C WILD-TYPE 
             22             371 
  DIP2C MUTATED DIP2C WILD-TYPE 
             22             371 
[1] "KLHL1 MUTATION ANALYSIS"
[1] 3
  KLHL1 MUTATED KLHL1 WILD-TYPE 
             15             378 
  KLHL1 MUTATED KLHL1 WILD-TYPE 
             15             378 
[1] "ZC3H3 MUTATION ANALYSIS"
[1] 3
  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
             19             374 
  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
             19             374 
[1] "SLC22A16 MUTATION ANALYSIS"
[1] 3
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                11                382 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                11                382 
[1] "NHLRC2 MUTATION ANALYSIS"
[1] 3
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               7              386 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               7              386 
[1] "CEACAM3 MUTATION ANALYSIS"
[1] 3
  CEACAM3 MUTATED CEACAM3 WILD-TYPE 
                9               384 
  CEACAM3 MUTATED CEACAM3 WILD-TYPE 
                9               384 
[1] "THBS3 MUTATION ANALYSIS"
[1] 3
  THBS3 MUTATED THBS3 WILD-TYPE 
             10             383 
  THBS3 MUTATED THBS3 WILD-TYPE 
             10             383 
[1] "GPC4 MUTATION ANALYSIS"
[1] 3
  GPC4 MUTATED GPC4 WILD-TYPE 
             8            385 
  GPC4 MUTATED GPC4 WILD-TYPE 
             8            385 
[1] "ABTB1 MUTATION ANALYSIS"
[1] 3
  ABTB1 MUTATED ABTB1 WILD-TYPE 
             10             383 
  ABTB1 MUTATED ABTB1 WILD-TYPE 
             10             383 
[1] "NEK7 MUTATION ANALYSIS"
[1] 3
  NEK7 MUTATED NEK7 WILD-TYPE 
             6            387 
  NEK7 MUTATED NEK7 WILD-TYPE 
             6            387 
[1] "QTRTD1 MUTATION ANALYSIS"
[1] 3
  QTRTD1 MUTATED QTRTD1 WILD-TYPE 
               6              387 
  QTRTD1 MUTATED QTRTD1 WILD-TYPE 
               6              387 
[1] "UACA MUTATION ANALYSIS"
[1] 3
  UACA MUTATED UACA WILD-TYPE 
            14            379 
  UACA MUTATED UACA WILD-TYPE 
            14            379 
[1] "TMEM206 MUTATION ANALYSIS"
[1] 3
  TMEM206 MUTATED TMEM206 WILD-TYPE 
                7               386 
  TMEM206 MUTATED TMEM206 WILD-TYPE 
                7               386 
[1] "CDKN2AIP MUTATION ANALYSIS"
[1] 3
  CDKN2AIP MUTATED CDKN2AIP WILD-TYPE 
                 3                390 
  CDKN2AIP MUTATED CDKN2AIP WILD-TYPE 
                 3                390 
[1] "CLGN MUTATION ANALYSIS"
[1] 3
  CLGN MUTATED CLGN WILD-TYPE 
             9            384 
  CLGN MUTATED CLGN WILD-TYPE 
             9            384 
[1] "ACAA2 MUTATION ANALYSIS"
[1] 3
  ACAA2 MUTATED ACAA2 WILD-TYPE 
              8             385 
  ACAA2 MUTATED ACAA2 WILD-TYPE 
              8             385 
[1] "SLC25A45 MUTATION ANALYSIS"
[1] 3
  SLC25A45 MUTATED SLC25A45 WILD-TYPE 
                 9                384 
  SLC25A45 MUTATED SLC25A45 WILD-TYPE 
                 9                384 
[1] "TMEFF2 MUTATION ANALYSIS"
[1] 3
  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
              10              383 
  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
              10              383 
[1] "IFNA17 MUTATION ANALYSIS"
[1] 3
  IFNA17 MUTATED IFNA17 WILD-TYPE 
               4              389 
  IFNA17 MUTATED IFNA17 WILD-TYPE 
               4              389 
[1] "PGBD1 MUTATION ANALYSIS"
[1] 3
  PGBD1 MUTATED PGBD1 WILD-TYPE 
             14             379 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
             14             379 
[1] "FCN2 MUTATION ANALYSIS"
[1] 3
  FCN2 MUTATED FCN2 WILD-TYPE 
            10            383 
  FCN2 MUTATED FCN2 WILD-TYPE 
            10            383 
[1] "PTPRJ MUTATION ANALYSIS"
[1] 3
  PTPRJ MUTATED PTPRJ WILD-TYPE 
             28             365 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
             28             365 
[1] "C11ORF63 MUTATION ANALYSIS"
[1] 3
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                20                373 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                20                373 
[1] "HSF4 MUTATION ANALYSIS"
[1] 3
  HSF4 MUTATED HSF4 WILD-TYPE 
             8            385 
  HSF4 MUTATED HSF4 WILD-TYPE 
             8            385 
[1] "CNPY4 MUTATION ANALYSIS"
[1] 3
  CNPY4 MUTATED CNPY4 WILD-TYPE 
              4             389 
  CNPY4 MUTATED CNPY4 WILD-TYPE 
              4             389 
[1] "FAM167A MUTATION ANALYSIS"
[1] 3
  FAM167A MUTATED FAM167A WILD-TYPE 
                8               385 
  FAM167A MUTATED FAM167A WILD-TYPE 
                8               385 
[1] "DMC1 MUTATION ANALYSIS"
[1] 3
  DMC1 MUTATED DMC1 WILD-TYPE 
             8            385 
  DMC1 MUTATED DMC1 WILD-TYPE 
             8            385 
[1] "DENND4C MUTATION ANALYSIS"
[1] 3
  DENND4C MUTATED DENND4C WILD-TYPE 
               16               377 
  DENND4C MUTATED DENND4C WILD-TYPE 
               16               377 
[1] "DEK MUTATION ANALYSIS"
[1] 3
  DEK MUTATED DEK WILD-TYPE 
            8           385 
  DEK MUTATED DEK WILD-TYPE 
            8           385 
[1] "SP140 MUTATION ANALYSIS"
[1] 3
  SP140 MUTATED SP140 WILD-TYPE 
             16             377 
  SP140 MUTATED SP140 WILD-TYPE 
             16             377 
[1] "EGR1 MUTATION ANALYSIS"
[1] 3
  EGR1 MUTATED EGR1 WILD-TYPE 
            12            381 
  EGR1 MUTATED EGR1 WILD-TYPE 
            12            381 
[1] "PKD2L2 MUTATION ANALYSIS"
[1] 3
  PKD2L2 MUTATED PKD2L2 WILD-TYPE 
              10              383 
  PKD2L2 MUTATED PKD2L2 WILD-TYPE 
              10              383 
[1] "FGF13 MUTATION ANALYSIS"
[1] 3
  FGF13 MUTATED FGF13 WILD-TYPE 
             15             378 
  FGF13 MUTATED FGF13 WILD-TYPE 
             15             378 
[1] "MAP4K5 MUTATION ANALYSIS"
[1] 3
  MAP4K5 MUTATED MAP4K5 WILD-TYPE 
               4              389 
  MAP4K5 MUTATED MAP4K5 WILD-TYPE 
               4              389 
[1] "ARID5B MUTATION ANALYSIS"
[1] 3
  ARID5B MUTATED ARID5B WILD-TYPE 
              15              378 
  ARID5B MUTATED ARID5B WILD-TYPE 
              15              378 
[1] "CCDC92 MUTATION ANALYSIS"
[1] 3
  CCDC92 MUTATED CCDC92 WILD-TYPE 
               7              386 
  CCDC92 MUTATED CCDC92 WILD-TYPE 
               7              386 
[1] "CNGA1 MUTATION ANALYSIS"
[1] 3
  CNGA1 MUTATED CNGA1 WILD-TYPE 
             10             383 
  CNGA1 MUTATED CNGA1 WILD-TYPE 
             10             383 
[1] "RAE1 MUTATION ANALYSIS"
[1] 3
  RAE1 MUTATED RAE1 WILD-TYPE 
             8            385 
  RAE1 MUTATED RAE1 WILD-TYPE 
             8            385 
[1] "ZC3H8 MUTATION ANALYSIS"
[1] 3
  ZC3H8 MUTATED ZC3H8 WILD-TYPE 
              4             389 
  ZC3H8 MUTATED ZC3H8 WILD-TYPE 
              4             389 
[1] "WDR53 MUTATION ANALYSIS"
[1] 3
  WDR53 MUTATED WDR53 WILD-TYPE 
              6             387 
  WDR53 MUTATED WDR53 WILD-TYPE 
              6             387 
[1] "EPB41L4B MUTATION ANALYSIS"
[1] 3
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
                18                375 
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
                18                375 
[1] "RNMT MUTATION ANALYSIS"
[1] 3
  RNMT MUTATED RNMT WILD-TYPE 
             8            385 
  RNMT MUTATED RNMT WILD-TYPE 
             8            385 
[1] "SUCNR1 MUTATION ANALYSIS"
[1] 3
  SUCNR1 MUTATED SUCNR1 WILD-TYPE 
               4              389 
  SUCNR1 MUTATED SUCNR1 WILD-TYPE 
               4              389 
[1] "NYNRIN MUTATION ANALYSIS"
[1] 3
  NYNRIN MUTATED NYNRIN WILD-TYPE 
              17              376 
  NYNRIN MUTATED NYNRIN WILD-TYPE 
              17              376 
[1] "PHTF1 MUTATION ANALYSIS"
[1] 3
  PHTF1 MUTATED PHTF1 WILD-TYPE 
             11             382 
  PHTF1 MUTATED PHTF1 WILD-TYPE 
             11             382 
[1] "CARD14 MUTATION ANALYSIS"
[1] 3
  CARD14 MUTATED CARD14 WILD-TYPE 
              13              380 
  CARD14 MUTATED CARD14 WILD-TYPE 
              13              380 
[1] "CASKIN1 MUTATION ANALYSIS"
[1] 3
  CASKIN1 MUTATED CASKIN1 WILD-TYPE 
               17               376 
  CASKIN1 MUTATED CASKIN1 WILD-TYPE 
               17               376 
[1] "C13ORF18 MUTATION ANALYSIS"
[1] 3
  C13ORF18 MUTATED C13ORF18 WILD-TYPE 
                10                383 
  C13ORF18 MUTATED C13ORF18 WILD-TYPE 
                10                383 
[1] "CCDC37 MUTATION ANALYSIS"
[1] 3
  CCDC37 MUTATED CCDC37 WILD-TYPE 
              14              379 
  CCDC37 MUTATED CCDC37 WILD-TYPE 
              14              379 
[1] "ETV1 MUTATION ANALYSIS"
[1] 3
  ETV1 MUTATED ETV1 WILD-TYPE 
             8            385 
  ETV1 MUTATED ETV1 WILD-TYPE 
             8            385 
[1] "TSPAN13 MUTATION ANALYSIS"
[1] 3
  TSPAN13 MUTATED TSPAN13 WILD-TYPE 
                4               389 
  TSPAN13 MUTATED TSPAN13 WILD-TYPE 
                4               389 
[1] "MAP1A MUTATION ANALYSIS"
[1] 3
  MAP1A MUTATED MAP1A WILD-TYPE 
             19             374 
  MAP1A MUTATED MAP1A WILD-TYPE 
             19             374 
[1] "FBXO32 MUTATION ANALYSIS"
[1] 3
  FBXO32 MUTATED FBXO32 WILD-TYPE 
               7              386 
  FBXO32 MUTATED FBXO32 WILD-TYPE 
               7              386 
[1] "PRAMEF2 MUTATION ANALYSIS"
[1] 3
  PRAMEF2 MUTATED PRAMEF2 WILD-TYPE 
               10               383 
  PRAMEF2 MUTATED PRAMEF2 WILD-TYPE 
               10               383 
[1] "C20ORF195 MUTATION ANALYSIS"
[1] 3
  C20ORF195 MUTATED C20ORF195 WILD-TYPE 
                  9                 384 
  C20ORF195 MUTATED C20ORF195 WILD-TYPE 
                  9                 384 
[1] "RERE MUTATION ANALYSIS"
[1] 3
  RERE MUTATED RERE WILD-TYPE 
            24            369 
  RERE MUTATED RERE WILD-TYPE 
            24            369 
[1] "WFIKKN2 MUTATION ANALYSIS"
[1] 3
  WFIKKN2 MUTATED WFIKKN2 WILD-TYPE 
               16               377 
  WFIKKN2 MUTATED WFIKKN2 WILD-TYPE 
               16               377 
[1] "OR1L3 MUTATION ANALYSIS"
[1] 3
  OR1L3 MUTATED OR1L3 WILD-TYPE 
              7             386 
  OR1L3 MUTATED OR1L3 WILD-TYPE 
              7             386 
[1] "MORC1 MUTATION ANALYSIS"
[1] 3
  MORC1 MUTATED MORC1 WILD-TYPE 
             13             380 
  MORC1 MUTATED MORC1 WILD-TYPE 
             13             380 
[1] "AP3B1 MUTATION ANALYSIS"
[1] 3
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              9             384 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              9             384 
[1] "OSBPL6 MUTATION ANALYSIS"
[1] 3
  OSBPL6 MUTATED OSBPL6 WILD-TYPE 
              18              375 
  OSBPL6 MUTATED OSBPL6 WILD-TYPE 
              18              375 
[1] "EFHC1 MUTATION ANALYSIS"
[1] 3
  EFHC1 MUTATED EFHC1 WILD-TYPE 
             10             383 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
             10             383 
[1] "DTNBP1 MUTATION ANALYSIS"
[1] 3
  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
               6              387 
  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
               6              387 
[1] "KCNH1 MUTATION ANALYSIS"
[1] 3
  KCNH1 MUTATED KCNH1 WILD-TYPE 
             20             373 
  KCNH1 MUTATED KCNH1 WILD-TYPE 
             20             373 
[1] "BBS10 MUTATION ANALYSIS"
[1] 3
  BBS10 MUTATED BBS10 WILD-TYPE 
              9             384 
  BBS10 MUTATED BBS10 WILD-TYPE 
              9             384 
[1] "SMARCC2 MUTATION ANALYSIS"
[1] 3
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
               18               375 
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
               18               375 
[1] "NRK MUTATION ANALYSIS"
[1] 3
  NRK MUTATED NRK WILD-TYPE 
           26           367 
  NRK MUTATED NRK WILD-TYPE 
           26           367 
[1] "WBP11 MUTATION ANALYSIS"
[1] 3
  WBP11 MUTATED WBP11 WILD-TYPE 
              5             388 
  WBP11 MUTATED WBP11 WILD-TYPE 
              5             388 
[1] "WSB2 MUTATION ANALYSIS"
[1] 3
  WSB2 MUTATED WSB2 WILD-TYPE 
             9            384 
  WSB2 MUTATED WSB2 WILD-TYPE 
             9            384 
[1] "SET MUTATION ANALYSIS"
[1] 3
  SET MUTATED SET WILD-TYPE 
            7           386 
  SET MUTATED SET WILD-TYPE 
            7           386 
[1] "CASC5 MUTATION ANALYSIS"
[1] 3
  CASC5 MUTATED CASC5 WILD-TYPE 
             21             372 
  CASC5 MUTATED CASC5 WILD-TYPE 
             21             372 
[1] "BEND5 MUTATION ANALYSIS"
[1] 3
  BEND5 MUTATED BEND5 WILD-TYPE 
              6             387 
  BEND5 MUTATED BEND5 WILD-TYPE 
              6             387 
[1] "FGF22 MUTATION ANALYSIS"
[1] 3
  FGF22 MUTATED FGF22 WILD-TYPE 
              4             389 
  FGF22 MUTATED FGF22 WILD-TYPE 
              4             389 
[1] "EIF2AK3 MUTATION ANALYSIS"
[1] 3
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
               19               374 
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
               19               374 
[1] "GALK1 MUTATION ANALYSIS"
[1] 3
  GALK1 MUTATED GALK1 WILD-TYPE 
              4             389 
  GALK1 MUTATED GALK1 WILD-TYPE 
              4             389 
[1] "ZNF334 MUTATION ANALYSIS"
[1] 3
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              13              380 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              13              380 
[1] "HORMAD1 MUTATION ANALYSIS"
[1] 3
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
                7               386 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
                7               386 
[1] "CSNK1G1 MUTATION ANALYSIS"
[1] 3
  CSNK1G1 MUTATED CSNK1G1 WILD-TYPE 
                7               386 
  CSNK1G1 MUTATED CSNK1G1 WILD-TYPE 
                7               386 
[1] "HIST1H1B MUTATION ANALYSIS"
[1] 3
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                11                382 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                11                382 
[1] "KIF20B MUTATION ANALYSIS"
[1] 3
  KIF20B MUTATED KIF20B WILD-TYPE 
              13              380 
  KIF20B MUTATED KIF20B WILD-TYPE 
              13              380 
[1] "SASH3 MUTATION ANALYSIS"
[1] 3
  SASH3 MUTATED SASH3 WILD-TYPE 
              8             385 
  SASH3 MUTATED SASH3 WILD-TYPE 
              8             385 
[1] "TCERG1 MUTATION ANALYSIS"
[1] 3
  TCERG1 MUTATED TCERG1 WILD-TYPE 
              12              381 
  TCERG1 MUTATED TCERG1 WILD-TYPE 
              12              381 
[1] "FBXL22 MUTATION ANALYSIS"
[1] 3
  FBXL22 MUTATED FBXL22 WILD-TYPE 
               5              388 
  FBXL22 MUTATED FBXL22 WILD-TYPE 
               5              388 
[1] "PARP15 MUTATION ANALYSIS"
[1] 3
  PARP15 MUTATED PARP15 WILD-TYPE 
               5              388 
  PARP15 MUTATED PARP15 WILD-TYPE 
               5              388 
[1] "NCAN MUTATION ANALYSIS"
[1] 3
  NCAN MUTATED NCAN WILD-TYPE 
            25            368 
  NCAN MUTATED NCAN WILD-TYPE 
            25            368 
[1] "SLC30A3 MUTATION ANALYSIS"
[1] 3
  SLC30A3 MUTATED SLC30A3 WILD-TYPE 
                9               384 
  SLC30A3 MUTATED SLC30A3 WILD-TYPE 
                9               384 
[1] "LRP1B MUTATION ANALYSIS"
[1] 3
  LRP1B MUTATED LRP1B WILD-TYPE 
            104             289 
  LRP1B MUTATED LRP1B WILD-TYPE 
            104             289 
[1] "GNAS MUTATION ANALYSIS"
[1] 3
  GNAS MUTATED GNAS WILD-TYPE 
            34            359 
  GNAS MUTATED GNAS WILD-TYPE 
            34            359 
[1] "FER MUTATION ANALYSIS"
[1] 3
  FER MUTATED FER WILD-TYPE 
           13           380 
  FER MUTATED FER WILD-TYPE 
           13           380 
[1] "GPATCH2 MUTATION ANALYSIS"
[1] 3
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
                9               384 
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
                9               384 
[1] "GFOD1 MUTATION ANALYSIS"
[1] 3
  GFOD1 MUTATED GFOD1 WILD-TYPE 
             13             380 
  GFOD1 MUTATED GFOD1 WILD-TYPE 
             13             380 
[1] "C3ORF33 MUTATION ANALYSIS"
[1] 3
  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
                7               386 
  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
                7               386 
[1] "MYCL1 MUTATION ANALYSIS"
[1] 3
  MYCL1 MUTATED MYCL1 WILD-TYPE 
              8             385 
  MYCL1 MUTATED MYCL1 WILD-TYPE 
              8             385 
[1] "SERPING1 MUTATION ANALYSIS"
[1] 3
  SERPING1 MUTATED SERPING1 WILD-TYPE 
                 8                385 
  SERPING1 MUTATED SERPING1 WILD-TYPE 
                 8                385 
[1] "TNFRSF13B MUTATION ANALYSIS"
[1] 3
  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE 
                  7                 386 
  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE 
                  7                 386 
[1] "ABCC1 MUTATION ANALYSIS"
[1] 3
  ABCC1 MUTATED ABCC1 WILD-TYPE 
             14             379 
  ABCC1 MUTATED ABCC1 WILD-TYPE 
             14             379 
[1] "CD1E MUTATION ANALYSIS"
[1] 3
  CD1E MUTATED CD1E WILD-TYPE 
            11            382 
  CD1E MUTATED CD1E WILD-TYPE 
            11            382 
[1] "ATG9A MUTATION ANALYSIS"
[1] 3
  ATG9A MUTATED ATG9A WILD-TYPE 
             11             382 
  ATG9A MUTATED ATG9A WILD-TYPE 
             11             382 
[1] "IGBP1 MUTATION ANALYSIS"
[1] 3
  IGBP1 MUTATED IGBP1 WILD-TYPE 
              6             387 
  IGBP1 MUTATED IGBP1 WILD-TYPE 
              6             387 
[1] "HIVEP2 MUTATION ANALYSIS"
[1] 3
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
              27              366 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
              27              366 
[1] "FAM60A MUTATION ANALYSIS"
[1] 3
  FAM60A MUTATED FAM60A WILD-TYPE 
               3              390 
  FAM60A MUTATED FAM60A WILD-TYPE 
               3              390 
[1] "ARV1 MUTATION ANALYSIS"
[1] 3
  ARV1 MUTATED ARV1 WILD-TYPE 
             5            388 
  ARV1 MUTATED ARV1 WILD-TYPE 
             5            388 
[1] "ERI1 MUTATION ANALYSIS"
[1] 3
  ERI1 MUTATED ERI1 WILD-TYPE 
             4            389 
  ERI1 MUTATED ERI1 WILD-TYPE 
             4            389 
[1] "TM9SF3 MUTATION ANALYSIS"
[1] 3
  TM9SF3 MUTATED TM9SF3 WILD-TYPE 
              13              380 
  TM9SF3 MUTATED TM9SF3 WILD-TYPE 
              13              380 
[1] "ATP2C1 MUTATION ANALYSIS"
[1] 3
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
              13              380 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
              13              380 
[1] "STK36 MUTATION ANALYSIS"
[1] 3
  STK36 MUTATED STK36 WILD-TYPE 
              8             385 
  STK36 MUTATED STK36 WILD-TYPE 
              8             385 
[1] "ISM1 MUTATION ANALYSIS"
[1] 3
  ISM1 MUTATED ISM1 WILD-TYPE 
            13            380 
  ISM1 MUTATED ISM1 WILD-TYPE 
            13            380 
[1] "GLTPD1 MUTATION ANALYSIS"
[1] 3
  GLTPD1 MUTATED GLTPD1 WILD-TYPE 
               4              389 
  GLTPD1 MUTATED GLTPD1 WILD-TYPE 
               4              389 
[1] "CLDN5 MUTATION ANALYSIS"
[1] 3
  CLDN5 MUTATED CLDN5 WILD-TYPE 
              4             389 
  CLDN5 MUTATED CLDN5 WILD-TYPE 
              4             389 
[1] "D4S234E MUTATION ANALYSIS"
[1] 3
  D4S234E MUTATED D4S234E WILD-TYPE 
                7               386 
  D4S234E MUTATED D4S234E WILD-TYPE 
                7               386 
[1] "EGLN1 MUTATION ANALYSIS"
[1] 3
  EGLN1 MUTATED EGLN1 WILD-TYPE 
              5             388 
  EGLN1 MUTATED EGLN1 WILD-TYPE 
              5             388 
[1] "C1ORF131 MUTATION ANALYSIS"
[1] 3
  C1ORF131 MUTATED C1ORF131 WILD-TYPE 
                 5                388 
  C1ORF131 MUTATED C1ORF131 WILD-TYPE 
                 5                388 
[1] "CSF1 MUTATION ANALYSIS"
[1] 3
  CSF1 MUTATED CSF1 WILD-TYPE 
             5            388 
  CSF1 MUTATED CSF1 WILD-TYPE 
             5            388 
[1] "TBC1D5 MUTATION ANALYSIS"
[1] 3
  TBC1D5 MUTATED TBC1D5 WILD-TYPE 
               9              384 
  TBC1D5 MUTATED TBC1D5 WILD-TYPE 
               9              384 
[1] "ZNF428 MUTATION ANALYSIS"
[1] 3
  ZNF428 MUTATED ZNF428 WILD-TYPE 
               5              388 
  ZNF428 MUTATED ZNF428 WILD-TYPE 
               5              388 
[1] "SLC38A1 MUTATION ANALYSIS"
[1] 3
  SLC38A1 MUTATED SLC38A1 WILD-TYPE 
                7               386 
  SLC38A1 MUTATED SLC38A1 WILD-TYPE 
                7               386 
[1] "ZNF570 MUTATION ANALYSIS"
[1] 3
  ZNF570 MUTATED ZNF570 WILD-TYPE 
              12              381 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
              12              381 
[1] "GPR115 MUTATION ANALYSIS"
[1] 3
  GPR115 MUTATED GPR115 WILD-TYPE 
               5              388 
  GPR115 MUTATED GPR115 WILD-TYPE 
               5              388 
[1] "SLC45A4 MUTATION ANALYSIS"
[1] 3
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
               19               374 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
               19               374 
[1] "NKX2-3 MUTATION ANALYSIS"
[1] 3
  NKX2-3 MUTATED NKX2-3 WILD-TYPE 
               8              385 
  NKX2-3 MUTATED NKX2-3 WILD-TYPE 
               8              385 
[1] "EPHA3 MUTATION ANALYSIS"
[1] 3
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             28             365 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             28             365 
[1] "GABRG3 MUTATION ANALYSIS"
[1] 3
  GABRG3 MUTATED GABRG3 WILD-TYPE 
               9              384 
  GABRG3 MUTATED GABRG3 WILD-TYPE 
               9              384 
[1] "EPHA10 MUTATION ANALYSIS"
[1] 3
  EPHA10 MUTATED EPHA10 WILD-TYPE 
              17              376 
  EPHA10 MUTATED EPHA10 WILD-TYPE 
              17              376 
[1] "SLC44A4 MUTATION ANALYSIS"
[1] 3
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
               15               378 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
               15               378 
[1] "PPL MUTATION ANALYSIS"
[1] 3
  PPL MUTATED PPL WILD-TYPE 
           18           375 
  PPL MUTATED PPL WILD-TYPE 
           18           375 
[1] "TMEM63A MUTATION ANALYSIS"
[1] 3
  TMEM63A MUTATED TMEM63A WILD-TYPE 
               13               380 
  TMEM63A MUTATED TMEM63A WILD-TYPE 
               13               380 
[1] "ANKRD42 MUTATION ANALYSIS"
[1] 3
  ANKRD42 MUTATED ANKRD42 WILD-TYPE 
                8               385 
  ANKRD42 MUTATED ANKRD42 WILD-TYPE 
                8               385 
[1] "AVPR1A MUTATION ANALYSIS"
[1] 3
  AVPR1A MUTATED AVPR1A WILD-TYPE 
              15              378 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
              15              378 
[1] "VILL MUTATION ANALYSIS"
[1] 3
  VILL MUTATED VILL WILD-TYPE 
            11            382 
  VILL MUTATED VILL WILD-TYPE 
            11            382 
[1] "ARRDC5 MUTATION ANALYSIS"
[1] 3
  ARRDC5 MUTATED ARRDC5 WILD-TYPE 
               4              389 
  ARRDC5 MUTATED ARRDC5 WILD-TYPE 
               4              389 
[1] "P2RY12 MUTATION ANALYSIS"
[1] 3
  P2RY12 MUTATED P2RY12 WILD-TYPE 
               9              384 
  P2RY12 MUTATED P2RY12 WILD-TYPE 
               9              384 
[1] "KIAA1217 MUTATION ANALYSIS"
[1] 3
  KIAA1217 MUTATED KIAA1217 WILD-TYPE 
                27                366 
  KIAA1217 MUTATED KIAA1217 WILD-TYPE 
                27                366 
[1] "MEPCE MUTATION ANALYSIS"
[1] 3
  MEPCE MUTATED MEPCE WILD-TYPE 
              8             385 
  MEPCE MUTATED MEPCE WILD-TYPE 
              8             385 
[1] "TRIM27 MUTATION ANALYSIS"
[1] 3
  TRIM27 MUTATED TRIM27 WILD-TYPE 
               5              388 
  TRIM27 MUTATED TRIM27 WILD-TYPE 
               5              388 
[1] "PTPN12 MUTATION ANALYSIS"
[1] 3
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              12              381 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              12              381 
[1] "ITGAV MUTATION ANALYSIS"
[1] 3
  ITGAV MUTATED ITGAV WILD-TYPE 
             18             375 
  ITGAV MUTATED ITGAV WILD-TYPE 
             18             375 
[1] "PATL1 MUTATION ANALYSIS"
[1] 3
  PATL1 MUTATED PATL1 WILD-TYPE 
              7             386 
  PATL1 MUTATED PATL1 WILD-TYPE 
              7             386 
[1] "KCNE1 MUTATION ANALYSIS"
[1] 3
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              4             389 
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              4             389 
[1] "TLR4 MUTATION ANALYSIS"
[1] 3
  TLR4 MUTATED TLR4 WILD-TYPE 
            27            366 
  TLR4 MUTATED TLR4 WILD-TYPE 
            27            366 
[1] "XRCC2 MUTATION ANALYSIS"
[1] 3
  XRCC2 MUTATED XRCC2 WILD-TYPE 
              6             387 
  XRCC2 MUTATED XRCC2 WILD-TYPE 
              6             387 
[1] "CRYBB1 MUTATION ANALYSIS"
[1] 3
  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
              10              383 
  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
              10              383 
[1] "MED23 MUTATION ANALYSIS"
[1] 3
  MED23 MUTATED MED23 WILD-TYPE 
             18             375 
  MED23 MUTATED MED23 WILD-TYPE 
             18             375 
[1] "SFRS2 MUTATION ANALYSIS"
[1] 3
  SFRS2 MUTATED SFRS2 WILD-TYPE 
              4             389 
  SFRS2 MUTATED SFRS2 WILD-TYPE 
              4             389 
[1] "SGK196 MUTATION ANALYSIS"
[1] 3
  SGK196 MUTATED SGK196 WILD-TYPE 
               7              386 
  SGK196 MUTATED SGK196 WILD-TYPE 
               7              386 
[1] "TDG MUTATION ANALYSIS"
[1] 3
  TDG MUTATED TDG WILD-TYPE 
            6           387 
  TDG MUTATED TDG WILD-TYPE 
            6           387 
[1] "KIAA0408 MUTATION ANALYSIS"
[1] 3
  KIAA0408 MUTATED KIAA0408 WILD-TYPE 
                14                379 
  KIAA0408 MUTATED KIAA0408 WILD-TYPE 
                14                379 
[1] "PIAS1 MUTATION ANALYSIS"
[1] 3
  PIAS1 MUTATED PIAS1 WILD-TYPE 
              9             384 
  PIAS1 MUTATED PIAS1 WILD-TYPE 
              9             384 
[1] "FLJ10357 MUTATION ANALYSIS"
[1] 3
  FLJ10357 MUTATED FLJ10357 WILD-TYPE 
                20                373 
  FLJ10357 MUTATED FLJ10357 WILD-TYPE 
                20                373 
[1] "SMC5 MUTATION ANALYSIS"
[1] 3
  SMC5 MUTATED SMC5 WILD-TYPE 
            10            383 
  SMC5 MUTATED SMC5 WILD-TYPE 
            10            383 
[1] "ATOH1 MUTATION ANALYSIS"
[1] 3
  ATOH1 MUTATED ATOH1 WILD-TYPE 
              6             387 
  ATOH1 MUTATED ATOH1 WILD-TYPE 
              6             387 
[1] "AAMP MUTATION ANALYSIS"
[1] 3
  AAMP MUTATED AAMP WILD-TYPE 
             3            390 
  AAMP MUTATED AAMP WILD-TYPE 
             3            390 
[1] "SYBU MUTATION ANALYSIS"
[1] 3
  SYBU MUTATED SYBU WILD-TYPE 
            15            378 
  SYBU MUTATED SYBU WILD-TYPE 
            15            378 
[1] "CPT2 MUTATION ANALYSIS"
[1] 3
  CPT2 MUTATED CPT2 WILD-TYPE 
             6            387 
  CPT2 MUTATED CPT2 WILD-TYPE 
             6            387 
[1] "SCNN1D MUTATION ANALYSIS"
[1] 3
  SCNN1D MUTATED SCNN1D WILD-TYPE 
              10              383 
  SCNN1D MUTATED SCNN1D WILD-TYPE 
              10              383 
[1] "OLFM3 MUTATION ANALYSIS"
[1] 3
  OLFM3 MUTATED OLFM3 WILD-TYPE 
              8             385 
  OLFM3 MUTATED OLFM3 WILD-TYPE 
              8             385 
[1] "LRRC43 MUTATION ANALYSIS"
[1] 3
  LRRC43 MUTATED LRRC43 WILD-TYPE 
              12              381 
  LRRC43 MUTATED LRRC43 WILD-TYPE 
              12              381 
[1] "TMC2 MUTATION ANALYSIS"
[1] 3
  TMC2 MUTATED TMC2 WILD-TYPE 
            17            376 
  TMC2 MUTATED TMC2 WILD-TYPE 
            17            376 
[1] "USP30 MUTATION ANALYSIS"
[1] 3
  USP30 MUTATED USP30 WILD-TYPE 
              9             384 
  USP30 MUTATED USP30 WILD-TYPE 
              9             384 
[1] "TRIP6 MUTATION ANALYSIS"
[1] 3
  TRIP6 MUTATED TRIP6 WILD-TYPE 
              8             385 
  TRIP6 MUTATED TRIP6 WILD-TYPE 
              8             385 
[1] "PBX2 MUTATION ANALYSIS"
[1] 3
  PBX2 MUTATED PBX2 WILD-TYPE 
            10            383 
  PBX2 MUTATED PBX2 WILD-TYPE 
            10            383 
[1] "TNNT3 MUTATION ANALYSIS"
[1] 3
  TNNT3 MUTATED TNNT3 WILD-TYPE 
              7             386 
  TNNT3 MUTATED TNNT3 WILD-TYPE 
              7             386 
[1] "OSTALPHA MUTATION ANALYSIS"
[1] 3
  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
                 4                389 
  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
                 4                389 
[1] "OXCT2 MUTATION ANALYSIS"
[1] 3
  OXCT2 MUTATED OXCT2 WILD-TYPE 
              5             388 
  OXCT2 MUTATED OXCT2 WILD-TYPE 
              5             388 
[1] "XIRP2 MUTATION ANALYSIS"
[1] 3
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             56             337 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             56             337 
[1] "CREBBP MUTATION ANALYSIS"
[1] 3
  CREBBP MUTATED CREBBP WILD-TYPE 
              36              357 
  CREBBP MUTATED CREBBP WILD-TYPE 
              36              357 
[1] "TJP2 MUTATION ANALYSIS"
[1] 3
  TJP2 MUTATED TJP2 WILD-TYPE 
            14            379 
  TJP2 MUTATED TJP2 WILD-TYPE 
            14            379 
[1] "PTPN11 MUTATION ANALYSIS"
[1] 3
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               8              385 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               8              385 
[1] "ASCL4 MUTATION ANALYSIS"
[1] 3
  ASCL4 MUTATED ASCL4 WILD-TYPE 
              7             386 
  ASCL4 MUTATED ASCL4 WILD-TYPE 
              7             386 
[1] "TESK1 MUTATION ANALYSIS"
[1] 3
  TESK1 MUTATED TESK1 WILD-TYPE 
             12             381 
  TESK1 MUTATED TESK1 WILD-TYPE 
             12             381 
[1] "ORC2L MUTATION ANALYSIS"
[1] 3
  ORC2L MUTATED ORC2L WILD-TYPE 
              7             386 
  ORC2L MUTATED ORC2L WILD-TYPE 
              7             386 
[1] "DHX15 MUTATION ANALYSIS"
[1] 3
  DHX15 MUTATED DHX15 WILD-TYPE 
             11             382 
  DHX15 MUTATED DHX15 WILD-TYPE 
             11             382 
[1] "LRRC4 MUTATION ANALYSIS"
[1] 3
  LRRC4 MUTATED LRRC4 WILD-TYPE 
             21             372 
  LRRC4 MUTATED LRRC4 WILD-TYPE 
             21             372 
[1] "FIGNL1 MUTATION ANALYSIS"
[1] 3
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               9              384 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               9              384 
[1] "CD6 MUTATION ANALYSIS"
[1] 3
  CD6 MUTATED CD6 WILD-TYPE 
           10           383 
  CD6 MUTATED CD6 WILD-TYPE 
           10           383 
[1] "POGZ MUTATION ANALYSIS"
[1] 3
  POGZ MUTATED POGZ WILD-TYPE 
            24            369 
  POGZ MUTATED POGZ WILD-TYPE 
            24            369 
[1] "RBM16 MUTATION ANALYSIS"
[1] 3
  RBM16 MUTATED RBM16 WILD-TYPE 
             13             380 
  RBM16 MUTATED RBM16 WILD-TYPE 
             13             380 
[1] "SPOCK1 MUTATION ANALYSIS"
[1] 3
  SPOCK1 MUTATED SPOCK1 WILD-TYPE 
              13              380 
  SPOCK1 MUTATED SPOCK1 WILD-TYPE 
              13              380 
[1] "FAH MUTATION ANALYSIS"
[1] 3
  FAH MUTATED FAH WILD-TYPE 
            7           386 
  FAH MUTATED FAH WILD-TYPE 
            7           386 
[1] "SERPINB8 MUTATION ANALYSIS"
[1] 3
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
                 8                385 
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
                 8                385 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RESIDUAL_TUMOR"                      
[15] "NUMBER_OF_LYMPH_NODES"               
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 393 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=53,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=125,	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=211,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'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 393 columns, 1 survival variables, and 12 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"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"       
[10] "NUMBER_OF_LYMPH_NODES" "RACE"                  "ETHNICITY"            
YEARS_TO_BIRTH, nv=53, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 22  92 173  97 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 22  92 173  97 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 22  92 173  97 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 22  92 173  97 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
118 104  77  77 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
118 104  77  77 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
118 104  77  77 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
118 104  77  77 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=7, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=28, 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   122  58
  TP53 WILD-TYPE 108  81
  TP53 MUTATED TP53 WILD-TYPE 
           180            189 
  TP53 MUTATED TP53 WILD-TYPE 
            58             81 
$`TP53 MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-KB-A93G TCGA-B7-5818 TCGA-B7-A5TI 
       47.05        21.99        79.07        20.15        11.70        19.56 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4255 TCGA-BR-4256 
       11.01         9.44         6.61         6.97         4.08         9.34 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-6852 
       17.29        13.68        19.33         9.17        31.20        44.94 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 
        9.21        36.16        33.63        39.78        28.73         3.45 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 
       11.44         0.69         9.60        32.25        29.42         2.66 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 
        7.40         6.18        31.10        14.04        14.79         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8678 
        5.39        25.18        20.22         1.12         9.34        24.79 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       32.58         9.86        10.68        13.87         7.53        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        1.48        27.55        12.89        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-5813 
        1.15        21.44        13.02        13.15        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-8533 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
       15.39         6.31        12.30        11.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 
       12.20        20.02         7.99        54.08         4.01        19.07 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5721 TCGA-CG-5723 
       18.97         7.07        30.97        36.00         6.02       105.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
        4.01        69.04        12.66        20.91        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.54        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-8578 
       12.79        12.36        11.31        12.33        14.66        21.14 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74B TCGA-EQ-8122 
       11.24        11.31        22.29        15.65         7.13         7.99 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 
       14.47        72.23        11.38         3.48        19.53        17.06 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HJ-7597 
        0.56        11.08         5.52         6.21        77.29        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8604 TCGA-HU-A4GC TCGA-HU-A4GD 
        1.51         5.92        24.39        22.82         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       25.81        11.77        29.98         8.98         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4HD 
       20.25         0.26        12.95        29.00        23.84        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-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-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        2.53         5.56        36.95        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
        8.52        37.91       115.69         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-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91U 
       37.41        38.14        22.19        17.85         1.87         1.71 
TCGA-VQ-A91V TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I 
       42.64        43.66        38.93        32.94        26.04        16.14 

$`TP53 WILD-TYPE`
TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-A5TK 
       22.98        16.24         0.23         9.86        26.70         9.47 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4257 
        4.64         7.43        18.35        30.90         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-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-7196 TCGA-BR-7704 
       12.16         8.98        40.21        30.90        21.90        35.24 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       35.84        18.15        15.32         9.07        29.56        33.21 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       37.25        14.43        29.59         8.05         0.56        19.96 
TCGA-BR-8295 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        2.20         0.26        22.19        17.52         0.95        26.33 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        4.31         3.32        11.80        31.27         7.36        25.05 
TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        9.21        12.79        27.12        28.14         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 
       26.73        31.96        20.88         8.22        34.13         6.08 
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-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 
        0.66        32.52        16.14         5.13        13.41        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8534 
       13.35        11.21         7.17        12.30        11.64        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
       12.82        12.43         6.58        11.77        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 
       27.02        15.95         1.02         8.05        14.01        29.98 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
       12.03         0.00         9.01         6.97         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 
        0.99        12.03        15.02        28.96        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8570 
        7.99        25.71        20.55        18.61        17.85        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YT 
       16.80        19.50        17.19        18.21        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-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A TCGA-EQ-5647 
       11.44        20.32         8.38         4.34        19.96         0.62 
TCGA-F1-A448 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       21.27        14.07        22.29        59.54         5.03        13.58 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
       63.06        52.21        30.51        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-A4GJ TCGA-HU-A4GT TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       21.37         6.51         2.10        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F7 
       15.68         3.39        19.53        15.75        13.51        63.62 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        3.72        19.73        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-A8N0 
       11.05         8.61         5.13        16.67       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-SW-A7EA TCGA-VQ-A8P3 TCGA-VQ-A8PQ 
      116.38        71.38        57.44        19.04        37.22        15.65 
TCGA-VQ-A91Q TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6F 
       20.81        66.81        11.24        18.41        28.41        54.12 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  TP53 MUTATED TP53 WILD-TYPE 
           0.1            0.0 
  TP53 MUTATED TP53 WILD-TYPE 
        115.69         122.30 
  TP53 MUTATED TP53 WILD-TYPE 
         13.20          15.95 
[1] "0.1 - 115.7 (13.2)" "0.0 - 122.3 (15.9)"
[1] "hr=" "1.3"
D1V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TP53 MUTATED         1        7       18       16        21        25
  TP53 WILD-TYPE       1        8       22       14        16        27
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TP53 MUTATED           0         38         23         15       14
  TP53 WILD-TYPE         3         32         30         17       24
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I               1              1
  STAGE IA              7              8
  STAGE IB             18             22
  STAGE II             16             14
  STAGE IIA            21             16
  STAGE IIB            25             27
  STAGE III             0              3
  STAGE IIIA           38             32
  STAGE IIIB           23             30
  STAGE IIIC           15             17
  STAGE IV             14             24
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  TP53 MUTATED   10 47 88 41
  TP53 WILD-TYPE 12 45 85 56
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           10             12
  T2           47             45
  T3           88             85
  T4           41             56
[1] 4 2
[1] TRUE
[1] "dimension of 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   59 50 38 34
  TP53 WILD-TYPE 59 54 39 43
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           59             59
  N1           50             54
  N2           38             39
  N3           34             43
[1] 4 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   167  10
  TP53 WILD-TYPE 179  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    167   10
  TP53 WILD-TYPE  179   19
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0          167            179
  1           10             19
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED    68 120
  TP53 WILD-TYPE  77 128
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     68  120
  TP53 WILD-TYPE   77  128
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           68             77
  MALE            120            128
[1] 2 2
[1] FALSE
D1V8, binary
                cls
clus               0   1
  TP53 MUTATED   145  29
  TP53 WILD-TYPE 147  30
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    145   29
  TP53 WILD-TYPE  147   30
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO           145            147
  YES           29             30
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TP53 MUTATED                                          5
  TP53 WILD-TYPE                                        3
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TP53 MUTATED                                      26
  TP53 WILD-TYPE                                    44
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TP53 MUTATED                                                       72
  TP53 WILD-TYPE                                                     86
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TP53 MUTATED                                                  10
  TP53 WILD-TYPE                                                11
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TP53 MUTATED                                                                  37
  TP53 WILD-TYPE                                                                31
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TP53 MUTATED                                                    3
  TP53 WILD-TYPE                                                  2
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TP53 MUTATED                                                 35
  TP53 WILD-TYPE                                               26
D1V9, multiclass
                                                                   clus
vv                                                                  TP53 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       26
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      72
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           10
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           37
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            35
                                                                   clus
vv                                                                  TP53 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         44
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        86
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             11
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             31
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              26
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED   154   5   4   9
  TP53 WILD-TYPE 157   9  11  15
D1V10, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0          154            157
  R1            5              9
  R2            4             11
  RX            9             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TP53 MUTATED      44                         5
  TP53 WILD-TYPE    43                         4
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TP53 MUTATED                                           0   118
  TP53 WILD-TYPE                                         1   125
D1V12, multiclass
                                           clus
vv                                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                               44             43
  BLACK OR AFRICAN AMERICAN                            5              4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                              118            125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
                cls
clus               0   1
  TP53 MUTATED     1 148
  TP53 WILD-TYPE   3 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1  148
  TP53 WILD-TYPE    3  162
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO          148            162
[1] 2 2
[1] FALSE

Clustering(2) Variable = ARID1A MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    57  34
  ARID1A WILD-TYPE 173 105
  ARID1A MUTATED ARID1A WILD-TYPE 
              91              278 
  ARID1A MUTATED ARID1A WILD-TYPE 
              34              105 
$`ARID1A MUTATED`
TCGA-CG-4460 TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-4184 
       21.99         9.86        26.70        19.56         9.47         6.97 
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6455 
        7.43        30.90         4.08         9.34        34.68        13.87 
TCGA-BR-6456 TCGA-BR-6707 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 
       17.29        19.89        30.90        44.94        21.90        35.84 
TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8361 
       33.63        15.32        14.43        29.59         8.05        31.10 
TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        0.26        17.52         4.31        31.27         7.36        25.05 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 
        1.12        27.12        28.14        31.96        20.88         8.22 
TCGA-BR-A453 TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QL 
        6.08         0.72        28.34        13.51        20.42        16.14 
TCGA-CD-5803 TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-4469 
       11.21        12.43        15.95         1.02         9.01         7.07 
TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-6521 TCGA-D7-6524 
        6.02        65.10        21.07        25.71        18.54        17.85 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6EY 
       20.91        14.27        16.44         5.92        36.43        11.44 
TCGA-D7-A6EZ TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BE 
       20.32        14.47        21.27        17.06         0.56        11.08 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8608 TCGA-HU-A4G3 
       77.29        52.21        30.51        26.47        21.07         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GQ 
       24.26        22.68        24.20        11.77        29.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-KB-A6F7 
        6.58        20.25        29.00        23.84        14.07        63.62 
TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7C1 TCGA-SW-A7EA TCGA-VQ-A8P2 
       19.73        74.53         4.60        16.67        19.04        38.14 
TCGA-VQ-AA6J 
       27.55 

$`ARID1A WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4191 
       11.70        11.01         9.44         6.61         4.64        18.35 
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-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-6803 
       25.61        18.05        12.16         8.98        40.21        31.20 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 
        9.21        36.16        35.24        39.78        18.15        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-8297 TCGA-BR-8360 TCGA-BR-8364 TCGA-BR-8366 
       19.96         2.20         7.40         6.18        22.19         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-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-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        34.13        13.87         7.53        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-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
        0.66        32.52        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-5804 
       13.41        13.02        13.15        13.18        13.35        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-4466 TCGA-CG-4477 
       29.98        19.07        12.03         0.00        18.97        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-5734 
       12.03        15.02        28.96         4.01        69.04         7.99 
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-D7-6525 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-A4YY TCGA-D7-A4Z0 
       17.19        18.21        14.66        21.14        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-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-8209 
       11.38         3.48        19.53        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HU-8238 
        5.03        13.58         5.52         6.21        63.06         1.51 
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-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GP 
       24.30         3.25        22.75        25.81        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-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-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       18.21         8.52         6.08         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-AA6K TCGA-ZA-A8F6 
       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 
           19.04            13.35 
[1] "0.1 - 77.3 (19.0)"  "0.0 - 122.3 (13.3)"
[1] "hr=" "1.2"
D2V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID1A MUTATED         1        4       11        5        10        14
  ARID1A WILD-TYPE       1       11       29       25        27        38
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID1A MUTATED           1         14          9         11       11
  ARID1A WILD-TYPE         2         56         44         21       27
D2V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                 1                1
  STAGE IA                4               11
  STAGE IB               11               29
  STAGE II                5               25
  STAGE IIA              10               27
  STAGE IIB              14               38
  STAGE III               1                2
  STAGE IIIA             14               56
  STAGE IIIB              9               44
  STAGE IIIC             11               21
  STAGE IV               11               27
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID1A MUTATED     8  21  35  31
  ARID1A WILD-TYPE  14  71 138  66
D2V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              8               14
  T2             21               71
  T3             35              138
  T4             31               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"
                  vv
clus               N0 N1 N2 N3
  ARID1A MUTATED   28 29 19 18
  ARID1A WILD-TYPE 90 75 58 59
D2V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0             28               90
  N1             29               75
  N2             19               58
  N3             18               59
[1] 4 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    85   8
  ARID1A WILD-TYPE 261  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     85    8
  ARID1A WILD-TYPE  261   21
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             85              261
  1              8               21
[1] 2 2
[1] FALSE
D2V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED    46  53
  ARID1A WILD-TYPE  99 195
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     46   53
  ARID1A WILD-TYPE   99  195
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE             46               99
  MALE               53              195
[1] 2 2
[1] FALSE
D2V8, binary
                  cls
clus                 0   1
  ARID1A MUTATED    78   8
  ARID1A WILD-TYPE 214  51
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     78    8
  ARID1A WILD-TYPE  214   51
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO              78              214
  YES              8               51
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARID1A MUTATED                                          2
  ARID1A WILD-TYPE                                        6
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARID1A MUTATED                                      14
  ARID1A WILD-TYPE                                    56
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARID1A MUTATED                                                       46
  ARID1A WILD-TYPE                                                    112
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARID1A MUTATED                                                   5
  ARID1A WILD-TYPE                                                16
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARID1A MUTATED                                                                  16
  ARID1A WILD-TYPE                                                                52
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARID1A MUTATED                                                    1
  ARID1A WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARID1A MUTATED                                                 15
  ARID1A WILD-TYPE                                               46
D2V9, multiclass
                                                                   clus
vv                                                                  ARID1A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         14
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        46
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             16
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              15
                                                                   clus
vv                                                                  ARID1A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           56
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         112
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               52
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                46
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    76   4   3  11
  ARID1A WILD-TYPE 235  10  12  13
D2V10, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             76              235
  R1              4               10
  R2              3               12
  RX             11               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ARID1A MUTATED      20                         4
  ARID1A WILD-TYPE    67                         5
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID1A MUTATED                                           0    63
  ARID1A WILD-TYPE                                         1   180
D2V12, multiclass
                                           clus
vv                                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                                 20               67
  BLACK OR AFRICAN AMERICAN                              4                5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 63              180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
                  cls
clus                 0   1
  ARID1A MUTATED     2  83
  ARID1A WILD-TYPE   2 227
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2   83
  ARID1A WILD-TYPE    2  227
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  2                2
  NOT HISPANIC OR LATINO             83              227
[1] 2 2
[1] FALSE

Clustering(3) Variable = RNF43 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  RNF43 MUTATED    26  13
  RNF43 WILD-TYPE 204 126
  RNF43 MUTATED RNF43 WILD-TYPE 
             39             330 
  RNF43 MUTATED RNF43 WILD-TYPE 
             13             126 
$`RNF43 MUTATED`
TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6852 
       11.01         6.97        30.90         9.34        34.68        44.94 
TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 
       35.84        32.25         6.18        31.10         4.31        31.27 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CG-4306 
       25.05         1.12        12.79        16.14         5.13         1.02 
TCGA-CG-4469 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 
        7.07         6.02        28.96        65.10        21.07         7.99 
TCGA-D7-A4YT TCGA-F1-A448 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4G9 TCGA-HU-A4GN 
       14.27        21.27        30.51        26.47        24.20        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-SW-A7EA 
        0.10         6.51        29.00        14.07        19.73        19.04 
TCGA-VQ-A8DT TCGA-VQ-A8P2 TCGA-VQ-A91U 
       48.79        38.14         1.71 

$`RNF43 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       21.44        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-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-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       15.02         4.01        69.04        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-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-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-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-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-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-A8DU 
       57.44         8.94        35.61         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-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 

  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           14.04 
[1] "0.1 - 65.1 (19.7)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.3"
D3V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RNF43 MUTATED         0        2        7        0         6         4
  RNF43 WILD-TYPE       2       13       33       30        31        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF43 MUTATED           0          9          3          6        4
  RNF43 WILD-TYPE         3         61         50         26       34
D3V3, multiclass
            clus
vv           RNF43 MUTATED RNF43 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               7              33
  STAGE II               0              30
  STAGE IIA              6              31
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             9              61
  STAGE IIIB             3              50
  STAGE IIIC             6              26
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RNF43 MUTATED     4  10  15  14
  RNF43 WILD-TYPE  18  82 158  83
D3V4, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  T1             4              18
  T2            10              82
  T3            15             158
  T4            14              83
[1] 4 2
[1] TRUE
[1] "dimension of 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    17   9   7   9
  RNF43 WILD-TYPE 101  95  70  68
D3V5, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  N0            17             101
  N1             9              95
  N2             7              70
  N3             9              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"
D3V6, binary
                 cls
clus                0   1
  RNF43 MUTATED    42   1
  RNF43 WILD-TYPE 304  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     42    1
  RNF43 WILD-TYPE  304   28
   clus
vv  RNF43 MUTATED RNF43 WILD-TYPE
  0            42             304
  1             1              28
[1] 2 2
[1] FALSE
D3V7, binary
                 cls
clus                0   1
  RNF43 MUTATED    24  21
  RNF43 WILD-TYPE 121 227
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     24   21
  RNF43 WILD-TYPE  121  227
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  FEMALE            24             121
  MALE              21             227
[1] 2 2
[1] FALSE
D3V8, binary
                 cls
clus                0   1
  RNF43 MUTATED    30   4
  RNF43 WILD-TYPE 262  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     30    4
  RNF43 WILD-TYPE  262   55
     clus
vv    RNF43 MUTATED RNF43 WILD-TYPE
  NO             30             262
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RNF43 MUTATED                                          1
  RNF43 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RNF43 MUTATED                                       2
  RNF43 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RNF43 MUTATED                                                       20
  RNF43 WILD-TYPE                                                    138
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RNF43 MUTATED                                                   3
  RNF43 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RNF43 MUTATED                                                                  12
  RNF43 WILD-TYPE                                                                56
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RNF43 MUTATED                                                    0
  RNF43 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RNF43 MUTATED                                                  7
  RNF43 WILD-TYPE                                               54
D3V9, multiclass
                                                                   clus
vv                                                                  RNF43 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       20
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              7
                                                                   clus
vv                                                                  RNF43 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        138
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              56
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RNF43 MUTATED    34   2   1   7
  RNF43 WILD-TYPE 277  12  14  17
D3V10, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  R0            34             277
  R1             2              12
  R2             1              14
  RX             7              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RNF43 MUTATED       7                         0
  RNF43 WILD-TYPE    80                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RNF43 MUTATED                                           0    28
  RNF43 WILD-TYPE                                         1   215
D3V12, multiclass
                                           clus
vv                                          RNF43 MUTATED RNF43 WILD-TYPE
  ASIAN                                                 7              80
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                28             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, binary
                 cls
clus                0   1
  RNF43 MUTATED     1  32
  RNF43 WILD-TYPE   3 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      1   32
  RNF43 WILD-TYPE    3  278
                        clus
vv                       RNF43 MUTATED RNF43 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            32             278
[1] 2 2
[1] FALSE

Clustering(4) Variable = XYLT2 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  XYLT2 MUTATED    24   9
  XYLT2 WILD-TYPE 206 130
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             33             336 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
              9             130 
$`XYLT2 MUTATED`
TCGA-CG-4460 TCGA-B7-A5TI TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-7723 
       21.99        19.56        34.68        32.78        35.84        28.73 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       29.59        32.25         8.05         6.18        31.10         0.26 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI 
       25.05         1.12        28.14        12.43         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-FP-A4BE 
       12.62         1.02       105.07        65.10        21.07        11.08 
TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 
       77.29        30.51        22.32         6.58        20.25        29.00 
TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       14.07        19.73        38.14 

$`XYLT2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 
       37.25        14.43        11.44         0.69         9.60         0.56 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8364 
       29.42         2.66        19.96         2.20         7.40        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-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-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-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-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 
       13.58         0.56         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-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-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10         6.51         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-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 

  XYLT2 MUTATED XYLT2 WILD-TYPE 
           0.26            0.00 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
         105.07          122.30 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
         21.990          14.025 
[1] "0.3 - 105.1 (22.0)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.9"
D4V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XYLT2 MUTATED         1        0        5        3         6         5
  XYLT2 WILD-TYPE       1       15       35       27        31        47
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XYLT2 MUTATED           0          5          1          8        3
  XYLT2 WILD-TYPE         3         65         52         24       35
D4V3, multiclass
            clus
vv           XYLT2 MUTATED XYLT2 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               5              35
  STAGE II               3              27
  STAGE IIA              6              31
  STAGE IIB              5              47
  STAGE III              0               3
  STAGE IIIA             5              65
  STAGE IIIB             1              52
  STAGE IIIC             8              24
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  XYLT2 MUTATED     3   7  12  16
  XYLT2 WILD-TYPE  19  85 161  81
D4V4, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  T1             3              19
  T2             7              85
  T3            12             161
  T4            16              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"
                 vv
clus               N0  N1  N2  N3
  XYLT2 MUTATED    16   8   6   7
  XYLT2 WILD-TYPE 102  96  71  70
D4V5, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  N0            16             102
  N1             8              96
  N2             6              71
  N3             7              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"
D4V6, binary
                 cls
clus                0   1
  XYLT2 MUTATED    35   2
  XYLT2 WILD-TYPE 311  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     35    2
  XYLT2 WILD-TYPE  311   27
   clus
vv  XYLT2 MUTATED XYLT2 WILD-TYPE
  0            35             311
  1             2              27
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus                0   1
  XYLT2 MUTATED    21  17
  XYLT2 WILD-TYPE 124 231
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     21   17
  XYLT2 WILD-TYPE  124  231
        clus
vv       XYLT2 MUTATED XYLT2 WILD-TYPE
  FEMALE            21             124
  MALE              17             231
[1] 2 2
[1] FALSE
D4V8, binary
                 cls
clus                0   1
  XYLT2 MUTATED    28   4
  XYLT2 WILD-TYPE 264  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     28    4
  XYLT2 WILD-TYPE  264   55
     clus
vv    XYLT2 MUTATED XYLT2 WILD-TYPE
  NO             28             264
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  XYLT2 MUTATED                                          0
  XYLT2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  XYLT2 MUTATED                                       6
  XYLT2 WILD-TYPE                                    64
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XYLT2 MUTATED                                                       21
  XYLT2 WILD-TYPE                                                    137
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  XYLT2 MUTATED                                                   3
  XYLT2 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XYLT2 MUTATED                                                                   6
  XYLT2 WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  XYLT2 MUTATED                                                    0
  XYLT2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  XYLT2 MUTATED                                                  2
  XYLT2 WILD-TYPE                                               59
D4V9, multiclass
                                                                   clus
vv                                                                  XYLT2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       21
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  XYLT2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        137
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  XYLT2 MUTATED    28   1   2   3
  XYLT2 WILD-TYPE 283  13  13  21
D4V10, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  R0            28             283
  R1             1              13
  R2             2              13
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  XYLT2 MUTATED       9                         2
  XYLT2 WILD-TYPE    78                         7
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XYLT2 MUTATED                                           0    20
  XYLT2 WILD-TYPE                                         1   223
D4V12, multiclass
                                           clus
vv                                          XYLT2 MUTATED XYLT2 WILD-TYPE
  ASIAN                                                 9              78
  BLACK OR AFRICAN AMERICAN                             2               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                20             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, binary
                 cls
clus                0   1
  XYLT2 MUTATED     0  30
  XYLT2 WILD-TYPE   4 280
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED      0   30
  XYLT2 WILD-TYPE    4  280
                        clus
vv                       XYLT2 MUTATED XYLT2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            30             280
[1] 2 2
[1] FALSE

Clustering(5) Variable = KRAS MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  KRAS MUTATED    22  11
  KRAS WILD-TYPE 208 128
  KRAS MUTATED KRAS WILD-TYPE 
            33            336 
  KRAS MUTATED KRAS WILD-TYPE 
            11            128 
$`KRAS MUTATED`
TCGA-CG-5727 TCGA-EQ-A4SO TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4201 
       79.07        16.24        11.01         9.47         6.97        30.90 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6705 TCGA-BR-6802 TCGA-BR-7703 
        9.67         6.18         6.61        25.61        30.90        36.16 
TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8370 
       35.84        14.43        29.59         0.95         4.31         3.32 
TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-8535 
       31.96         8.22        34.98        16.14        13.41        12.82 
TCGA-CD-A4MJ TCGA-D7-A74A TCGA-HF-A5NB TCGA-HU-8604 TCGA-HU-A4GQ TCGA-HU-A4H3 
       12.62        19.96        30.51        22.82         0.10        29.00 
TCGA-SW-A7EA TCGA-VQ-A94T TCGA-VQ-AA69 
       19.04        11.24        28.41 

$`KRAS WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       47.05        21.99        22.98         0.23        20.15         9.86 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 
       26.70        11.70        19.56         9.44         6.61         4.64 
TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 
        7.43        18.35         4.08         4.08         9.34         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-6706 TCGA-BR-6707 
       39.12        26.10         9.17        32.78        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-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-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-8367 TCGA-BR-8369 
       31.10         0.26        22.19        17.52        26.33        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-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-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-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       21.44         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-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-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-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-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-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-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-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       42.64        66.81        18.41        43.66        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 

  KRAS MUTATED KRAS WILD-TYPE 
           0.1            0.0 
  KRAS MUTATED KRAS WILD-TYPE 
         79.07         122.30 
  KRAS MUTATED KRAS WILD-TYPE 
         16.14          14.12 
[1] "0.1 - 79.1 (16.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D5V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRAS MUTATED         0        1        7        2         2         2
  KRAS WILD-TYPE       2       14       33       28        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRAS MUTATED           2          8          5          4        2
  KRAS WILD-TYPE         1         62         48         28       36
D5V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              7             33
  STAGE II              2             28
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             2              1
  STAGE IIIA            8             62
  STAGE IIIB            5             48
  STAGE IIIC            4             28
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KRAS MUTATED     1   9  13  13
  KRAS WILD-TYPE  21  83 160  84
D5V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            1             21
  T2            9             83
  T3           13            160
  T4           13             84
[1] 4 2
[1] TRUE
[1] "dimension of 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    14   6   8   5
  KRAS WILD-TYPE 104  98  69  72
D5V5, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0           14            104
  N1            6             98
  N2            8             69
  N3            5             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"
D5V6, binary
                cls
clus               0   1
  KRAS MUTATED    34   1
  KRAS WILD-TYPE 312  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     34    1
  KRAS WILD-TYPE  312   28
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0           34            312
  1            1             28
[1] 2 2
[1] FALSE
D5V7, binary
                cls
clus               0   1
  KRAS MUTATED    18  19
  KRAS WILD-TYPE 127 229
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     18   19
  KRAS WILD-TYPE  127  229
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           18            127
  MALE             19            229
[1] 2 2
[1] FALSE
D5V8, binary
                cls
clus               0   1
  KRAS MUTATED    30   3
  KRAS WILD-TYPE 262  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     30    3
  KRAS WILD-TYPE  262   56
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO            30            262
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KRAS MUTATED                                          0
  KRAS WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KRAS MUTATED                                       4
  KRAS WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KRAS MUTATED                                                       19
  KRAS WILD-TYPE                                                    139
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KRAS MUTATED                                                   2
  KRAS WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KRAS MUTATED                                                                   6
  KRAS WILD-TYPE                                                                62
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KRAS MUTATED                                                    1
  KRAS WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KRAS MUTATED                                                  4
  KRAS WILD-TYPE                                               57
D5V9, multiclass
                                                                   clus
vv                                                                  KRAS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      19
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  KRAS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       139
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KRAS MUTATED    24   2   0   7
  KRAS WILD-TYPE 287  12  15  17
D5V10, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           24            287
  R1            2             12
  R2            0             15
  RX            7             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  KRAS MUTATED       7                         0
  KRAS WILD-TYPE    80                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KRAS MUTATED                                           0    26
  KRAS WILD-TYPE                                         1   217
D5V12, multiclass
                                           clus
vv                                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                                7             80
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               26            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
                cls
clus               0   1
  KRAS MUTATED     0  32
  KRAS WILD-TYPE   4 278
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0   32
  KRAS WILD-TYPE    4  278
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           32            278
[1] 2 2
[1] FALSE

Clustering(6) Variable = LARP4B MUTATION ANALYSIS
D6V1, survival
                  sevent
clus2                0   1
  LARP4B MUTATED    18   7
  LARP4B WILD-TYPE 212 132
  LARP4B MUTATED LARP4B WILD-TYPE 
              25              344 
  LARP4B MUTATED LARP4B WILD-TYPE 
               7              132 
$`LARP4B MUTATED`
TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8368 TCGA-BR-8372 
       30.90         9.67        32.78        35.84         4.31        31.27 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8535 TCGA-CD-A4MG TCGA-CD-A4MI 
       28.14        31.96        16.14        12.82         6.58        11.77 
TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5733 TCGA-F1-6874 TCGA-HF-A5NB TCGA-HU-8602 
        6.02        65.10        21.07        14.47        30.51        22.32 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-IN-A6RN TCGA-R5-A7ZI TCGA-RD-A7C1 
       22.68        29.98         6.51        19.53        74.53        16.67 
TCGA-VQ-A8P2 
       38.14 

$`LARP4B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-F1-6875 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-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-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-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-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-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 

  LARP4B MUTATED LARP4B WILD-TYPE 
            4.31             0.00 
  LARP4B MUTATED LARP4B WILD-TYPE 
           74.53           122.30 
  LARP4B MUTATED LARP4B WILD-TYPE 
          22.320           14.025 
[1] "4.3 - 74.5 (22.3)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.8"
D6V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LARP4B MUTATED         0        0        5        0         5         2
  LARP4B WILD-TYPE       2       15       35       30        32        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LARP4B MUTATED           0          5          1          3        4
  LARP4B WILD-TYPE         3         65         52         29       34
D6V3, multiclass
            clus
vv           LARP4B MUTATED LARP4B WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                5               35
  STAGE II                0               30
  STAGE IIA               5               32
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              5               65
  STAGE IIIB              1               52
  STAGE IIIC              3               29
  STAGE IV                4               34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LARP4B MUTATED     2   8   8  10
  LARP4B WILD-TYPE  20  84 165  87
D6V4, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  T1              2               20
  T2              8               84
  T3              8              165
  T4             10               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
  LARP4B MUTATED    10   7   4   4
  LARP4B WILD-TYPE 108  97  73  73
D6V5, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  N0             10              108
  N1              7               97
  N2              4               73
  N3              4               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"
D6V6, binary
                  cls
clus                 0   1
  LARP4B MUTATED    27   2
  LARP4B WILD-TYPE 319  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     27    2
  LARP4B WILD-TYPE  319   27
   clus
vv  LARP4B MUTATED LARP4B WILD-TYPE
  0             27              319
  1              2               27
[1] 2 2
[1] FALSE
D6V7, binary
                  cls
clus                 0   1
  LARP4B MUTATED    19  11
  LARP4B WILD-TYPE 126 237
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     19   11
  LARP4B WILD-TYPE  126  237
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  FEMALE             19              126
  MALE               11              237
[1] 2 2
[1] FALSE
D6V8, binary
                  cls
clus                 0   1
  LARP4B MUTATED    22   2
  LARP4B WILD-TYPE 270  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     22    2
  LARP4B WILD-TYPE  270   57
     clus
vv    LARP4B MUTATED LARP4B WILD-TYPE
  NO              22              270
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LARP4B MUTATED                                          0
  LARP4B WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LARP4B MUTATED                                       5
  LARP4B WILD-TYPE                                    65
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LARP4B MUTATED                                                       16
  LARP4B WILD-TYPE                                                    142
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LARP4B MUTATED                                                   2
  LARP4B WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LARP4B MUTATED                                                                   4
  LARP4B WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LARP4B MUTATED                                                    0
  LARP4B WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LARP4B MUTATED                                                  3
  LARP4B WILD-TYPE                                               58
D6V9, multiclass
                                                                   clus
vv                                                                  LARP4B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  LARP4B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LARP4B MUTATED    19   1   0   7
  LARP4B WILD-TYPE 292  13  15  17
D6V10, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  R0             19              292
  R1              1               13
  R2              0               15
  RX              7               17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  LARP4B MUTATED       8                         0
  LARP4B WILD-TYPE    79                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LARP4B MUTATED                                           0    18
  LARP4B WILD-TYPE                                         1   225
D6V12, multiclass
                                           clus
vv                                          LARP4B MUTATED LARP4B WILD-TYPE
  ASIAN                                                  8               79
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 18              225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
                  cls
clus                 0   1
  LARP4B MUTATED     1  24
  LARP4B WILD-TYPE   3 286
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED      1   24
  LARP4B WILD-TYPE    3  286
                        clus
vv                       LARP4B MUTATED LARP4B WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             24              286
[1] 2 2
[1] FALSE

Clustering(7) Variable = HLA-B MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  HLA-B MUTATED    17   8
  HLA-B WILD-TYPE 213 131
  HLA-B MUTATED HLA-B WILD-TYPE 
             25             344 
  HLA-B MUTATED HLA-B WILD-TYPE 
              8             131 
$`HLA-B MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-4280 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8363 
       21.99        26.70         6.61        44.94        29.59         0.26 
TCGA-BR-8366 TCGA-BR-8372 TCGA-BR-8589 TCGA-BR-8591 TCGA-CD-8531 TCGA-CD-A4MG 
        0.95        31.27        27.12        28.14        12.59         6.58 
TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 
       12.62         1.02         9.01         6.02        28.96        65.10 
TCGA-F1-6874 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-KB-A93J TCGA-MX-A5UJ 
       14.47        22.68         0.10        29.00        36.95        19.73 
TCGA-SW-A7EA 
       19.04 

$`HLA-B WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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-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-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-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-D7-6525 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-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-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-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-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 

  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 
          19.73           14.07 
[1] "0.1 - 65.1 (19.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D7V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HLA-B MUTATED         0        2        6        1         3         3
  HLA-B WILD-TYPE       2       13       34       29        34        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HLA-B MUTATED           1          2          1          4        4
  HLA-B WILD-TYPE         2         68         52         28       34
D7V3, multiclass
            clus
vv           HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               6              34
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              3              49
  STAGE III              1               2
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             4              28
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HLA-B MUTATED     2   8   8  10
  HLA-B WILD-TYPE  20  84 165  87
D7V4, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  T1             2              20
  T2             8              84
  T3             8             165
  T4            10              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
  HLA-B MUTATED    13   7   3   4
  HLA-B WILD-TYPE 105  97  74  73
D7V5, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  N0            13             105
  N1             7              97
  N2             3              74
  N3             4              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"
D7V6, binary
                 cls
clus                0   1
  HLA-B MUTATED    24   3
  HLA-B WILD-TYPE 322  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     24    3
  HLA-B WILD-TYPE  322   26
   clus
vv  HLA-B MUTATED HLA-B WILD-TYPE
  0            24             322
  1             3              26
[1] 2 2
[1] FALSE
D7V7, binary
                 cls
clus                0   1
  HLA-B MUTATED    15  13
  HLA-B WILD-TYPE 130 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     15   13
  HLA-B WILD-TYPE  130  235
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  FEMALE            15             130
  MALE              13             235
[1] 2 2
[1] FALSE
D7V8, binary
                 cls
clus                0   1
  HLA-B MUTATED    18   3
  HLA-B WILD-TYPE 274  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     18    3
  HLA-B WILD-TYPE  274   56
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  NO             18             274
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HLA-B MUTATED                                          0
  HLA-B WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HLA-B MUTATED                                       8
  HLA-B WILD-TYPE                                    62
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HLA-B MUTATED                                                       12
  HLA-B WILD-TYPE                                                    146
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HLA-B MUTATED                                                   0
  HLA-B WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HLA-B MUTATED                                                                   6
  HLA-B WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HLA-B MUTATED                                                    0
  HLA-B WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HLA-B MUTATED                                                  2
  HLA-B WILD-TYPE                                               59
D7V9, multiclass
                                                                   clus
vv                                                                  HLA-B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  HLA-B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          62
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HLA-B MUTATED    20   0   3   2
  HLA-B WILD-TYPE 291  14  12  22
D7V10, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  R0            20             291
  R1             0              14
  R2             3              12
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HLA-B MUTATED       7                         0
  HLA-B WILD-TYPE    80                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HLA-B MUTATED                                           0    14
  HLA-B WILD-TYPE                                         1   229
D7V12, multiclass
                                           clus
vv                                          HLA-B MUTATED HLA-B WILD-TYPE
  ASIAN                                                 7              80
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, binary
                 cls
clus                0   1
  HLA-B MUTATED     0  20
  HLA-B WILD-TYPE   4 290
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      0   20
  HLA-B WILD-TYPE    4  290
                        clus
vv                       HLA-B MUTATED HLA-B WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            20             290
[1] 2 2
[1] FALSE

Clustering(8) Variable = RHOA MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  RHOA MUTATED    12   7
  RHOA WILD-TYPE 218 132
  RHOA MUTATED RHOA WILD-TYPE 
            19            350 
  RHOA MUTATED RHOA WILD-TYPE 
             7            132 
$`RHOA MUTATED`
TCGA-BR-4188 TCGA-BR-6563 TCGA-BR-6802 TCGA-BR-7722 TCGA-BR-8366 TCGA-BR-A4IV 
        7.43        39.12        30.90        15.32         0.95        28.57 
TCGA-BR-A4QM TCGA-CG-4465 TCGA-CG-5720 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-8574 
        5.13         9.01         0.99        18.84        18.54        17.19 
TCGA-D7-A4YU TCGA-F1-A448 TCGA-HU-A4H0 TCGA-R5-A804 TCGA-VQ-A8P2 TCGA-VQ-A8PM 
       16.44        21.27         2.10         4.60        38.14         1.87 
TCGA-ZA-A8F6 
       17.26 

$`RHOA WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98         1.48        27.55        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-CD-5798 
       20.65        20.42         1.15        21.44        16.14        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-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         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-D7-6522 
       25.71        12.66        20.91        19.13        20.55        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-D7-8575 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-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-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-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       74.53         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-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 
       27.55        12.43 

  RHOA MUTATED RHOA WILD-TYPE 
          0.95           0.00 
  RHOA MUTATED RHOA WILD-TYPE 
         39.12         122.30 
  RHOA MUTATED RHOA WILD-TYPE 
         16.44          14.12 
[1] "0.9 - 39.1 (16.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D8V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RHOA MUTATED         0        0        2        0         1         2
  RHOA WILD-TYPE       2       15       38       30        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RHOA MUTATED           0          5          3          1        3
  RHOA WILD-TYPE         3         65         50         31       35
D8V3, multiclass
            clus
vv           RHOA MUTATED RHOA WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            5             65
  STAGE IIIB            3             50
  STAGE IIIC            1             31
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RHOA MUTATED     0   5   8   5
  RHOA WILD-TYPE  22  87 165  92
D8V4, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  T1            0             22
  T2            5             87
  T3            8            165
  T4            5             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
  RHOA MUTATED     3   4   6   6
  RHOA WILD-TYPE 115 100  71  71
D8V5, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  N0            3            115
  N1            4            100
  N2            6             71
  N3            6             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"
D8V6, binary
                cls
clus               0   1
  RHOA MUTATED    16   2
  RHOA WILD-TYPE 330  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED     16    2
  RHOA WILD-TYPE  330   27
   clus
vv  RHOA MUTATED RHOA WILD-TYPE
  0           16            330
  1            2             27
[1] 2 2
[1] FALSE
D8V7, binary
                cls
clus               0   1
  RHOA MUTATED     3  16
  RHOA WILD-TYPE 142 232
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      3   16
  RHOA WILD-TYPE  142  232
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  FEMALE            3            142
  MALE             16            232
[1] 2 2
[1] FALSE
D8V8, binary
                cls
clus               0   1
  RHOA MUTATED    15   2
  RHOA WILD-TYPE 277  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED     15    2
  RHOA WILD-TYPE  277   57
     clus
vv    RHOA MUTATED RHOA WILD-TYPE
  NO            15            277
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RHOA MUTATED                                          1
  RHOA WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RHOA MUTATED                                       5
  RHOA WILD-TYPE                                    65
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RHOA MUTATED                                                        8
  RHOA WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RHOA MUTATED                                                   2
  RHOA WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RHOA MUTATED                                                                   1
  RHOA WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RHOA MUTATED                                                    0
  RHOA WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RHOA MUTATED                                                  2
  RHOA WILD-TYPE                                               59
D8V9, multiclass
                                                                   clus
vv                                                                  RHOA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  RHOA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RHOA MUTATED    16   0   1   1
  RHOA WILD-TYPE 295  14  14  23
D8V10, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  R0           16            295
  R1            0             14
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RHOA MUTATED       2                         1
  RHOA WILD-TYPE    85                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RHOA MUTATED                                           0    14
  RHOA WILD-TYPE                                         1   229
D8V12, multiclass
                                           clus
vv                                          RHOA MUTATED RHOA WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               14            229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
                cls
clus               0   1
  RHOA MUTATED     1  14
  RHOA WILD-TYPE   3 296
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      1   14
  RHOA WILD-TYPE    3  296
                        clus
vv                       RHOA MUTATED RHOA WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           14            296
[1] 2 2
[1] FALSE

Clustering(9) Variable = SMAD4 MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2               0   1
  SMAD4 MUTATED    18  10
  SMAD4 WILD-TYPE 212 129
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             28             341 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             10             129 
$`SMAD4 MUTATED`
TCGA-BR-4184 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6564 TCGA-BR-7722 TCGA-BR-7958 
        6.97         6.18         9.57        26.10        15.32        29.56 
TCGA-BR-8361 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-A4J6 
       31.10         0.95         3.32        31.27         1.12         0.66 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8529 TCGA-CG-4469 TCGA-CG-5719 TCGA-D7-6815 
       11.21        12.10        12.30         7.07         1.02        15.98 
TCGA-D7-A6EV TCGA-F1-A72C TCGA-FP-7829 TCGA-HU-8243 TCGA-HU-A4G2 TCGA-HU-A4H4 
       11.24        11.38        19.53         5.92        24.30        23.84 
TCGA-IN-8462 TCGA-KB-A6F7 TCGA-R5-A7ZF TCGA-VQ-A91U 
       18.81        63.62         8.52         1.71 

$`SMAD4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-4280 
       30.90         4.08         4.08         9.34         9.67         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-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         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-7959 
       39.78        18.15        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-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-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53        28.34        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-5813 
       13.41        13.02        13.15        13.18        13.35        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-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-D7-6817 
       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-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-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23        21.27         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-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-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         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-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-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-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 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           0.66            0.00 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          63.62          122.30 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          11.31           14.66 
[1] "0.7 - 63.6 (11.3)"  "0.0 - 122.3 (14.7)"
[1] "hr=" "1.2"
D9V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMAD4 MUTATED         0        0        2        2         4         7
  SMAD4 WILD-TYPE       2       15       38       28        33        45
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMAD4 MUTATED           0          3          2          3        4
  SMAD4 WILD-TYPE         3         67         51         29       34
D9V3, multiclass
            clus
vv           SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               2              28
  STAGE IIA              4              33
  STAGE IIB              7              45
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             3              29
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMAD4 MUTATED     1   6  14   7
  SMAD4 WILD-TYPE  21  86 159  90
D9V4, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  T1             1              21
  T2             6              86
  T3            14             159
  T4             7              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
  SMAD4 MUTATED     9  10   5   4
  SMAD4 WILD-TYPE 109  94  72  73
D9V5, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0             9             109
  N1            10              94
  N2             5              72
  N3             4              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"
D9V6, binary
                 cls
clus                0   1
  SMAD4 MUTATED    24   3
  SMAD4 WILD-TYPE 322  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     24    3
  SMAD4 WILD-TYPE  322   26
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0            24             322
  1             3              26
[1] 2 2
[1] FALSE
D9V7, binary
                 cls
clus                0   1
  SMAD4 MUTATED    12  16
  SMAD4 WILD-TYPE 133 232
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     12   16
  SMAD4 WILD-TYPE  133  232
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE            12             133
  MALE              16             232
[1] 2 2
[1] FALSE
D9V8, binary
                 cls
clus                0   1
  SMAD4 MUTATED    23   3
  SMAD4 WILD-TYPE 269  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     23    3
  SMAD4 WILD-TYPE  269   56
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  NO             23             269
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SMAD4 MUTATED                                          0
  SMAD4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SMAD4 MUTATED                                       3
  SMAD4 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMAD4 MUTATED                                                       14
  SMAD4 WILD-TYPE                                                    144
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SMAD4 MUTATED                                                   2
  SMAD4 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMAD4 MUTATED                                                                   5
  SMAD4 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SMAD4 MUTATED                                                    0
  SMAD4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SMAD4 MUTATED                                                  4
  SMAD4 WILD-TYPE                                               57
D9V9, multiclass
                                                                   clus
vv                                                                  SMAD4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  SMAD4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SMAD4 MUTATED    22   1   0   3
  SMAD4 WILD-TYPE 289  13  15  21
D9V10, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0            22             289
  R1             1              13
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SMAD4 MUTATED       8                         1
  SMAD4 WILD-TYPE    79                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMAD4 MUTATED                                           0    16
  SMAD4 WILD-TYPE                                         1   227
D9V12, multiclass
                                           clus
vv                                          SMAD4 MUTATED SMAD4 WILD-TYPE
  ASIAN                                                 8              79
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                16             227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, binary
                 cls
clus                0   1
  SMAD4 MUTATED     0  24
  SMAD4 WILD-TYPE   4 286
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      0   24
  SMAD4 WILD-TYPE    4  286
                        clus
vv                       SMAD4 MUTATED SMAD4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            24             286
[1] 2 2
[1] FALSE

Clustering(10) Variable = B2M MUTATION ANALYSIS
D10V1, survival
               sevent
clus2             0   1
  B2M MUTATED    12   4
  B2M WILD-TYPE 218 135
  B2M MUTATED B2M WILD-TYPE 
           16           353 
  B2M MUTATED B2M WILD-TYPE 
            4           135 
$`B2M MUTATED`
TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 
       32.78        44.94        35.84        25.05         1.12        28.14 
TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-8570 
       16.14        12.43        11.77         6.02        65.10        24.72 
TCGA-D7-A6EY TCGA-D7-A74A TCGA-HU-A4GX TCGA-HU-A4H8 
       11.44        19.96        20.25        14.07 

$`B2M WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-D7-8572 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-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-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-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-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 

  B2M MUTATED B2M WILD-TYPE 
         1.12          0.00 
  B2M MUTATED B2M WILD-TYPE 
         65.1         122.3 
  B2M MUTATED B2M WILD-TYPE 
       20.105        14.070 
[1] "1.1 - 65.1 (20.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D10V2, 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       1       15       37       29        34        52
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B2M MUTATED           0          2          3          3        1
  B2M WILD-TYPE         3         68         50         29       37
D10V3, multiclass
            clus
vv           B2M MUTATED B2M WILD-TYPE
  STAGE I              1             1
  STAGE IA             0            15
  STAGE IB             3            37
  STAGE II             1            29
  STAGE IIA            3            34
  STAGE IIB            0            52
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           3            50
  STAGE IIIC           3            29
  STAGE IV             1            37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  B2M MUTATED     2   2   9   4
  B2M WILD-TYPE  20  90 164  93
D10V4, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  T1           2            20
  T2           2            90
  T3           9           164
  T4           4            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
  B2M MUTATED     6   5   2   5
  B2M WILD-TYPE 112  99  75  72
D10V5, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  N0           6           112
  N1           5            99
  N2           2            75
  N3           5            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"
D10V6, binary
               cls
clus              0   1
  B2M MUTATED    17   0
  B2M WILD-TYPE 329  29
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     17    0
  B2M WILD-TYPE  329   29
   clus
vv  B2M MUTATED B2M WILD-TYPE
  0          17           329
  1           0            29
[1] 2 2
[1] FALSE
D10V7, binary
               cls
clus              0   1
  B2M MUTATED    11   7
  B2M WILD-TYPE 134 241
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     11    7
  B2M WILD-TYPE  134  241
        clus
vv       B2M MUTATED B2M WILD-TYPE
  FEMALE          11           134
  MALE             7           241
[1] 2 2
[1] FALSE
D10V8, binary
               cls
clus              0   1
  B2M MUTATED    16   0
  B2M WILD-TYPE 276  59
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     16    0
  B2M WILD-TYPE  276   59
     clus
vv    B2M MUTATED B2M WILD-TYPE
  NO           16           276
  YES           0            59
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  B2M MUTATED                                          0
  B2M WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  B2M MUTATED                                       1
  B2M WILD-TYPE                                    69
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  B2M MUTATED                                                       11
  B2M WILD-TYPE                                                    147
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  B2M MUTATED                                                   0
  B2M WILD-TYPE                                                21
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  B2M MUTATED                                                                   2
  B2M WILD-TYPE                                                                66
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  B2M MUTATED                                                    0
  B2M WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  B2M MUTATED                                                  4
  B2M WILD-TYPE                                               57
D10V9, multiclass
                                                                   clus
vv                                                                  B2M MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                     11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            4
                                                                   clus
vv                                                                  B2M WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  B2M MUTATED    16   0   0   1
  B2M WILD-TYPE 295  14  15  23
D10V10, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  R0          16           295
  R1           0            14
  R2           0            15
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  B2M MUTATED       4                         1
  B2M WILD-TYPE    83                         8
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  B2M MUTATED                                           0    11
  B2M WILD-TYPE                                         1   232
D10V12, multiclass
                                           clus
vv                                          B2M MUTATED B2M WILD-TYPE
  ASIAN                                               4            83
  BLACK OR AFRICAN AMERICAN                           1             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              11           232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, binary
               cls
clus              0   1
  B2M MUTATED     0  16
  B2M WILD-TYPE   4 294
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      0   16
  B2M WILD-TYPE    4  294
                        clus
vv                       B2M MUTATED B2M WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          16           294
[1] 2 2
[1] FALSE

Clustering(11) Variable = C7ORF50 MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  C7ORF50 MUTATED     7   5
  C7ORF50 WILD-TYPE 223 134
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
               12               357 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                5               134 
$`C7ORF50 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-A4QL 
       21.99        34.68         6.18        31.10         1.12        16.14 
TCGA-CG-5726 TCGA-D7-A4YY TCGA-D7-A6EY TCGA-F1-6874 TCGA-HU-A4G8 TCGA-HU-A4GQ 
       28.96        13.78        11.44        14.47        22.68         0.10 

$`C7ORF50 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        36.43        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-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-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 

  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
              0.1               0.0 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
            34.68            122.30 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
           15.305            14.170 
[1] "0.1 - 34.7 (15.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C7ORF50 MUTATED         0        1        1        0         3         1
  C7ORF50 WILD-TYPE       2       14       39       30        34        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF50 MUTATED           0          0          3          2        1
  C7ORF50 WILD-TYPE         3         70         50         30       37
D11V3, multiclass
            clus
vv           C7ORF50 MUTATED C7ORF50 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                3                34
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               3                50
  STAGE IIIC               2                30
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C7ORF50 MUTATED     1   1   7   3
  C7ORF50 WILD-TYPE  21  91 166  94
D11V4, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  T1               1                21
  T2               1                91
  T3               7               166
  T4               3                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
  C7ORF50 MUTATED     5   2   2   3
  C7ORF50 WILD-TYPE 113 102  75  74
D11V5, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  N0               5               113
  N1               2               102
  N2               2                75
  N3               3                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"
D11V6, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED    11   1
  C7ORF50 WILD-TYPE 335  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED     11    1
  C7ORF50 WILD-TYPE  335   28
   clus
vv  C7ORF50 MUTATED C7ORF50 WILD-TYPE
  0              11               335
  1               1                28
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     7   5
  C7ORF50 WILD-TYPE 138 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      7    5
  C7ORF50 WILD-TYPE  138  243
        clus
vv       C7ORF50 MUTATED C7ORF50 WILD-TYPE
  FEMALE               7               138
  MALE                 5               243
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED    10   1
  C7ORF50 WILD-TYPE 282  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED     10    1
  C7ORF50 WILD-TYPE  282   58
     clus
vv    C7ORF50 MUTATED C7ORF50 WILD-TYPE
  NO               10               282
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C7ORF50 MUTATED                                          0
  C7ORF50 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C7ORF50 MUTATED                                       1
  C7ORF50 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C7ORF50 MUTATED                                                        5
  C7ORF50 WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C7ORF50 MUTATED                                                   0
  C7ORF50 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C7ORF50 MUTATED                                                                   4
  C7ORF50 WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C7ORF50 MUTATED                                                    0
  C7ORF50 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C7ORF50 MUTATED                                                  2
  C7ORF50 WILD-TYPE                                               59
D11V9, multiclass
                                                                   clus
vv                                                                  C7ORF50 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  C7ORF50 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C7ORF50 MUTATED    10   0   1   0
  C7ORF50 WILD-TYPE 301  14  14  24
D11V10, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  R0              10               301
  R1               0                14
  R2               1                14
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C7ORF50 MUTATED       2                         0
  C7ORF50 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C7ORF50 MUTATED                                           0     8
  C7ORF50 WILD-TYPE                                         1   235
D11V12, multiclass
                                           clus
vv                                          C7ORF50 MUTATED C7ORF50 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     0  10
  C7ORF50 WILD-TYPE   4 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      0   10
  C7ORF50 WILD-TYPE    4  300
                        clus
vv                       C7ORF50 MUTATED C7ORF50 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              10               300
[1] 2 2
[1] FALSE

Clustering(12) Variable = MLL4 MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  MLL4 MUTATED    26  15
  MLL4 WILD-TYPE 204 124
  MLL4 MUTATED MLL4 WILD-TYPE 
            41            328 
  MLL4 MUTATED MLL4 WILD-TYPE 
            15            124 
$`MLL4 MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6456 
       19.56         6.97         7.43         6.61        34.68        17.29 
TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8363 
       19.33        32.78        44.94        29.59        32.25         0.26 
TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 
        4.31        31.27         7.36        25.05         1.12        28.14 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 
       12.43         6.58        11.77        12.62        15.95         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A4YV TCGA-D7-A6EY TCGA-F1-A448 
        0.99         6.02        28.96         5.92        11.44        21.27 
TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GX 
       11.08        30.51        26.47        22.32        29.98        20.25 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-RD-A8MV TCGA-SW-A7EA TCGA-VQ-A8P2 
       29.00        14.07       122.30        19.04        38.14 

$`MLL4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        26.70        11.70        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        9.44         6.61         4.64        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-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.87        13.68        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-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-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-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         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-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-4436 
       11.61        12.20        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-5722 TCGA-CG-5723 TCGA-CG-5724 
        6.97        36.00         1.02         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-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-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-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-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-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-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 

  MLL4 MUTATED MLL4 WILD-TYPE 
          0.26           0.00 
  MLL4 MUTATED MLL4 WILD-TYPE 
        122.30         116.38 
  MLL4 MUTATED MLL4 WILD-TYPE 
        19.040         14.055 
[1] "0.3 - 122.3 (19.0)" "0.0 - 116.4 (14.1)"
[1] "hr=" "1.1"
D12V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLL4 MUTATED         1        1        8        2         7         8
  MLL4 WILD-TYPE       1       14       32       28        30        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MLL4 MUTATED           1          4          3          7        2
  MLL4 WILD-TYPE         2         66         50         25       36
D12V3, multiclass
            clus
vv           MLL4 MUTATED MLL4 WILD-TYPE
  STAGE I               1              1
  STAGE IA              1             14
  STAGE IB              8             32
  STAGE II              2             28
  STAGE IIA             7             30
  STAGE IIB             8             44
  STAGE III             1              2
  STAGE IIIA            4             66
  STAGE IIIB            3             50
  STAGE IIIC            7             25
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MLL4 MUTATED     3  10  17  14
  MLL4 WILD-TYPE  19  82 156  83
D12V4, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  T1            3             19
  T2           10             82
  T3           17            156
  T4           14             83
[1] 4 2
[1] TRUE
[1] "dimension of 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   20 14  3  8
  MLL4 WILD-TYPE 98 90 74 69
D12V5, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  N0           20             98
  N1           14             90
  N2            3             74
  N3            8             69
[1] 4 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
  MLL4 MUTATED    41   1
  MLL4 WILD-TYPE 305  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     41    1
  MLL4 WILD-TYPE  305   28
   clus
vv  MLL4 MUTATED MLL4 WILD-TYPE
  0           41            305
  1            1             28
[1] 2 2
[1] FALSE
D12V7, binary
                cls
clus               0   1
  MLL4 MUTATED    22  23
  MLL4 WILD-TYPE 123 225
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     22   23
  MLL4 WILD-TYPE  123  225
        clus
vv       MLL4 MUTATED MLL4 WILD-TYPE
  FEMALE           22            123
  MALE             23            225
[1] 2 2
[1] FALSE
D12V8, binary
                cls
clus               0   1
  MLL4 MUTATED    34   5
  MLL4 WILD-TYPE 258  54
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     34    5
  MLL4 WILD-TYPE  258   54
     clus
vv    MLL4 MUTATED MLL4 WILD-TYPE
  NO            34            258
  YES            5             54
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MLL4 MUTATED                                          1
  MLL4 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MLL4 MUTATED                                       6
  MLL4 WILD-TYPE                                    64
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MLL4 MUTATED                                                       26
  MLL4 WILD-TYPE                                                    132
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MLL4 MUTATED                                                   3
  MLL4 WILD-TYPE                                                18
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MLL4 MUTATED                                                                   5
  MLL4 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MLL4 MUTATED                                                    0
  MLL4 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MLL4 MUTATED                                                  4
  MLL4 WILD-TYPE                                               57
D12V9, multiclass
                                                                   clus
vv                                                                  MLL4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      26
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  MLL4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       132
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MLL4 MUTATED    35   1   1   4
  MLL4 WILD-TYPE 276  13  14  20
D12V10, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  R0           35            276
  R1            1             13
  R2            1             14
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MLL4 MUTATED       9                         2
  MLL4 WILD-TYPE    78                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MLL4 MUTATED                                           0    27
  MLL4 WILD-TYPE                                         1   216
D12V12, multiclass
                                           clus
vv                                          MLL4 MUTATED MLL4 WILD-TYPE
  ASIAN                                                9             78
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               27            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, binary
                cls
clus               0   1
  MLL4 MUTATED     1  36
  MLL4 WILD-TYPE   3 274
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      1   36
  MLL4 WILD-TYPE    3  274
                        clus
vv                       MLL4 MUTATED MLL4 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           36            274
[1] 2 2
[1] FALSE

Clustering(13) Variable = PTEN MUTATION ANALYSIS
D13V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    17  11
  PTEN WILD-TYPE 213 128
  PTEN MUTATED PTEN WILD-TYPE 
            28            341 
  PTEN MUTATED PTEN WILD-TYPE 
            11            128 
$`PTEN MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4257 
       26.70        19.56        30.90         4.08         9.34         9.67 
TCGA-BR-6452 TCGA-BR-6707 TCGA-BR-7704 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8368 
       34.68        19.89        35.24        29.59         8.05         4.31 
TCGA-BR-8381 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-8531 TCGA-CG-4305 TCGA-CG-5725 
        7.36         1.12        28.14        12.59        15.95        15.02 
TCGA-CG-5728 TCGA-D7-5577 TCGA-FP-7735 TCGA-FP-8211 TCGA-FP-A4BE TCGA-HU-A4GT 
       65.10        25.71         3.48        13.58        11.08         6.51 
TCGA-IN-A6RN TCGA-R5-A7O7 TCGA-R5-A805 TCGA-VQ-A8DL 
       19.53        45.67         9.24         0.92 

$`PTEN WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        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-4255 
        6.61         6.97         4.64         7.43        18.35         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-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-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-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-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-8382 TCGA-BR-8384 TCGA-BR-8483 
       11.80        31.27        14.79        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-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-5726 TCGA-CG-5730 TCGA-CG-5732 
        0.99       105.07        12.03        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-D7-8579 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-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-8631 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 
       59.54         5.03         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-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-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        13.35         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-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-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 

  PTEN MUTATED PTEN WILD-TYPE 
          0.92           0.00 
  PTEN MUTATED PTEN WILD-TYPE 
          65.1          122.3 
  PTEN MUTATED PTEN WILD-TYPE 
         14.30          14.27 
[1] "0.9 - 65.1 (14.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D13V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTEN MUTATED         0        0        4        2         7         5
  PTEN WILD-TYPE       2       15       36       28        30        47
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTEN MUTATED           0          3          1          3        1
  PTEN WILD-TYPE         3         67         52         29       37
D13V3, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              4             36
  STAGE II              2             28
  STAGE IIA             7             30
  STAGE IIB             5             47
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            1             52
  STAGE IIIC            3             29
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PTEN MUTATED     1   7  13   6
  PTEN WILD-TYPE  21  85 160  91
D13V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            1             21
  T2            7             85
  T3           13            160
  T4            6             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
  PTEN MUTATED    14   8   2   4
  PTEN WILD-TYPE 104  96  75  73
D13V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0           14            104
  N1            8             96
  N2            2             75
  N3            4             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"
D13V6, binary
                cls
clus               0   1
  PTEN MUTATED    27   1
  PTEN WILD-TYPE 319  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     27    1
  PTEN WILD-TYPE  319   28
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0           27            319
  1            1             28
[1] 2 2
[1] FALSE
D13V7, binary
                cls
clus               0   1
  PTEN MUTATED    17  13
  PTEN WILD-TYPE 128 235
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     17   13
  PTEN WILD-TYPE  128  235
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE           17            128
  MALE             13            235
[1] 2 2
[1] FALSE
D13V8, binary
                cls
clus               0   1
  PTEN MUTATED    24   3
  PTEN WILD-TYPE 268  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     24    3
  PTEN WILD-TYPE  268   56
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO            24            268
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PTEN MUTATED                                          0
  PTEN WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PTEN MUTATED                                       3
  PTEN WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTEN MUTATED                                                       18
  PTEN WILD-TYPE                                                    140
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PTEN MUTATED                                                   0
  PTEN WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTEN MUTATED                                                                   5
  PTEN WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PTEN MUTATED                                                    0
  PTEN WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PTEN MUTATED                                                  4
  PTEN WILD-TYPE                                               57
D13V9, multiclass
                                                                   clus
vv                                                                  PTEN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      18
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  PTEN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       140
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED    21   1   0   5
  PTEN WILD-TYPE 290  13  15  19
D13V10, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0           21            290
  R1            1             13
  R2            0             15
  RX            5             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PTEN MUTATED       2                         2
  PTEN WILD-TYPE    85                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTEN MUTATED                                           0    23
  PTEN WILD-TYPE                                         1   220
D13V12, multiclass
                                           clus
vv                                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               23            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, binary
                cls
clus               0   1
  PTEN MUTATED     1  25
  PTEN WILD-TYPE   3 285
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1   25
  PTEN WILD-TYPE    3  285
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           25            285
[1] 2 2
[1] FALSE

Clustering(14) Variable = CDH1 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  CDH1 MUTATED    16  14
  CDH1 WILD-TYPE 214 125
  CDH1 MUTATED CDH1 WILD-TYPE 
            30            339 
  CDH1 MUTATED CDH1 WILD-TYPE 
            14            125 
$`CDH1 MUTATED`
TCGA-FP-A8CX TCGA-B7-A5TI TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6566 
        0.23        19.56         7.43         9.57        34.68        32.78 
TCGA-BR-6803 TCGA-BR-8058 TCGA-BR-8364 TCGA-BR-8370 TCGA-BR-8592 TCGA-BR-8686 
       31.20        37.25        22.19         3.32         6.28        20.88 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5813 
       34.13         6.08        28.57         5.13        13.02        12.39 
TCGA-CD-A4MG TCGA-D7-6518 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-A4YU TCGA-D7-A6EY 
        6.58        19.13        16.80        17.19        16.44        11.44 
TCGA-D7-A748 TCGA-F1-6874 TCGA-FP-8210 TCGA-IN-7808 TCGA-MX-A5UG TCGA-R5-A804 
        4.34        14.47         5.03         3.45         3.72         4.60 

$`CDH1 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       47.05        21.99        22.98        79.07        16.24        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        26.70        11.70        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         4.64        18.35        30.90         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-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-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        30.90        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-8059 
       28.73         3.45         9.07        29.56        33.21        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-8365 TCGA-BR-8366 TCGA-BR-8367 
        6.18        31.10         0.26        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-8591 TCGA-BR-8676 
        1.12        12.79        27.12         9.34        28.14         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-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       10.68        13.87         7.53        34.98         1.48        27.55 
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-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       21.44        16.14        13.41        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-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-D7-6519 
       21.07         7.99        25.71        12.66        20.91        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-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        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-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-F1-6875 
        8.38        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-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       17.06        59.54        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-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-A5UJ 
       13.51         2.53         5.56        63.62        36.95        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-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 

  CDH1 MUTATED CDH1 WILD-TYPE 
          0.23           0.00 
  CDH1 MUTATED CDH1 WILD-TYPE 
         37.25         122.30 
  CDH1 MUTATED CDH1 WILD-TYPE 
        12.705         14.430 
[1] "0.2 - 37.2 (12.7)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.6"
D14V2, 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       2       15       39       27        32        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDH1 MUTATED           0          5          7          3        4
  CDH1 WILD-TYPE         3         65         46         29       34
D14V3, multiclass
            clus
vv           CDH1 MUTATED CDH1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              3             27
  STAGE IIA             5             32
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            5             65
  STAGE IIIB            7             46
  STAGE IIIC            3             29
  STAGE IV              4             34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CDH1 MUTATED     1   6  14  10
  CDH1 WILD-TYPE  21  86 159  87
D14V4, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  T1            1             21
  T2            6             86
  T3           14            159
  T4           10             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
  CDH1 MUTATED     7   7   7  10
  CDH1 WILD-TYPE 111  97  70  67
D14V5, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  N0            7            111
  N1            7             97
  N2            7             70
  N3           10             67
[1] 4 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
  CDH1 MUTATED    26   5
  CDH1 WILD-TYPE 320  24
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     26    5
  CDH1 WILD-TYPE  320   24
   clus
vv  CDH1 MUTATED CDH1 WILD-TYPE
  0           26            320
  1            5             24
[1] 2 2
[1] FALSE
D14V7, binary
                cls
clus               0   1
  CDH1 MUTATED    12  20
  CDH1 WILD-TYPE 133 228
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     12   20
  CDH1 WILD-TYPE  133  228
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  FEMALE           12            133
  MALE             20            228
[1] 2 2
[1] FALSE
D14V8, binary
                cls
clus               0   1
  CDH1 MUTATED    27   2
  CDH1 WILD-TYPE 265  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     27    2
  CDH1 WILD-TYPE  265   57
     clus
vv    CDH1 MUTATED CDH1 WILD-TYPE
  NO            27            265
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CDH1 MUTATED                                          2
  CDH1 WILD-TYPE                                        6
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CDH1 MUTATED                                      15
  CDH1 WILD-TYPE                                    55
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDH1 MUTATED                                                        9
  CDH1 WILD-TYPE                                                    149
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CDH1 MUTATED                                                   1
  CDH1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDH1 MUTATED                                                                   2
  CDH1 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CDH1 MUTATED                                                    0
  CDH1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CDH1 MUTATED                                                  3
  CDH1 WILD-TYPE                                               58
D14V9, multiclass
                                                                   clus
vv                                                                  CDH1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       15
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  CDH1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         55
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CDH1 MUTATED    20   1   1   3
  CDH1 WILD-TYPE 291  13  14  21
D14V10, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  R0           20            291
  R1            1             13
  R2            1             14
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CDH1 MUTATED       8                         1
  CDH1 WILD-TYPE    79                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDH1 MUTATED                                           0    22
  CDH1 WILD-TYPE                                         1   221
D14V12, multiclass
                                           clus
vv                                          CDH1 MUTATED CDH1 WILD-TYPE
  ASIAN                                                8             79
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               22            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, binary
                cls
clus               0   1
  CDH1 MUTATED     0  31
  CDH1 WILD-TYPE   4 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED      0   31
  CDH1 WILD-TYPE    4  279
                        clus
vv                       CDH1 MUTATED CDH1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           31            279
[1] 2 2
[1] FALSE

Clustering(15) Variable = GNG12 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  GNG12 MUTATED     7   3
  GNG12 WILD-TYPE 223 136
  GNG12 MUTATED GNG12 WILD-TYPE 
             10             359 
  GNG12 MUTATED GNG12 WILD-TYPE 
              3             136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  GNG12 MUTATED GNG12 WILD-TYPE 
           0.26            0.00 
  GNG12 MUTATED GNG12 WILD-TYPE 
          34.68          122.30 
  GNG12 MUTATED GNG12 WILD-TYPE 
          11.46           14.27 
[1] "0.3 - 34.7 (11.5)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "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       2       15       38       29        34        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GNG12 MUTATED           0          1          0          0        2
  GNG12 WILD-TYPE         3         69         53         32       36
D15V3, multiclass
            clus
vv           GNG12 MUTATED GNG12 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GNG12 MUTATED     0   3   4   4
  GNG12 WILD-TYPE  22  89 169  93
D15V4, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             4             169
  T4             4              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
  GNG12 MUTATED     7   4   1   0
  GNG12 WILD-TYPE 111 100  76  77
D15V5, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  N0             7             111
  N1             4             100
  N2             1              76
  N3             0              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"
D15V6, binary
                 cls
clus                0   1
  GNG12 MUTATED    11   0
  GNG12 WILD-TYPE 335  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED     11    0
  GNG12 WILD-TYPE  335   29
   clus
vv  GNG12 MUTATED GNG12 WILD-TYPE
  0            11             335
  1             0              29
[1] 2 2
[1] FALSE
D15V7, binary
                 cls
clus                0   1
  GNG12 MUTATED     8   4
  GNG12 WILD-TYPE 137 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      8    4
  GNG12 WILD-TYPE  137  244
        clus
vv       GNG12 MUTATED GNG12 WILD-TYPE
  FEMALE             8             137
  MALE               4             244
[1] 2 2
[1] FALSE
D15V8, binary
                 cls
clus                0   1
  GNG12 MUTATED    10   0
  GNG12 WILD-TYPE 282  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED     10    0
  GNG12 WILD-TYPE  282   59
     clus
vv    GNG12 MUTATED GNG12 WILD-TYPE
  NO             10             282
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GNG12 MUTATED                                          0
  GNG12 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GNG12 MUTATED                                       3
  GNG12 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GNG12 MUTATED                                                        7
  GNG12 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GNG12 MUTATED                                                   0
  GNG12 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GNG12 MUTATED                                                                   1
  GNG12 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GNG12 MUTATED                                                    0
  GNG12 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GNG12 MUTATED                                                  1
  GNG12 WILD-TYPE                                               60
D15V9, multiclass
                                                                   clus
vv                                                                  GNG12 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  GNG12 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GNG12 MUTATED     8   0   0   3
  GNG12 WILD-TYPE 303  14  15  21
D15V10, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GNG12 MUTATED       3                         0
  GNG12 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GNG12 MUTATED                                           0     7
  GNG12 WILD-TYPE                                         1   236
D15V12, multiclass
                                           clus
vv                                          GNG12 MUTATED GNG12 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, binary
                 cls
clus                0   1
  GNG12 MUTATED     0  10
  GNG12 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      0   10
  GNG12 WILD-TYPE    4  300
                        clus
vv                       GNG12 MUTATED GNG12 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(16) Variable = PGM5 MUTATION ANALYSIS
D16V1, survival
                sevent
clus2              0   1
  PGM5 MUTATED    23  11
  PGM5 WILD-TYPE 207 128
  PGM5 MUTATED PGM5 WILD-TYPE 
            34            335 
  PGM5 MUTATED PGM5 WILD-TYPE 
            11            128 
$`PGM5 MUTATED`
TCGA-CG-4460 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 
       21.99        30.90        34.68        36.16        35.84        29.59 
TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 
       32.25        31.10         0.26         4.31        31.27        25.05 
TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4305 
        1.12        31.96        16.14        12.43         6.58        15.95 
TCGA-CG-4306 TCGA-CG-4462 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6521 TCGA-D7-A4YV 
        1.02         0.00       105.07        21.07        18.54         5.92 
TCGA-D7-A4YY TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4G9 
       13.78        11.08        30.51        22.32        22.68        24.20 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H8 
        0.10         6.51        29.00        14.07 

$`PGM5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
       14.04         3.32        11.80        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-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-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-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-D7-6522 
       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-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       14.27        16.44        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-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-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-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-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-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 

  PGM5 MUTATED PGM5 WILD-TYPE 
          0.00           0.23 
  PGM5 MUTATED PGM5 WILD-TYPE 
        105.07         122.30 
  PGM5 MUTATED PGM5 WILD-TYPE 
         21.53          14.04 
[1] "0.0 - 105.1 (21.5)" "0.2 - 122.3 (14.0)"
[1] "hr=" "1.4"
D16V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PGM5 MUTATED         1        2        5        3         5         5
  PGM5 WILD-TYPE       1       13       35       27        32        47
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PGM5 MUTATED           0          1          2          6        4
  PGM5 WILD-TYPE         3         69         51         26       34
D16V3, multiclass
            clus
vv           PGM5 MUTATED PGM5 WILD-TYPE
  STAGE I               1              1
  STAGE IA              2             13
  STAGE IB              5             35
  STAGE II              3             27
  STAGE IIA             5             32
  STAGE IIB             5             47
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            2             51
  STAGE IIIC            6             26
  STAGE IV              4             34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PGM5 MUTATED     5   9  12  11
  PGM5 WILD-TYPE  17  83 161  86
D16V4, multiclass
    clus
vv   PGM5 MUTATED PGM5 WILD-TYPE
  T1            5             17
  T2            9             83
  T3           12            161
  T4           11             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
  PGM5 MUTATED    15   8   6   7
  PGM5 WILD-TYPE 103  96  71  70
D16V5, multiclass
    clus
vv   PGM5 MUTATED PGM5 WILD-TYPE
  N0           15            103
  N1            8             96
  N2            6             71
  N3            7             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"
D16V6, binary
                cls
clus               0   1
  PGM5 MUTATED    34   4
  PGM5 WILD-TYPE 312  25
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM5 MUTATED     34    4
  PGM5 WILD-TYPE  312   25
   clus
vv  PGM5 MUTATED PGM5 WILD-TYPE
  0           34            312
  1            4             25
[1] 2 2
[1] FALSE
D16V7, binary
                cls
clus               0   1
  PGM5 MUTATED    24  15
  PGM5 WILD-TYPE 121 233
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM5 MUTATED     24   15
  PGM5 WILD-TYPE  121  233
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  FEMALE           24            121
  MALE             15            233
[1] 2 2
[1] FALSE
D16V8, binary
                cls
clus               0   1
  PGM5 MUTATED    29   3
  PGM5 WILD-TYPE 263  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM5 MUTATED     29    3
  PGM5 WILD-TYPE  263   56
     clus
vv    PGM5 MUTATED PGM5 WILD-TYPE
  NO            29            263
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PGM5 MUTATED                                          0
  PGM5 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PGM5 MUTATED                                       6
  PGM5 WILD-TYPE                                    64
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PGM5 MUTATED                                                       22
  PGM5 WILD-TYPE                                                    136
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PGM5 MUTATED                                                   1
  PGM5 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PGM5 MUTATED                                                                   3
  PGM5 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PGM5 MUTATED                                                    1
  PGM5 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PGM5 MUTATED                                                  6
  PGM5 WILD-TYPE                                               55
D16V9, multiclass
                                                                   clus
vv                                                                  PGM5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             6
                                                                   clus
vv                                                                  PGM5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       136
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PGM5 MUTATED    29   1   3   4
  PGM5 WILD-TYPE 282  13  12  20
D16V10, multiclass
    clus
vv   PGM5 MUTATED PGM5 WILD-TYPE
  R0           29            282
  R1            1             13
  R2            3             12
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PGM5 MUTATED      10                         2
  PGM5 WILD-TYPE    77                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PGM5 MUTATED                                           0    19
  PGM5 WILD-TYPE                                         1   224
D16V12, multiclass
                                           clus
vv                                          PGM5 MUTATED PGM5 WILD-TYPE
  ASIAN                                               10             77
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               19            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, binary
                cls
clus               0   1
  PGM5 MUTATED     0  31
  PGM5 WILD-TYPE   4 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM5 MUTATED      0   31
  PGM5 WILD-TYPE    4  279
                        clus
vv                       PGM5 MUTATED PGM5 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           31            279
[1] 2 2
[1] FALSE

Clustering(17) Variable = CBWD1 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  CBWD1 MUTATED    12   6
  CBWD1 WILD-TYPE 218 133
  CBWD1 MUTATED CBWD1 WILD-TYPE 
             18             351 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
              6             133 
$`CBWD1 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8372 
       26.70        34.68        32.78        35.84        29.59        31.27 
TCGA-BR-8382 TCGA-BR-8591 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 
       25.05        28.14         6.58        12.62        15.95         1.02 
TCGA-CG-5733 TCGA-F1-A448 TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-A4GQ TCGA-HU-A4GT 
       21.07        21.27        77.29        26.47         0.10         6.51 

$`CBWD1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 
       12.20        11.77        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-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-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-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-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-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 

  CBWD1 MUTATED CBWD1 WILD-TYPE 
            0.1             0.0 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
          77.29          122.30 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
          25.76           14.04 
[1] "0.1 - 77.3 (25.8)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.5"
D17V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CBWD1 MUTATED         0        0        3        2         4         3
  CBWD1 WILD-TYPE       2       15       37       28        33        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CBWD1 MUTATED           0          1          1          4        2
  CBWD1 WILD-TYPE         3         69         52         28       36
D17V3, multiclass
            clus
vv           CBWD1 MUTATED CBWD1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               2              28
  STAGE IIA              4              33
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             4              28
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CBWD1 MUTATED     0   6   6   8
  CBWD1 WILD-TYPE  22  86 167  89
D17V4, multiclass
    clus
vv   CBWD1 MUTATED CBWD1 WILD-TYPE
  T1             0              22
  T2             6              86
  T3             6             167
  T4             8              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
  CBWD1 MUTATED    10   3   4   4
  CBWD1 WILD-TYPE 108 101  73  73
D17V5, multiclass
    clus
vv   CBWD1 MUTATED CBWD1 WILD-TYPE
  N0            10             108
  N1             3             101
  N2             4              73
  N3             4              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"
D17V6, binary
                 cls
clus                0   1
  CBWD1 MUTATED    19   1
  CBWD1 WILD-TYPE 327  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD1 MUTATED     19    1
  CBWD1 WILD-TYPE  327   28
   clus
vv  CBWD1 MUTATED CBWD1 WILD-TYPE
  0            19             327
  1             1              28
[1] 2 2
[1] FALSE
D17V7, binary
                 cls
clus                0   1
  CBWD1 MUTATED    11  10
  CBWD1 WILD-TYPE 134 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD1 MUTATED     11   10
  CBWD1 WILD-TYPE  134  238
        clus
vv       CBWD1 MUTATED CBWD1 WILD-TYPE
  FEMALE            11             134
  MALE              10             238
[1] 2 2
[1] FALSE
D17V8, binary
                 cls
clus                0   1
  CBWD1 MUTATED    16   2
  CBWD1 WILD-TYPE 276  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD1 MUTATED     16    2
  CBWD1 WILD-TYPE  276   57
     clus
vv    CBWD1 MUTATED CBWD1 WILD-TYPE
  NO             16             276
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CBWD1 MUTATED                                          1
  CBWD1 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CBWD1 MUTATED                                       2
  CBWD1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CBWD1 MUTATED                                                       12
  CBWD1 WILD-TYPE                                                    146
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CBWD1 MUTATED                                                   2
  CBWD1 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CBWD1 MUTATED                                                                   2
  CBWD1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CBWD1 MUTATED                                                    0
  CBWD1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CBWD1 MUTATED                                                  2
  CBWD1 WILD-TYPE                                               59
D17V9, multiclass
                                                                   clus
vv                                                                  CBWD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  CBWD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CBWD1 MUTATED    16   0   1   2
  CBWD1 WILD-TYPE 295  14  14  22
D17V10, multiclass
    clus
vv   CBWD1 MUTATED CBWD1 WILD-TYPE
  R0            16             295
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CBWD1 MUTATED       4                         0
  CBWD1 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CBWD1 MUTATED                                           0    13
  CBWD1 WILD-TYPE                                         1   230
D17V12, multiclass
                                           clus
vv                                          CBWD1 MUTATED CBWD1 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, binary
                 cls
clus                0   1
  CBWD1 MUTATED     1  16
  CBWD1 WILD-TYPE   3 294
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD1 MUTATED      1   16
  CBWD1 WILD-TYPE    3  294
                        clus
vv                       CBWD1 MUTATED CBWD1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            16             294
[1] 2 2
[1] FALSE

Clustering(18) Variable = ZBTB20 MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  ZBTB20 MUTATED    21  11
  ZBTB20 WILD-TYPE 209 128
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              32              337 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              11              128 
$`ZBTB20 MUTATED`
TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7707 
       30.90         9.34         6.61        34.68        36.16        35.84 
TCGA-BR-7958 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-A4QL 
       29.56        25.05         1.12        12.79        28.14        16.14 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5723 
        6.58        12.62         1.02         9.01         6.02       105.07 
TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-A4YY TCGA-D7-A6EY TCGA-HF-A5NB TCGA-HU-A4G8 
       28.96        21.07        13.78        11.44        30.51        22.68 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-MX-A5UJ 
       29.98         6.51         6.58        29.00        14.07        19.73 
TCGA-R5-A7ZI TCGA-VQ-A8P2 
       74.53        38.14 

$`ZBTB20 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
           20.40            14.07 
[1] "1.0 - 105.1 (20.4)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D18V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZBTB20 MUTATED         1        2        4        1         5         3
  ZBTB20 WILD-TYPE       1       13       36       29        32        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB20 MUTATED           1          4          4          4        5
  ZBTB20 WILD-TYPE         2         66         49         28       33
D18V3, multiclass
            clus
vv           ZBTB20 MUTATED ZBTB20 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                2               13
  STAGE IB                4               36
  STAGE II                1               29
  STAGE IIA               5               32
  STAGE IIB               3               49
  STAGE III               1                2
  STAGE IIIA              4               66
  STAGE IIIB              4               49
  STAGE IIIC              4               28
  STAGE IV                5               33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB20 MUTATED     4   8  11  12
  ZBTB20 WILD-TYPE  18  84 162  85
D18V4, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  T1              4               18
  T2              8               84
  T3             11              162
  T4             12               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
  ZBTB20 MUTATED    12  12   4   8
  ZBTB20 WILD-TYPE 106  92  73  69
D18V5, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  N0             12              106
  N1             12               92
  N2              4               73
  N3              8               69
[1] 4 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
  ZBTB20 MUTATED    33   3
  ZBTB20 WILD-TYPE 313  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     33    3
  ZBTB20 WILD-TYPE  313   26
   clus
vv  ZBTB20 MUTATED ZBTB20 WILD-TYPE
  0             33              313
  1              3               26
[1] 2 2
[1] FALSE
D18V7, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    20  17
  ZBTB20 WILD-TYPE 125 231
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     20   17
  ZBTB20 WILD-TYPE  125  231
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  FEMALE             20              125
  MALE               17              231
[1] 2 2
[1] FALSE
D18V8, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    26   3
  ZBTB20 WILD-TYPE 266  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     26    3
  ZBTB20 WILD-TYPE  266   56
     clus
vv    ZBTB20 MUTATED ZBTB20 WILD-TYPE
  NO              26              266
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZBTB20 MUTATED                                          0
  ZBTB20 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZBTB20 MUTATED                                       6
  ZBTB20 WILD-TYPE                                    64
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZBTB20 MUTATED                                                       19
  ZBTB20 WILD-TYPE                                                    139
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZBTB20 MUTATED                                                   2
  ZBTB20 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZBTB20 MUTATED                                                                   4
  ZBTB20 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZBTB20 MUTATED                                                    1
  ZBTB20 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZBTB20 MUTATED                                                  5
  ZBTB20 WILD-TYPE                                               56
D18V9, multiclass
                                                                   clus
vv                                                                  ZBTB20 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        19
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               5
                                                                   clus
vv                                                                  ZBTB20 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         139
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZBTB20 MUTATED    25   1   2   6
  ZBTB20 WILD-TYPE 286  13  13  18
D18V10, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  R0             25              286
  R1              1               13
  R2              2               13
  RX              6               18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZBTB20 MUTATED       8                         1
  ZBTB20 WILD-TYPE    79                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZBTB20 MUTATED                                           0    20
  ZBTB20 WILD-TYPE                                         1   223
D18V12, multiclass
                                           clus
vv                                          ZBTB20 MUTATED ZBTB20 WILD-TYPE
  ASIAN                                                  8               79
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 20              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED     1  27
  ZBTB20 WILD-TYPE   3 283
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED      1   27
  ZBTB20 WILD-TYPE    3  283
                        clus
vv                       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             27              283
[1] 2 2
[1] FALSE

Clustering(19) Variable = ARID4A MUTATION ANALYSIS
D19V1, survival
                  sevent
clus2                0   1
  ARID4A MUTATED    15   5
  ARID4A WILD-TYPE 215 134
  ARID4A MUTATED ARID4A WILD-TYPE 
              20              349 
  ARID4A MUTATED ARID4A WILD-TYPE 
               5              134 
$`ARID4A MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8284 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8591 
       34.68        44.94         8.05         4.31        31.27        28.14 
TCGA-BR-8680 TCGA-BR-A4J2 TCGA-CD-5813 TCGA-CD-8536 TCGA-CD-A4MJ TCGA-CG-4305 
       31.96        14.17        12.39        12.43        12.62        15.95 
TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-A6EY TCGA-HU-A4GU 
        1.02         4.01       105.07        65.10        11.44         6.58 
TCGA-HU-A4H8 TCGA-VQ-A8P2 
       14.07        38.14 

$`ARID4A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-4436 TCGA-CG-4437 
       11.77        20.02         3.02        27.02         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-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-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-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-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 

  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            14.43 
[1] "1.0 - 105.1 (14.1)" "0.0 - 122.3 (14.4)"
[1] "hr=" "1.8"
D19V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID4A MUTATED         0        0        4        4         2         2
  ARID4A WILD-TYPE       2       15       36       26        35        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID4A MUTATED           0          1          1          4        3
  ARID4A WILD-TYPE         3         69         52         28       35
D19V3, multiclass
            clus
vv           ARID4A MUTATED ARID4A WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                4               36
  STAGE II                4               26
  STAGE IIA               2               35
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              4               28
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID4A MUTATED     1   5   8   7
  ARID4A WILD-TYPE  21  87 165  90
D19V4, multiclass
    clus
vv   ARID4A MUTATED ARID4A WILD-TYPE
  T1              1               21
  T2              5               87
  T3              8              165
  T4              7               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
  ARID4A MUTATED     8   5   2   6
  ARID4A WILD-TYPE 110  99  75  71
D19V5, multiclass
    clus
vv   ARID4A MUTATED ARID4A WILD-TYPE
  N0              8              110
  N1              5               99
  N2              2               75
  N3              6               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"
D19V6, binary
                  cls
clus                 0   1
  ARID4A MUTATED    19   3
  ARID4A WILD-TYPE 327  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4A MUTATED     19    3
  ARID4A WILD-TYPE  327   26
   clus
vv  ARID4A MUTATED ARID4A WILD-TYPE
  0             19              327
  1              3               26
[1] 2 2
[1] FALSE
D19V7, binary
                  cls
clus                 0   1
  ARID4A MUTATED     7  15
  ARID4A WILD-TYPE 138 233
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4A MUTATED      7   15
  ARID4A WILD-TYPE  138  233
        clus
vv       ARID4A MUTATED ARID4A WILD-TYPE
  FEMALE              7              138
  MALE               15              233
[1] 2 2
[1] FALSE
D19V8, binary
                  cls
clus                 0   1
  ARID4A MUTATED    17   1
  ARID4A WILD-TYPE 275  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4A MUTATED     17    1
  ARID4A WILD-TYPE  275   58
     clus
vv    ARID4A MUTATED ARID4A WILD-TYPE
  NO              17              275
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARID4A MUTATED                                          0
  ARID4A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARID4A MUTATED                                       2
  ARID4A WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARID4A MUTATED                                                       12
  ARID4A WILD-TYPE                                                    146
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARID4A MUTATED                                                   2
  ARID4A WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARID4A MUTATED                                                                   3
  ARID4A WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARID4A MUTATED                                                    0
  ARID4A WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARID4A MUTATED                                                  3
  ARID4A WILD-TYPE                                               58
D19V9, multiclass
                                                                   clus
vv                                                                  ARID4A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  ARID4A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARID4A MUTATED    16   1   2   1
  ARID4A WILD-TYPE 295  13  13  23
D19V10, multiclass
    clus
vv   ARID4A MUTATED ARID4A WILD-TYPE
  R0             16              295
  R1              1               13
  R2              2               13
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ARID4A MUTATED       7                         0
  ARID4A WILD-TYPE    80                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID4A MUTATED                                           0    10
  ARID4A WILD-TYPE                                         1   233
D19V12, multiclass
                                           clus
vv                                          ARID4A MUTATED ARID4A WILD-TYPE
  ASIAN                                                  7               80
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, binary
                  cls
clus                 0   1
  ARID4A MUTATED     0  16
  ARID4A WILD-TYPE   4 294
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4A MUTATED      0   16
  ARID4A WILD-TYPE    4  294
                        clus
vv                       ARID4A MUTATED ARID4A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             16              294
[1] 2 2
[1] FALSE

Clustering(20) Variable = MLL2 MUTATION ANALYSIS
D20V1, survival
                sevent
clus2              0   1
  MLL2 MUTATED    40  21
  MLL2 WILD-TYPE 190 118
  MLL2 MUTATED MLL2 WILD-TYPE 
            61            308 
  MLL2 MUTATED MLL2 WILD-TYPE 
            21            118 
$`MLL2 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4257 
       21.99        26.70        19.56        30.90         9.34         9.67 
TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6566 TCGA-BR-6802 
        6.18         6.61        34.68        13.87        32.78        30.90 
TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8368 
       35.84        29.59         6.18        31.10         0.26         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-8676 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 
        7.53        16.14         6.58        11.77        12.62        15.95 
TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
        1.02        54.08        29.98         6.02       105.07        28.96 
TCGA-CG-5728 TCGA-D7-6526 TCGA-D7-8570 TCGA-D7-A4YV TCGA-D7-A6EY TCGA-HF-7132 
       65.10        17.19        24.72         5.92        11.44        77.29 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GQ 
       30.51        26.47        22.32        22.68        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HD 
        6.51         6.58        20.25        29.00        14.07        33.40 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A8MV TCGA-VQ-A8P2 
       19.53         6.74        74.53         4.60       122.30        38.14 
TCGA-VQ-A91Q 
       20.81 

$`MLL2 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
        9.86        11.70        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-4279 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        9.57        15.95        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-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-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-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       11.80        14.79         3.72         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 
       20.22        12.79         9.34         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-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-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4437 
       12.20        20.02         3.02        27.02         7.99         8.05 
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-5730 TCGA-CG-5732 
        0.99         0.99        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-D7-6527 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-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-7133 
       13.58         0.56        11.08         5.52         6.21        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-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-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-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        36.36         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT 
       12.46        13.35         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-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-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-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 

  MLL2 MUTATED MLL2 WILD-TYPE 
           0.1            0.0 
  MLL2 MUTATED MLL2 WILD-TYPE 
        122.30         116.38 
  MLL2 MUTATED MLL2 WILD-TYPE 
        20.810         13.825 
[1] "0.1 - 122.3 (20.8)" "0.0 - 116.4 (13.8)"
[1] "hr=" "1.4"
D20V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLL2 MUTATED         1        2        9        3         8         8
  MLL2 WILD-TYPE       1       13       31       27        29        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MLL2 MUTATED           1          7          6          9        8
  MLL2 WILD-TYPE         2         63         47         23       30
D20V3, multiclass
            clus
vv           MLL2 MUTATED MLL2 WILD-TYPE
  STAGE I               1              1
  STAGE IA              2             13
  STAGE IB              9             31
  STAGE II              3             27
  STAGE IIA             8             29
  STAGE IIB             8             44
  STAGE III             1              2
  STAGE IIIA            7             63
  STAGE IIIB            6             47
  STAGE IIIC            9             23
  STAGE IV              8             30
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MLL2 MUTATED     5  14  25  20
  MLL2 WILD-TYPE  17  78 148  77
D20V4, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  T1            5             17
  T2           14             78
  T3           25            148
  T4           20             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
  MLL2 MUTATED   20 21 12 11
  MLL2 WILD-TYPE 98 83 65 66
D20V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  N0           20             98
  N1           21             83
  N2           12             65
  N3           11             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"
D20V6, binary
                cls
clus               0   1
  MLL2 MUTATED    60   4
  MLL2 WILD-TYPE 286  25
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     60    4
  MLL2 WILD-TYPE  286   25
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0           60            286
  1            4             25
[1] 2 2
[1] FALSE
D20V7, binary
                cls
clus               0   1
  MLL2 MUTATED    32  35
  MLL2 WILD-TYPE 113 213
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     32   35
  MLL2 WILD-TYPE  113  213
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE           32            113
  MALE             35            213
[1] 2 2
[1] FALSE
D20V8, binary
                cls
clus               0   1
  MLL2 MUTATED    51   5
  MLL2 WILD-TYPE 241  54
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     51    5
  MLL2 WILD-TYPE  241   54
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO            51            241
  YES            5             54
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MLL2 MUTATED                                          1
  MLL2 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MLL2 MUTATED                                      10
  MLL2 WILD-TYPE                                    60
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MLL2 MUTATED                                                       33
  MLL2 WILD-TYPE                                                    125
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MLL2 MUTATED                                                   3
  MLL2 WILD-TYPE                                                18
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MLL2 MUTATED                                                                  10
  MLL2 WILD-TYPE                                                                58
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MLL2 MUTATED                                                    0
  MLL2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MLL2 MUTATED                                                 10
  MLL2 WILD-TYPE                                               51
D20V9, multiclass
                                                                   clus
vv                                                                  MLL2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       10
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      33
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           10
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            10
                                                                   clus
vv                                                                  MLL2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       125
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             58
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              51
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MLL2 MUTATED    49   1   2   9
  MLL2 WILD-TYPE 262  13  13  15
D20V10, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  R0           49            262
  R1            1             13
  R2            2             13
  RX            9             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MLL2 MUTATED      13                         2
  MLL2 WILD-TYPE    74                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MLL2 MUTATED                                           0    39
  MLL2 WILD-TYPE                                         1   204
D20V12, multiclass
                                           clus
vv                                          MLL2 MUTATED MLL2 WILD-TYPE
  ASIAN                                               13             74
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               39            204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, binary
                cls
clus               0   1
  MLL2 MUTATED     1  52
  MLL2 WILD-TYPE   3 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      1   52
  MLL2 WILD-TYPE    3  258
                        clus
vv                       MLL2 MUTATED MLL2 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           52            258
[1] 2 2
[1] FALSE

Clustering(21) Variable = FBXW7 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED    22   7
  FBXW7 WILD-TYPE 208 132
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             29             340 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              7             132 
$`FBXW7 MUTATED`
TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8360 TCGA-BR-8372 
       30.90         9.34        44.94        35.84         6.18        31.27 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8536 
        9.21         1.12        24.79        31.96        16.14        12.43 
TCGA-CD-A4MJ TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-A4YV 
       12.62         6.02       105.07        65.10        21.07         5.92 
TCGA-D7-A6EY TCGA-F1-A448 TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4GN 
       11.44        21.27        77.29        30.51        22.32        29.98 
TCGA-HU-A4H3 TCGA-KB-A6F5 TCGA-MX-A5UJ TCGA-VQ-A8DU TCGA-VQ-A8P2 
       29.00         5.56        19.73         5.46        38.14 

$`FBXW7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        5.39        25.18        20.22        12.79        27.12         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 
       28.14         6.28         7.53        26.73        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-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-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-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-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-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-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-A6F7 
       10.62        11.70        15.75        13.51         2.53        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 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           1.12            0.00 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         105.07          122.30 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         21.270          14.055 
[1] "1.1 - 105.1 (21.3)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.1"
D21V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXW7 MUTATED         0        0        4        3         4         3
  FBXW7 WILD-TYPE       2       15       36       27        33        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXW7 MUTATED           0          5          3          5        2
  FBXW7 WILD-TYPE         3         65         50         27       36
D21V3, multiclass
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               4              36
  STAGE II               3              27
  STAGE IIA              4              33
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             5              65
  STAGE IIIB             3              50
  STAGE IIIC             5              27
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FBXW7 MUTATED     0  10  11  10
  FBXW7 WILD-TYPE  22  82 162  87
D21V4, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  T1             0              22
  T2            10              82
  T3            11             162
  T4            10              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
  FBXW7 MUTATED    10   7   5   8
  FBXW7 WILD-TYPE 108  97  72  69
D21V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0            10             108
  N1             7              97
  N2             5              72
  N3             8              69
[1] 4 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
  FBXW7 MUTATED    31   1
  FBXW7 WILD-TYPE 315  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     31    1
  FBXW7 WILD-TYPE  315   28
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0            31             315
  1             1              28
[1] 2 2
[1] FALSE
D21V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED    15  17
  FBXW7 WILD-TYPE 130 231
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     15   17
  FBXW7 WILD-TYPE  130  231
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE            15             130
  MALE              17             231
[1] 2 2
[1] FALSE
D21V8, binary
                 cls
clus                0   1
  FBXW7 MUTATED    25   4
  FBXW7 WILD-TYPE 267  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     25    4
  FBXW7 WILD-TYPE  267   55
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO             25             267
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FBXW7 MUTATED                                          0
  FBXW7 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FBXW7 MUTATED                                       2
  FBXW7 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBXW7 MUTATED                                                       14
  FBXW7 WILD-TYPE                                                    144
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FBXW7 MUTATED                                                   4
  FBXW7 WILD-TYPE                                                17
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBXW7 MUTATED                                                                   6
  FBXW7 WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FBXW7 MUTATED                                                    0
  FBXW7 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FBXW7 MUTATED                                                  6
  FBXW7 WILD-TYPE                                               55
D21V9, multiclass
                                                                   clus
vv                                                                  FBXW7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              6
                                                                   clus
vv                                                                  FBXW7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FBXW7 MUTATED    26   2   0   3
  FBXW7 WILD-TYPE 285  12  15  21
D21V10, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0            26             285
  R1             2              12
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FBXW7 MUTATED       6                         0
  FBXW7 WILD-TYPE    81                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXW7 MUTATED                                           0    19
  FBXW7 WILD-TYPE                                         1   224
D21V12, multiclass
                                           clus
vv                                          FBXW7 MUTATED FBXW7 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                19             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, binary
                 cls
clus                0   1
  FBXW7 MUTATED     1  22
  FBXW7 WILD-TYPE   3 288
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      1   22
  FBXW7 WILD-TYPE    3  288
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            22             288
[1] 2 2
[1] FALSE

Clustering(22) Variable = MBD6 MUTATION ANALYSIS
D22V1, survival
                sevent
clus2              0   1
  MBD6 MUTATED    13   7
  MBD6 WILD-TYPE 217 132
  MBD6 MUTATED MBD6 WILD-TYPE 
            20            349 
  MBD6 MUTATED MBD6 WILD-TYPE 
             7            132 
$`MBD6 MUTATED`
TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6852 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4QL 
       30.90         9.67        44.94         1.12        28.14        16.14 
TCGA-CD-A4MG TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-6815 TCGA-F1-6874 TCGA-FP-A4BE 
        6.58       105.07        65.10        15.98        14.47        11.08 
TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-A4GU TCGA-IN-A6RR TCGA-MX-A5UJ 
       26.47        28.96        22.32         6.58         6.74        19.73 
TCGA-R5-A804 TCGA-VQ-A8P2 
        4.60        38.14 

$`MBD6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        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-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8604 
       52.21        30.51         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-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-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-A805 
       45.67        18.21         8.52        74.53         6.08         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 

  MBD6 MUTATED MBD6 WILD-TYPE 
          1.12           0.00 
  MBD6 MUTATED MBD6 WILD-TYPE 
        105.07         122.30 
  MBD6 MUTATED MBD6 WILD-TYPE 
        17.935         14.070 
[1] "1.1 - 105.1 (17.9)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D22V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MBD6 MUTATED         0        0        4        1         4         3
  MBD6 WILD-TYPE       2       15       36       29        33        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MBD6 MUTATED           0          5          1          1        1
  MBD6 WILD-TYPE         3         65         52         31       37
D22V3, multiclass
            clus
vv           MBD6 MUTATED MBD6 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              4             36
  STAGE II              1             29
  STAGE IIA             4             33
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            5             65
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MBD6 MUTATED     1   7  10   4
  MBD6 WILD-TYPE  21  85 163  93
D22V4, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  T1            1             21
  T2            7             85
  T3           10            163
  T4            4             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
  MBD6 MUTATED    10   5   4   2
  MBD6 WILD-TYPE 108  99  73  75
D22V5, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  N0           10            108
  N1            5             99
  N2            4             73
  N3            2             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"
D22V6, binary
                cls
clus               0   1
  MBD6 MUTATED    22   1
  MBD6 WILD-TYPE 324  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     22    1
  MBD6 WILD-TYPE  324   28
   clus
vv  MBD6 MUTATED MBD6 WILD-TYPE
  0           22            324
  1            1             28
[1] 2 2
[1] FALSE
D22V7, binary
                cls
clus               0   1
  MBD6 MUTATED    13  11
  MBD6 WILD-TYPE 132 237
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     13   11
  MBD6 WILD-TYPE  132  237
        clus
vv       MBD6 MUTATED MBD6 WILD-TYPE
  FEMALE           13            132
  MALE             11            237
[1] 2 2
[1] FALSE
D22V8, binary
                cls
clus               0   1
  MBD6 MUTATED    17   2
  MBD6 WILD-TYPE 275  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     17    2
  MBD6 WILD-TYPE  275   57
     clus
vv    MBD6 MUTATED MBD6 WILD-TYPE
  NO            17            275
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MBD6 MUTATED                                          1
  MBD6 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MBD6 MUTATED                                       4
  MBD6 WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MBD6 MUTATED                                                       12
  MBD6 WILD-TYPE                                                    146
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MBD6 MUTATED                                                   1
  MBD6 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MBD6 MUTATED                                                                   3
  MBD6 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MBD6 MUTATED                                                    0
  MBD6 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MBD6 MUTATED                                                  3
  MBD6 WILD-TYPE                                               58
D22V9, multiclass
                                                                   clus
vv                                                                  MBD6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  MBD6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MBD6 MUTATED    17   0   0   5
  MBD6 WILD-TYPE 294  14  15  19
D22V10, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  R0           17            294
  R1            0             14
  R2            0             15
  RX            5             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MBD6 MUTATED       4                         2
  MBD6 WILD-TYPE    83                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MBD6 MUTATED                                           0    15
  MBD6 WILD-TYPE                                         1   228
D22V12, multiclass
                                           clus
vv                                          MBD6 MUTATED MBD6 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               15            228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, binary
                cls
clus               0   1
  MBD6 MUTATED     0  20
  MBD6 WILD-TYPE   4 290
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED      0   20
  MBD6 WILD-TYPE    4  290
                        clus
vv                       MBD6 MUTATED MBD6 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           20            290
[1] 2 2
[1] FALSE

Clustering(23) Variable = MUC6 MUTATION ANALYSIS
D23V1, survival
                sevent
clus2              0   1
  MUC6 MUTATED    28  15
  MUC6 WILD-TYPE 202 124
  MUC6 MUTATED MUC6 WILD-TYPE 
            43            326 
  MUC6 MUTATED MUC6 WILD-TYPE 
            15            124 
$`MUC6 MUTATED`
TCGA-CG-4475 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6801 TCGA-BR-7703 
       22.98        26.70         6.97        34.68        40.21        36.16 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8382 TCGA-BR-8487 
       11.44        29.59        32.25        31.10        25.05         1.12 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-8525 TCGA-CD-8529 
       28.14        31.96        20.42        16.14        12.59        12.30 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-8578 
        6.58        11.77         1.02         6.02       105.07        21.14 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GX TCGA-HU-A4H3 
       13.58         0.56        24.30         3.25        20.25        29.00 
TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-AB1V TCGA-R5-A7ZE TCGA-R5-A7ZI 
       36.36         3.39        19.53        15.75        18.21        74.53 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8N6 TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8P2 
        8.61         5.13         8.94        13.25        13.02        38.14 
TCGA-VQ-A94T 
       11.24 

$`MUC6 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        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-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 
       37.25        14.43         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-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-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-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-8526 
       13.35        11.21        12.10        12.39        12.76        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-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-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-D7-8579 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-A4BE 
       14.07        22.29        17.06        59.54         5.03        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-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-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-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       33.40         3.45        18.81        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-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-A7ZR TCGA-R5-A804 
       19.73        14.04        45.67         8.52         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        9.24        11.05        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-A8E2 TCGA-VQ-A8E7 
        5.79         0.92        48.79         5.46        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-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 

  MUC6 MUTATED MUC6 WILD-TYPE 
          0.56           0.00 
  MUC6 MUTATED MUC6 WILD-TYPE 
        105.07         122.30 
  MUC6 MUTATED MUC6 WILD-TYPE 
         18.21          14.07 
[1] "0.6 - 105.1 (18.2)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D23V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MUC6 MUTATED         0        2        4        1         5         9
  MUC6 WILD-TYPE       2       13       36       29        32        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MUC6 MUTATED           0          8          3          5        7
  MUC6 WILD-TYPE         3         62         50         27       31
D23V3, multiclass
            clus
vv           MUC6 MUTATED MUC6 WILD-TYPE
  STAGE I               0              2
  STAGE IA              2             13
  STAGE IB              4             36
  STAGE II              1             29
  STAGE IIA             5             32
  STAGE IIB             9             43
  STAGE III             0              3
  STAGE IIIA            8             62
  STAGE IIIB            3             50
  STAGE IIIC            5             27
  STAGE IV              7             31
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MUC6 MUTATED     4   8  17  16
  MUC6 WILD-TYPE  18  84 156  81
D23V4, multiclass
    clus
vv   MUC6 MUTATED MUC6 WILD-TYPE
  T1            4             18
  T2            8             84
  T3           17            156
  T4           16             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"
                vv
clus              N0  N1  N2  N3
  MUC6 MUTATED    15  12  12   6
  MUC6 WILD-TYPE 103  92  65  71
D23V5, multiclass
    clus
vv   MUC6 MUTATED MUC6 WILD-TYPE
  N0           15            103
  N1           12             92
  N2           12             65
  N3            6             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"
D23V6, binary
                cls
clus               0   1
  MUC6 MUTATED    38   5
  MUC6 WILD-TYPE 308  24
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     38    5
  MUC6 WILD-TYPE  308   24
   clus
vv  MUC6 MUTATED MUC6 WILD-TYPE
  0           38            308
  1            5             24
[1] 2 2
[1] FALSE
D23V7, binary
                cls
clus               0   1
  MUC6 MUTATED    21  25
  MUC6 WILD-TYPE 124 223
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     21   25
  MUC6 WILD-TYPE  124  223
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  FEMALE           21            124
  MALE             25            223
[1] 2 2
[1] FALSE
D23V8, binary
                cls
clus               0   1
  MUC6 MUTATED    35   5
  MUC6 WILD-TYPE 257  54
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     35    5
  MUC6 WILD-TYPE  257   54
     clus
vv    MUC6 MUTATED MUC6 WILD-TYPE
  NO            35            257
  YES            5             54
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MUC6 MUTATED                                          1
  MUC6 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MUC6 MUTATED                                      10
  MUC6 WILD-TYPE                                    60
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MUC6 MUTATED                                                       23
  MUC6 WILD-TYPE                                                    135
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MUC6 MUTATED                                                   3
  MUC6 WILD-TYPE                                                18
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MUC6 MUTATED                                                                   5
  MUC6 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MUC6 MUTATED                                                    1
  MUC6 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MUC6 MUTATED                                                  2
  MUC6 WILD-TYPE                                               59
D23V9, multiclass
                                                                   clus
vv                                                                  MUC6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       10
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      23
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  MUC6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       135
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MUC6 MUTATED    35   1   3   4
  MUC6 WILD-TYPE 276  13  12  20
D23V10, multiclass
    clus
vv   MUC6 MUTATED MUC6 WILD-TYPE
  R0           35            276
  R1            1             13
  R2            3             12
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MUC6 MUTATED       9                         1
  MUC6 WILD-TYPE    78                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MUC6 MUTATED                                           1    30
  MUC6 WILD-TYPE                                         0   213
D23V12, multiclass
                                           clus
vv                                          MUC6 MUTATED MUC6 WILD-TYPE
  ASIAN                                                9             78
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                               30            213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, binary
                cls
clus               0   1
  MUC6 MUTATED     1  37
  MUC6 WILD-TYPE   3 273
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED      1   37
  MUC6 WILD-TYPE    3  273
                        clus
vv                       MUC6 MUTATED MUC6 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           37            273
[1] 2 2
[1] FALSE

Clustering(24) Variable = DDX17 MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  DDX17 MUTATED     7   5
  DDX17 WILD-TYPE 223 134
  DDX17 MUTATED DDX17 WILD-TYPE 
             12             357 
  DDX17 MUTATED DDX17 WILD-TYPE 
              5             134 
$`DDX17 MUTATED`
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8372 TCGA-CD-8529 
       29.59        32.25        31.10         0.26        31.27        12.30 
TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5726 TCGA-CG-5733 TCGA-HF-A5NB TCGA-HU-A4H8 
        6.58         9.01        28.96        21.07        30.51        14.07 

$`DDX17 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       15.02        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-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 

  DDX17 MUTATED DDX17 WILD-TYPE 
           0.26            0.00 
  DDX17 MUTATED DDX17 WILD-TYPE 
          32.25          122.30 
  DDX17 MUTATED DDX17 WILD-TYPE 
         25.015          14.170 
[1] "0.3 - 32.2 (25.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D24V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX17 MUTATED         0        1        2        0         1         3
  DDX17 WILD-TYPE       2       14       38       30        36        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDX17 MUTATED           0          2          0          3        2
  DDX17 WILD-TYPE         3         68         53         29       36
D24V3, multiclass
            clus
vv           DDX17 MUTATED DDX17 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX17 MUTATED     2   2   2   9
  DDX17 WILD-TYPE  20  90 171  88
D24V4, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  T1             2              20
  T2             2              90
  T3             2             171
  T4             9              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
  DDX17 MUTATED     8   1   2   3
  DDX17 WILD-TYPE 110 103  75  74
D24V5, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  N0             8             110
  N1             1             103
  N2             2              75
  N3             3              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"
D24V6, binary
                 cls
clus                0   1
  DDX17 MUTATED    12   2
  DDX17 WILD-TYPE 334  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED     12    2
  DDX17 WILD-TYPE  334   27
   clus
vv  DDX17 MUTATED DDX17 WILD-TYPE
  0            12             334
  1             2              27
[1] 2 2
[1] FALSE
D24V7, binary
                 cls
clus                0   1
  DDX17 MUTATED     9   6
  DDX17 WILD-TYPE 136 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      9    6
  DDX17 WILD-TYPE  136  242
        clus
vv       DDX17 MUTATED DDX17 WILD-TYPE
  FEMALE             9             136
  MALE               6             242
[1] 2 2
[1] FALSE
D24V8, binary
                 cls
clus                0   1
  DDX17 MUTATED     9   2
  DDX17 WILD-TYPE 283  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      9    2
  DDX17 WILD-TYPE  283   57
     clus
vv    DDX17 MUTATED DDX17 WILD-TYPE
  NO              9             283
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DDX17 MUTATED                                          0
  DDX17 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DDX17 MUTATED                                       2
  DDX17 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DDX17 MUTATED                                                        7
  DDX17 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DDX17 MUTATED                                                   2
  DDX17 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DDX17 MUTATED                                                                   3
  DDX17 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DDX17 MUTATED                                                    0
  DDX17 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DDX17 MUTATED                                                  1
  DDX17 WILD-TYPE                                               60
D24V9, multiclass
                                                                   clus
vv                                                                  DDX17 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  DDX17 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DDX17 MUTATED    10   1   1   2
  DDX17 WILD-TYPE 301  13  14  22
D24V10, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  R0            10             301
  R1             1              13
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DDX17 MUTATED       3                         0
  DDX17 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDX17 MUTATED                                           0     8
  DDX17 WILD-TYPE                                         1   235
D24V12, multiclass
                                           clus
vv                                          DDX17 MUTATED DDX17 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, binary
                 cls
clus                0   1
  DDX17 MUTATED     0  11
  DDX17 WILD-TYPE   4 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      0   11
  DDX17 WILD-TYPE    4  299
                        clus
vv                       DDX17 MUTATED DDX17 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(25) Variable = HOXD8 MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  HOXD8 MUTATED     8   4
  HOXD8 WILD-TYPE 222 135
  HOXD8 MUTATED HOXD8 WILD-TYPE 
             12             357 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
              4             135 
$`HOXD8 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8360 TCGA-CD-A4MG 
       30.90        34.68        44.94        35.84         6.18         6.58 
TCGA-CG-4306 TCGA-CG-5721 TCGA-HU-A4GT TCGA-IN-8663 TCGA-MX-A5UJ TCGA-VQ-A8P2 
        1.02         6.02         6.51         3.39        19.73        38.14 

$`HOXD8 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  HOXD8 MUTATED HOXD8 WILD-TYPE 
           1.02            0.00 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
          44.94          122.30 
  HOXD8 MUTATED HOXD8 WILD-TYPE 
         13.155          14.270 
[1] "1.0 - 44.9 (13.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D25V2, 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       2       15       39       30        32        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HOXD8 MUTATED           0          3          0          0        2
  HOXD8 WILD-TYPE         3         67         53         32       36
D25V3, multiclass
            clus
vv           HOXD8 MUTATED HOXD8 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              5              32
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HOXD8 MUTATED     0   3   7   3
  HOXD8 WILD-TYPE  22  89 166  94
D25V4, multiclass
    clus
vv   HOXD8 MUTATED HOXD8 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             7             166
  T4             3              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
  HOXD8 MUTATED     7   2   3   0
  HOXD8 WILD-TYPE 111 102  74  77
D25V5, multiclass
    clus
vv   HOXD8 MUTATED HOXD8 WILD-TYPE
  N0             7             111
  N1             2             102
  N2             3              74
  N3             0              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
  HOXD8 MUTATED    12   1
  HOXD8 WILD-TYPE 334  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD8 MUTATED     12    1
  HOXD8 WILD-TYPE  334   28
   clus
vv  HOXD8 MUTATED HOXD8 WILD-TYPE
  0            12             334
  1             1              28
[1] 2 2
[1] FALSE
D25V7, binary
                 cls
clus                0   1
  HOXD8 MUTATED     7   6
  HOXD8 WILD-TYPE 138 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD8 MUTATED      7    6
  HOXD8 WILD-TYPE  138  242
        clus
vv       HOXD8 MUTATED HOXD8 WILD-TYPE
  FEMALE             7             138
  MALE               6             242
[1] 2 2
[1] FALSE
D25V8, binary
                 cls
clus                0   1
  HOXD8 MUTATED    10   1
  HOXD8 WILD-TYPE 282  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD8 MUTATED     10    1
  HOXD8 WILD-TYPE  282   58
     clus
vv    HOXD8 MUTATED HOXD8 WILD-TYPE
  NO             10             282
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HOXD8 MUTATED                                          0
  HOXD8 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HOXD8 MUTATED                                       1
  HOXD8 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HOXD8 MUTATED                                                        7
  HOXD8 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HOXD8 MUTATED                                                   1
  HOXD8 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HOXD8 MUTATED                                                                   2
  HOXD8 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HOXD8 MUTATED                                                    0
  HOXD8 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HOXD8 MUTATED                                                  2
  HOXD8 WILD-TYPE                                               59
D25V9, multiclass
                                                                   clus
vv                                                                  HOXD8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  HOXD8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HOXD8 MUTATED     9   0   1   2
  HOXD8 WILD-TYPE 302  14  14  22
D25V10, multiclass
    clus
vv   HOXD8 MUTATED HOXD8 WILD-TYPE
  R0             9             302
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HOXD8 MUTATED       2                         0
  HOXD8 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HOXD8 MUTATED                                           0     9
  HOXD8 WILD-TYPE                                         1   234
D25V12, multiclass
                                           clus
vv                                          HOXD8 MUTATED HOXD8 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, binary
                 cls
clus                0   1
  HOXD8 MUTATED     0  10
  HOXD8 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD8 MUTATED      0   10
  HOXD8 WILD-TYPE    4  300
                        clus
vv                       HOXD8 MUTATED HOXD8 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(26) Variable = ZBTB7C MUTATION ANALYSIS
D26V1, survival
                  sevent
clus2                0   1
  ZBTB7C MUTATED    10   4
  ZBTB7C WILD-TYPE 220 135
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              14              355 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
               4              135 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-AA69 TCGA-VQ-AA6A 
       42.64        66.81        11.24        18.41        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 

  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           14.070 
[1] "1.1 - 65.1 (21.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D26V2, 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       1       14       38       30        33        48
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB7C MUTATED           0          2          1          1        0
  ZBTB7C WILD-TYPE         3         68         52         31       38
D26V3, multiclass
            clus
vv           ZBTB7C MUTATED ZBTB7C WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               4               33
  STAGE IIB               4               48
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB7C MUTATED     3   2   8   4
  ZBTB7C WILD-TYPE  19  90 165  93
D26V4, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  T1              3               19
  T2              2               90
  T3              8              165
  T4              4               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
  ZBTB7C MUTATED     9   4   1   2
  ZBTB7C WILD-TYPE 109 100  76  75
D26V5, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  N0              9              109
  N1              4              100
  N2              1               76
  N3              2               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"
D26V6, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED    16   0
  ZBTB7C WILD-TYPE 330  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED     16    0
  ZBTB7C WILD-TYPE  330   29
   clus
vv  ZBTB7C MUTATED ZBTB7C WILD-TYPE
  0             16              330
  1              0               29
[1] 2 2
[1] FALSE
D26V7, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED    11   6
  ZBTB7C WILD-TYPE 134 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED     11    6
  ZBTB7C WILD-TYPE  134  242
        clus
vv       ZBTB7C MUTATED ZBTB7C WILD-TYPE
  FEMALE             11              134
  MALE                6              242
[1] 2 2
[1] FALSE
D26V8, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED    12   2
  ZBTB7C WILD-TYPE 280  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED     12    2
  ZBTB7C WILD-TYPE  280   57
     clus
vv    ZBTB7C MUTATED ZBTB7C WILD-TYPE
  NO              12              280
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZBTB7C MUTATED                                          0
  ZBTB7C WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZBTB7C MUTATED                                       2
  ZBTB7C WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZBTB7C MUTATED                                                        7
  ZBTB7C WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZBTB7C MUTATED                                                   1
  ZBTB7C WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZBTB7C MUTATED                                                                   4
  ZBTB7C WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZBTB7C MUTATED                                                    0
  ZBTB7C WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZBTB7C MUTATED                                                  3
  ZBTB7C WILD-TYPE                                               58
D26V9, multiclass
                                                                   clus
vv                                                                  ZBTB7C MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  ZBTB7C WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZBTB7C MUTATED    14   0   0   1
  ZBTB7C WILD-TYPE 297  14  15  23
D26V10, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  R0             14              297
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZBTB7C MUTATED       2                         1
  ZBTB7C WILD-TYPE    85                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZBTB7C MUTATED                                           0    12
  ZBTB7C WILD-TYPE                                         1   231
D26V12, multiclass
                                           clus
vv                                          ZBTB7C MUTATED ZBTB7C WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED     0  13
  ZBTB7C WILD-TYPE   4 297
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED      0   13
  ZBTB7C WILD-TYPE    4  297
                        clus
vv                       ZBTB7C MUTATED ZBTB7C WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             13              297
[1] 2 2
[1] FALSE

Clustering(27) Variable = KLF3 MUTATION ANALYSIS
D27V1, survival
                sevent
clus2              0   1
  KLF3 MUTATED    11   6
  KLF3 WILD-TYPE 219 133
  KLF3 MUTATED KLF3 WILD-TYPE 
            17            352 
  KLF3 MUTATED KLF3 WILD-TYPE 
             6            133 
$`KLF3 MUTATED`
TCGA-MX-A663 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8284 
        9.86        32.78        44.94        35.84        29.59         8.05 
TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8680 TCGA-BR-8682 TCGA-CD-A4MG TCGA-D7-A4YV 
        2.66         7.40        31.96        32.58         6.58         5.92 
TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H2 
       77.29        22.32        29.98         0.10        12.95 

$`KLF3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15        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-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-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
        9.60        32.25         0.56        29.42        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-8683 
       28.14         6.28         7.53        26.73        24.79         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-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-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-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        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 

  KLF3 MUTATED KLF3 WILD-TYPE 
           0.1            0.0 
  KLF3 MUTATED KLF3 WILD-TYPE 
         77.29         122.30 
  KLF3 MUTATED KLF3 WILD-TYPE 
         22.32          14.22 
[1] "0.1 - 77.3 (22.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D27V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLF3 MUTATED         0        0        1        1         5         5
  KLF3 WILD-TYPE       2       15       39       29        32        47
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLF3 MUTATED           0          1          1          3        2
  KLF3 WILD-TYPE         3         69         52         29       36
D27V3, multiclass
            clus
vv           KLF3 MUTATED KLF3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             5             32
  STAGE IIB             5             47
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            3             29
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KLF3 MUTATED     0   3   6  10
  KLF3 WILD-TYPE  22  89 167  87
D27V4, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  T1            0             22
  T2            3             89
  T3            6            167
  T4           10             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
  KLF3 MUTATED    10   3   2   4
  KLF3 WILD-TYPE 108 101  75  73
D27V5, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  N0           10            108
  N1            3            101
  N2            2             75
  N3            4             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"
D27V6, binary
                cls
clus               0   1
  KLF3 MUTATED    17   2
  KLF3 WILD-TYPE 329  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED     17    2
  KLF3 WILD-TYPE  329   27
   clus
vv  KLF3 MUTATED KLF3 WILD-TYPE
  0           17            329
  1            2             27
[1] 2 2
[1] FALSE
D27V7, binary
                cls
clus               0   1
  KLF3 MUTATED     9  10
  KLF3 WILD-TYPE 136 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      9   10
  KLF3 WILD-TYPE  136  238
        clus
vv       KLF3 MUTATED KLF3 WILD-TYPE
  FEMALE            9            136
  MALE             10            238
[1] 2 2
[1] FALSE
D27V8, binary
                cls
clus               0   1
  KLF3 MUTATED    17   1
  KLF3 WILD-TYPE 275  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED     17    1
  KLF3 WILD-TYPE  275   58
     clus
vv    KLF3 MUTATED KLF3 WILD-TYPE
  NO            17            275
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KLF3 MUTATED                                          0
  KLF3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KLF3 MUTATED                                       3
  KLF3 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KLF3 MUTATED                                                        6
  KLF3 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KLF3 MUTATED                                                   2
  KLF3 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KLF3 MUTATED                                                                   3
  KLF3 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KLF3 MUTATED                                                    0
  KLF3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KLF3 MUTATED                                                  5
  KLF3 WILD-TYPE                                               56
D27V9, multiclass
                                                                   clus
vv                                                                  KLF3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             5
                                                                   clus
vv                                                                  KLF3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KLF3 MUTATED    17   0   0   1
  KLF3 WILD-TYPE 294  14  15  23
D27V10, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  R0           17            294
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  KLF3 MUTATED       7                         0
  KLF3 WILD-TYPE    80                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLF3 MUTATED                                           0    11
  KLF3 WILD-TYPE                                         1   232
D27V12, multiclass
                                           clus
vv                                          KLF3 MUTATED KLF3 WILD-TYPE
  ASIAN                                                7             80
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, binary
                cls
clus               0   1
  KLF3 MUTATED     0  18
  KLF3 WILD-TYPE   4 292
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      0   18
  KLF3 WILD-TYPE    4  292
                        clus
vv                       KLF3 MUTATED KLF3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           18            292
[1] 2 2
[1] FALSE

Clustering(28) Variable = TENC1 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2               0   1
  TENC1 MUTATED    12   7
  TENC1 WILD-TYPE 218 132
  TENC1 MUTATED TENC1 WILD-TYPE 
             19             350 
  TENC1 MUTATED TENC1 WILD-TYPE 
              7             132 
$`TENC1 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-4280 TCGA-BR-6852 TCGA-BR-8297 TCGA-BR-8372 
       21.99        26.70         6.61        44.94         7.40        31.27 
TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-5721 TCGA-D7-6526 TCGA-D7-A4YV TCGA-HF-A5NB 
        6.58        15.95         6.02        17.19         5.92        30.51 
TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-RD-A7BT 
       26.47        29.98         0.10        20.25        29.00         8.61 
TCGA-VQ-A8P2 
       38.14 

$`TENC1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-D7-6527 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-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-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-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-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-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 

  TENC1 MUTATED TENC1 WILD-TYPE 
            0.1             0.0 
  TENC1 MUTATED TENC1 WILD-TYPE 
          44.94          122.30 
  TENC1 MUTATED TENC1 WILD-TYPE 
          20.25           14.07 
[1] "0.1 - 44.9 (20.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D28V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TENC1 MUTATED         0        0        1        1         3         2
  TENC1 WILD-TYPE       2       15       39       29        34        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TENC1 MUTATED           1          2          0          6        3
  TENC1 WILD-TYPE         2         68         53         26       35
D28V3, multiclass
            clus
vv           TENC1 MUTATED TENC1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              2              50
  STAGE III              1               2
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             6              26
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TENC1 MUTATED     0   4   5  10
  TENC1 WILD-TYPE  22  88 168  87
D28V4, multiclass
    clus
vv   TENC1 MUTATED TENC1 WILD-TYPE
  T1             0              22
  T2             4              88
  T3             5             168
  T4            10              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
  TENC1 MUTATED     4   7   3   5
  TENC1 WILD-TYPE 114  97  74  72
D28V5, multiclass
    clus
vv   TENC1 MUTATED TENC1 WILD-TYPE
  N0             4             114
  N1             7              97
  N2             3              74
  N3             5              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"
D28V6, binary
                 cls
clus                0   1
  TENC1 MUTATED    18   1
  TENC1 WILD-TYPE 328  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TENC1 MUTATED     18    1
  TENC1 WILD-TYPE  328   28
   clus
vv  TENC1 MUTATED TENC1 WILD-TYPE
  0            18             328
  1             1              28
[1] 2 2
[1] FALSE
D28V7, binary
                 cls
clus                0   1
  TENC1 MUTATED    11   9
  TENC1 WILD-TYPE 134 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TENC1 MUTATED     11    9
  TENC1 WILD-TYPE  134  239
        clus
vv       TENC1 MUTATED TENC1 WILD-TYPE
  FEMALE            11             134
  MALE               9             239
[1] 2 2
[1] FALSE
D28V8, binary
                 cls
clus                0   1
  TENC1 MUTATED    16   2
  TENC1 WILD-TYPE 276  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TENC1 MUTATED     16    2
  TENC1 WILD-TYPE  276   57
     clus
vv    TENC1 MUTATED TENC1 WILD-TYPE
  NO             16             276
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TENC1 MUTATED                                          1
  TENC1 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TENC1 MUTATED                                       5
  TENC1 WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TENC1 MUTATED                                                        5
  TENC1 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TENC1 MUTATED                                                   2
  TENC1 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TENC1 MUTATED                                                                   3
  TENC1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TENC1 MUTATED                                                    0
  TENC1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TENC1 MUTATED                                                  4
  TENC1 WILD-TYPE                                               57
D28V9, multiclass
                                                                   clus
vv                                                                  TENC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  TENC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TENC1 MUTATED    14   1   2   2
  TENC1 WILD-TYPE 297  13  13  22
D28V10, multiclass
    clus
vv   TENC1 MUTATED TENC1 WILD-TYPE
  R0            14             297
  R1             1              13
  R2             2              13
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TENC1 MUTATED       5                         0
  TENC1 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TENC1 MUTATED                                           1    10
  TENC1 WILD-TYPE                                         0   233
D28V12, multiclass
                                           clus
vv                                          TENC1 MUTATED TENC1 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               0
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, binary
                 cls
clus                0   1
  TENC1 MUTATED     0  15
  TENC1 WILD-TYPE   4 295
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TENC1 MUTATED      0   15
  TENC1 WILD-TYPE    4  295
                        clus
vv                       TENC1 MUTATED TENC1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            15             295
[1] 2 2
[1] FALSE

Clustering(29) Variable = MTG1 MUTATION ANALYSIS
D29V1, survival
                sevent
clus2              0   1
  MTG1 MUTATED     5   4
  MTG1 WILD-TYPE 225 135
  MTG1 MUTATED MTG1 WILD-TYPE 
             9            360 
  MTG1 MUTATED MTG1 WILD-TYPE 
             4            135 
$`MTG1 MUTATED`
TCGA-BR-4184 TCGA-BR-8081 TCGA-CG-4306 TCGA-D7-A4YV TCGA-F1-6874 TCGA-FP-A4BE 
        6.97        32.25         1.02         5.92        14.47        11.08 
TCGA-HU-8602 TCGA-HU-A4GQ TCGA-VQ-A8P2 
       22.32         0.10        38.14 

$`MTG1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-F1-6875 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-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 

  MTG1 MUTATED MTG1 WILD-TYPE 
           0.1            0.0 
  MTG1 MUTATED MTG1 WILD-TYPE 
         38.14         122.30 
  MTG1 MUTATED MTG1 WILD-TYPE 
         11.08          14.35 
[1] "0.1 - 38.1 (11.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D29V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTG1 MUTATED         0        0        1        0         1         3
  MTG1 WILD-TYPE       2       15       39       30        36        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MTG1 MUTATED           0          2          0          1        1
  MTG1 WILD-TYPE         3         68         53         31       37
D29V3, multiclass
            clus
vv           MTG1 MUTATED MTG1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MTG1 MUTATED     0   1   4   4
  MTG1 WILD-TYPE  22  91 169  93
D29V4, multiclass
    clus
vv   MTG1 MUTATED MTG1 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            4            169
  T4            4             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
  MTG1 MUTATED     4   3   2   0
  MTG1 WILD-TYPE 114 101  75  77
D29V5, multiclass
    clus
vv   MTG1 MUTATED MTG1 WILD-TYPE
  N0            4            114
  N1            3            101
  N2            2             75
  N3            0             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"
D29V6, binary
                cls
clus               0   1
  MTG1 MUTATED     7   1
  MTG1 WILD-TYPE 339  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTG1 MUTATED      7    1
  MTG1 WILD-TYPE  339   28
   clus
vv  MTG1 MUTATED MTG1 WILD-TYPE
  0            7            339
  1            1             28
[1] 2 2
[1] FALSE
D29V7, binary
                cls
clus               0   1
  MTG1 MUTATED     3   6
  MTG1 WILD-TYPE 142 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTG1 MUTATED      3    6
  MTG1 WILD-TYPE  142  242
        clus
vv       MTG1 MUTATED MTG1 WILD-TYPE
  FEMALE            3            142
  MALE              6            242
[1] 2 2
[1] FALSE
D29V8, binary
                cls
clus               0   1
  MTG1 MUTATED     6   2
  MTG1 WILD-TYPE 286  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTG1 MUTATED      6    2
  MTG1 WILD-TYPE  286   57
     clus
vv    MTG1 MUTATED MTG1 WILD-TYPE
  NO             6            286
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MTG1 MUTATED                                          0
  MTG1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MTG1 MUTATED                                       1
  MTG1 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MTG1 MUTATED                                                        4
  MTG1 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MTG1 MUTATED                                                   1
  MTG1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MTG1 MUTATED                                                                   1
  MTG1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MTG1 MUTATED                                                    0
  MTG1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MTG1 MUTATED                                                  2
  MTG1 WILD-TYPE                                               59
D29V9, multiclass
                                                                   clus
vv                                                                  MTG1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  MTG1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MTG1 MUTATED     7   0   1   1
  MTG1 WILD-TYPE 304  14  14  23
D29V10, multiclass
    clus
vv   MTG1 MUTATED MTG1 WILD-TYPE
  R0            7            304
  R1            0             14
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MTG1 MUTATED       2                         1
  MTG1 WILD-TYPE    85                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MTG1 MUTATED                                           0     5
  MTG1 WILD-TYPE                                         1   238
D29V12, multiclass
                                           clus
vv                                          MTG1 MUTATED MTG1 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, binary
                cls
clus               0   1
  MTG1 MUTATED     0   7
  MTG1 WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTG1 MUTATED      0    7
  MTG1 WILD-TYPE    4  303
                        clus
vv                       MTG1 MUTATED MTG1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(30) Variable = LARP7 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  LARP7 MUTATED    11   3
  LARP7 WILD-TYPE 219 136
  LARP7 MUTATED LARP7 WILD-TYPE 
             14             355 
  LARP7 MUTATED LARP7 WILD-TYPE 
              3             136 
$`LARP7 MUTATED`
TCGA-B7-A5TI TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8372 TCGA-CD-A486 
       19.56        31.20        44.94         6.18        31.27         6.31 
TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4H4 TCGA-MX-A5UJ TCGA-R5-A7O7 
       11.44        22.32        22.68        23.84        19.73        45.67 
TCGA-SW-A7EA TCGA-VQ-A8DU 
       19.04         5.46 

$`LARP7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       30.90        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-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-A487 TCGA-CD-A489 
       15.39        12.07        12.82        12.43        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-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-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-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-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
        8.94        35.61         5.79         0.92        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 

  LARP7 MUTATED LARP7 WILD-TYPE 
           5.46            0.00 
  LARP7 MUTATED LARP7 WILD-TYPE 
          45.67          122.30 
  LARP7 MUTATED LARP7 WILD-TYPE 
         21.025          14.070 
[1] "5.5 - 45.7 (21.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.2"
D30V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LARP7 MUTATED         1        0        2        0         4         3
  LARP7 WILD-TYPE       1       15       38       30        33        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LARP7 MUTATED           0          3          1          2        1
  LARP7 WILD-TYPE         3         67         52         30       37
D30V3, multiclass
            clus
vv           LARP7 MUTATED LARP7 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              4              33
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LARP7 MUTATED     1   3   9   4
  LARP7 WILD-TYPE  21  89 164  93
D30V4, multiclass
    clus
vv   LARP7 MUTATED LARP7 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             9             164
  T4             4              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
  LARP7 MUTATED     8   4   3   3
  LARP7 WILD-TYPE 110 100  74  74
D30V5, multiclass
    clus
vv   LARP7 MUTATED LARP7 WILD-TYPE
  N0             8             110
  N1             4             100
  N2             3              74
  N3             3              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"
D30V6, binary
                 cls
clus                0   1
  LARP7 MUTATED    16   1
  LARP7 WILD-TYPE 330  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED     16    1
  LARP7 WILD-TYPE  330   28
   clus
vv  LARP7 MUTATED LARP7 WILD-TYPE
  0            16             330
  1             1              28
[1] 2 2
[1] FALSE
D30V7, binary
                 cls
clus                0   1
  LARP7 MUTATED    10   8
  LARP7 WILD-TYPE 135 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED     10    8
  LARP7 WILD-TYPE  135  240
        clus
vv       LARP7 MUTATED LARP7 WILD-TYPE
  FEMALE            10             135
  MALE               8             240
[1] 2 2
[1] FALSE
D30V8, binary
                 cls
clus                0   1
  LARP7 MUTATED    15   0
  LARP7 WILD-TYPE 277  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED     15    0
  LARP7 WILD-TYPE  277   59
     clus
vv    LARP7 MUTATED LARP7 WILD-TYPE
  NO             15             277
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LARP7 MUTATED                                          0
  LARP7 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LARP7 MUTATED                                       5
  LARP7 WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LARP7 MUTATED                                                        6
  LARP7 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LARP7 MUTATED                                                   0
  LARP7 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LARP7 MUTATED                                                                   2
  LARP7 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LARP7 MUTATED                                                    0
  LARP7 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LARP7 MUTATED                                                  5
  LARP7 WILD-TYPE                                               56
D30V9, multiclass
                                                                   clus
vv                                                                  LARP7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              5
                                                                   clus
vv                                                                  LARP7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LARP7 MUTATED    12   0   0   2
  LARP7 WILD-TYPE 299  14  15  22
D30V10, multiclass
    clus
vv   LARP7 MUTATED LARP7 WILD-TYPE
  R0            12             299
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LARP7 MUTATED       4                         1
  LARP7 WILD-TYPE    83                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LARP7 MUTATED                                           0    12
  LARP7 WILD-TYPE                                         1   231
D30V12, multiclass
                                           clus
vv                                          LARP7 MUTATED LARP7 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, binary
                 cls
clus                0   1
  LARP7 MUTATED     1  15
  LARP7 WILD-TYPE   3 295
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP7 MUTATED      1   15
  LARP7 WILD-TYPE    3  295
                        clus
vv                       LARP7 MUTATED LARP7 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            15             295
[1] 2 2
[1] FALSE

Clustering(31) Variable = MVK MUTATION ANALYSIS
D31V1, survival
               sevent
clus2             0   1
  MVK MUTATED     8   5
  MVK WILD-TYPE 222 134
  MVK MUTATED MVK WILD-TYPE 
           13           356 
  MVK MUTATED MVK WILD-TYPE 
            5           134 
$`MVK MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8589 TCGA-CD-A4MG 
        6.97         6.61        35.84        31.10        27.12         6.58 
TCGA-CD-A4MI TCGA-CG-5733 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-HU-A4H3 
       11.77        21.07        30.51        22.68         6.58        29.00 
TCGA-MX-A5UJ 
       19.73 

$`MVK WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  MVK MUTATED MVK WILD-TYPE 
         6.58          0.00 
  MVK MUTATED MVK WILD-TYPE 
        35.84        122.30 
  MVK MUTATED MVK WILD-TYPE 
        21.07         14.12 
[1] "6.6 - 35.8 (21.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D31V2, 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       2       15       38       30        36        50
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MVK MUTATED           1          4          1          3        0
  MVK WILD-TYPE         2         66         52         29       38
D31V3, multiclass
            clus
vv           MVK MUTATED MVK WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             2            38
  STAGE II             0            30
  STAGE IIA            1            36
  STAGE IIB            2            50
  STAGE III            1             2
  STAGE IIIA           4            66
  STAGE IIIB           1            52
  STAGE IIIC           3            29
  STAGE IV             0            38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MVK MUTATED     1   4   6   4
  MVK WILD-TYPE  21  88 167  93
D31V4, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  T1           1            21
  T2           4            88
  T3           6           167
  T4           4            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
  MVK MUTATED     3   6   3   2
  MVK WILD-TYPE 115  98  74  75
D31V5, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  N0           3           115
  N1           6            98
  N2           3            74
  N3           2            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
  MVK MUTATED    14   0
  MVK WILD-TYPE 332  29
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED     14    0
  MVK WILD-TYPE  332   29
   clus
vv  MVK MUTATED MVK WILD-TYPE
  0          14           332
  1           0            29
[1] 2 2
[1] FALSE
D31V7, binary
               cls
clus              0   1
  MVK MUTATED     9   6
  MVK WILD-TYPE 136 242
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED      9    6
  MVK WILD-TYPE  136  242
        clus
vv       MVK MUTATED MVK WILD-TYPE
  FEMALE           9           136
  MALE             6           242
[1] 2 2
[1] FALSE
D31V8, binary
               cls
clus              0   1
  MVK MUTATED    11   1
  MVK WILD-TYPE 281  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED     11    1
  MVK WILD-TYPE  281   58
     clus
vv    MVK MUTATED MVK WILD-TYPE
  NO           11           281
  YES           1            58
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MVK MUTATED                                          0
  MVK WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MVK MUTATED                                       4
  MVK WILD-TYPE                                    66
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MVK MUTATED                                                        7
  MVK WILD-TYPE                                                    151
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MVK MUTATED                                                   1
  MVK WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MVK MUTATED                                                                   2
  MVK WILD-TYPE                                                                66
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MVK MUTATED                                                    0
  MVK WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MVK MUTATED                                                  1
  MVK WILD-TYPE                                               60
D31V9, multiclass
                                                                   clus
vv                                                                  MVK MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            1
                                                                   clus
vv                                                                  MVK WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  MVK MUTATED     8   1   0   3
  MVK WILD-TYPE 303  13  15  21
D31V10, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  R0           8           303
  R1           1            13
  R2           0            15
  RX           3            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  MVK MUTATED       5                         0
  MVK WILD-TYPE    82                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MVK MUTATED                                           0     7
  MVK WILD-TYPE                                         1   236
D31V12, multiclass
                                           clus
vv                                          MVK MUTATED MVK WILD-TYPE
  ASIAN                                               5            82
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               7           236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, binary
               cls
clus              0   1
  MVK MUTATED     0  12
  MVK WILD-TYPE   4 298
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED      0   12
  MVK WILD-TYPE    4  298
                        clus
vv                       MVK MUTATED MVK WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          12           298
[1] 2 2
[1] FALSE

Clustering(32) Variable = KIAA0406 MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  KIAA0406 MUTATED    11  11
  KIAA0406 WILD-TYPE 219 128
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                22                347 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                11                128 
$`KIAA0406 MUTATED`
TCGA-CG-4475 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 
       22.98         9.34        34.68        11.44        29.59        32.25 
TCGA-BR-8363 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4CS TCGA-BR-A4QL 
        0.26        27.12        28.14        31.96         1.48        16.14 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5726 TCGA-CG-5728 
       12.43         6.58        11.77         1.02        28.96        65.10 
TCGA-D7-A6EY TCGA-HU-A4GN TCGA-HU-A4GX TCGA-VQ-A8PE 
       11.44        29.98        20.25        22.19 

$`KIAA0406 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-8077 
        9.07        29.56        33.21        37.25        14.43         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-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-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-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-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-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-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-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-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-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-A8PK TCGA-VQ-A8PM 
       43.36        37.41        38.14        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 

  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
              0.26               0.00 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
              65.1              122.3 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
             21.22              14.07 
[1] "0.3 - 65.1 (21.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0406 MUTATED         0        1        3        1         3         4
  KIAA0406 WILD-TYPE       2       14       37       29        34        48
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0406 MUTATED           0          1          4          3        2
  KIAA0406 WILD-TYPE         3         69         49         29       36
D32V3, multiclass
            clus
vv           KIAA0406 MUTATED KIAA0406 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  3                 37
  STAGE II                  1                 29
  STAGE IIA                 3                 34
  STAGE IIB                 4                 48
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                4                 49
  STAGE IIIC                3                 29
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0406 MUTATED     1   5   9   7
  KIAA0406 WILD-TYPE  21  87 164  90
D32V4, multiclass
    clus
vv   KIAA0406 MUTATED KIAA0406 WILD-TYPE
  T1                1                 21
  T2                5                 87
  T3                9                164
  T4                7                 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
  KIAA0406 MUTATED     9   5   4   5
  KIAA0406 WILD-TYPE 109  99  73  72
D32V5, multiclass
    clus
vv   KIAA0406 MUTATED KIAA0406 WILD-TYPE
  N0                9                109
  N1                5                 99
  N2                4                 73
  N3                5                 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"
D32V6, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED    21   2
  KIAA0406 WILD-TYPE 325  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED     21    2
  KIAA0406 WILD-TYPE  325   27
   clus
vv  KIAA0406 MUTATED KIAA0406 WILD-TYPE
  0               21                325
  1                2                 27
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED     9  14
  KIAA0406 WILD-TYPE 136 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED      9   14
  KIAA0406 WILD-TYPE  136  234
        clus
vv       KIAA0406 MUTATED KIAA0406 WILD-TYPE
  FEMALE                9                136
  MALE                 14                234
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED    19   0
  KIAA0406 WILD-TYPE 273  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED     19    0
  KIAA0406 WILD-TYPE  273   59
     clus
vv    KIAA0406 MUTATED KIAA0406 WILD-TYPE
  NO                19                273
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA0406 MUTATED                                          0
  KIAA0406 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA0406 MUTATED                                       2
  KIAA0406 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0406 MUTATED                                                       13
  KIAA0406 WILD-TYPE                                                    145
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA0406 MUTATED                                                   0
  KIAA0406 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0406 MUTATED                                                                   3
  KIAA0406 WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA0406 MUTATED                                                    0
  KIAA0406 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA0406 MUTATED                                                  4
  KIAA0406 WILD-TYPE                                               57
D32V9, multiclass
                                                                   clus
vv                                                                  KIAA0406 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 4
                                                                   clus
vv                                                                  KIAA0406 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0406 MUTATED    19   0   1   1
  KIAA0406 WILD-TYPE 292  14  14  23
D32V10, multiclass
    clus
vv   KIAA0406 MUTATED KIAA0406 WILD-TYPE
  R0               19                292
  R1                0                 14
  R2                1                 14
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0406 MUTATED       6                         0
  KIAA0406 WILD-TYPE    81                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0406 MUTATED                                           0    12
  KIAA0406 WILD-TYPE                                         1   231
D32V12, multiclass
                                           clus
vv                                          KIAA0406 MUTATED KIAA0406 WILD-TYPE
  ASIAN                                                    6                 81
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   12                231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED     0  17
  KIAA0406 WILD-TYPE   4 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED      0   17
  KIAA0406 WILD-TYPE    4  293
                        clus
vv                       KIAA0406 MUTATED KIAA0406 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               17                293
[1] 2 2
[1] FALSE

Clustering(33) Variable = FRMD4A MUTATION ANALYSIS
D33V1, survival
                  sevent
clus2                0   1
  FRMD4A MUTATED    15   4
  FRMD4A WILD-TYPE 215 135
  FRMD4A MUTATED FRMD4A WILD-TYPE 
              19              350 
  FRMD4A MUTATED FRMD4A WILD-TYPE 
               4              135 
$`FRMD4A MUTATED`
TCGA-B7-5816 TCGA-B7-A5TJ TCGA-BR-4256 TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8487 
       26.70        11.01         9.34        35.84        31.10         1.12 
TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-6822 
       28.14        31.96         6.58         6.02        28.96        12.33 
TCGA-F1-6874 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4GQ TCGA-HU-A4H6 
       14.47        11.08        77.29        30.51         0.10        21.17 
TCGA-HU-A4H8 
       14.07 

$`FRMD4A WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        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-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-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-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-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-D7-8570 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-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-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-A4HB TCGA-HU-A4HD 
       12.95        29.00        23.84        23.80        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 

  FRMD4A MUTATED FRMD4A WILD-TYPE 
             0.1              0.0 
  FRMD4A MUTATED FRMD4A WILD-TYPE 
           77.29           122.30 
  FRMD4A MUTATED FRMD4A WILD-TYPE 
           14.47            14.22 
[1] "0.1 - 77.3 (14.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.1"
D33V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FRMD4A MUTATED         0        2        4        1         3         2
  FRMD4A WILD-TYPE       2       13       36       29        34        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FRMD4A MUTATED           0          1          0          4        2
  FRMD4A WILD-TYPE         3         69         53         28       36
D33V3, multiclass
            clus
vv           FRMD4A MUTATED FRMD4A WILD-TYPE
  STAGE I                 0                2
  STAGE IA                2               13
  STAGE IB                4               36
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              4               28
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FRMD4A MUTATED     3   4   4   8
  FRMD4A WILD-TYPE  19  88 169  89
D33V4, multiclass
    clus
vv   FRMD4A MUTATED FRMD4A WILD-TYPE
  T1              3               19
  T2              4               88
  T3              4              169
  T4              8               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
  FRMD4A MUTATED     9   5   4   2
  FRMD4A WILD-TYPE 109  99  73  75
D33V5, multiclass
    clus
vv   FRMD4A MUTATED FRMD4A WILD-TYPE
  N0              9              109
  N1              5               99
  N2              4               73
  N3              2               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"
D33V6, binary
                  cls
clus                 0   1
  FRMD4A MUTATED    20   1
  FRMD4A WILD-TYPE 326  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4A MUTATED     20    1
  FRMD4A WILD-TYPE  326   28
   clus
vv  FRMD4A MUTATED FRMD4A WILD-TYPE
  0             20              326
  1              1               28
[1] 2 2
[1] FALSE
D33V7, binary
                  cls
clus                 0   1
  FRMD4A MUTATED     7  14
  FRMD4A WILD-TYPE 138 234
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4A MUTATED      7   14
  FRMD4A WILD-TYPE  138  234
        clus
vv       FRMD4A MUTATED FRMD4A WILD-TYPE
  FEMALE              7              138
  MALE               14              234
[1] 2 2
[1] FALSE
D33V8, binary
                  cls
clus                 0   1
  FRMD4A MUTATED    15   4
  FRMD4A WILD-TYPE 277  55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4A MUTATED     15    4
  FRMD4A WILD-TYPE  277   55
     clus
vv    FRMD4A MUTATED FRMD4A WILD-TYPE
  NO              15              277
  YES              4               55
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FRMD4A MUTATED                                          0
  FRMD4A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FRMD4A MUTATED                                       2
  FRMD4A WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FRMD4A MUTATED                                                        8
  FRMD4A WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FRMD4A MUTATED                                                   2
  FRMD4A WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FRMD4A MUTATED                                                                   4
  FRMD4A WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FRMD4A MUTATED                                                    0
  FRMD4A WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FRMD4A MUTATED                                                  5
  FRMD4A WILD-TYPE                                               56
D33V9, multiclass
                                                                   clus
vv                                                                  FRMD4A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               5
                                                                   clus
vv                                                                  FRMD4A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FRMD4A MUTATED    16   1   0   2
  FRMD4A WILD-TYPE 295  13  15  22
D33V10, multiclass
    clus
vv   FRMD4A MUTATED FRMD4A WILD-TYPE
  R0             16              295
  R1              1               13
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FRMD4A MUTATED       6                         1
  FRMD4A WILD-TYPE    81                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FRMD4A MUTATED                                           0    10
  FRMD4A WILD-TYPE                                         1   233
D33V12, multiclass
                                           clus
vv                                          FRMD4A MUTATED FRMD4A WILD-TYPE
  ASIAN                                                  6               81
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, binary
                  cls
clus                 0   1
  FRMD4A MUTATED     0  17
  FRMD4A WILD-TYPE   4 293
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4A MUTATED      0   17
  FRMD4A WILD-TYPE    4  293
                        clus
vv                       FRMD4A MUTATED FRMD4A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             17              293
[1] 2 2
[1] FALSE

Clustering(34) Variable = MCM8 MUTATION ANALYSIS
D34V1, survival
                sevent
clus2              0   1
  MCM8 MUTATED    17   7
  MCM8 WILD-TYPE 213 132
  MCM8 MUTATED MCM8 WILD-TYPE 
            24            345 
  MCM8 MUTATED MCM8 WILD-TYPE 
             7            132 
$`MCM8 MUTATED`
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
        9.67        34.68        14.43        29.59        32.25         8.05 
TCGA-BR-8360 TCGA-BR-8680 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
        6.18        31.96        12.76        12.59        12.53        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CG-4437 TCGA-D7-8572 TCGA-D7-8574 
       12.30        12.39        12.59         8.05        16.80        17.19 
TCGA-D7-8576 TCGA-D7-A6EZ TCGA-FP-8209 TCGA-HF-7132 TCGA-HU-8243 TCGA-VQ-A8P2 
       14.66        20.32        59.54        77.29         5.92        38.14 

$`MCM8 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8060 
        3.45         9.07        29.56        33.21        37.25        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-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-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-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
        7.17        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-D7-8573 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-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-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       17.06         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-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 

  MCM8 MUTATED MCM8 WILD-TYPE 
          5.92           0.00 
  MCM8 MUTATED MCM8 WILD-TYPE 
         77.29         122.30 
  MCM8 MUTATED MCM8 WILD-TYPE 
        13.595         14.270 
[1] "5.9 - 77.3 (13.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D34V2, 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       1       15       39       26        35        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MCM8 MUTATED           1          7          1          2        2
  MCM8 WILD-TYPE         2         63         52         30       36
D34V3, multiclass
            clus
vv           MCM8 MUTATED MCM8 WILD-TYPE
  STAGE I               1              1
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              4             26
  STAGE IIA             2             35
  STAGE IIB             3             49
  STAGE III             1              2
  STAGE IIIA            7             63
  STAGE IIIB            1             52
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MCM8 MUTATED     1   5   9   9
  MCM8 WILD-TYPE  21  87 164  88
D34V4, multiclass
    clus
vv   MCM8 MUTATED MCM8 WILD-TYPE
  T1            1             21
  T2            5             87
  T3            9            164
  T4            9             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
  MCM8 MUTATED     9   8   3   4
  MCM8 WILD-TYPE 109  96  74  73
D34V5, multiclass
    clus
vv   MCM8 MUTATED MCM8 WILD-TYPE
  N0            9            109
  N1            8             96
  N2            3             74
  N3            4             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"
D34V6, binary
                cls
clus               0   1
  MCM8 MUTATED    22   2
  MCM8 WILD-TYPE 324  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM8 MUTATED     22    2
  MCM8 WILD-TYPE  324   27
   clus
vv  MCM8 MUTATED MCM8 WILD-TYPE
  0           22            324
  1            2             27
[1] 2 2
[1] FALSE
D34V7, binary
                cls
clus               0   1
  MCM8 MUTATED    11  14
  MCM8 WILD-TYPE 134 234
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM8 MUTATED     11   14
  MCM8 WILD-TYPE  134  234
        clus
vv       MCM8 MUTATED MCM8 WILD-TYPE
  FEMALE           11            134
  MALE             14            234
[1] 2 2
[1] FALSE
D34V8, binary
                cls
clus               0   1
  MCM8 MUTATED    17   8
  MCM8 WILD-TYPE 275  51
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM8 MUTATED     17    8
  MCM8 WILD-TYPE  275   51
     clus
vv    MCM8 MUTATED MCM8 WILD-TYPE
  NO            17            275
  YES            8             51
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MCM8 MUTATED                                          0
  MCM8 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MCM8 MUTATED                                       3
  MCM8 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MCM8 MUTATED                                                        8
  MCM8 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MCM8 MUTATED                                                   4
  MCM8 WILD-TYPE                                                17
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MCM8 MUTATED                                                                   7
  MCM8 WILD-TYPE                                                                61
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MCM8 MUTATED                                                    0
  MCM8 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MCM8 MUTATED                                                  3
  MCM8 WILD-TYPE                                               58
D34V9, multiclass
                                                                   clus
vv                                                                  MCM8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            7
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  MCM8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             61
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MCM8 MUTATED    24   0   0   1
  MCM8 WILD-TYPE 287  14  15  23
D34V10, multiclass
    clus
vv   MCM8 MUTATED MCM8 WILD-TYPE
  R0           24            287
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MCM8 MUTATED       9                         1
  MCM8 WILD-TYPE    78                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MCM8 MUTATED                                           0    13
  MCM8 WILD-TYPE                                         1   230
D34V12, multiclass
                                           clus
vv                                          MCM8 MUTATED MCM8 WILD-TYPE
  ASIAN                                                9             78
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, binary
                cls
clus               0   1
  MCM8 MUTATED     0  22
  MCM8 WILD-TYPE   4 288
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM8 MUTATED      0   22
  MCM8 WILD-TYPE    4  288
                        clus
vv                       MCM8 MUTATED MCM8 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           22            288
[1] 2 2
[1] FALSE

Clustering(35) Variable = APC MUTATION ANALYSIS
D35V1, survival
               sevent
clus2             0   1
  APC MUTATED    23  21
  APC WILD-TYPE 207 118
  APC MUTATED APC WILD-TYPE 
           44           325 
  APC MUTATED APC WILD-TYPE 
           21           118 
$`APC MUTATED`
TCGA-KB-A93G TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6563 
       20.15         6.97        18.35         6.18        34.68        39.12 
TCGA-BR-6565 TCGA-BR-6802 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-8081 
        9.17        30.90         9.21        36.16        35.24        32.25 
TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A452 TCGA-CD-8535 TCGA-CD-8536 
        0.26         1.12        31.96         7.53        12.82        12.43 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5718 
        6.58        12.62         1.02         9.01         7.07        36.00 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6528 TCGA-D7-A4YV TCGA-D7-A6EY 
        6.02       105.07        21.07        15.22         5.92        11.44 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-8211 TCGA-HU-8243 TCGA-HU-8604 TCGA-HU-A4GU 
       72.23         3.48        13.58         5.92        22.82         6.58 
TCGA-HU-A4H3 TCGA-IN-A6RP TCGA-MX-A666 TCGA-R5-A7ZF TCGA-VQ-A8DV TCGA-VQ-A8P2 
       29.00         6.44        14.04         8.52        13.25        38.14 
TCGA-VQ-A8PE TCGA-VQ-A91U 
       22.19         1.71 

$`APC WILD-TYPE`
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-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-4279 TCGA-BR-4280 TCGA-BR-6453 
        4.08         9.34         9.67         9.57         6.61        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6566 
       13.87        17.29        13.68        19.33        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-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       31.20        44.94        21.90        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-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-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-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-A486 TCGA-CD-A487 TCGA-CD-A489 
       11.64        15.39        12.07         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-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 TCGA-CG-5724 
       30.97         6.97         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-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-D7-6815 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-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27        11.38        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-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        1.51        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-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-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-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZI 
       36.95         3.72        19.73        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-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 
        0.92        48.79         5.46        13.02        43.36        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91V 
       37.22        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 

  APC MUTATED APC WILD-TYPE 
         0.26          0.00 
  APC MUTATED APC WILD-TYPE 
       105.07        122.30 
  APC MUTATED APC WILD-TYPE 
        12.72         14.76 
[1] "0.3 - 105.1 (12.7)" "0.0 - 122.3 (14.8)"
[1] "hr=" "1.4"
D35V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  APC MUTATED         0        2        8        5         5         6
  APC WILD-TYPE       2       13       32       25        32        46
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  APC MUTATED           0          8          2          4        6
  APC WILD-TYPE         3         62         51         28       32
D35V3, multiclass
            clus
vv           APC MUTATED APC WILD-TYPE
  STAGE I              0             2
  STAGE IA             2            13
  STAGE IB             8            32
  STAGE II             5            25
  STAGE IIA            5            32
  STAGE IIB            6            46
  STAGE III            0             3
  STAGE IIIA           8            62
  STAGE IIIB           2            51
  STAGE IIIC           4            28
  STAGE IV             6            32
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  APC MUTATED     2  13  19  12
  APC WILD-TYPE  20  79 154  85
D35V4, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T1           2            20
  T2          13            79
  T3          19           154
  T4          12            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
  APC MUTATED   20 15  4  8
  APC WILD-TYPE 98 89 73 69
D35V5, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  N0          20            98
  N1          15            89
  N2           4            73
  N3           8            69
[1] 4 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
  APC MUTATED    40   4
  APC WILD-TYPE 306  25
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     40    4
  APC WILD-TYPE  306   25
   clus
vv  APC MUTATED APC WILD-TYPE
  0          40           306
  1           4            25
[1] 2 2
[1] FALSE
D35V7, binary
               cls
clus              0   1
  APC MUTATED    16  32
  APC WILD-TYPE 129 216
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     16   32
  APC WILD-TYPE  129  216
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          16           129
  MALE            32           216
[1] 2 2
[1] FALSE
D35V8, binary
               cls
clus              0   1
  APC MUTATED    37   3
  APC WILD-TYPE 255  56
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     37    3
  APC WILD-TYPE  255   56
     clus
vv    APC MUTATED APC WILD-TYPE
  NO           37           255
  YES           3            56
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  APC MUTATED                                          1
  APC WILD-TYPE                                        7
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  APC MUTATED                                       5
  APC WILD-TYPE                                    65
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  APC MUTATED                                                       23
  APC WILD-TYPE                                                    135
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  APC MUTATED                                                   1
  APC WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  APC MUTATED                                                                   8
  APC WILD-TYPE                                                                60
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  APC MUTATED                                                    1
  APC WILD-TYPE                                                  4
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  APC MUTATED                                                  9
  APC WILD-TYPE                                               52
D35V9, multiclass
                                                                   clus
vv                                                                  APC MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                     23
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           8
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            9
                                                                   clus
vv                                                                  APC WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      135
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            60
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             52
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  APC MUTATED    35   2   2   5
  APC WILD-TYPE 276  12  13  19
D35V10, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0          35           276
  R1           2            12
  R2           2            13
  RX           5            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  APC MUTATED      11                         3
  APC WILD-TYPE    76                         6
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  APC MUTATED                                           0    25
  APC WILD-TYPE                                         1   218
D35V12, multiclass
                                           clus
vv                                          APC MUTATED APC WILD-TYPE
  ASIAN                                              11            76
  BLACK OR AFRICAN AMERICAN                           3             6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              25           218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, binary
               cls
clus              0   1
  APC MUTATED     0  34
  APC WILD-TYPE   4 276
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      0   34
  APC WILD-TYPE    4  276
                        clus
vv                       APC MUTATED APC WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          34           276
[1] 2 2
[1] FALSE

Clustering(36) Variable = TRIP4 MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2               0   1
  TRIP4 MUTATED     7   4
  TRIP4 WILD-TYPE 223 135
  TRIP4 MUTATED TRIP4 WILD-TYPE 
             11             358 
  TRIP4 MUTATED TRIP4 WILD-TYPE 
              4             135 
$`TRIP4 MUTATED`
TCGA-CG-4460 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8382 TCGA-BR-8487 
       21.99        14.43        32.25         8.05        25.05         1.12 
TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-5723 TCGA-HF-7132 
       31.96        15.95         8.05       105.07        77.29 

$`TRIP4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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 

  TRIP4 MUTATED TRIP4 WILD-TYPE 
           1.12            0.00 
  TRIP4 MUTATED TRIP4 WILD-TYPE 
         105.07          122.30 
  TRIP4 MUTATED TRIP4 WILD-TYPE 
          21.99           14.07 
[1] "1.1 - 105.1 (22.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D36V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIP4 MUTATED         0        0        0        4         1         1
  TRIP4 WILD-TYPE       2       15       40       26        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIP4 MUTATED           1          0          0          2        2
  TRIP4 WILD-TYPE         2         70         53         30       36
D36V3, multiclass
            clus
vv           TRIP4 MUTATED TRIP4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               4              26
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRIP4 MUTATED     1   4   1   6
  TRIP4 WILD-TYPE  21  88 172  91
D36V4, multiclass
    clus
vv   TRIP4 MUTATED TRIP4 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             1             172
  T4             6              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
  TRIP4 MUTATED     2   6   1   2
  TRIP4 WILD-TYPE 116  98  76  75
D36V5, multiclass
    clus
vv   TRIP4 MUTATED TRIP4 WILD-TYPE
  N0             2             116
  N1             6              98
  N2             1              76
  N3             2              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"
D36V6, binary
                 cls
clus                0   1
  TRIP4 MUTATED    10   2
  TRIP4 WILD-TYPE 336  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP4 MUTATED     10    2
  TRIP4 WILD-TYPE  336   27
   clus
vv  TRIP4 MUTATED TRIP4 WILD-TYPE
  0            10             336
  1             2              27
[1] 2 2
[1] FALSE
D36V7, binary
                 cls
clus                0   1
  TRIP4 MUTATED     6   6
  TRIP4 WILD-TYPE 139 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP4 MUTATED      6    6
  TRIP4 WILD-TYPE  139  242
        clus
vv       TRIP4 MUTATED TRIP4 WILD-TYPE
  FEMALE             6             139
  MALE               6             242
[1] 2 2
[1] FALSE
D36V8, binary
                 cls
clus                0   1
  TRIP4 MUTATED    10   1
  TRIP4 WILD-TYPE 282  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP4 MUTATED     10    1
  TRIP4 WILD-TYPE  282   58
     clus
vv    TRIP4 MUTATED TRIP4 WILD-TYPE
  NO             10             282
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TRIP4 MUTATED                                          0
  TRIP4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TRIP4 MUTATED                                       0
  TRIP4 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRIP4 MUTATED                                                        6
  TRIP4 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TRIP4 MUTATED                                                   1
  TRIP4 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRIP4 MUTATED                                                                   4
  TRIP4 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TRIP4 MUTATED                                                    0
  TRIP4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TRIP4 MUTATED                                                  1
  TRIP4 WILD-TYPE                                               60
D36V9, multiclass
                                                                   clus
vv                                                                  TRIP4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  TRIP4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRIP4 MUTATED    10   0   1   1
  TRIP4 WILD-TYPE 301  14  14  23
D36V10, multiclass
    clus
vv   TRIP4 MUTATED TRIP4 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TRIP4 MUTATED       1                         0
  TRIP4 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRIP4 MUTATED                                           0     6
  TRIP4 WILD-TYPE                                         1   237
D36V12, multiclass
                                           clus
vv                                          TRIP4 MUTATED TRIP4 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, binary
                 cls
clus                0   1
  TRIP4 MUTATED     0   7
  TRIP4 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP4 MUTATED      0    7
  TRIP4 WILD-TYPE    4  303
                        clus
vv                       TRIP4 MUTATED TRIP4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(37) Variable = CTNND1 MUTATION ANALYSIS
D37V1, survival
                  sevent
clus2                0   1
  CTNND1 MUTATED    17   5
  CTNND1 WILD-TYPE 213 134
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              22              347 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
               5              134 
$`CTNND1 MUTATED`
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-8284 
        9.44         6.97        34.68        21.90        36.16         8.05 
TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8678 TCGA-BR-8680 TCGA-CD-8536 
        0.26        31.27        25.05        24.79        31.96        12.43 
TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-A4Z0 TCGA-HF-A5NB 
       12.62        15.95         6.02        21.07        14.76        30.51 
TCGA-HU-A4GN TCGA-HU-A4H3 TCGA-VQ-A8P2 TCGA-VQ-A91V 
       29.98        29.00        38.14        42.64 

$`CTNND1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         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-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       44.94         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-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-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-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-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-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-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-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-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-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-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 

  CTNND1 MUTATED CTNND1 WILD-TYPE 
            0.26             0.00 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
           42.64           122.30 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
          23.345           14.040 
[1] "0.3 - 42.6 (23.3)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "2.1"
D37V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTNND1 MUTATED         1        1        3        2         2         3
  CTNND1 WILD-TYPE       1       14       37       28        35        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNND1 MUTATED           0          4          0          5        3
  CTNND1 WILD-TYPE         3         66         53         27       35
D37V3, multiclass
            clus
vv           CTNND1 MUTATED CTNND1 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                3               37
  STAGE II                2               28
  STAGE IIA               2               35
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              0               53
  STAGE IIIC              5               27
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CTNND1 MUTATED     2   7   5  10
  CTNND1 WILD-TYPE  20  85 168  87
D37V4, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  T1              2               20
  T2              7               85
  T3              5              168
  T4             10               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
  CTNND1 MUTATED     7   6   4   6
  CTNND1 WILD-TYPE 111  98  73  71
D37V5, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  N0              7              111
  N1              6               98
  N2              4               73
  N3              6               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"
D37V6, binary
                  cls
clus                 0   1
  CTNND1 MUTATED    20   2
  CTNND1 WILD-TYPE 326  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED     20    2
  CTNND1 WILD-TYPE  326   27
   clus
vv  CTNND1 MUTATED CTNND1 WILD-TYPE
  0             20              326
  1              2               27
[1] 2 2
[1] FALSE
D37V7, binary
                  cls
clus                 0   1
  CTNND1 MUTATED     8  16
  CTNND1 WILD-TYPE 137 232
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED      8   16
  CTNND1 WILD-TYPE  137  232
        clus
vv       CTNND1 MUTATED CTNND1 WILD-TYPE
  FEMALE              8              137
  MALE               16              232
[1] 2 2
[1] FALSE
D37V8, binary
                  cls
clus                 0   1
  CTNND1 MUTATED    19   4
  CTNND1 WILD-TYPE 273  55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED     19    4
  CTNND1 WILD-TYPE  273   55
     clus
vv    CTNND1 MUTATED CTNND1 WILD-TYPE
  NO              19              273
  YES              4               55
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CTNND1 MUTATED                                          0
  CTNND1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CTNND1 MUTATED                                       1
  CTNND1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTNND1 MUTATED                                                       12
  CTNND1 WILD-TYPE                                                    146
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CTNND1 MUTATED                                                   3
  CTNND1 WILD-TYPE                                                18
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTNND1 MUTATED                                                                   4
  CTNND1 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CTNND1 MUTATED                                                    1
  CTNND1 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CTNND1 MUTATED                                                  3
  CTNND1 WILD-TYPE                                               58
D37V9, multiclass
                                                                   clus
vv                                                                  CTNND1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  CTNND1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CTNND1 MUTATED    20   1   0   1
  CTNND1 WILD-TYPE 291  13  15  23
D37V10, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  R0             20              291
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CTNND1 MUTATED       5                         1
  CTNND1 WILD-TYPE    82                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTNND1 MUTATED                                           0    13
  CTNND1 WILD-TYPE                                         1   230
D37V12, multiclass
                                           clus
vv                                          CTNND1 MUTATED CTNND1 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                  cls
clus                 0   1
  CTNND1 MUTATED     0  18
  CTNND1 WILD-TYPE   4 292
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED      0   18
  CTNND1 WILD-TYPE    4  292
                        clus
vv                       CTNND1 MUTATED CTNND1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             18              292
[1] 2 2
[1] FALSE

Clustering(38) Variable = FAM9A MUTATION ANALYSIS
D38V1, survival
                 sevent
clus2               0   1
  FAM9A MUTATED     6   3
  FAM9A WILD-TYPE 224 136
  FAM9A MUTATED FAM9A WILD-TYPE 
              9             360 
  FAM9A MUTATED FAM9A WILD-TYPE 
              3             136 
$`FAM9A MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-7715 TCGA-CD-A4MG TCGA-CG-5721 
       21.99         6.97        44.94        33.63         6.58         6.02 
TCGA-D7-A4Z0 TCGA-SW-A7EA TCGA-VQ-A8P2 
       14.76        19.04        38.14 

$`FAM9A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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 

  FAM9A MUTATED FAM9A WILD-TYPE 
           6.02            0.00 
  FAM9A MUTATED FAM9A WILD-TYPE 
          44.94          122.30 
  FAM9A MUTATED FAM9A WILD-TYPE 
          19.04           14.12 
[1] "6.0 - 44.9 (19.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D38V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM9A MUTATED         1        0        1        0         3         1
  FAM9A WILD-TYPE       1       15       39       30        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM9A MUTATED           0          2          0          0        3
  FAM9A WILD-TYPE         3         68         53         32       35
D38V3, multiclass
            clus
vv           FAM9A MUTATED FAM9A WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FAM9A MUTATED     1   2   4   4
  FAM9A WILD-TYPE  21  90 169  93
D38V4, multiclass
    clus
vv   FAM9A MUTATED FAM9A WILD-TYPE
  T1             1              21
  T2             2              90
  T3             4             169
  T4             4              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
  FAM9A MUTATED     4   5   2   0
  FAM9A WILD-TYPE 114  99  75  77
D38V5, multiclass
    clus
vv   FAM9A MUTATED FAM9A WILD-TYPE
  N0             4             114
  N1             5              99
  N2             2              75
  N3             0              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"
D38V6, binary
                 cls
clus                0   1
  FAM9A MUTATED     9   1
  FAM9A WILD-TYPE 337  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      9    1
  FAM9A WILD-TYPE  337   28
   clus
vv  FAM9A MUTATED FAM9A WILD-TYPE
  0             9             337
  1             1              28
[1] 2 2
[1] FALSE
D38V7, binary
                 cls
clus                0   1
  FAM9A MUTATED     6   6
  FAM9A WILD-TYPE 139 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      6    6
  FAM9A WILD-TYPE  139  242
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  FEMALE             6             139
  MALE               6             242
[1] 2 2
[1] FALSE
D38V8, binary
                 cls
clus                0   1
  FAM9A MUTATED     8   2
  FAM9A WILD-TYPE 284  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      8    2
  FAM9A WILD-TYPE  284   57
     clus
vv    FAM9A MUTATED FAM9A WILD-TYPE
  NO              8             284
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM9A MUTATED                                          0
  FAM9A WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM9A MUTATED                                       2
  FAM9A WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM9A MUTATED                                                        6
  FAM9A WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM9A MUTATED                                                   2
  FAM9A WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM9A MUTATED                                                                   2
  FAM9A WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM9A MUTATED                                                    0
  FAM9A WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM9A MUTATED                                                  0
  FAM9A WILD-TYPE                                               61
D38V9, multiclass
                                                                   clus
vv                                                                  FAM9A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  FAM9A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FAM9A MUTATED     7   0   1   3
  FAM9A WILD-TYPE 304  14  14  21
D38V10, multiclass
    clus
vv   FAM9A MUTATED FAM9A WILD-TYPE
  R0             7             304
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FAM9A MUTATED       1                         1
  FAM9A WILD-TYPE    86                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM9A MUTATED                                           0     8
  FAM9A WILD-TYPE                                         1   235
D38V12, multiclass
                                           clus
vv                                          FAM9A MUTATED FAM9A WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, binary
                 cls
clus                0   1
  FAM9A MUTATED     0   9
  FAM9A WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      0    9
  FAM9A WILD-TYPE    4  301
                        clus
vv                       FAM9A MUTATED FAM9A WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(39) Variable = SLC27A3 MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  SLC27A3 MUTATED     1   5
  SLC27A3 WILD-TYPE 229 134
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                6               363 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                5               134 
$`SLC27A3 MUTATED`
TCGA-BR-8059 TCGA-BR-8382 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-HF-7132 TCGA-HJ-7597 
       14.43        25.05        16.14         6.58        77.29        26.47 

$`SLC27A3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
             6.58              0.00 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
            77.29            122.30 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
           20.595            14.070 
[1] "6.6 - 77.3 (20.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D39V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC27A3 MUTATED         1        0        2        1         1         0
  SLC27A3 WILD-TYPE       1       15       38       29        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC27A3 MUTATED           1          0          1          1        0
  SLC27A3 WILD-TYPE         2         70         52         31       38
D39V3, multiclass
            clus
vv           SLC27A3 MUTATED SLC27A3 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                1                 2
  STAGE IIIA               0                70
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC27A3 MUTATED     2   3   2   2
  SLC27A3 WILD-TYPE  20  89 171  95
D39V4, multiclass
    clus
vv   SLC27A3 MUTATED SLC27A3 WILD-TYPE
  T1               2                20
  T2               3                89
  T3               2               171
  T4               2                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
  SLC27A3 MUTATED     3   3   0   2
  SLC27A3 WILD-TYPE 115 101  77  75
D39V5, multiclass
    clus
vv   SLC27A3 MUTATED SLC27A3 WILD-TYPE
  N0               3               115
  N1               3               101
  N2               0                77
  N3               2                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"
D39V6, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     7   0
  SLC27A3 WILD-TYPE 339  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      7    0
  SLC27A3 WILD-TYPE  339   29
   clus
vv  SLC27A3 MUTATED SLC27A3 WILD-TYPE
  0               7               339
  1               0                29
[1] 2 2
[1] FALSE
D39V7, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     4   5
  SLC27A3 WILD-TYPE 141 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      4    5
  SLC27A3 WILD-TYPE  141  243
        clus
vv       SLC27A3 MUTATED SLC27A3 WILD-TYPE
  FEMALE               4               141
  MALE                 5               243
[1] 2 2
[1] FALSE
D39V8, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     6   1
  SLC27A3 WILD-TYPE 286  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      6    1
  SLC27A3 WILD-TYPE  286   58
     clus
vv    SLC27A3 MUTATED SLC27A3 WILD-TYPE
  NO                6               286
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC27A3 MUTATED                                          1
  SLC27A3 WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC27A3 MUTATED                                       1
  SLC27A3 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC27A3 MUTATED                                                        4
  SLC27A3 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC27A3 MUTATED                                                   1
  SLC27A3 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC27A3 MUTATED                                                                   2
  SLC27A3 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC27A3 MUTATED                                                    0
  SLC27A3 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC27A3 MUTATED                                                  0
  SLC27A3 WILD-TYPE                                               61
D39V9, multiclass
                                                                   clus
vv                                                                  SLC27A3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  SLC27A3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC27A3 MUTATED     7   0   0   1
  SLC27A3 WILD-TYPE 304  14  15  23
D39V10, multiclass
    clus
vv   SLC27A3 MUTATED SLC27A3 WILD-TYPE
  R0               7               304
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC27A3 MUTATED       1                         1
  SLC27A3 WILD-TYPE    86                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC27A3 MUTATED                                           0     5
  SLC27A3 WILD-TYPE                                         1   238
D39V12, multiclass
                                           clus
vv                                          SLC27A3 MUTATED SLC27A3 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     0   7
  SLC27A3 WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      0    7
  SLC27A3 WILD-TYPE    4  303
                        clus
vv                       SLC27A3 MUTATED SLC27A3 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(40) Variable = PAX6 MUTATION ANALYSIS
D40V1, survival
                sevent
clus2              0   1
  PAX6 MUTATED    13   5
  PAX6 WILD-TYPE 217 134
  PAX6 MUTATED PAX6 WILD-TYPE 
            18            351 
  PAX6 MUTATED PAX6 WILD-TYPE 
             5            134 
$`PAX6 MUTATED`
TCGA-BR-4257 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8372 
        9.67        32.78        36.16        29.59        31.10        31.27 
TCGA-BR-8382 TCGA-BR-A4CQ TCGA-CD-8529 TCGA-CG-5721 TCGA-CG-5733 TCGA-FP-7916 
       25.05        34.98        12.30         6.02        21.07        14.07 
TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-R5-A7ZI TCGA-RD-A7BT 
       30.51        22.68         6.51         6.58        74.53         8.61 

$`PAX6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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-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-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-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 

  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         14.070 
[1] "6.0 - 74.5 (23.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D40V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAX6 MUTATED         0        1        1        0         2         3
  PAX6 WILD-TYPE       2       14       39       30        35        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAX6 MUTATED           0          2          0          5        4
  PAX6 WILD-TYPE         3         68         53         27       34
D40V3, multiclass
            clus
vv           PAX6 MUTATED PAX6 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            5             27
  STAGE IV              4             34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAX6 MUTATED     1   2   6  10
  PAX6 WILD-TYPE  21  90 167  87
D40V4, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  T1            1             21
  T2            2             90
  T3            6            167
  T4           10             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
  PAX6 MUTATED     6   5   2   5
  PAX6 WILD-TYPE 112  99  75  72
D40V5, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  N0            6            112
  N1            5             99
  N2            2             75
  N3            5             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"
D40V6, binary
                cls
clus               0   1
  PAX6 MUTATED    16   2
  PAX6 WILD-TYPE 330  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED     16    2
  PAX6 WILD-TYPE  330   27
   clus
vv  PAX6 MUTATED PAX6 WILD-TYPE
  0           16            330
  1            2             27
[1] 2 2
[1] FALSE
D40V7, binary
                cls
clus               0   1
  PAX6 MUTATED    11   9
  PAX6 WILD-TYPE 134 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED     11    9
  PAX6 WILD-TYPE  134  239
        clus
vv       PAX6 MUTATED PAX6 WILD-TYPE
  FEMALE           11            134
  MALE              9            239
[1] 2 2
[1] FALSE
D40V8, binary
                cls
clus               0   1
  PAX6 MUTATED    16   2
  PAX6 WILD-TYPE 276  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED     16    2
  PAX6 WILD-TYPE  276   57
     clus
vv    PAX6 MUTATED PAX6 WILD-TYPE
  NO            16            276
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PAX6 MUTATED                                          0
  PAX6 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PAX6 MUTATED                                       4
  PAX6 WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAX6 MUTATED                                                        8
  PAX6 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PAX6 MUTATED                                                   2
  PAX6 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAX6 MUTATED                                                                   4
  PAX6 WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PAX6 MUTATED                                                    1
  PAX6 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PAX6 MUTATED                                                  1
  PAX6 WILD-TYPE                                               60
D40V9, multiclass
                                                                   clus
vv                                                                  PAX6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  PAX6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PAX6 MUTATED    14   1   1   2
  PAX6 WILD-TYPE 297  13  14  22
D40V10, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  R0           14            297
  R1            1             13
  R2            1             14
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PAX6 MUTATED       5                         0
  PAX6 WILD-TYPE    82                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAX6 MUTATED                                           1    10
  PAX6 WILD-TYPE                                         0   233
D40V12, multiclass
                                           clus
vv                                          PAX6 MUTATED PAX6 WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                               10            233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, binary
                cls
clus               0   1
  PAX6 MUTATED     1  15
  PAX6 WILD-TYPE   3 295
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED      1   15
  PAX6 WILD-TYPE    3  295
                        clus
vv                       PAX6 MUTATED PAX6 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           15            295
[1] 2 2
[1] FALSE

Clustering(41) Variable = KRT75 MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2               0   1
  KRT75 MUTATED    26  10
  KRT75 WILD-TYPE 204 129
  KRT75 MUTATED KRT75 WILD-TYPE 
             36             333 
  KRT75 MUTATED KRT75 WILD-TYPE 
             10             129 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-8297 TCGA-BR-8361 
        0.56        29.42         2.66        19.96         7.40        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-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-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-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98         0.72         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-8527 
       13.18        13.35        11.21        12.10        12.39         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-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-D7-8575 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-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-8210 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       14.07        22.29         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-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
       21.07         5.59        22.68        24.20        22.75        25.81 
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-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 

  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          14.790 
[1] "0.3 - 74.5 (12.7)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.3"
D41V2, 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       2       12       37       26        32        46
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRT75 MUTATED           1          7          4          1        2
  KRT75 WILD-TYPE         2         63         49         31       36
D41V3, multiclass
            clus
vv           KRT75 MUTATED KRT75 WILD-TYPE
  STAGE I                0               2
  STAGE IA               3              12
  STAGE IB               3              37
  STAGE II               4              26
  STAGE IIA              5              32
  STAGE IIB              6              46
  STAGE III              1               2
  STAGE IIIA             7              63
  STAGE IIIB             4              49
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KRT75 MUTATED     3   6  17  11
  KRT75 WILD-TYPE  19  86 156  86
D41V4, multiclass
    clus
vv   KRT75 MUTATED KRT75 WILD-TYPE
  T1             3              19
  T2             6              86
  T3            17             156
  T4            11              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
  KRT75 MUTATED   19 11  1  5
  KRT75 WILD-TYPE 99 93 76 72
D41V5, multiclass
    clus
vv   KRT75 MUTATED KRT75 WILD-TYPE
  N0            19              99
  N1            11              93
  N2             1              76
  N3             5              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"
D41V6, binary
                 cls
clus                0   1
  KRT75 MUTATED    32   2
  KRT75 WILD-TYPE 314  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT75 MUTATED     32    2
  KRT75 WILD-TYPE  314   27
   clus
vv  KRT75 MUTATED KRT75 WILD-TYPE
  0            32             314
  1             2              27
[1] 2 2
[1] FALSE
D41V7, binary
                 cls
clus                0   1
  KRT75 MUTATED    14  23
  KRT75 WILD-TYPE 131 225
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT75 MUTATED     14   23
  KRT75 WILD-TYPE  131  225
        clus
vv       KRT75 MUTATED KRT75 WILD-TYPE
  FEMALE            14             131
  MALE              23             225
[1] 2 2
[1] FALSE
D41V8, binary
                 cls
clus                0   1
  KRT75 MUTATED    29   7
  KRT75 WILD-TYPE 263  52
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT75 MUTATED     29    7
  KRT75 WILD-TYPE  263   52
     clus
vv    KRT75 MUTATED KRT75 WILD-TYPE
  NO             29             263
  YES             7              52
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KRT75 MUTATED                                          0
  KRT75 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KRT75 MUTATED                                       9
  KRT75 WILD-TYPE                                    61
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KRT75 MUTATED                                                       15
  KRT75 WILD-TYPE                                                    143
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KRT75 MUTATED                                                   3
  KRT75 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KRT75 MUTATED                                                                   6
  KRT75 WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KRT75 MUTATED                                                    1
  KRT75 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KRT75 MUTATED                                                  3
  KRT75 WILD-TYPE                                               58
D41V9, multiclass
                                                                   clus
vv                                                                  KRT75 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  KRT75 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          61
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KRT75 MUTATED    34   1   0   2
  KRT75 WILD-TYPE 277  13  15  22
D41V10, multiclass
    clus
vv   KRT75 MUTATED KRT75 WILD-TYPE
  R0            34             277
  R1             1              13
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KRT75 MUTATED      15                         0
  KRT75 WILD-TYPE    72                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KRT75 MUTATED                                           0    21
  KRT75 WILD-TYPE                                         1   222
D41V12, multiclass
                                           clus
vv                                          KRT75 MUTATED KRT75 WILD-TYPE
  ASIAN                                                15              72
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                21             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, binary
                 cls
clus                0   1
  KRT75 MUTATED     1  34
  KRT75 WILD-TYPE   3 276
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT75 MUTATED      1   34
  KRT75 WILD-TYPE    3  276
                        clus
vv                       KRT75 MUTATED KRT75 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            34             276
[1] 2 2
[1] FALSE

Clustering(42) Variable = P4HTM MUTATION ANALYSIS
D42V1, survival
                 sevent
clus2               0   1
  P4HTM MUTATED    18   6
  P4HTM WILD-TYPE 212 133
  P4HTM MUTATED P4HTM WILD-TYPE 
             24             345 
  P4HTM MUTATED P4HTM WILD-TYPE 
              6             133 
$`P4HTM MUTATED`
TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-7197 TCGA-BR-8059 TCGA-BR-8078 
       26.70         9.67         6.61         9.21        14.43        29.59 
TCGA-BR-8372 TCGA-BR-A44U TCGA-BR-A4J2 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       31.27        13.87        14.17        12.76        12.59        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CG-5723 TCGA-CG-5728 
       12.33        12.30        12.59        11.64       105.07        65.10 
TCGA-D7-8576 TCGA-FP-8211 TCGA-HU-8610 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GY 
       14.66        13.58         0.76        11.77         8.98         0.26 

$`P4HTM WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90        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-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-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-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98         0.72         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-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-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-D7-8578 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-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-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.82        21.07        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-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58        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-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 

  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           15.22 
[1] "0.3 - 105.1 (12.6)" "0.0 - 122.3 (15.2)"
[1] "hr=" "1.4"
D42V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  P4HTM MUTATED         0        2        1        4         1         4
  P4HTM WILD-TYPE       2       13       39       26        36        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  P4HTM MUTATED           2          5          2          1        2
  P4HTM WILD-TYPE         1         65         51         31       36
D42V3, multiclass
            clus
vv           P4HTM MUTATED P4HTM WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               1              39
  STAGE II               4              26
  STAGE IIA              1              36
  STAGE IIB              4              48
  STAGE III              2               1
  STAGE IIIA             5              65
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  P4HTM MUTATED     2   4   9   9
  P4HTM WILD-TYPE  20  88 164  88
D42V4, multiclass
    clus
vv   P4HTM MUTATED P4HTM WILD-TYPE
  T1             2              20
  T2             4              88
  T3             9             164
  T4             9              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
  P4HTM MUTATED    11   9   1   3
  P4HTM WILD-TYPE 107  95  76  74
D42V5, multiclass
    clus
vv   P4HTM MUTATED P4HTM WILD-TYPE
  N0            11             107
  N1             9              95
  N2             1              76
  N3             3              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"
D42V6, binary
                 cls
clus                0   1
  P4HTM MUTATED    24   1
  P4HTM WILD-TYPE 322  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P4HTM MUTATED     24    1
  P4HTM WILD-TYPE  322   28
   clus
vv  P4HTM MUTATED P4HTM WILD-TYPE
  0            24             322
  1             1              28
[1] 2 2
[1] FALSE
D42V7, binary
                 cls
clus                0   1
  P4HTM MUTATED    14  12
  P4HTM WILD-TYPE 131 236
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P4HTM MUTATED     14   12
  P4HTM WILD-TYPE  131  236
        clus
vv       P4HTM MUTATED P4HTM WILD-TYPE
  FEMALE            14             131
  MALE              12             236
[1] 2 2
[1] FALSE
D42V8, binary
                 cls
clus                0   1
  P4HTM MUTATED    18   5
  P4HTM WILD-TYPE 274  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P4HTM MUTATED     18    5
  P4HTM WILD-TYPE  274   54
     clus
vv    P4HTM MUTATED P4HTM WILD-TYPE
  NO             18             274
  YES             5              54
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  P4HTM MUTATED                                          0
  P4HTM WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  P4HTM MUTATED                                       5
  P4HTM WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  P4HTM MUTATED                                                       12
  P4HTM WILD-TYPE                                                    146
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  P4HTM MUTATED                                                   2
  P4HTM WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  P4HTM MUTATED                                                                   4
  P4HTM WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  P4HTM MUTATED                                                    0
  P4HTM WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  P4HTM MUTATED                                                  3
  P4HTM WILD-TYPE                                               58
D42V9, multiclass
                                                                   clus
vv                                                                  P4HTM MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  P4HTM WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  P4HTM MUTATED    21   1   0   4
  P4HTM WILD-TYPE 290  13  15  20
D42V10, multiclass
    clus
vv   P4HTM MUTATED P4HTM WILD-TYPE
  R0            21             290
  R1             1              13
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  P4HTM MUTATED      12                         0
  P4HTM WILD-TYPE    75                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  P4HTM MUTATED                                           0    12
  P4HTM WILD-TYPE                                         1   231
D42V12, multiclass
                                           clus
vv                                          P4HTM MUTATED P4HTM WILD-TYPE
  ASIAN                                                12              75
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, binary
                 cls
clus                0   1
  P4HTM MUTATED     0  24
  P4HTM WILD-TYPE   4 286
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P4HTM MUTATED      0   24
  P4HTM WILD-TYPE    4  286
                        clus
vv                       P4HTM MUTATED P4HTM WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            24             286
[1] 2 2
[1] FALSE

Clustering(43) Variable = DSTN MUTATION ANALYSIS
D43V1, survival
                sevent
clus2              0   1
  DSTN MUTATED     3   3
  DSTN WILD-TYPE 227 136
  DSTN MUTATED DSTN WILD-TYPE 
             6            363 
  DSTN MUTATED DSTN WILD-TYPE 
             3            136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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         14.270 
[1] "6.6 - 21.1 (15.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D43V2, 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       2       15       39       30        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DSTN MUTATED           0          1          1          0        1
  DSTN WILD-TYPE         3         69         52         32       37
D43V3, multiclass
            clus
vv           DSTN MUTATED DSTN WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DSTN MUTATED     1   1   4   1
  DSTN WILD-TYPE  21  91 169  96
D43V4, multiclass
    clus
vv   DSTN MUTATED DSTN WILD-TYPE
  T1            1             21
  T2            1             91
  T3            4            169
  T4            1             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
  DSTN MUTATED     1   3   2   1
  DSTN WILD-TYPE 117 101  75  76
D43V5, multiclass
    clus
vv   DSTN MUTATED DSTN WILD-TYPE
  N0            1            117
  N1            3            101
  N2            2             75
  N3            1             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"
D43V6, binary
                cls
clus               0   1
  DSTN MUTATED     7   0
  DSTN WILD-TYPE 339  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      7    0
  DSTN WILD-TYPE  339   29
   clus
vv  DSTN MUTATED DSTN WILD-TYPE
  0            7            339
  1            0             29
[1] 2 2
[1] FALSE
D43V7, binary
                cls
clus               0   1
  DSTN MUTATED     3   4
  DSTN WILD-TYPE 142 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      3    4
  DSTN WILD-TYPE  142  244
        clus
vv       DSTN MUTATED DSTN WILD-TYPE
  FEMALE            3            142
  MALE              4            244
[1] 2 2
[1] FALSE
D43V8, binary
                cls
clus               0   1
  DSTN MUTATED     5   1
  DSTN WILD-TYPE 287  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      5    1
  DSTN WILD-TYPE  287   58
     clus
vv    DSTN MUTATED DSTN WILD-TYPE
  NO             5            287
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DSTN MUTATED                                          0
  DSTN WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DSTN MUTATED                                       2
  DSTN WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DSTN MUTATED                                                        3
  DSTN WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DSTN MUTATED                                                   0
  DSTN WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DSTN MUTATED                                                                   1
  DSTN WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DSTN MUTATED                                                    0
  DSTN WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DSTN MUTATED                                                  1
  DSTN WILD-TYPE                                               60
D43V9, multiclass
                                                                   clus
vv                                                                  DSTN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  DSTN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DSTN MUTATED     6   0   0   1
  DSTN WILD-TYPE 305  14  15  23
D43V10, multiclass
    clus
vv   DSTN MUTATED DSTN WILD-TYPE
  R0            6            305
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DSTN MUTATED       2                         1
  DSTN WILD-TYPE    85                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DSTN MUTATED                                           0     3
  DSTN WILD-TYPE                                         1   240
D43V12, multiclass
                                           clus
vv                                          DSTN MUTATED DSTN WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, binary
                cls
clus               0   1
  DSTN MUTATED     0   6
  DSTN WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      0    6
  DSTN WILD-TYPE    4  304
                        clus
vv                       DSTN MUTATED DSTN WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(44) Variable = CIC MUTATION ANALYSIS
D44V1, survival
               sevent
clus2             0   1
  CIC MUTATED    30  13
  CIC WILD-TYPE 200 126
  CIC MUTATED CIC WILD-TYPE 
           43           326 
  CIC MUTATED CIC WILD-TYPE 
           13           126 
$`CIC MUTATED`
TCGA-EQ-A4SO TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       16.24        30.90        34.68        14.43         0.69        29.59 
TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8372 TCGA-BR-8382 
       32.25         6.18         0.95        26.33        31.27        25.05 
TCGA-BR-8487 TCGA-BR-A4J2 TCGA-BR-A4QL TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 
        1.12        14.17        16.14        12.76        12.53        12.33 
TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-A4MI TCGA-CG-4465 TCGA-CG-5723 
       12.39        11.64        12.07        11.77         9.01       105.07 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-A6EY TCGA-F1-6874 
       65.10        21.07        19.50        17.19        11.44        14.47 
TCGA-FP-8099 TCGA-FP-8209 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8610 
       17.06        59.54        26.47         5.92        22.32         0.76 
TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-R5-A7ZI 
       22.68        11.77         8.98         6.58        29.00        74.53 
TCGA-VQ-A8P2 
       38.14 

$`CIC WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-8060 TCGA-BR-8080 
        9.07        29.56        33.21        37.25        11.44         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-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8368 
        7.40        31.10         0.26        22.19        17.52         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
       14.04         3.32        11.80        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-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-8525 
       13.18        13.35        11.21        12.10        12.39        12.59 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        7.17        12.30        12.59        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-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-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-D7-8575 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-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-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       14.07        22.29         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-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
        1.51        24.39        28.96        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-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-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-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 

  CIC MUTATED CIC WILD-TYPE 
         0.69          0.00 
  CIC MUTATED CIC WILD-TYPE 
       105.07        122.30 
  CIC MUTATED CIC WILD-TYPE 
       16.140        14.055 
[1] "0.7 - 105.1 (16.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D44V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CIC MUTATED         1        2        5        5         7         6
  CIC WILD-TYPE       1       13       35       25        30        46
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CIC MUTATED           1          6          5          4        3
  CIC WILD-TYPE         2         64         48         28       35
D44V3, multiclass
            clus
vv           CIC MUTATED CIC WILD-TYPE
  STAGE I              1             1
  STAGE IA             2            13
  STAGE IB             5            35
  STAGE II             5            25
  STAGE IIA            7            30
  STAGE IIB            6            46
  STAGE III            1             2
  STAGE IIIA           6            64
  STAGE IIIB           5            48
  STAGE IIIC           4            28
  STAGE IV             3            35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CIC MUTATED     3  10  18  16
  CIC WILD-TYPE  19  82 155  81
D44V4, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  T1           3            19
  T2          10            82
  T3          18           155
  T4          16            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"
               vv
clus            N0 N1 N2 N3
  CIC MUTATED   22 12  2  9
  CIC WILD-TYPE 96 92 75 68
D44V5, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  N0          22            96
  N1          12            92
  N2           2            75
  N3           9            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"
D44V6, binary
               cls
clus              0   1
  CIC MUTATED    40   2
  CIC WILD-TYPE 306  27
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     40    2
  CIC WILD-TYPE  306   27
   clus
vv  CIC MUTATED CIC WILD-TYPE
  0          40           306
  1           2            27
[1] 2 2
[1] FALSE
D44V7, binary
               cls
clus              0   1
  CIC MUTATED    24  23
  CIC WILD-TYPE 121 225
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     24   23
  CIC WILD-TYPE  121  225
        clus
vv       CIC MUTATED CIC WILD-TYPE
  FEMALE          24           121
  MALE            23           225
[1] 2 2
[1] FALSE
D44V8, binary
               cls
clus              0   1
  CIC MUTATED    35   5
  CIC WILD-TYPE 257  54
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     35    5
  CIC WILD-TYPE  257   54
     clus
vv    CIC MUTATED CIC WILD-TYPE
  NO           35           257
  YES           5            54
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CIC MUTATED                                          1
  CIC WILD-TYPE                                        7
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CIC MUTATED                                      11
  CIC WILD-TYPE                                    59
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CIC MUTATED                                                       19
  CIC WILD-TYPE                                                    139
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CIC MUTATED                                                   1
  CIC WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CIC MUTATED                                                                   9
  CIC WILD-TYPE                                                                59
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CIC MUTATED                                                    0
  CIC WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CIC MUTATED                                                  5
  CIC WILD-TYPE                                               56
D44V9, multiclass
                                                                   clus
vv                                                                  CIC MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                      11
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                     19
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           9
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            5
                                                                   clus
vv                                                                  CIC WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        59
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      139
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            59
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  CIC MUTATED    41   0   1   3
  CIC WILD-TYPE 270  14  14  21
D44V10, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  R0          41           270
  R1           0            14
  R2           1            14
  RX           3            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CIC MUTATED      16                         1
  CIC WILD-TYPE    71                         8
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CIC MUTATED                                           0    25
  CIC WILD-TYPE                                         1   218
D44V12, multiclass
                                           clus
vv                                          CIC MUTATED CIC WILD-TYPE
  ASIAN                                              16            71
  BLACK OR AFRICAN AMERICAN                           1             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              25           218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, binary
               cls
clus              0   1
  CIC MUTATED     1  40
  CIC WILD-TYPE   3 270
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED      1   40
  CIC WILD-TYPE    3  270
                        clus
vv                       CIC MUTATED CIC WILD-TYPE
  HISPANIC OR LATINO               1             3
  NOT HISPANIC OR LATINO          40           270
[1] 2 2
[1] FALSE

Clustering(45) Variable = OSBP2 MUTATION ANALYSIS
D45V1, survival
                 sevent
clus2               0   1
  OSBP2 MUTATED     9   5
  OSBP2 WILD-TYPE 221 134
  OSBP2 MUTATED OSBP2 WILD-TYPE 
             14             355 
  OSBP2 MUTATED OSBP2 WILD-TYPE 
              5             134 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-A8P2 TCGA-VQ-A8P3 
        5.46        13.25        13.02        43.36        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-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 

  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          14.040 
[1] "1.0 - 44.9 (23.9)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.5"
D45V2, 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       2       15       39       30        34        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSBP2 MUTATED           0          0          2          2        3
  OSBP2 WILD-TYPE         3         70         51         30       35
D45V3, multiclass
            clus
vv           OSBP2 MUTATED OSBP2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OSBP2 MUTATED     0   2   9   4
  OSBP2 WILD-TYPE  22  90 164  93
D45V4, multiclass
    clus
vv   OSBP2 MUTATED OSBP2 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             9             164
  T4             4              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
  OSBP2 MUTATED     5   3   4   2
  OSBP2 WILD-TYPE 113 101  73  75
D45V5, multiclass
    clus
vv   OSBP2 MUTATED OSBP2 WILD-TYPE
  N0             5             113
  N1             3             101
  N2             4              73
  N3             2              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"
D45V6, binary
                 cls
clus                0   1
  OSBP2 MUTATED    13   2
  OSBP2 WILD-TYPE 333  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSBP2 MUTATED     13    2
  OSBP2 WILD-TYPE  333   27
   clus
vv  OSBP2 MUTATED OSBP2 WILD-TYPE
  0            13             333
  1             2              27
[1] 2 2
[1] FALSE
D45V7, binary
                 cls
clus                0   1
  OSBP2 MUTATED    11   4
  OSBP2 WILD-TYPE 134 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSBP2 MUTATED     11    4
  OSBP2 WILD-TYPE  134  244
        clus
vv       OSBP2 MUTATED OSBP2 WILD-TYPE
  FEMALE            11             134
  MALE               4             244
[1] 2 2
[1] FALSE
D45V8, binary
                 cls
clus                0   1
  OSBP2 MUTATED    12   1
  OSBP2 WILD-TYPE 280  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSBP2 MUTATED     12    1
  OSBP2 WILD-TYPE  280   58
     clus
vv    OSBP2 MUTATED OSBP2 WILD-TYPE
  NO             12             280
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OSBP2 MUTATED                                          0
  OSBP2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OSBP2 MUTATED                                       4
  OSBP2 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OSBP2 MUTATED                                                        9
  OSBP2 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OSBP2 MUTATED                                                   0
  OSBP2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OSBP2 MUTATED                                                                   1
  OSBP2 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OSBP2 MUTATED                                                    0
  OSBP2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OSBP2 MUTATED                                                  1
  OSBP2 WILD-TYPE                                               60
D45V9, multiclass
                                                                   clus
vv                                                                  OSBP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  OSBP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OSBP2 MUTATED    11   0   1   2
  OSBP2 WILD-TYPE 300  14  14  22
D45V10, multiclass
    clus
vv   OSBP2 MUTATED OSBP2 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OSBP2 MUTATED       4                         0
  OSBP2 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OSBP2 MUTATED                                           0    10
  OSBP2 WILD-TYPE                                         1   233
D45V12, multiclass
                                           clus
vv                                          OSBP2 MUTATED OSBP2 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, binary
                 cls
clus                0   1
  OSBP2 MUTATED     0  12
  OSBP2 WILD-TYPE   4 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSBP2 MUTATED      0   12
  OSBP2 WILD-TYPE    4  298
                        clus
vv                       OSBP2 MUTATED OSBP2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(46) Variable = CEP57 MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2               0   1
  CEP57 MUTATED     7   5
  CEP57 WILD-TYPE 223 134
  CEP57 MUTATED CEP57 WILD-TYPE 
             12             357 
  CEP57 MUTATED CEP57 WILD-TYPE 
              5             134 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        9.44         6.61         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-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-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-F1-6875 
        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-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-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-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 

  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          14.170 
[1] "1.0 - 38.1 (16.8)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D46V2, 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       2       15       38       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP57 MUTATED           0          3          0          2        3
  CEP57 WILD-TYPE         3         67         53         30       35
D46V3, multiclass
            clus
vv           CEP57 MUTATED CEP57 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CEP57 MUTATED     0   2   4   6
  CEP57 WILD-TYPE  22  90 169  91
D46V4, multiclass
    clus
vv   CEP57 MUTATED CEP57 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             4             169
  T4             6              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
  CEP57 MUTATED     4   4   2   2
  CEP57 WILD-TYPE 114 100  75  75
D46V5, multiclass
    clus
vv   CEP57 MUTATED CEP57 WILD-TYPE
  N0             4             114
  N1             4             100
  N2             2              75
  N3             2              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"
D46V6, binary
                 cls
clus                0   1
  CEP57 MUTATED    10   2
  CEP57 WILD-TYPE 336  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP57 MUTATED     10    2
  CEP57 WILD-TYPE  336   27
   clus
vv  CEP57 MUTATED CEP57 WILD-TYPE
  0            10             336
  1             2              27
[1] 2 2
[1] FALSE
D46V7, binary
                 cls
clus                0   1
  CEP57 MUTATED     6   7
  CEP57 WILD-TYPE 139 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP57 MUTATED      6    7
  CEP57 WILD-TYPE  139  241
        clus
vv       CEP57 MUTATED CEP57 WILD-TYPE
  FEMALE             6             139
  MALE               7             241
[1] 2 2
[1] FALSE
D46V8, binary
                 cls
clus                0   1
  CEP57 MUTATED     9   1
  CEP57 WILD-TYPE 283  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP57 MUTATED      9    1
  CEP57 WILD-TYPE  283   58
     clus
vv    CEP57 MUTATED CEP57 WILD-TYPE
  NO              9             283
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CEP57 MUTATED                                          0
  CEP57 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CEP57 MUTATED                                       2
  CEP57 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CEP57 MUTATED                                                        6
  CEP57 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CEP57 MUTATED                                                   1
  CEP57 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CEP57 MUTATED                                                                   3
  CEP57 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CEP57 MUTATED                                                    0
  CEP57 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CEP57 MUTATED                                                  1
  CEP57 WILD-TYPE                                               60
D46V9, multiclass
                                                                   clus
vv                                                                  CEP57 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  CEP57 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CEP57 MUTATED     8   0   2   3
  CEP57 WILD-TYPE 303  14  13  21
D46V10, multiclass
    clus
vv   CEP57 MUTATED CEP57 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             2              13
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CEP57 MUTATED       2                         0
  CEP57 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CEP57 MUTATED                                           0     8
  CEP57 WILD-TYPE                                         1   235
D46V12, multiclass
                                           clus
vv                                          CEP57 MUTATED CEP57 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, binary
                 cls
clus                0   1
  CEP57 MUTATED     0   9
  CEP57 WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP57 MUTATED      0    9
  CEP57 WILD-TYPE    4  301
                        clus
vv                       CEP57 MUTATED CEP57 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(47) Variable = PRRG1 MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2               0   1
  PRRG1 MUTATED     4   3
  PRRG1 WILD-TYPE 226 136
  PRRG1 MUTATED PRRG1 WILD-TYPE 
              7             362 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
              3             136 
$`PRRG1 MUTATED`
TCGA-BR-8078 TCGA-BR-8363 TCGA-CD-A4MG TCGA-CG-5726 TCGA-HU-8602 TCGA-MX-A5UJ 
       29.59         0.26         6.58        28.96        22.32        19.73 
TCGA-VQ-A8P2 
       38.14 

$`PRRG1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  PRRG1 MUTATED PRRG1 WILD-TYPE 
           0.26            0.00 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
          38.14          122.30 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
          22.32           14.12 
[1] "0.3 - 38.1 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D47V2, 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       2       14       39       30        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRRG1 MUTATED           0          3          0          0        1
  PRRG1 WILD-TYPE         3         67         53         32       37
D47V3, multiclass
            clus
vv           PRRG1 MUTATED PRRG1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRRG1 MUTATED     1   1   2   5
  PRRG1 WILD-TYPE  21  91 171  92
D47V4, multiclass
    clus
vv   PRRG1 MUTATED PRRG1 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             2             171
  T4             5              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
  PRRG1 MUTATED     6   2   2   0
  PRRG1 WILD-TYPE 112 102  75  77
D47V5, multiclass
    clus
vv   PRRG1 MUTATED PRRG1 WILD-TYPE
  N0             6             112
  N1             2             102
  N2             2              75
  N3             0              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"
D47V6, binary
                 cls
clus                0   1
  PRRG1 MUTATED    10   0
  PRRG1 WILD-TYPE 336  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED     10    0
  PRRG1 WILD-TYPE  336   29
   clus
vv  PRRG1 MUTATED PRRG1 WILD-TYPE
  0            10             336
  1             0              29
[1] 2 2
[1] FALSE
D47V7, binary
                 cls
clus                0   1
  PRRG1 MUTATED     7   3
  PRRG1 WILD-TYPE 138 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      7    3
  PRRG1 WILD-TYPE  138  245
        clus
vv       PRRG1 MUTATED PRRG1 WILD-TYPE
  FEMALE             7             138
  MALE               3             245
[1] 2 2
[1] FALSE
D47V8, binary
                 cls
clus                0   1
  PRRG1 MUTATED     5   1
  PRRG1 WILD-TYPE 287  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      5    1
  PRRG1 WILD-TYPE  287   58
     clus
vv    PRRG1 MUTATED PRRG1 WILD-TYPE
  NO              5             287
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PRRG1 MUTATED                                          0
  PRRG1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PRRG1 MUTATED                                       2
  PRRG1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRRG1 MUTATED                                                        5
  PRRG1 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PRRG1 MUTATED                                                   1
  PRRG1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRRG1 MUTATED                                                                   1
  PRRG1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PRRG1 MUTATED                                                    0
  PRRG1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PRRG1 MUTATED                                                  1
  PRRG1 WILD-TYPE                                               60
D47V9, multiclass
                                                                   clus
vv                                                                  PRRG1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  PRRG1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRRG1 MUTATED     6   0   0   3
  PRRG1 WILD-TYPE 305  14  15  21
D47V10, multiclass
    clus
vv   PRRG1 MUTATED PRRG1 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PRRG1 MUTATED       2                         0
  PRRG1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRRG1 MUTATED                                           0     7
  PRRG1 WILD-TYPE                                         1   236
D47V12, multiclass
                                           clus
vv                                          PRRG1 MUTATED PRRG1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, binary
                 cls
clus                0   1
  PRRG1 MUTATED     0   8
  PRRG1 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      0    8
  PRRG1 WILD-TYPE    4  302
                        clus
vv                       PRRG1 MUTATED PRRG1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(48) Variable = BCOR MUTATION ANALYSIS
D48V1, survival
                sevent
clus2              0   1
  BCOR MUTATED    17   8
  BCOR WILD-TYPE 213 131
  BCOR MUTATED BCOR WILD-TYPE 
            25            344 
  BCOR MUTATED BCOR WILD-TYPE 
             8            131 
$`BCOR MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6455 TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-7196 
       26.70         6.97        13.87        32.78        19.89        21.90 
TCGA-BR-7707 TCGA-BR-8366 TCGA-BR-8487 TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-4306 
       35.84         0.95         1.12        12.43        11.77         1.02 
TCGA-CG-4455 TCGA-CG-5721 TCGA-CG-5724 TCGA-D7-A6ET TCGA-D7-A6F0 TCGA-F1-A448 
       12.03         6.02        12.03        26.43        22.29        21.27 
TCGA-HJ-7597 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-SW-A7EA 
       26.47        22.82        21.07         0.10         6.51        19.04 
TCGA-VQ-A8P2 
       38.14 

$`BCOR WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-6705 TCGA-BR-6706 TCGA-BR-6709 
       39.12        26.10         9.17        25.61        18.05        12.16 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        44.94         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-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-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-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-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-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-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        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-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-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       22.32         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-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 

  BCOR MUTATED BCOR WILD-TYPE 
           0.1            0.0 
  BCOR MUTATED BCOR WILD-TYPE 
         38.14         122.30 
  BCOR MUTATED BCOR WILD-TYPE 
         19.04          14.22 
[1] "0.1 - 38.1 (19.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D48V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCOR MUTATED         0        0        5        2         6         2
  BCOR WILD-TYPE       2       15       35       28        31        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCOR MUTATED           0          4          3          1        4
  BCOR WILD-TYPE         3         66         50         31       34
D48V3, multiclass
            clus
vv           BCOR MUTATED BCOR WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              5             35
  STAGE II              2             28
  STAGE IIA             6             31
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            4             66
  STAGE IIIB            3             50
  STAGE IIIC            1             31
  STAGE IV              4             34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BCOR MUTATED     0   6  16   6
  BCOR WILD-TYPE  22  86 157  91
D48V4, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  T1            0             22
  T2            6             86
  T3           16            157
  T4            6             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
  BCOR MUTATED    14   6   3   4
  BCOR WILD-TYPE 104  98  74  73
D48V5, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  N0           14            104
  N1            6             98
  N2            3             74
  N3            4             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"
D48V6, binary
                cls
clus               0   1
  BCOR MUTATED    22   3
  BCOR WILD-TYPE 324  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     22    3
  BCOR WILD-TYPE  324   26
   clus
vv  BCOR MUTATED BCOR WILD-TYPE
  0           22            324
  1            3             26
[1] 2 2
[1] FALSE
D48V7, binary
                cls
clus               0   1
  BCOR MUTATED    12  16
  BCOR WILD-TYPE 133 232
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     12   16
  BCOR WILD-TYPE  133  232
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  FEMALE           12            133
  MALE             16            232
[1] 2 2
[1] FALSE
D48V8, binary
                cls
clus               0   1
  BCOR MUTATED    21   3
  BCOR WILD-TYPE 271  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     21    3
  BCOR WILD-TYPE  271   56
     clus
vv    BCOR MUTATED BCOR WILD-TYPE
  NO            21            271
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BCOR MUTATED                                          1
  BCOR WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BCOR MUTATED                                       4
  BCOR WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BCOR MUTATED                                                       13
  BCOR WILD-TYPE                                                    145
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BCOR MUTATED                                                   3
  BCOR WILD-TYPE                                                18
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BCOR MUTATED                                                                   3
  BCOR WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BCOR MUTATED                                                    0
  BCOR WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BCOR MUTATED                                                  4
  BCOR WILD-TYPE                                               57
D48V9, multiclass
                                                                   clus
vv                                                                  BCOR MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  BCOR WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BCOR MUTATED    22   0   2   3
  BCOR WILD-TYPE 289  14  13  21
D48V10, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  R0           22            289
  R1            0             14
  R2            2             13
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BCOR MUTATED       6                         0
  BCOR WILD-TYPE    81                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BCOR MUTATED                                           0    17
  BCOR WILD-TYPE                                         1   226
D48V12, multiclass
                                           clus
vv                                          BCOR MUTATED BCOR WILD-TYPE
  ASIAN                                                6             81
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               17            226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, binary
                cls
clus               0   1
  BCOR MUTATED     1  21
  BCOR WILD-TYPE   3 289
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      1   21
  BCOR WILD-TYPE    3  289
                        clus
vv                       BCOR MUTATED BCOR WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           21            289
[1] 2 2
[1] FALSE

Clustering(49) Variable = KIAA1967 MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                  0   1
  KIAA1967 MUTATED    14   7
  KIAA1967 WILD-TYPE 216 132
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                21                348 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                 7                132 
$`KIAA1967 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 
        6.97        30.90         9.67        34.68        44.94        35.84 
TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8372 TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-5733 
       14.43        32.25        31.27        11.77        15.95        21.07 
TCGA-D7-A6EY TCGA-F1-A448 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GT 
       11.44        21.27        30.51        22.32        22.68         6.51 
TCGA-HU-A4H3 TCGA-SW-A7EA TCGA-VQ-A8P2 
       29.00        19.04        38.14 

$`KIAA1967 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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-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-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 

  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
              6.51               0.00 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
             44.94             122.30 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
            22.320             14.025 
[1] "6.5 - 44.9 (22.3)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.5"
D49V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1967 MUTATED         0        0        2        1         3         3
  KIAA1967 WILD-TYPE       2       15       38       29        34        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1967 MUTATED           1          4          2          3        0
  KIAA1967 WILD-TYPE         2         66         51         29       38
D49V3, multiclass
            clus
vv           KIAA1967 MUTATED KIAA1967 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  2                 38
  STAGE II                  1                 29
  STAGE IIA                 3                 34
  STAGE IIB                 3                 49
  STAGE III                 1                  2
  STAGE IIIA                4                 66
  STAGE IIIB                2                 51
  STAGE IIIC                3                 29
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1967 MUTATED     0   5   8   7
  KIAA1967 WILD-TYPE  22  87 165  90
D49V4, multiclass
    clus
vv   KIAA1967 MUTATED KIAA1967 WILD-TYPE
  T1                0                 22
  T2                5                 87
  T3                8                165
  T4                7                 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
  KIAA1967 MUTATED     7   7   1   5
  KIAA1967 WILD-TYPE 111  97  76  72
D49V5, multiclass
    clus
vv   KIAA1967 MUTATED KIAA1967 WILD-TYPE
  N0                7                111
  N1                7                 97
  N2                1                 76
  N3                5                 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"
D49V6, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED    21   0
  KIAA1967 WILD-TYPE 325  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED     21    0
  KIAA1967 WILD-TYPE  325   29
   clus
vv  KIAA1967 MUTATED KIAA1967 WILD-TYPE
  0               21                325
  1                0                 29
[1] 2 2
[1] FALSE
D49V7, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED    15   7
  KIAA1967 WILD-TYPE 130 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED     15    7
  KIAA1967 WILD-TYPE  130  241
        clus
vv       KIAA1967 MUTATED KIAA1967 WILD-TYPE
  FEMALE               15                130
  MALE                  7                241
[1] 2 2
[1] FALSE
D49V8, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED    17   3
  KIAA1967 WILD-TYPE 275  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED     17    3
  KIAA1967 WILD-TYPE  275   56
     clus
vv    KIAA1967 MUTATED KIAA1967 WILD-TYPE
  NO                17                275
  YES                3                 56
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA1967 MUTATED                                          0
  KIAA1967 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA1967 MUTATED                                       4
  KIAA1967 WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1967 MUTATED                                                       11
  KIAA1967 WILD-TYPE                                                    147
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA1967 MUTATED                                                   3
  KIAA1967 WILD-TYPE                                                18
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1967 MUTATED                                                                   2
  KIAA1967 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA1967 MUTATED                                                    0
  KIAA1967 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA1967 MUTATED                                                  2
  KIAA1967 WILD-TYPE                                               59
D49V9, multiclass
                                                                   clus
vv                                                                  KIAA1967 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  KIAA1967 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1967 MUTATED    15   1   0   4
  KIAA1967 WILD-TYPE 296  13  15  20
D49V10, multiclass
    clus
vv   KIAA1967 MUTATED KIAA1967 WILD-TYPE
  R0               15                296
  R1                1                 13
  R2                0                 15
  RX                4                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1967 MUTATED       5                         0
  KIAA1967 WILD-TYPE    82                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1967 MUTATED                                           0    14
  KIAA1967 WILD-TYPE                                         1   229
D49V12, multiclass
                                           clus
vv                                          KIAA1967 MUTATED KIAA1967 WILD-TYPE
  ASIAN                                                    5                 82
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED     1  17
  KIAA1967 WILD-TYPE   3 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED      1   17
  KIAA1967 WILD-TYPE    3  293
                        clus
vv                       KIAA1967 MUTATED KIAA1967 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               17                293
[1] 2 2
[1] FALSE

Clustering(50) Variable = KIAA1267 MUTATION ANALYSIS
D50V1, survival
                    sevent
clus2                  0   1
  KIAA1267 MUTATED     8   7
  KIAA1267 WILD-TYPE 222 132
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                15                354 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                 7                132 
$`KIAA1267 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6563 TCGA-BR-7703 
       21.99        26.70         6.97        30.90        39.12        36.16 
TCGA-BR-8059 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 
       14.43         0.26        31.27        25.05         1.12        28.14 
TCGA-CD-8536 TCGA-IN-7808 TCGA-VQ-A8P2 
       12.43         3.45        38.14 

$`KIAA1267 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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-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-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-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 

  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
              0.26               0.00 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
             39.12             122.30 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
             25.05              14.07 
[1] "0.3 - 39.1 (25.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D50V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1267 MUTATED         1        1        2        1         1         2
  KIAA1267 WILD-TYPE       1       14       38       29        36        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1267 MUTATED           1          2          0          3        1
  KIAA1267 WILD-TYPE         2         68         53         29       37
D50V3, multiclass
            clus
vv           KIAA1267 MUTATED KIAA1267 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  1                 14
  STAGE IB                  2                 38
  STAGE II                  1                 29
  STAGE IIA                 1                 36
  STAGE IIB                 2                 50
  STAGE III                 1                  2
  STAGE IIIA                2                 68
  STAGE IIIB                0                 53
  STAGE IIIC                3                 29
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1267 MUTATED     2   3   5   7
  KIAA1267 WILD-TYPE  20  89 168  90
D50V4, multiclass
    clus
vv   KIAA1267 MUTATED KIAA1267 WILD-TYPE
  T1                2                 20
  T2                3                 89
  T3                5                168
  T4                7                 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
  KIAA1267 MUTATED     6   7   0   4
  KIAA1267 WILD-TYPE 112  97  77  73
D50V5, multiclass
    clus
vv   KIAA1267 MUTATED KIAA1267 WILD-TYPE
  N0                6                112
  N1                7                 97
  N2                0                 77
  N3                4                 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"
D50V6, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED    15   2
  KIAA1267 WILD-TYPE 331  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED     15    2
  KIAA1267 WILD-TYPE  331   27
   clus
vv  KIAA1267 MUTATED KIAA1267 WILD-TYPE
  0               15                331
  1                2                 27
[1] 2 2
[1] FALSE
D50V7, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED     8  11
  KIAA1267 WILD-TYPE 137 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED      8   11
  KIAA1267 WILD-TYPE  137  237
        clus
vv       KIAA1267 MUTATED KIAA1267 WILD-TYPE
  FEMALE                8                137
  MALE                 11                237
[1] 2 2
[1] FALSE
D50V8, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED    15   1
  KIAA1267 WILD-TYPE 277  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED     15    1
  KIAA1267 WILD-TYPE  277   58
     clus
vv    KIAA1267 MUTATED KIAA1267 WILD-TYPE
  NO                15                277
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA1267 MUTATED                                          0
  KIAA1267 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA1267 MUTATED                                       2
  KIAA1267 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1267 MUTATED                                                       12
  KIAA1267 WILD-TYPE                                                    146
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA1267 MUTATED                                                   1
  KIAA1267 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1267 MUTATED                                                                   3
  KIAA1267 WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA1267 MUTATED                                                    1
  KIAA1267 WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA1267 MUTATED                                                  0
  KIAA1267 WILD-TYPE                                               61
D50V9, multiclass
                                                                   clus
vv                                                                  KIAA1267 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 0
                                                                   clus
vv                                                                  KIAA1267 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1267 MUTATED    13   0   1   4
  KIAA1267 WILD-TYPE 298  14  14  20
D50V10, multiclass
    clus
vv   KIAA1267 MUTATED KIAA1267 WILD-TYPE
  R0               13                298
  R1                0                 14
  R2                1                 14
  RX                4                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1267 MUTATED       1                         1
  KIAA1267 WILD-TYPE    86                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1267 MUTATED                                           0    15
  KIAA1267 WILD-TYPE                                         1   228
D50V12, multiclass
                                           clus
vv                                          KIAA1267 MUTATED KIAA1267 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   15                228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED     0  16
  KIAA1267 WILD-TYPE   4 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED      0   16
  KIAA1267 WILD-TYPE    4  294
                        clus
vv                       KIAA1267 MUTATED KIAA1267 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               16                294
[1] 2 2
[1] FALSE

Clustering(51) Variable = ZNF48 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2               0   1
  ZNF48 MUTATED     9   2
  ZNF48 WILD-TYPE 221 137
  ZNF48 MUTATED ZNF48 WILD-TYPE 
             11             358 
  ZNF48 MUTATED ZNF48 WILD-TYPE 
              2             137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8369 
       31.10        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-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-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-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-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-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 

  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           14.12 
[1] "0.1 - 44.9 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.4"
D51V2, 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       2       15       37       30        34        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF48 MUTATED           0          2          0          1        0
  ZNF48 WILD-TYPE         3         68         53         31       38
D51V3, multiclass
            clus
vv           ZNF48 MUTATED ZNF48 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZNF48 MUTATED     1   3   5   4
  ZNF48 WILD-TYPE  21  89 168  93
D51V4, multiclass
    clus
vv   ZNF48 MUTATED ZNF48 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             5             168
  T4             4              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
  ZNF48 MUTATED     8   2   2   0
  ZNF48 WILD-TYPE 110 102  75  77
D51V5, multiclass
    clus
vv   ZNF48 MUTATED ZNF48 WILD-TYPE
  N0             8             110
  N1             2             102
  N2             2              75
  N3             0              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"
D51V6, binary
                 cls
clus                0   1
  ZNF48 MUTATED    13   0
  ZNF48 WILD-TYPE 333  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF48 MUTATED     13    0
  ZNF48 WILD-TYPE  333   29
   clus
vv  ZNF48 MUTATED ZNF48 WILD-TYPE
  0            13             333
  1             0              29
[1] 2 2
[1] FALSE
D51V7, binary
                 cls
clus                0   1
  ZNF48 MUTATED     9   4
  ZNF48 WILD-TYPE 136 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF48 MUTATED      9    4
  ZNF48 WILD-TYPE  136  244
        clus
vv       ZNF48 MUTATED ZNF48 WILD-TYPE
  FEMALE             9             136
  MALE               4             244
[1] 2 2
[1] FALSE
D51V8, binary
                 cls
clus                0   1
  ZNF48 MUTATED     9   2
  ZNF48 WILD-TYPE 283  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF48 MUTATED      9    2
  ZNF48 WILD-TYPE  283   57
     clus
vv    ZNF48 MUTATED ZNF48 WILD-TYPE
  NO              9             283
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF48 MUTATED                                          0
  ZNF48 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF48 MUTATED                                       2
  ZNF48 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF48 MUTATED                                                        7
  ZNF48 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF48 MUTATED                                                   1
  ZNF48 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF48 MUTATED                                                                   1
  ZNF48 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF48 MUTATED                                                    0
  ZNF48 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF48 MUTATED                                                  2
  ZNF48 WILD-TYPE                                               59
D51V9, multiclass
                                                                   clus
vv                                                                  ZNF48 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  ZNF48 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZNF48 MUTATED    10   0   0   1
  ZNF48 WILD-TYPE 301  14  15  23
D51V10, multiclass
    clus
vv   ZNF48 MUTATED ZNF48 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZNF48 MUTATED       4                         0
  ZNF48 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF48 MUTATED                                           0     8
  ZNF48 WILD-TYPE                                         1   235
D51V12, multiclass
                                           clus
vv                                          ZNF48 MUTATED ZNF48 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, binary
                 cls
clus                0   1
  ZNF48 MUTATED     0  11
  ZNF48 WILD-TYPE   4 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF48 MUTATED      0   11
  ZNF48 WILD-TYPE    4  299
                        clus
vv                       ZNF48 MUTATED ZNF48 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(52) Variable = WASF3 MUTATION ANALYSIS
D52V1, survival
                 sevent
clus2               0   1
  WASF3 MUTATED    14   3
  WASF3 WILD-TYPE 216 136
  WASF3 MUTATED WASF3 WILD-TYPE 
             17             352 
  WASF3 MUTATED WASF3 WILD-TYPE 
              3             136 
$`WASF3 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8682 TCGA-BR-A4CQ 
       26.70        34.68        44.94        35.84        32.58        34.98 
TCGA-CG-4306 TCGA-CG-5728 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-HF-7132 TCGA-HU-A4GT 
        1.02        65.10         5.92        13.78        77.29         6.51 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
        6.58         2.10        38.14        37.22        22.19 

$`WASF3 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-8683 TCGA-BR-8686 
        7.53        26.73        24.79        31.96         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-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-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-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-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        0.10        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-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       13.02        43.36        37.41        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 

  WASF3 MUTATED WASF3 WILD-TYPE 
           1.02            0.00 
  WASF3 MUTATED WASF3 WILD-TYPE 
          77.29          122.30 
  WASF3 MUTATED WASF3 WILD-TYPE 
          32.58           14.07 
[1] "1.0 - 77.3 (32.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3"  
D52V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WASF3 MUTATED         1        0        3        1         3         4
  WASF3 WILD-TYPE       1       15       37       29        34        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WASF3 MUTATED           0          3          2          1        1
  WASF3 WILD-TYPE         3         67         51         31       37
D52V3, multiclass
            clus
vv           WASF3 MUTATED WASF3 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WASF3 MUTATED     1   4   8   6
  WASF3 WILD-TYPE  21  88 165  91
D52V4, multiclass
    clus
vv   WASF3 MUTATED WASF3 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             8             165
  T4             6              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
  WASF3 MUTATED     8   7   1   3
  WASF3 WILD-TYPE 110  97  76  74
D52V5, multiclass
    clus
vv   WASF3 MUTATED WASF3 WILD-TYPE
  N0             8             110
  N1             7              97
  N2             1              76
  N3             3              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"
D52V6, binary
                 cls
clus                0   1
  WASF3 MUTATED    17   1
  WASF3 WILD-TYPE 329  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED     17    1
  WASF3 WILD-TYPE  329   28
   clus
vv  WASF3 MUTATED WASF3 WILD-TYPE
  0            17             329
  1             1              28
[1] 2 2
[1] FALSE
D52V7, binary
                 cls
clus                0   1
  WASF3 MUTATED     7  12
  WASF3 WILD-TYPE 138 236
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED      7   12
  WASF3 WILD-TYPE  138  236
        clus
vv       WASF3 MUTATED WASF3 WILD-TYPE
  FEMALE             7             138
  MALE              12             236
[1] 2 2
[1] FALSE
D52V8, binary
                 cls
clus                0   1
  WASF3 MUTATED    12   4
  WASF3 WILD-TYPE 280  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED     12    4
  WASF3 WILD-TYPE  280   55
     clus
vv    WASF3 MUTATED WASF3 WILD-TYPE
  NO             12             280
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  WASF3 MUTATED                                          0
  WASF3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  WASF3 MUTATED                                       3
  WASF3 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WASF3 MUTATED                                                        7
  WASF3 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  WASF3 MUTATED                                                   3
  WASF3 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WASF3 MUTATED                                                                   2
  WASF3 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  WASF3 MUTATED                                                    0
  WASF3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  WASF3 MUTATED                                                  4
  WASF3 WILD-TYPE                                               57
D52V9, multiclass
                                                                   clus
vv                                                                  WASF3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  WASF3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WASF3 MUTATED    18   0   1   0
  WASF3 WILD-TYPE 293  14  14  24
D52V10, multiclass
    clus
vv   WASF3 MUTATED WASF3 WILD-TYPE
  R0            18             293
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  WASF3 MUTATED       4                         1
  WASF3 WILD-TYPE    83                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WASF3 MUTATED                                           0    10
  WASF3 WILD-TYPE                                         1   233
D52V12, multiclass
                                           clus
vv                                          WASF3 MUTATED WASF3 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, binary
                 cls
clus                0   1
  WASF3 MUTATED     0  12
  WASF3 WILD-TYPE   4 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED      0   12
  WASF3 WILD-TYPE    4  298
                        clus
vv                       WASF3 MUTATED WASF3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(53) Variable = NLK MUTATION ANALYSIS
D53V1, survival
               sevent
clus2             0   1
  NLK MUTATED     7   5
  NLK WILD-TYPE 223 134
  NLK MUTATED NLK WILD-TYPE 
           12           357 
  NLK MUTATED NLK WILD-TYPE 
            5           134 
$`NLK MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7715 TCGA-BR-8360 TCGA-BR-8363 
       21.99         6.97        34.68        33.63         6.18         0.26 
TCGA-BR-8368 TCGA-BR-8372 TCGA-CD-A4MG TCGA-CG-5725 TCGA-HU-A4G8 TCGA-HU-A4GN 
        4.31        31.27         6.58        15.02        22.68        29.98 

$`NLK WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-D7-6526 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-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 

  NLK MUTATED NLK WILD-TYPE 
         0.26          0.00 
  NLK MUTATED NLK WILD-TYPE 
        34.68        122.30 
  NLK MUTATED NLK WILD-TYPE 
       18.505        14.170 
[1] "0.3 - 34.7 (18.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D53V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NLK MUTATED         0        0        3        0         5         1
  NLK WILD-TYPE       2       15       37       30        32        51
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NLK MUTATED           0          2          0          1        1
  NLK WILD-TYPE         3         68         53         31       37
D53V3, multiclass
            clus
vv           NLK MUTATED NLK WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             3            37
  STAGE II             0            30
  STAGE IIA            5            32
  STAGE IIB            1            51
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           0            53
  STAGE IIIC           1            31
  STAGE IV             1            37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NLK MUTATED     0   4   7   3
  NLK WILD-TYPE  22  88 166  94
D53V4, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  T1           0            22
  T2           4            88
  T3           7           166
  T4           3            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
  NLK MUTATED     8   4   0   1
  NLK WILD-TYPE 110 100  77  76
D53V5, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  N0           8           110
  N1           4           100
  N2           0            77
  N3           1            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"
D53V6, binary
               cls
clus              0   1
  NLK MUTATED    11   1
  NLK WILD-TYPE 335  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED     11    1
  NLK WILD-TYPE  335   28
   clus
vv  NLK MUTATED NLK WILD-TYPE
  0          11           335
  1           1            28
[1] 2 2
[1] FALSE
D53V7, binary
               cls
clus              0   1
  NLK MUTATED     7   7
  NLK WILD-TYPE 138 241
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED      7    7
  NLK WILD-TYPE  138  241
        clus
vv       NLK MUTATED NLK WILD-TYPE
  FEMALE           7           138
  MALE             7           241
[1] 2 2
[1] FALSE
D53V8, binary
               cls
clus              0   1
  NLK MUTATED    12   0
  NLK WILD-TYPE 280  59
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED     12    0
  NLK WILD-TYPE  280   59
     clus
vv    NLK MUTATED NLK WILD-TYPE
  NO           12           280
  YES           0            59
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NLK MUTATED                                          0
  NLK WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NLK MUTATED                                       2
  NLK WILD-TYPE                                    68
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NLK MUTATED                                                        9
  NLK WILD-TYPE                                                    149
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NLK MUTATED                                                   0
  NLK WILD-TYPE                                                21
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NLK MUTATED                                                                   2
  NLK WILD-TYPE                                                                66
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NLK MUTATED                                                    0
  NLK WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NLK MUTATED                                                  1
  NLK WILD-TYPE                                               60
D53V9, multiclass
                                                                   clus
vv                                                                  NLK MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            1
                                                                   clus
vv                                                                  NLK WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  NLK MUTATED     8   0   1   3
  NLK WILD-TYPE 303  14  14  21
D53V10, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  R0           8           303
  R1           0            14
  R2           1            14
  RX           3            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  NLK MUTATED       3                         0
  NLK WILD-TYPE    84                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NLK MUTATED                                           0     9
  NLK WILD-TYPE                                         1   234
D53V12, multiclass
                                           clus
vv                                          NLK MUTATED NLK WILD-TYPE
  ASIAN                                               3            84
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               9           234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, binary
               cls
clus              0   1
  NLK MUTATED     0  12
  NLK WILD-TYPE   4 298
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED      0   12
  NLK WILD-TYPE    4  298
                        clus
vv                       NLK MUTATED NLK WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          12           298
[1] 2 2
[1] FALSE

Clustering(54) Variable = CYP27B1 MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  CYP27B1 MUTATED     4   5
  CYP27B1 WILD-TYPE 226 134
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                9               360 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                5               134 
$`CYP27B1 MUTATED`
TCGA-BR-4184 TCGA-BR-8059 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5728 TCGA-CG-5733 
        6.97        14.43        31.96         6.58        65.10        21.07 
TCGA-D7-A6EY TCGA-HU-A4GX TCGA-HU-A4H4 
       11.44        20.25        23.84 

$`CYP27B1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-F1-6874 
        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-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-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 

  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
             6.58              0.00 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
             65.1             122.3 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
            20.25             14.12 
[1] "6.6 - 65.1 (20.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D54V2, 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       2       15       39       30        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP27B1 MUTATED           1          2          1          1        1
  CYP27B1 WILD-TYPE         2         68         52         31       37
D54V3, multiclass
            clus
vv           CYP27B1 MUTATED CYP27B1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                1                 2
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYP27B1 MUTATED     0   3   3   3
  CYP27B1 WILD-TYPE  22  89 170  94
D54V4, multiclass
    clus
vv   CYP27B1 MUTATED CYP27B1 WILD-TYPE
  T1               0                22
  T2               3                89
  T3               3               170
  T4               3                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
  CYP27B1 MUTATED     2   2   4   1
  CYP27B1 WILD-TYPE 116 102  73  76
D54V5, multiclass
    clus
vv   CYP27B1 MUTATED CYP27B1 WILD-TYPE
  N0               2               116
  N1               2               102
  N2               4                73
  N3               1                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"
D54V6, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     7   1
  CYP27B1 WILD-TYPE 339  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      7    1
  CYP27B1 WILD-TYPE  339   28
   clus
vv  CYP27B1 MUTATED CYP27B1 WILD-TYPE
  0               7               339
  1               1                28
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     5   4
  CYP27B1 WILD-TYPE 140 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      5    4
  CYP27B1 WILD-TYPE  140  244
        clus
vv       CYP27B1 MUTATED CYP27B1 WILD-TYPE
  FEMALE               5               140
  MALE                 4               244
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     8   0
  CYP27B1 WILD-TYPE 284  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      8    0
  CYP27B1 WILD-TYPE  284   59
     clus
vv    CYP27B1 MUTATED CYP27B1 WILD-TYPE
  NO                8               284
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CYP27B1 MUTATED                                          0
  CYP27B1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CYP27B1 MUTATED                                       2
  CYP27B1 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CYP27B1 MUTATED                                                        1
  CYP27B1 WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CYP27B1 MUTATED                                                   0
  CYP27B1 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CYP27B1 MUTATED                                                                   3
  CYP27B1 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CYP27B1 MUTATED                                                    0
  CYP27B1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CYP27B1 MUTATED                                                  3
  CYP27B1 WILD-TYPE                                               58
D54V9, multiclass
                                                                   clus
vv                                                                  CYP27B1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  CYP27B1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CYP27B1 MUTATED     7   0   0   1
  CYP27B1 WILD-TYPE 304  14  15  23
D54V10, multiclass
    clus
vv   CYP27B1 MUTATED CYP27B1 WILD-TYPE
  R0               7               304
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CYP27B1 MUTATED       4                         0
  CYP27B1 WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CYP27B1 MUTATED                                           0     3
  CYP27B1 WILD-TYPE                                         1   240
D54V12, multiclass
                                           clus
vv                                          CYP27B1 MUTATED CYP27B1 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     0   7
  CYP27B1 WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      0    7
  CYP27B1 WILD-TYPE    4  303
                        clus
vv                       CYP27B1 MUTATED CYP27B1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(55) Variable = C14ORF43 MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                  0   1
  C14ORF43 MUTATED    18   5
  C14ORF43 WILD-TYPE 212 134
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                23                346 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                 5                134 
$`C14ORF43 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        0.10        20.25         0.26         2.10        12.95        23.84 
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 

  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
              6.02               0.00 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
             74.53             122.30 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
             22.68              14.07 
[1] "6.0 - 74.5 (22.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.3"
D55V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C14ORF43 MUTATED         0        0        3        1         4         4
  C14ORF43 WILD-TYPE       2       15       37       29        33        48
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF43 MUTATED           1          2          3          2        4
  C14ORF43 WILD-TYPE         2         68         50         30       34
D55V3, multiclass
            clus
vv           C14ORF43 MUTATED C14ORF43 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  3                 37
  STAGE II                  1                 29
  STAGE IIA                 4                 33
  STAGE IIB                 4                 48
  STAGE III                 1                  2
  STAGE IIIA                2                 68
  STAGE IIIB                3                 50
  STAGE IIIC                2                 30
  STAGE IV                  4                 34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C14ORF43 MUTATED     1   5  11   9
  C14ORF43 WILD-TYPE  21  87 162  88
D55V4, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  T1                1                 21
  T2                5                 87
  T3               11                162
  T4                9                 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
  C14ORF43 MUTATED     9   8   2   5
  C14ORF43 WILD-TYPE 109  96  75  72
D55V5, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  N0                9                109
  N1                8                 96
  N2                2                 75
  N3                5                 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"
D55V6, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    22   2
  C14ORF43 WILD-TYPE 324  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     22    2
  C14ORF43 WILD-TYPE  324   27
   clus
vv  C14ORF43 MUTATED C14ORF43 WILD-TYPE
  0               22                324
  1                2                 27
[1] 2 2
[1] FALSE
D55V7, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    16  10
  C14ORF43 WILD-TYPE 129 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     16   10
  C14ORF43 WILD-TYPE  129  238
        clus
vv       C14ORF43 MUTATED C14ORF43 WILD-TYPE
  FEMALE               16                129
  MALE                 10                238
[1] 2 2
[1] FALSE
D55V8, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    20   1
  C14ORF43 WILD-TYPE 272  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     20    1
  C14ORF43 WILD-TYPE  272   58
     clus
vv    C14ORF43 MUTATED C14ORF43 WILD-TYPE
  NO                20                272
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C14ORF43 MUTATED                                          1
  C14ORF43 WILD-TYPE                                        7
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C14ORF43 MUTATED                                       5
  C14ORF43 WILD-TYPE                                    65
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C14ORF43 MUTATED                                                       11
  C14ORF43 WILD-TYPE                                                    147
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C14ORF43 MUTATED                                                   1
  C14ORF43 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C14ORF43 MUTATED                                                                   3
  C14ORF43 WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C14ORF43 MUTATED                                                    1
  C14ORF43 WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C14ORF43 MUTATED                                                  4
  C14ORF43 WILD-TYPE                                               57
D55V9, multiclass
                                                                   clus
vv                                                                  C14ORF43 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 4
                                                                   clus
vv                                                                  C14ORF43 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C14ORF43 MUTATED    20   0   0   4
  C14ORF43 WILD-TYPE 291  14  15  20
D55V10, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  R0               20                291
  R1                0                 14
  R2                0                 15
  RX                4                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C14ORF43 MUTATED      10                         0
  C14ORF43 WILD-TYPE    77                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C14ORF43 MUTATED                                           0    14
  C14ORF43 WILD-TYPE                                         1   229
D55V12, multiclass
                                           clus
vv                                          C14ORF43 MUTATED C14ORF43 WILD-TYPE
  ASIAN                                                   10                 77
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V13, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED     1  22
  C14ORF43 WILD-TYPE   3 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED      1   22
  C14ORF43 WILD-TYPE    3  288
                        clus
vv                       C14ORF43 MUTATED C14ORF43 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               22                288
[1] 2 2
[1] FALSE

Clustering(56) Variable = PRSS36 MUTATION ANALYSIS
D56V1, survival
                  sevent
clus2                0   1
  PRSS36 MUTATED     6   9
  PRSS36 WILD-TYPE 224 130
  PRSS36 MUTATED PRSS36 WILD-TYPE 
              15              354 
  PRSS36 MUTATED PRSS36 WILD-TYPE 
               9              130 
$`PRSS36 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  PRSS36 MUTATED PRSS36 WILD-TYPE 
             0.1              0.0 
  PRSS36 MUTATED PRSS36 WILD-TYPE 
            65.1            122.3 
  PRSS36 MUTATED PRSS36 WILD-TYPE 
           16.14            14.12 
[1] "0.1 - 65.1 (16.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D56V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRSS36 MUTATED         0        1        2        1         2         2
  PRSS36 WILD-TYPE       2       14       38       29        35        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRSS36 MUTATED           0          1          2          2        1
  PRSS36 WILD-TYPE         3         69         51         30       37
D56V3, multiclass
            clus
vv           PRSS36 MUTATED PRSS36 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              2               51
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PRSS36 MUTATED     1   5   6   3
  PRSS36 WILD-TYPE  21  87 167  94
D56V4, multiclass
    clus
vv   PRSS36 MUTATED PRSS36 WILD-TYPE
  T1              1               21
  T2              5               87
  T3              6              167
  T4              3               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
  PRSS36 MUTATED     6   4   3   2
  PRSS36 WILD-TYPE 112 100  74  75
D56V5, multiclass
    clus
vv   PRSS36 MUTATED PRSS36 WILD-TYPE
  N0              6              112
  N1              4              100
  N2              3               74
  N3              2               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"
D56V6, binary
                  cls
clus                 0   1
  PRSS36 MUTATED    15   1
  PRSS36 WILD-TYPE 331  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS36 MUTATED     15    1
  PRSS36 WILD-TYPE  331   28
   clus
vv  PRSS36 MUTATED PRSS36 WILD-TYPE
  0             15              331
  1              1               28
[1] 2 2
[1] FALSE
D56V7, binary
                  cls
clus                 0   1
  PRSS36 MUTATED     9   7
  PRSS36 WILD-TYPE 136 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS36 MUTATED      9    7
  PRSS36 WILD-TYPE  136  241
        clus
vv       PRSS36 MUTATED PRSS36 WILD-TYPE
  FEMALE              9              136
  MALE                7              241
[1] 2 2
[1] FALSE
D56V8, binary
                  cls
clus                 0   1
  PRSS36 MUTATED    12   0
  PRSS36 WILD-TYPE 280  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS36 MUTATED     12    0
  PRSS36 WILD-TYPE  280   59
     clus
vv    PRSS36 MUTATED PRSS36 WILD-TYPE
  NO              12              280
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PRSS36 MUTATED                                          0
  PRSS36 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PRSS36 MUTATED                                       0
  PRSS36 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRSS36 MUTATED                                                       10
  PRSS36 WILD-TYPE                                                    148
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PRSS36 MUTATED                                                   0
  PRSS36 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRSS36 MUTATED                                                                   3
  PRSS36 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PRSS36 MUTATED                                                    0
  PRSS36 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PRSS36 MUTATED                                                  3
  PRSS36 WILD-TYPE                                               58
D56V9, multiclass
                                                                   clus
vv                                                                  PRSS36 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  PRSS36 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PRSS36 MUTATED    13   0   1   2
  PRSS36 WILD-TYPE 298  14  14  22
D56V10, multiclass
    clus
vv   PRSS36 MUTATED PRSS36 WILD-TYPE
  R0             13              298
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PRSS36 MUTATED       1                         0
  PRSS36 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRSS36 MUTATED                                           0    10
  PRSS36 WILD-TYPE                                         1   233
D56V12, multiclass
                                           clus
vv                                          PRSS36 MUTATED PRSS36 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, binary
                  cls
clus                 0   1
  PRSS36 MUTATED     0  11
  PRSS36 WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS36 MUTATED      0   11
  PRSS36 WILD-TYPE    4  299
                        clus
vv                       PRSS36 MUTATED PRSS36 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(57) Variable = FZD3 MUTATION ANALYSIS
D57V1, survival
                sevent
clus2              0   1
  FZD3 MUTATED     5   5
  FZD3 WILD-TYPE 225 134
  FZD3 MUTATED FZD3 WILD-TYPE 
            10            359 
  FZD3 MUTATED FZD3 WILD-TYPE 
             5            134 
$`FZD3 MUTATED`
TCGA-BR-4184 TCGA-BR-6458 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-A4QL 
        6.97        19.33        29.59         6.18         4.31        16.14 
TCGA-CD-A4MG TCGA-CG-5723 TCGA-D7-A6EY TCGA-MX-A5UJ 
        6.58       105.07        11.44        19.73 

$`FZD3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  FZD3 MUTATED FZD3 WILD-TYPE 
          4.31           0.00 
  FZD3 MUTATED FZD3 WILD-TYPE 
        105.07         122.30 
  FZD3 MUTATED FZD3 WILD-TYPE 
         13.79          14.27 
[1] "4.3 - 105.1 (13.8)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D57V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FZD3 MUTATED         0        0        1        1         2         3
  FZD3 WILD-TYPE       2       15       39       29        35        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FZD3 MUTATED           0          2          2          0        0
  FZD3 WILD-TYPE         3         68         51         32       38
D57V3, multiclass
            clus
vv           FZD3 MUTATED FZD3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            2             51
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FZD3 MUTATED     0   2   7   2
  FZD3 WILD-TYPE  22  90 166  95
D57V4, multiclass
    clus
vv   FZD3 MUTATED FZD3 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            7            166
  T4            2             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
  FZD3 MUTATED     5   3   1   2
  FZD3 WILD-TYPE 113 101  76  75
D57V5, multiclass
    clus
vv   FZD3 MUTATED FZD3 WILD-TYPE
  N0            5            113
  N1            3            101
  N2            1             76
  N3            2             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"
D57V6, binary
                cls
clus               0   1
  FZD3 MUTATED    10   0
  FZD3 WILD-TYPE 336  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED     10    0
  FZD3 WILD-TYPE  336   29
   clus
vv  FZD3 MUTATED FZD3 WILD-TYPE
  0           10            336
  1            0             29
[1] 2 2
[1] FALSE
D57V7, binary
                cls
clus               0   1
  FZD3 MUTATED     6   5
  FZD3 WILD-TYPE 139 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED      6    5
  FZD3 WILD-TYPE  139  243
        clus
vv       FZD3 MUTATED FZD3 WILD-TYPE
  FEMALE            6            139
  MALE              5            243
[1] 2 2
[1] FALSE
D57V8, binary
                cls
clus               0   1
  FZD3 MUTATED    11   0
  FZD3 WILD-TYPE 281  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED     11    0
  FZD3 WILD-TYPE  281   59
     clus
vv    FZD3 MUTATED FZD3 WILD-TYPE
  NO            11            281
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FZD3 MUTATED                                          0
  FZD3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FZD3 MUTATED                                       1
  FZD3 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FZD3 MUTATED                                                        6
  FZD3 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FZD3 MUTATED                                                   0
  FZD3 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FZD3 MUTATED                                                                   2
  FZD3 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FZD3 MUTATED                                                    0
  FZD3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FZD3 MUTATED                                                  2
  FZD3 WILD-TYPE                                               59
D57V9, multiclass
                                                                   clus
vv                                                                  FZD3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  FZD3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FZD3 MUTATED     9   0   0   1
  FZD3 WILD-TYPE 302  14  15  23
D57V10, multiclass
    clus
vv   FZD3 MUTATED FZD3 WILD-TYPE
  R0            9            302
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FZD3 MUTATED       1                         0
  FZD3 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FZD3 MUTATED                                           0     9
  FZD3 WILD-TYPE                                         1   234
D57V12, multiclass
                                           clus
vv                                          FZD3 MUTATED FZD3 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V13, binary
                cls
clus               0   1
  FZD3 MUTATED     0  10
  FZD3 WILD-TYPE   4 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED      0   10
  FZD3 WILD-TYPE    4  300
                        clus
vv                       FZD3 MUTATED FZD3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           10            300
[1] 2 2
[1] FALSE

Clustering(58) Variable = NFASC MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2               0   1
  NFASC MUTATED    21   5
  NFASC WILD-TYPE 209 134
  NFASC MUTATED NFASC WILD-TYPE 
             26             343 
  NFASC MUTATED NFASC WILD-TYPE 
              5             134 
$`NFASC MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15         9.86        26.70        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-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-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-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-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-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-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-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-D7-6519 
       69.04         7.99        25.71        12.66        20.91        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-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-A4G3 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
        5.59        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-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-A7ZF TCGA-R5-A7ZR TCGA-R5-A804 
       19.73        14.04        45.67         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 

  NFASC MUTATED NFASC WILD-TYPE 
           1.12            0.00 
  NFASC MUTATED NFASC WILD-TYPE 
          77.29          122.30 
  NFASC MUTATED NFASC WILD-TYPE 
          20.10           14.04 
[1] "1.1 - 77.3 (20.1)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "2.5"
D58V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NFASC MUTATED         0        1        3        3         3         8
  NFASC WILD-TYPE       2       14       37       27        34        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFASC MUTATED           0          4          1          1        3
  NFASC WILD-TYPE         3         66         52         31       35
D58V3, multiclass
            clus
vv           NFASC MUTATED NFASC WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               3              27
  STAGE IIA              3              34
  STAGE IIB              8              44
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NFASC MUTATED     1   8  10   9
  NFASC WILD-TYPE  21  84 163  88
D58V4, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  T1             1              21
  T2             8              84
  T3            10             163
  T4             9              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
  NFASC MUTATED    10  11   3   3
  NFASC WILD-TYPE 108  93  74  74
D58V5, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  N0            10             108
  N1            11              93
  N2             3              74
  N3             3              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"
D58V6, binary
                 cls
clus                0   1
  NFASC MUTATED    28   2
  NFASC WILD-TYPE 318  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     28    2
  NFASC WILD-TYPE  318   27
   clus
vv  NFASC MUTATED NFASC WILD-TYPE
  0            28             318
  1             2              27
[1] 2 2
[1] FALSE
D58V7, binary
                 cls
clus                0   1
  NFASC MUTATED    15  16
  NFASC WILD-TYPE 130 232
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     15   16
  NFASC WILD-TYPE  130  232
        clus
vv       NFASC MUTATED NFASC WILD-TYPE
  FEMALE            15             130
  MALE              16             232
[1] 2 2
[1] FALSE
D58V8, binary
                 cls
clus                0   1
  NFASC MUTATED    24   3
  NFASC WILD-TYPE 268  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     24    3
  NFASC WILD-TYPE  268   56
     clus
vv    NFASC MUTATED NFASC WILD-TYPE
  NO             24             268
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NFASC MUTATED                                          0
  NFASC WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NFASC MUTATED                                       7
  NFASC WILD-TYPE                                    63
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NFASC MUTATED                                                       12
  NFASC WILD-TYPE                                                    146
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NFASC MUTATED                                                   2
  NFASC WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NFASC MUTATED                                                                   6
  NFASC WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NFASC MUTATED                                                    2
  NFASC WILD-TYPE                                                  3
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NFASC MUTATED                                                  2
  NFASC WILD-TYPE                                               59
D58V9, multiclass
                                                                   clus
vv                                                                  NFASC MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  NFASC WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NFASC MUTATED    23   1   0   4
  NFASC WILD-TYPE 288  13  15  20
D58V10, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  R0            23             288
  R1             1              13
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NFASC MUTATED       7                         1
  NFASC WILD-TYPE    80                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NFASC MUTATED                                           0    17
  NFASC WILD-TYPE                                         1   226
D58V12, multiclass
                                           clus
vv                                          NFASC MUTATED NFASC WILD-TYPE
  ASIAN                                                 7              80
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, binary
                 cls
clus                0   1
  NFASC MUTATED     1  23
  NFASC WILD-TYPE   3 287
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED      1   23
  NFASC WILD-TYPE    3  287
                        clus
vv                       NFASC MUTATED NFASC WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            23             287
[1] 2 2
[1] FALSE

Clustering(59) Variable = GRK4 MUTATION ANALYSIS
D59V1, survival
                sevent
clus2              0   1
  GRK4 MUTATED     8   2
  GRK4 WILD-TYPE 222 137
  GRK4 MUTATED GRK4 WILD-TYPE 
            10            359 
  GRK4 MUTATED GRK4 WILD-TYPE 
             2            137 
$`GRK4 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8487 
       26.70         6.97        34.68         6.18        31.10         1.12 
TCGA-CG-5721 TCGA-FP-A4BE TCGA-VQ-A8P2 TCGA-VQ-AA64 
        6.02        11.08        38.14        18.41 

$`GRK4 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  GRK4 MUTATED GRK4 WILD-TYPE 
          1.12           0.00 
  GRK4 MUTATED GRK4 WILD-TYPE 
         38.14         122.30 
  GRK4 MUTATED GRK4 WILD-TYPE 
        14.745         14.270 
[1] "1.1 - 38.1 (14.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.9"
D59V2, 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       2       15       39       30        33        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GRK4 MUTATED           0          2          1          1        1
  GRK4 WILD-TYPE         3         68         52         31       37
D59V3, multiclass
            clus
vv           GRK4 MUTATED GRK4 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             4             33
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GRK4 MUTATED     0   1   6   4
  GRK4 WILD-TYPE  22  91 167  93
D59V4, multiclass
    clus
vv   GRK4 MUTATED GRK4 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            6            167
  T4            4             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
  GRK4 MUTATED     6   3   2   0
  GRK4 WILD-TYPE 112 101  75  77
D59V5, multiclass
    clus
vv   GRK4 MUTATED GRK4 WILD-TYPE
  N0            6            112
  N1            3            101
  N2            2             75
  N3            0             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"
D59V6, binary
                cls
clus               0   1
  GRK4 MUTATED    10   0
  GRK4 WILD-TYPE 336  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK4 MUTATED     10    0
  GRK4 WILD-TYPE  336   29
   clus
vv  GRK4 MUTATED GRK4 WILD-TYPE
  0           10            336
  1            0             29
[1] 2 2
[1] FALSE
D59V7, binary
                cls
clus               0   1
  GRK4 MUTATED     4   7
  GRK4 WILD-TYPE 141 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK4 MUTATED      4    7
  GRK4 WILD-TYPE  141  241
        clus
vv       GRK4 MUTATED GRK4 WILD-TYPE
  FEMALE            4            141
  MALE              7            241
[1] 2 2
[1] FALSE
D59V8, binary
                cls
clus               0   1
  GRK4 MUTATED     7   3
  GRK4 WILD-TYPE 285  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK4 MUTATED      7    3
  GRK4 WILD-TYPE  285   56
     clus
vv    GRK4 MUTATED GRK4 WILD-TYPE
  NO             7            285
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GRK4 MUTATED                                          0
  GRK4 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GRK4 MUTATED                                       1
  GRK4 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GRK4 MUTATED                                                        5
  GRK4 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GRK4 MUTATED                                                   1
  GRK4 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GRK4 MUTATED                                                                   4
  GRK4 WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GRK4 MUTATED                                                    0
  GRK4 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GRK4 MUTATED                                                  0
  GRK4 WILD-TYPE                                               61
D59V9, multiclass
                                                                   clus
vv                                                                  GRK4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  GRK4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GRK4 MUTATED    10   0   0   1
  GRK4 WILD-TYPE 301  14  15  23
D59V10, multiclass
    clus
vv   GRK4 MUTATED GRK4 WILD-TYPE
  R0           10            301
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GRK4 MUTATED       0                         1
  GRK4 WILD-TYPE    87                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GRK4 MUTATED                                           0     8
  GRK4 WILD-TYPE                                         1   235
D59V12, multiclass
                                           clus
vv                                          GRK4 MUTATED GRK4 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, binary
                cls
clus               0   1
  GRK4 MUTATED     0   7
  GRK4 WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK4 MUTATED      0    7
  GRK4 WILD-TYPE    4  303
                        clus
vv                       GRK4 MUTATED GRK4 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(60) Variable = ATXN2L MUTATION ANALYSIS
D60V1, survival
                  sevent
clus2                0   1
  ATXN2L MUTATED    14   7
  ATXN2L WILD-TYPE 216 132
  ATXN2L MUTATED ATXN2L WILD-TYPE 
              21              348 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
               7              132 
$`ATXN2L MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-8059 TCGA-BR-8078 
       21.99        34.68        32.78        36.16        14.43        29.59 
TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8487 TCGA-CD-5813 TCGA-CD-A4MI 
       29.42        31.10        31.27         1.12        12.39        11.77 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4465 TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4GN 
       12.62        20.02         9.01        11.44        22.32        29.98 
TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-MX-A5UJ 
        6.51        29.00        19.73 

$`ATXN2L WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-CG-4301 
       11.31        12.43        11.61         6.58        12.20         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-D7-5578 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-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-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-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 

  ATXN2L MUTATED ATXN2L WILD-TYPE 
            1.12             0.00 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
           36.16           122.30 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
          21.990           14.055 
[1] "1.1 - 36.2 (22.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D60V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATXN2L MUTATED         0        1        1        2         5         2
  ATXN2L WILD-TYPE       2       14       39       28        32        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATXN2L MUTATED           1          2          2          3        2
  ATXN2L WILD-TYPE         2         68         51         29       36
D60V3, multiclass
            clus
vv           ATXN2L MUTATED ATXN2L WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               5               32
  STAGE IIB               2               50
  STAGE III               1                2
  STAGE IIIA              2               68
  STAGE IIIB              2               51
  STAGE IIIC              3               29
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATXN2L MUTATED     2   2  10   8
  ATXN2L WILD-TYPE  20  90 163  89
D60V4, multiclass
    clus
vv   ATXN2L MUTATED ATXN2L WILD-TYPE
  T1              2               20
  T2              2               90
  T3             10              163
  T4              8               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
  ATXN2L MUTATED    10   5   3   4
  ATXN2L WILD-TYPE 108  99  74  73
D60V5, multiclass
    clus
vv   ATXN2L MUTATED ATXN2L WILD-TYPE
  N0             10              108
  N1              5               99
  N2              3               74
  N3              4               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"
D60V6, binary
                  cls
clus                 0   1
  ATXN2L MUTATED    21   2
  ATXN2L WILD-TYPE 325  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED     21    2
  ATXN2L WILD-TYPE  325   27
   clus
vv  ATXN2L MUTATED ATXN2L WILD-TYPE
  0             21              325
  1              2               27
[1] 2 2
[1] FALSE
D60V7, binary
                  cls
clus                 0   1
  ATXN2L MUTATED    14   9
  ATXN2L WILD-TYPE 131 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED     14    9
  ATXN2L WILD-TYPE  131  239
        clus
vv       ATXN2L MUTATED ATXN2L WILD-TYPE
  FEMALE             14              131
  MALE                9              239
[1] 2 2
[1] FALSE
D60V8, binary
                  cls
clus                 0   1
  ATXN2L MUTATED    18   0
  ATXN2L WILD-TYPE 274  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED     18    0
  ATXN2L WILD-TYPE  274   59
     clus
vv    ATXN2L MUTATED ATXN2L WILD-TYPE
  NO              18              274
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ATXN2L MUTATED                                          0
  ATXN2L WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ATXN2L MUTATED                                       3
  ATXN2L WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATXN2L MUTATED                                                       12
  ATXN2L WILD-TYPE                                                    146
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ATXN2L MUTATED                                                   1
  ATXN2L WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATXN2L MUTATED                                                                   2
  ATXN2L WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ATXN2L MUTATED                                                    1
  ATXN2L WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ATXN2L MUTATED                                                  4
  ATXN2L WILD-TYPE                                               57
D60V9, multiclass
                                                                   clus
vv                                                                  ATXN2L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  ATXN2L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATXN2L MUTATED    16   0   2   2
  ATXN2L WILD-TYPE 295  14  13  22
D60V10, multiclass
    clus
vv   ATXN2L MUTATED ATXN2L WILD-TYPE
  R0             16              295
  R1              0               14
  R2              2               13
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ATXN2L MUTATED       7                         0
  ATXN2L WILD-TYPE    80                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATXN2L MUTATED                                           0    13
  ATXN2L WILD-TYPE                                         1   230
D60V12, multiclass
                                           clus
vv                                          ATXN2L MUTATED ATXN2L WILD-TYPE
  ASIAN                                                  7               80
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, binary
                  cls
clus                 0   1
  ATXN2L MUTATED     0  20
  ATXN2L WILD-TYPE   4 290
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED      0   20
  ATXN2L WILD-TYPE    4  290
                        clus
vv                       ATXN2L MUTATED ATXN2L WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             20              290
[1] 2 2
[1] FALSE

Clustering(61) Variable = GLI1 MUTATION ANALYSIS
D61V1, survival
                sevent
clus2              0   1
  GLI1 MUTATED    11   5
  GLI1 WILD-TYPE 219 134
  GLI1 MUTATED GLI1 WILD-TYPE 
            16            353 
  GLI1 MUTATED GLI1 WILD-TYPE 
             5            134 
$`GLI1 MUTATED`
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8078 TCGA-CD-8536 TCGA-CG-4465 TCGA-CG-5723 
        9.67        34.68        29.59        12.43         9.01       105.07 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GQ 
       28.96        65.10        21.07        22.32        22.68         0.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-IN-A6RJ TCGA-MX-A5UJ 
       29.00        23.84        12.46        19.73 

$`GLI1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
         22.50          14.07 
[1] "0.1 - 105.1 (22.5)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D61V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLI1 MUTATED         0        2        2        2         1         5
  GLI1 WILD-TYPE       2       13       38       28        36        47
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLI1 MUTATED           0          2          0          2        2
  GLI1 WILD-TYPE         3         68         53         30       36
D61V3, multiclass
            clus
vv           GLI1 MUTATED GLI1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              2             13
  STAGE IB              2             38
  STAGE II              2             28
  STAGE IIA             1             36
  STAGE IIB             5             47
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GLI1 MUTATED     2   5   4   7
  GLI1 WILD-TYPE  20  87 169  90
D61V4, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  T1            2             20
  T2            5             87
  T3            4            169
  T4            7             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
  GLI1 MUTATED     9   3   5   2
  GLI1 WILD-TYPE 109 101  72  75
D61V5, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  N0            9            109
  N1            3            101
  N2            5             72
  N3            2             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"
D61V6, binary
                cls
clus               0   1
  GLI1 MUTATED    19   1
  GLI1 WILD-TYPE 327  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     19    1
  GLI1 WILD-TYPE  327   28
   clus
vv  GLI1 MUTATED GLI1 WILD-TYPE
  0           19            327
  1            1             28
[1] 2 2
[1] FALSE
D61V7, binary
                cls
clus               0   1
  GLI1 MUTATED    13   7
  GLI1 WILD-TYPE 132 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     13    7
  GLI1 WILD-TYPE  132  241
        clus
vv       GLI1 MUTATED GLI1 WILD-TYPE
  FEMALE           13            132
  MALE              7            241
[1] 2 2
[1] FALSE
D61V8, binary
                cls
clus               0   1
  GLI1 MUTATED    13   0
  GLI1 WILD-TYPE 279  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     13    0
  GLI1 WILD-TYPE  279   59
     clus
vv    GLI1 MUTATED GLI1 WILD-TYPE
  NO            13            279
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GLI1 MUTATED                                          0
  GLI1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GLI1 MUTATED                                       4
  GLI1 WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GLI1 MUTATED                                                        8
  GLI1 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GLI1 MUTATED                                                   0
  GLI1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GLI1 MUTATED                                                                   5
  GLI1 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GLI1 MUTATED                                                    0
  GLI1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GLI1 MUTATED                                                  3
  GLI1 WILD-TYPE                                               58
D61V9, multiclass
                                                                   clus
vv                                                                  GLI1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  GLI1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GLI1 MUTATED    15   0   1   3
  GLI1 WILD-TYPE 296  14  14  21
D61V10, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  R0           15            296
  R1            0             14
  R2            1             14
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GLI1 MUTATED       6                         0
  GLI1 WILD-TYPE    81                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GLI1 MUTATED                                           0     8
  GLI1 WILD-TYPE                                         1   235
D61V12, multiclass
                                           clus
vv                                          GLI1 MUTATED GLI1 WILD-TYPE
  ASIAN                                                6             81
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V13, binary
                cls
clus               0   1
  GLI1 MUTATED     0  14
  GLI1 WILD-TYPE   4 296
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED      0   14
  GLI1 WILD-TYPE    4  296
                        clus
vv                       GLI1 MUTATED GLI1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           14            296
[1] 2 2
[1] FALSE

Clustering(62) Variable = INPPL1 MUTATION ANALYSIS
D62V1, survival
                  sevent
clus2                0   1
  INPPL1 MUTATED    14   5
  INPPL1 WILD-TYPE 216 134
  INPPL1 MUTATED INPPL1 WILD-TYPE 
              19              350 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
               5              134 
$`INPPL1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-4279 TCGA-BR-6452 
       26.70         6.97        30.90         9.67         9.57        34.68 
TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8361 TCGA-CD-8536 TCGA-CG-4305 
       21.90        35.84        29.59        31.10        12.43        15.95 
TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5728 TCGA-F1-A448 TCGA-HU-A4GT TCGA-HU-A4GU 
        1.02         6.02        65.10        21.27         6.51         6.58 
TCGA-MX-A5UJ 
       19.73 

$`INPPL1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-4280 TCGA-BR-6453 TCGA-BR-6455 
        4.08         9.34         6.18         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-7197 TCGA-BR-7703 
       40.21        30.90        31.20        44.94         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-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-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-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-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-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-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 

  INPPL1 MUTATED INPPL1 WILD-TYPE 
            1.02             0.00 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
            65.1            122.3 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
           19.73            14.12 
[1] "1.0 - 65.1 (19.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D62V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INPPL1 MUTATED         0        0        3        3         2         4
  INPPL1 WILD-TYPE       2       15       37       27        35        48
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INPPL1 MUTATED           0          2          1          1        4
  INPPL1 WILD-TYPE         3         68         52         31       34
D62V3, multiclass
            clus
vv           INPPL1 MUTATED INPPL1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                3               27
  STAGE IIA               2               35
  STAGE IIB               4               48
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                4               34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  INPPL1 MUTATED     0   6  10   6
  INPPL1 WILD-TYPE  22  86 163  91
D62V4, multiclass
    clus
vv   INPPL1 MUTATED INPPL1 WILD-TYPE
  T1              0               22
  T2              6               86
  T3             10              163
  T4              6               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
  INPPL1 MUTATED     9   6   4   2
  INPPL1 WILD-TYPE 109  98  73  75
D62V5, multiclass
    clus
vv   INPPL1 MUTATED INPPL1 WILD-TYPE
  N0              9              109
  N1              6               98
  N2              4               73
  N3              2               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"
D62V6, binary
                  cls
clus                 0   1
  INPPL1 MUTATED    20   2
  INPPL1 WILD-TYPE 326  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED     20    2
  INPPL1 WILD-TYPE  326   27
   clus
vv  INPPL1 MUTATED INPPL1 WILD-TYPE
  0             20              326
  1              2               27
[1] 2 2
[1] FALSE
D62V7, binary
                  cls
clus                 0   1
  INPPL1 MUTATED    13  11
  INPPL1 WILD-TYPE 132 237
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED     13   11
  INPPL1 WILD-TYPE  132  237
        clus
vv       INPPL1 MUTATED INPPL1 WILD-TYPE
  FEMALE             13              132
  MALE               11              237
[1] 2 2
[1] FALSE
D62V8, binary
                  cls
clus                 0   1
  INPPL1 MUTATED    17   1
  INPPL1 WILD-TYPE 275  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED     17    1
  INPPL1 WILD-TYPE  275   58
     clus
vv    INPPL1 MUTATED INPPL1 WILD-TYPE
  NO              17              275
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  INPPL1 MUTATED                                          0
  INPPL1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  INPPL1 MUTATED                                       2
  INPPL1 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  INPPL1 MUTATED                                                       15
  INPPL1 WILD-TYPE                                                    143
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  INPPL1 MUTATED                                                   1
  INPPL1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  INPPL1 MUTATED                                                                   4
  INPPL1 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  INPPL1 MUTATED                                                    0
  INPPL1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  INPPL1 MUTATED                                                  2
  INPPL1 WILD-TYPE                                               59
D62V9, multiclass
                                                                   clus
vv                                                                  INPPL1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  INPPL1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  INPPL1 MUTATED    16   0   1   7
  INPPL1 WILD-TYPE 295  14  14  17
D62V10, multiclass
    clus
vv   INPPL1 MUTATED INPPL1 WILD-TYPE
  R0             16              295
  R1              0               14
  R2              1               14
  RX              7               17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  INPPL1 MUTATED       3                         0
  INPPL1 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INPPL1 MUTATED                                           0    16
  INPPL1 WILD-TYPE                                         1   227
D62V12, multiclass
                                           clus
vv                                          INPPL1 MUTATED INPPL1 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 16              227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V13, binary
                  cls
clus                 0   1
  INPPL1 MUTATED     1  18
  INPPL1 WILD-TYPE   3 292
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED      1   18
  INPPL1 WILD-TYPE    3  292
                        clus
vv                       INPPL1 MUTATED INPPL1 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             18              292
[1] 2 2
[1] FALSE

Clustering(63) Variable = SOX7 MUTATION ANALYSIS
D63V1, survival
                sevent
clus2              0   1
  SOX7 MUTATED    10   6
  SOX7 WILD-TYPE 220 133
  SOX7 MUTATED SOX7 WILD-TYPE 
            16            353 
  SOX7 MUTATED SOX7 WILD-TYPE 
             6            133 
$`SOX7 MUTATED`
TCGA-CG-4460 TCGA-BR-6453 TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8680 TCGA-CG-5721 
       21.99        15.95         0.26        25.05        31.96         6.02 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-F1-6874 TCGA-HU-A4G8 TCGA-HU-A4GC 
       12.03        28.96        65.10        14.47        22.68         3.25 
TCGA-HU-A4H4 TCGA-IN-A6RL TCGA-MX-A5UJ TCGA-RD-A8N1 
       23.84        13.35        19.73       115.69 

$`SOX7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
      105.07        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-F1-6875 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-A4GD 
        0.76        24.30         5.59        24.26        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-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-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-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 

  SOX7 MUTATED SOX7 WILD-TYPE 
          0.26           0.00 
  SOX7 MUTATED SOX7 WILD-TYPE 
        115.69         122.30 
  SOX7 MUTATED SOX7 WILD-TYPE 
         20.86          14.07 
[1] "0.3 - 115.7 (20.9)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D63V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SOX7 MUTATED         0        2        3        0         1         2
  SOX7 WILD-TYPE       2       13       37       30        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SOX7 MUTATED           0          3          2          1        4
  SOX7 WILD-TYPE         3         67         51         31       34
D63V3, multiclass
            clus
vv           SOX7 MUTATED SOX7 WILD-TYPE
  STAGE I               0              2
  STAGE IA              2             13
  STAGE IB              3             37
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            2             51
  STAGE IIIC            1             31
  STAGE IV              4             34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SOX7 MUTATED     2   6   4   6
  SOX7 WILD-TYPE  20  86 169  91
D63V4, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  T1            2             20
  T2            6             86
  T3            4            169
  T4            6             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
  SOX7 MUTATED     6   5   5   2
  SOX7 WILD-TYPE 112  99  72  75
D63V5, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  N0            6            112
  N1            5             99
  N2            5             72
  N3            2             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"
D63V6, binary
                cls
clus               0   1
  SOX7 MUTATED    16   3
  SOX7 WILD-TYPE 330  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED     16    3
  SOX7 WILD-TYPE  330   26
   clus
vv  SOX7 MUTATED SOX7 WILD-TYPE
  0           16            330
  1            3             26
[1] 2 2
[1] FALSE
D63V7, binary
                cls
clus               0   1
  SOX7 MUTATED     9  10
  SOX7 WILD-TYPE 136 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED      9   10
  SOX7 WILD-TYPE  136  238
        clus
vv       SOX7 MUTATED SOX7 WILD-TYPE
  FEMALE            9            136
  MALE             10            238
[1] 2 2
[1] FALSE
D63V8, binary
                cls
clus               0   1
  SOX7 MUTATED    13   2
  SOX7 WILD-TYPE 279  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED     13    2
  SOX7 WILD-TYPE  279   57
     clus
vv    SOX7 MUTATED SOX7 WILD-TYPE
  NO            13            279
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SOX7 MUTATED                                          0
  SOX7 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SOX7 MUTATED                                       4
  SOX7 WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SOX7 MUTATED                                                        7
  SOX7 WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SOX7 MUTATED                                                   0
  SOX7 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SOX7 MUTATED                                                                   5
  SOX7 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SOX7 MUTATED                                                    0
  SOX7 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SOX7 MUTATED                                                  3
  SOX7 WILD-TYPE                                               58
D63V9, multiclass
                                                                   clus
vv                                                                  SOX7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  SOX7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SOX7 MUTATED    13   1   2   2
  SOX7 WILD-TYPE 298  13  13  22
D63V10, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  R0           13            298
  R1            1             13
  R2            2             13
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SOX7 MUTATED       5                         0
  SOX7 WILD-TYPE    82                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SOX7 MUTATED                                           0     9
  SOX7 WILD-TYPE                                         1   234
D63V12, multiclass
                                           clus
vv                                          SOX7 MUTATED SOX7 WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, binary
                cls
clus               0   1
  SOX7 MUTATED     0  14
  SOX7 WILD-TYPE   4 296
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED      0   14
  SOX7 WILD-TYPE    4  296
                        clus
vv                       SOX7 MUTATED SOX7 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           14            296
[1] 2 2
[1] FALSE

Clustering(64) Variable = FHOD3 MUTATION ANALYSIS
D64V1, survival
                 sevent
clus2               0   1
  FHOD3 MUTATED    19   8
  FHOD3 WILD-TYPE 211 131
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             27             342 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
              8             131 
$`FHOD3 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7197 
       21.99         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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-8080 TCGA-BR-8081 TCGA-BR-8285 
       14.43        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-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-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-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       27.02         7.99        54.08         4.01        14.01        29.98 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-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-5723 
        6.97        36.00         1.02         0.99         6.02       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-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-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-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-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-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 

  FHOD3 MUTATED FHOD3 WILD-TYPE 
           0.26            0.00 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
          38.14          122.30 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
          9.210          14.565 
[1] "0.3 - 38.1 (9.2)"   "0.0 - 122.3 (14.6)"
[1] "hr=" "1"  
D64V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FHOD3 MUTATED         0        1        5        3         4         3
  FHOD3 WILD-TYPE       2       14       35       27        33        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FHOD3 MUTATED           1          3          1          2        5
  FHOD3 WILD-TYPE         2         67         52         30       33
D64V3, multiclass
            clus
vv           FHOD3 MUTATED FHOD3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               5              35
  STAGE II               3              27
  STAGE IIA              4              33
  STAGE IIB              3              49
  STAGE III              1               2
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               5              33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FHOD3 MUTATED     4   7  11   7
  FHOD3 WILD-TYPE  18  85 162  90
D64V4, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  T1             4              18
  T2             7              85
  T3            11             162
  T4             7              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
  FHOD3 MUTATED    13  11   3   2
  FHOD3 WILD-TYPE 105  93  74  75
D64V5, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  N0            13             105
  N1            11              93
  N2             3              74
  N3             2              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"
D64V6, binary
                 cls
clus                0   1
  FHOD3 MUTATED    25   4
  FHOD3 WILD-TYPE 321  25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     25    4
  FHOD3 WILD-TYPE  321   25
   clus
vv  FHOD3 MUTATED FHOD3 WILD-TYPE
  0            25             321
  1             4              25
[1] 2 2
[1] FALSE
D64V7, binary
                 cls
clus                0   1
  FHOD3 MUTATED    15  15
  FHOD3 WILD-TYPE 130 233
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     15   15
  FHOD3 WILD-TYPE  130  233
        clus
vv       FHOD3 MUTATED FHOD3 WILD-TYPE
  FEMALE            15             130
  MALE              15             233
[1] 2 2
[1] FALSE
D64V8, binary
                 cls
clus                0   1
  FHOD3 MUTATED    22   3
  FHOD3 WILD-TYPE 270  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     22    3
  FHOD3 WILD-TYPE  270   56
     clus
vv    FHOD3 MUTATED FHOD3 WILD-TYPE
  NO             22             270
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FHOD3 MUTATED                                          0
  FHOD3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FHOD3 MUTATED                                       3
  FHOD3 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FHOD3 MUTATED                                                       16
  FHOD3 WILD-TYPE                                                    142
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FHOD3 MUTATED                                                   2
  FHOD3 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FHOD3 MUTATED                                                                   6
  FHOD3 WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FHOD3 MUTATED                                                    0
  FHOD3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FHOD3 MUTATED                                                  3
  FHOD3 WILD-TYPE                                               58
D64V9, multiclass
                                                                   clus
vv                                                                  FHOD3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  FHOD3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FHOD3 MUTATED    20   0   3   6
  FHOD3 WILD-TYPE 291  14  12  18
D64V10, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  R0            20             291
  R1             0              14
  R2             3              12
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FHOD3 MUTATED       4                         0
  FHOD3 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FHOD3 MUTATED                                           0    20
  FHOD3 WILD-TYPE                                         1   223
D64V12, multiclass
                                           clus
vv                                          FHOD3 MUTATED FHOD3 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                20             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, binary
                 cls
clus                0   1
  FHOD3 MUTATED     0  22
  FHOD3 WILD-TYPE   4 288
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED      0   22
  FHOD3 WILD-TYPE    4  288
                        clus
vv                       FHOD3 MUTATED FHOD3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            22             288
[1] 2 2
[1] FALSE

Clustering(65) Variable = RNF128 MUTATION ANALYSIS
D65V1, survival
                  sevent
clus2                0   1
  RNF128 MUTATED    10   3
  RNF128 WILD-TYPE 220 136
  RNF128 MUTATED RNF128 WILD-TYPE 
              13              356 
  RNF128 MUTATED RNF128 WILD-TYPE 
               3              136 
$`RNF128 MUTATED`
TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-A4QL TCGA-CG-5721 
       34.68         0.26         4.31        31.27        16.14         6.02 
TCGA-HU-8602 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-VQ-A8DU 
       22.32        24.26        24.20         6.51        29.00         5.46 
TCGA-VQ-A8P2 
       38.14 

$`RNF128 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  RNF128 MUTATED RNF128 WILD-TYPE 
            0.26             0.00 
  RNF128 MUTATED RNF128 WILD-TYPE 
           38.14           122.30 
  RNF128 MUTATED RNF128 WILD-TYPE 
           22.32            14.12 
[1] "0.3 - 38.1 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D65V2, 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       2       13       38       30        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF128 MUTATED           0          2          1          2        1
  RNF128 WILD-TYPE         3         68         52         30       37
D65V3, multiclass
            clus
vv           RNF128 MUTATED RNF128 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                2               13
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF128 MUTATED     2   2   4   5
  RNF128 WILD-TYPE  20  90 169  92
D65V4, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  T1              2               20
  T2              2               90
  T3              4              169
  T4              5               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
  RNF128 MUTATED     7   2   1   3
  RNF128 WILD-TYPE 111 102  76  74
D65V5, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  N0              7              111
  N1              2              102
  N2              1               76
  N3              3               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"
D65V6, binary
                  cls
clus                 0   1
  RNF128 MUTATED    14   0
  RNF128 WILD-TYPE 332  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED     14    0
  RNF128 WILD-TYPE  332   29
   clus
vv  RNF128 MUTATED RNF128 WILD-TYPE
  0             14              332
  1              0               29
[1] 2 2
[1] FALSE
D65V7, binary
                  cls
clus                 0   1
  RNF128 MUTATED     9   5
  RNF128 WILD-TYPE 136 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED      9    5
  RNF128 WILD-TYPE  136  243
        clus
vv       RNF128 MUTATED RNF128 WILD-TYPE
  FEMALE              9              136
  MALE                5              243
[1] 2 2
[1] FALSE
D65V8, binary
                  cls
clus                 0   1
  RNF128 MUTATED    11   1
  RNF128 WILD-TYPE 281  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED     11    1
  RNF128 WILD-TYPE  281   58
     clus
vv    RNF128 MUTATED RNF128 WILD-TYPE
  NO              11              281
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RNF128 MUTATED                                          0
  RNF128 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RNF128 MUTATED                                       2
  RNF128 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RNF128 MUTATED                                                        6
  RNF128 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RNF128 MUTATED                                                   1
  RNF128 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RNF128 MUTATED                                                                   1
  RNF128 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RNF128 MUTATED                                                    1
  RNF128 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RNF128 MUTATED                                                  3
  RNF128 WILD-TYPE                                               58
D65V9, multiclass
                                                                   clus
vv                                                                  RNF128 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  RNF128 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RNF128 MUTATED    13   0   0   1
  RNF128 WILD-TYPE 298  14  15  23
D65V10, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  R0             13              298
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RNF128 MUTATED       5                         0
  RNF128 WILD-TYPE    82                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RNF128 MUTATED                                           0     8
  RNF128 WILD-TYPE                                         1   235
D65V12, multiclass
                                           clus
vv                                          RNF128 MUTATED RNF128 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V13, binary
                  cls
clus                 0   1
  RNF128 MUTATED     0  11
  RNF128 WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED      0   11
  RNF128 WILD-TYPE    4  299
                        clus
vv                       RNF128 MUTATED RNF128 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(66) Variable = HLA-A MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2               0   1
  HLA-A MUTATED    12   4
  HLA-A WILD-TYPE 218 135
  HLA-A MUTATED HLA-A WILD-TYPE 
             16             353 
  HLA-A MUTATED HLA-A WILD-TYPE 
              4             135 
$`HLA-A MUTATED`
TCGA-BR-4257 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8372 TCGA-CD-8536 
        9.67        44.94        29.59        32.25        31.27        12.43 
TCGA-CD-A4MG TCGA-CG-4438 TCGA-CG-5718 TCGA-D7-A6EZ TCGA-F1-6874 TCGA-HU-8602 
        6.58        54.08        36.00        20.32        14.47        22.32 
TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-R5-A7ZI TCGA-VQ-A8P2 
       22.68         6.51        74.53        38.14 

$`HLA-A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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-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 

  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 
         26.135          14.040 
[1] "6.5 - 74.5 (26.1)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "2.2"
D66V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HLA-A MUTATED         0        0        1        2         3         4
  HLA-A WILD-TYPE       2       15       39       28        34        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HLA-A MUTATED           0          3          0          1        2
  HLA-A WILD-TYPE         3         67         53         31       36
D66V3, multiclass
            clus
vv           HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              3              34
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HLA-A MUTATED     0   2   6   8
  HLA-A WILD-TYPE  22  90 167  89
D66V4, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  T1             0              22
  T2             2              90
  T3             6             167
  T4             8              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
  HLA-A MUTATED     9   5   2   1
  HLA-A WILD-TYPE 109  99  75  76
D66V5, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  N0             9             109
  N1             5              99
  N2             2              75
  N3             1              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"
D66V6, binary
                 cls
clus                0   1
  HLA-A MUTATED    18   1
  HLA-A WILD-TYPE 328  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     18    1
  HLA-A WILD-TYPE  328   28
   clus
vv  HLA-A MUTATED HLA-A WILD-TYPE
  0            18             328
  1             1              28
[1] 2 2
[1] FALSE
D66V7, binary
                 cls
clus                0   1
  HLA-A MUTATED    12   7
  HLA-A WILD-TYPE 133 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     12    7
  HLA-A WILD-TYPE  133  241
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  FEMALE            12             133
  MALE               7             241
[1] 2 2
[1] FALSE
D66V8, binary
                 cls
clus                0   1
  HLA-A MUTATED    14   1
  HLA-A WILD-TYPE 278  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     14    1
  HLA-A WILD-TYPE  278   58
     clus
vv    HLA-A MUTATED HLA-A WILD-TYPE
  NO             14             278
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HLA-A MUTATED                                          0
  HLA-A WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HLA-A MUTATED                                       4
  HLA-A WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HLA-A MUTATED                                                        9
  HLA-A WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HLA-A MUTATED                                                   1
  HLA-A WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HLA-A MUTATED                                                                   4
  HLA-A WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HLA-A MUTATED                                                    0
  HLA-A WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HLA-A MUTATED                                                  1
  HLA-A WILD-TYPE                                               60
D66V9, multiclass
                                                                   clus
vv                                                                  HLA-A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  HLA-A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HLA-A MUTATED    13   0   0   4
  HLA-A WILD-TYPE 298  14  15  20
D66V10, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  R0            13             298
  R1             0              14
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HLA-A MUTATED       5                         0
  HLA-A WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HLA-A MUTATED                                           0    12
  HLA-A WILD-TYPE                                         1   231
D66V12, multiclass
                                           clus
vv                                          HLA-A MUTATED HLA-A WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V13, binary
                 cls
clus                0   1
  HLA-A MUTATED     1  15
  HLA-A WILD-TYPE   3 295
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      1   15
  HLA-A WILD-TYPE    3  295
                        clus
vv                       HLA-A MUTATED HLA-A WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            15             295
[1] 2 2
[1] FALSE

Clustering(67) Variable = MFRP MUTATION ANALYSIS
D67V1, survival
                sevent
clus2              0   1
  MFRP MUTATED     8   4
  MFRP WILD-TYPE 222 135
  MFRP MUTATED MFRP WILD-TYPE 
            12            357 
  MFRP MUTATED MFRP WILD-TYPE 
             4            135 
$`MFRP MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8591 
       21.99        34.68        32.25        31.10         1.12        28.14 
TCGA-BR-8680 TCGA-BR-A4J4 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5728 
       31.96         0.53        16.14         6.58         1.02        65.10 

$`MFRP WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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 

  MFRP MUTATED MFRP WILD-TYPE 
          0.53           0.00 
  MFRP MUTATED MFRP WILD-TYPE 
          65.1          122.3 
  MFRP MUTATED MFRP WILD-TYPE 
        25.065         14.070 
[1] "0.5 - 65.1 (25.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D67V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MFRP MUTATED         0        0        1        0         3         2
  MFRP WILD-TYPE       2       15       39       30        34        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MFRP MUTATED           0          1          2          2        3
  MFRP WILD-TYPE         3         69         51         30       35
D67V3, multiclass
            clus
vv           MFRP MUTATED MFRP WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             3             34
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            2             51
  STAGE IIIC            2             30
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MFRP MUTATED     0   1   5   8
  MFRP WILD-TYPE  22  91 168  89
D67V4, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  T1            0             22
  T2            1             91
  T3            5            168
  T4            8             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
  MFRP MUTATED     7   2   4   2
  MFRP WILD-TYPE 111 102  73  75
D67V5, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  N0            7            111
  N1            2            102
  N2            4             73
  N3            2             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"
D67V6, binary
                cls
clus               0   1
  MFRP MUTATED    12   3
  MFRP WILD-TYPE 334  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED     12    3
  MFRP WILD-TYPE  334   26
   clus
vv  MFRP MUTATED MFRP WILD-TYPE
  0           12            334
  1            3             26
[1] 2 2
[1] FALSE
D67V7, binary
                cls
clus               0   1
  MFRP MUTATED     9   6
  MFRP WILD-TYPE 136 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      9    6
  MFRP WILD-TYPE  136  242
        clus
vv       MFRP MUTATED MFRP WILD-TYPE
  FEMALE            9            136
  MALE              6            242
[1] 2 2
[1] FALSE
D67V8, binary
                cls
clus               0   1
  MFRP MUTATED    10   0
  MFRP WILD-TYPE 282  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED     10    0
  MFRP WILD-TYPE  282   59
     clus
vv    MFRP MUTATED MFRP WILD-TYPE
  NO            10            282
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MFRP MUTATED                                          0
  MFRP WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MFRP MUTATED                                       1
  MFRP WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MFRP MUTATED                                                       10
  MFRP WILD-TYPE                                                    148
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MFRP MUTATED                                                   0
  MFRP WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MFRP MUTATED                                                                   3
  MFRP WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MFRP MUTATED                                                    0
  MFRP WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MFRP MUTATED                                                  1
  MFRP WILD-TYPE                                               60
D67V9, multiclass
                                                                   clus
vv                                                                  MFRP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  MFRP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MFRP MUTATED    10   0   2   2
  MFRP WILD-TYPE 301  14  13  22
D67V10, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  R0           10            301
  R1            0             14
  R2            2             13
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MFRP MUTATED       3                         0
  MFRP WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MFRP MUTATED                                           0     9
  MFRP WILD-TYPE                                         1   234
D67V12, multiclass
                                           clus
vv                                          MFRP MUTATED MFRP WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V13, binary
                cls
clus               0   1
  MFRP MUTATED     0  12
  MFRP WILD-TYPE   4 298
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      0   12
  MFRP WILD-TYPE    4  298
                        clus
vv                       MFRP MUTATED MFRP WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           12            298
[1] 2 2
[1] FALSE

Clustering(68) Variable = EIF5B MUTATION ANALYSIS
D68V1, survival
                 sevent
clus2               0   1
  EIF5B MUTATED    18   4
  EIF5B WILD-TYPE 212 135
  EIF5B MUTATED EIF5B WILD-TYPE 
             22             347 
  EIF5B MUTATED EIF5B WILD-TYPE 
              4             135 
$`EIF5B MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         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-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-F1-6875 
        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-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-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 

  EIF5B MUTATED EIF5B WILD-TYPE 
           1.12            0.00 
  EIF5B MUTATED EIF5B WILD-TYPE 
           65.1           122.3 
  EIF5B MUTATED EIF5B WILD-TYPE 
          23.26           14.04 
[1] "1.1 - 65.1 (23.3)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "2.7"
D68V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EIF5B MUTATED         0        2        4        0         4         2
  EIF5B WILD-TYPE       2       13       36       30        33        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF5B MUTATED           0          3          2          3        2
  EIF5B WILD-TYPE         3         67         51         29       36
D68V3, multiclass
            clus
vv           EIF5B MUTATED EIF5B WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               4              36
  STAGE II               0              30
  STAGE IIA              4              33
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EIF5B MUTATED     3   6   5   9
  EIF5B WILD-TYPE  19  86 168  88
D68V4, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  T1             3              19
  T2             6              86
  T3             5             168
  T4             9              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
  EIF5B MUTATED    11   6   3   3
  EIF5B WILD-TYPE 107  98  74  74
D68V5, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  N0            11             107
  N1             6              98
  N2             3              74
  N3             3              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"
D68V6, binary
                 cls
clus                0   1
  EIF5B MUTATED    23   1
  EIF5B WILD-TYPE 323  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     23    1
  EIF5B WILD-TYPE  323   28
   clus
vv  EIF5B MUTATED EIF5B WILD-TYPE
  0            23             323
  1             1              28
[1] 2 2
[1] FALSE
D68V7, binary
                 cls
clus                0   1
  EIF5B MUTATED    14  11
  EIF5B WILD-TYPE 131 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     14   11
  EIF5B WILD-TYPE  131  237
        clus
vv       EIF5B MUTATED EIF5B WILD-TYPE
  FEMALE            14             131
  MALE              11             237
[1] 2 2
[1] FALSE
D68V8, binary
                 cls
clus                0   1
  EIF5B MUTATED    18   2
  EIF5B WILD-TYPE 274  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     18    2
  EIF5B WILD-TYPE  274   57
     clus
vv    EIF5B MUTATED EIF5B WILD-TYPE
  NO             18             274
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EIF5B MUTATED                                          0
  EIF5B WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EIF5B MUTATED                                       4
  EIF5B WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EIF5B MUTATED                                                        9
  EIF5B WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EIF5B MUTATED                                                   2
  EIF5B WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EIF5B MUTATED                                                                   5
  EIF5B WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EIF5B MUTATED                                                    0
  EIF5B WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EIF5B MUTATED                                                  5
  EIF5B WILD-TYPE                                               56
D68V9, multiclass
                                                                   clus
vv                                                                  EIF5B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              5
                                                                   clus
vv                                                                  EIF5B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EIF5B MUTATED    20   1   0   4
  EIF5B WILD-TYPE 291  13  15  20
D68V10, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  R0            20             291
  R1             1              13
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EIF5B MUTATED       6                         0
  EIF5B WILD-TYPE    81                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EIF5B MUTATED                                           0    14
  EIF5B WILD-TYPE                                         1   229
D68V12, multiclass
                                           clus
vv                                          EIF5B MUTATED EIF5B WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V13, binary
                 cls
clus                0   1
  EIF5B MUTATED     0  19
  EIF5B WILD-TYPE   4 291
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED      0   19
  EIF5B WILD-TYPE    4  291
                        clus
vv                       EIF5B MUTATED EIF5B WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            19             291
[1] 2 2
[1] FALSE

Clustering(69) Variable = C9ORF131 MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  C9ORF131 MUTATED    12   5
  C9ORF131 WILD-TYPE 218 134
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                17                352 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                 5                134 
$`C9ORF131 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8060 TCGA-BR-8078 
        6.97        30.90         9.34        34.68        11.44        29.59 
TCGA-BR-8680 TCGA-CD-5802 TCGA-CG-5728 TCGA-D7-A6EY TCGA-HF-A5NB TCGA-HU-A4G9 
       31.96        13.35        65.10        11.44        30.51        24.20 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-VQ-A8P2 
       29.00        14.07        19.73        74.53        38.14 

$`C9ORF131 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
              6.97               0.00 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
             74.53             122.30 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
            29.000             14.055 
[1] "7.0 - 74.5 (29.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C9ORF131 MUTATED         1        1        2        1         1         2
  C9ORF131 WILD-TYPE       1       14       38       29        36        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF131 MUTATED           0          4          1          2        2
  C9ORF131 WILD-TYPE         3         66         52         30       36
D69V3, multiclass
            clus
vv           C9ORF131 MUTATED C9ORF131 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  1                 14
  STAGE IB                  2                 38
  STAGE II                  1                 29
  STAGE IIA                 1                 36
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                4                 66
  STAGE IIIB                1                 52
  STAGE IIIC                2                 30
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C9ORF131 MUTATED     3   3   5   7
  C9ORF131 WILD-TYPE  19  89 168  90
D69V4, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  T1                3                 19
  T2                3                 89
  T3                5                168
  T4                7                 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
  C9ORF131 MUTATED     6   6   3   3
  C9ORF131 WILD-TYPE 112  98  74  74
D69V5, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  N0                6                112
  N1                6                 98
  N2                3                 74
  N3                3                 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"
D69V6, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED    15   2
  C9ORF131 WILD-TYPE 331  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED     15    2
  C9ORF131 WILD-TYPE  331   27
   clus
vv  C9ORF131 MUTATED C9ORF131 WILD-TYPE
  0               15                331
  1                2                 27
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED    12   7
  C9ORF131 WILD-TYPE 133 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED     12    7
  C9ORF131 WILD-TYPE  133  241
        clus
vv       C9ORF131 MUTATED C9ORF131 WILD-TYPE
  FEMALE               12                133
  MALE                  7                241
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED    13   3
  C9ORF131 WILD-TYPE 279  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED     13    3
  C9ORF131 WILD-TYPE  279   56
     clus
vv    C9ORF131 MUTATED C9ORF131 WILD-TYPE
  NO                13                279
  YES                3                 56
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C9ORF131 MUTATED                                          0
  C9ORF131 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C9ORF131 MUTATED                                       2
  C9ORF131 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C9ORF131 MUTATED                                                        9
  C9ORF131 WILD-TYPE                                                    149
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C9ORF131 MUTATED                                                   2
  C9ORF131 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C9ORF131 MUTATED                                                                   1
  C9ORF131 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C9ORF131 MUTATED                                                    0
  C9ORF131 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C9ORF131 MUTATED                                                  5
  C9ORF131 WILD-TYPE                                               56
D69V9, multiclass
                                                                   clus
vv                                                                  C9ORF131 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 5
                                                                   clus
vv                                                                  C9ORF131 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C9ORF131 MUTATED    13   1   0   4
  C9ORF131 WILD-TYPE 298  13  15  20
D69V10, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  R0               13                298
  R1                1                 13
  R2                0                 15
  RX                4                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C9ORF131 MUTATED       5                         1
  C9ORF131 WILD-TYPE    82                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C9ORF131 MUTATED                                           0    11
  C9ORF131 WILD-TYPE                                         1   232
D69V12, multiclass
                                           clus
vv                                          C9ORF131 MUTATED C9ORF131 WILD-TYPE
  ASIAN                                                    5                 82
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   11                232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V13, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED     1  15
  C9ORF131 WILD-TYPE   3 295
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED      1   15
  C9ORF131 WILD-TYPE    3  295
                        clus
vv                       C9ORF131 MUTATED C9ORF131 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               15                295
[1] 2 2
[1] FALSE

Clustering(70) Variable = BCORL1 MUTATION ANALYSIS
D70V1, survival
                  sevent
clus2                0   1
  BCORL1 MUTATED    16   7
  BCORL1 WILD-TYPE 214 132
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              23              346 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
               7              132 
$`BCORL1 MUTATED`
TCGA-CG-4460 TCGA-B7-A5TI TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8284 
       21.99        19.56         6.61        34.68        32.25         8.05 
TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-5723 TCGA-D7-5577 
        0.26        31.27         1.12        16.14       105.07        25.71 
TCGA-D7-6528 TCGA-F1-6874 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4H3 
       15.22        14.47        30.51        26.47        22.68        29.00 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7ZI TCGA-VQ-A8P2 TCGA-VQ-AA6A 
       19.73        14.04        74.53        38.14        38.93 

$`BCORL1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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-D7-5578 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-D7-6815 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-F1-6875 
        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-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-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-R5-A7O7 TCGA-R5-A7ZE 
        5.56        63.62        36.95         3.72        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-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 

  BCORL1 MUTATED BCORL1 WILD-TYPE 
            0.26             0.00 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
          105.07           122.30 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
           22.68            13.87 
[1] "0.3 - 105.1 (22.7)" "0.0 - 122.3 (13.9)"
[1] "hr=" "1.8"
D70V2, 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       2       15       36       29        34        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCORL1 MUTATED           1          4          1          6        2
  BCORL1 WILD-TYPE         2         66         52         26       36
D70V3, multiclass
            clus
vv           BCORL1 MUTATED BCORL1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                4               36
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               3               49
  STAGE III               1                2
  STAGE IIIA              4               66
  STAGE IIIB              1               52
  STAGE IIIC              6               26
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BCORL1 MUTATED     0   8   5  12
  BCORL1 WILD-TYPE  22  84 168  85
D70V4, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  T1              0               22
  T2              8               84
  T3              5              168
  T4             12               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
  BCORL1 MUTATED     9   7   1   8
  BCORL1 WILD-TYPE 109  97  76  69
D70V5, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  N0              9              109
  N1              7               97
  N2              1               76
  N3              8               69
[1] 4 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
  BCORL1 MUTATED    22   2
  BCORL1 WILD-TYPE 324  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     22    2
  BCORL1 WILD-TYPE  324   27
   clus
vv  BCORL1 MUTATED BCORL1 WILD-TYPE
  0             22              324
  1              2               27
[1] 2 2
[1] FALSE
D70V7, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    18   8
  BCORL1 WILD-TYPE 127 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     18    8
  BCORL1 WILD-TYPE  127  240
        clus
vv       BCORL1 MUTATED BCORL1 WILD-TYPE
  FEMALE             18              127
  MALE                8              240
[1] 2 2
[1] FALSE
D70V8, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    20   3
  BCORL1 WILD-TYPE 272  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     20    3
  BCORL1 WILD-TYPE  272   56
     clus
vv    BCORL1 MUTATED BCORL1 WILD-TYPE
  NO              20              272
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BCORL1 MUTATED                                          1
  BCORL1 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BCORL1 MUTATED                                       4
  BCORL1 WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BCORL1 MUTATED                                                       11
  BCORL1 WILD-TYPE                                                    147
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BCORL1 MUTATED                                                   2
  BCORL1 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BCORL1 MUTATED                                                                   5
  BCORL1 WILD-TYPE                                                                63
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BCORL1 MUTATED                                                    0
  BCORL1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BCORL1 MUTATED                                                  3
  BCORL1 WILD-TYPE                                               58
D70V9, multiclass
                                                                   clus
vv                                                                  BCORL1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  BCORL1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BCORL1 MUTATED    18   1   1   3
  BCORL1 WILD-TYPE 293  13  14  21
D70V10, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  R0             18              293
  R1              1               13
  R2              1               14
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  BCORL1 MUTATED       2                         0
  BCORL1 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BCORL1 MUTATED                                           0    21
  BCORL1 WILD-TYPE                                         1   222
D70V12, multiclass
                                           clus
vv                                          BCORL1 MUTATED BCORL1 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 21              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V13, binary
                  cls
clus                 0   1
  BCORL1 MUTATED     1  20
  BCORL1 WILD-TYPE   3 290
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED      1   20
  BCORL1 WILD-TYPE    3  290
                        clus
vv                       BCORL1 MUTATED BCORL1 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             20              290
[1] 2 2
[1] FALSE

Clustering(71) Variable = PAFAH1B1 MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  PAFAH1B1 MUTATED     8   3
  PAFAH1B1 WILD-TYPE 222 136
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
                11                358 
  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE 
                 3                136 
$`PAFAH1B1 MUTATED`
TCGA-BR-6452 TCGA-BR-6709 TCGA-BR-8372 TCGA-BR-8680 TCGA-CG-4306 TCGA-CG-5721 
       34.68        12.16        31.27        31.96         1.02         6.02 
TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-IN-A7NR 
       11.08        22.32        29.98         0.10         6.51 

$`PAFAH1B1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         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-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-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-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-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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        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 
             12.16              14.35 
[1] "0.1 - 34.7 (12.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAFAH1B1 MUTATED         1        1        0        0         3         1
  PAFAH1B1 WILD-TYPE       1       14       40       30        34        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAFAH1B1 MUTATED           0          0          1          2        4
  PAFAH1B1 WILD-TYPE         3         70         52         30       34
D71V3, multiclass
            clus
vv           PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  1                 14
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 3                 34
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                1                 52
  STAGE IIIC                2                 30
  STAGE IV                  4                 34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PAFAH1B1 MUTATED     3   1   5   5
  PAFAH1B1 WILD-TYPE  19  91 168  92
D71V4, multiclass
    clus
vv   PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  T1                3                 19
  T2                1                 91
  T3                5                168
  T4                5                 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
  PAFAH1B1 MUTATED     4   3   3   3
  PAFAH1B1 WILD-TYPE 114 101  74  74
D71V5, multiclass
    clus
vv   PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  N0                4                114
  N1                3                101
  N2                3                 74
  N3                3                 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"
D71V6, binary
                    cls
clus                   0   1
  PAFAH1B1 MUTATED    11   3
  PAFAH1B1 WILD-TYPE 335  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PAFAH1B1 MUTATED     11    3
  PAFAH1B1 WILD-TYPE  335   26
   clus
vv  PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  0               11                335
  1                3                 26
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  PAFAH1B1 MUTATED     6   9
  PAFAH1B1 WILD-TYPE 139 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PAFAH1B1 MUTATED      6    9
  PAFAH1B1 WILD-TYPE  139  239
        clus
vv       PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  FEMALE                6                139
  MALE                  9                239
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  PAFAH1B1 MUTATED    10   2
  PAFAH1B1 WILD-TYPE 282  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PAFAH1B1 MUTATED     10    2
  PAFAH1B1 WILD-TYPE  282   57
     clus
vv    PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  NO                10                282
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PAFAH1B1 MUTATED                                          0
  PAFAH1B1 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PAFAH1B1 MUTATED                                       1
  PAFAH1B1 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAFAH1B1 MUTATED                                                       10
  PAFAH1B1 WILD-TYPE                                                    148
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PAFAH1B1 MUTATED                                                   0
  PAFAH1B1 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAFAH1B1 MUTATED                                                                   1
  PAFAH1B1 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PAFAH1B1 MUTATED                                                    0
  PAFAH1B1 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PAFAH1B1 MUTATED                                                  3
  PAFAH1B1 WILD-TYPE                                               58
D71V9, multiclass
                                                                   clus
vv                                                                  PAFAH1B1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 3
                                                                   clus
vv                                                                  PAFAH1B1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  PAFAH1B1 MUTATED    11   1   1   2
  PAFAH1B1 WILD-TYPE 300  13  14  22
D71V10, multiclass
    clus
vv   PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  R0               11                300
  R1                1                 13
  R2                1                 14
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PAFAH1B1 MUTATED       5                         2
  PAFAH1B1 WILD-TYPE    82                         7
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAFAH1B1 MUTATED                                           0     6
  PAFAH1B1 WILD-TYPE                                         1   237
D71V12, multiclass
                                           clus
vv                                          PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  ASIAN                                                    5                 82
  BLACK OR AFRICAN AMERICAN                                2                  7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, binary
                    cls
clus                   0   1
  PAFAH1B1 MUTATED     0  13
  PAFAH1B1 WILD-TYPE   4 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PAFAH1B1 MUTATED      0   13
  PAFAH1B1 WILD-TYPE    4  297
                        clus
vv                       PAFAH1B1 MUTATED PAFAH1B1 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               13                297
[1] 2 2
[1] FALSE

Clustering(72) Variable = EPB49 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2               0   1
  EPB49 MUTATED     8   2
  EPB49 WILD-TYPE 222 137
  EPB49 MUTATED EPB49 WILD-TYPE 
             10             359 
  EPB49 MUTATED EPB49 WILD-TYPE 
              2             137 
$`EPB49 MUTATED`
TCGA-BR-4201 TCGA-BR-8368 TCGA-BR-8487 TCGA-CG-5723 TCGA-FP-7916 TCGA-HU-8602 
       30.90         4.31         1.12       105.07        14.07        22.32 
TCGA-HU-A4H4 TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-VQ-A8P2 
       23.84        19.73        74.53        38.14 

$`EPB49 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  EPB49 MUTATED EPB49 WILD-TYPE 
           1.12            0.00 
  EPB49 MUTATED EPB49 WILD-TYPE 
         105.07          122.30 
  EPB49 MUTATED EPB49 WILD-TYPE 
          23.08           14.07 
[1] "1.1 - 105.1 (23.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.9"
D72V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPB49 MUTATED         0        0        1        1         1         2
  EPB49 WILD-TYPE       2       15       39       29        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPB49 MUTATED           0          3          0          1        1
  EPB49 WILD-TYPE         3         67         53         31       37
D72V3, multiclass
            clus
vv           EPB49 MUTATED EPB49 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPB49 MUTATED     1   4   2   5
  EPB49 WILD-TYPE  21  88 171  92
D72V4, multiclass
    clus
vv   EPB49 MUTATED EPB49 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             2             171
  T4             5              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
  EPB49 MUTATED     4   4   2   1
  EPB49 WILD-TYPE 114 100  75  76
D72V5, multiclass
    clus
vv   EPB49 MUTATED EPB49 WILD-TYPE
  N0             4             114
  N1             4             100
  N2             2              75
  N3             1              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"
D72V6, binary
                 cls
clus                0   1
  EPB49 MUTATED    11   1
  EPB49 WILD-TYPE 335  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB49 MUTATED     11    1
  EPB49 WILD-TYPE  335   28
   clus
vv  EPB49 MUTATED EPB49 WILD-TYPE
  0            11             335
  1             1              28
[1] 2 2
[1] FALSE
D72V7, binary
                 cls
clus                0   1
  EPB49 MUTATED    10   3
  EPB49 WILD-TYPE 135 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB49 MUTATED     10    3
  EPB49 WILD-TYPE  135  245
        clus
vv       EPB49 MUTATED EPB49 WILD-TYPE
  FEMALE            10             135
  MALE               3             245
[1] 2 2
[1] FALSE
D72V8, binary
                 cls
clus                0   1
  EPB49 MUTATED     9   1
  EPB49 WILD-TYPE 283  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB49 MUTATED      9    1
  EPB49 WILD-TYPE  283   58
     clus
vv    EPB49 MUTATED EPB49 WILD-TYPE
  NO              9             283
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EPB49 MUTATED                                          0
  EPB49 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EPB49 MUTATED                                       3
  EPB49 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPB49 MUTATED                                                        7
  EPB49 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EPB49 MUTATED                                                   1
  EPB49 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPB49 MUTATED                                                                   0
  EPB49 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EPB49 MUTATED                                                    0
  EPB49 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EPB49 MUTATED                                                  2
  EPB49 WILD-TYPE                                               59
D72V9, multiclass
                                                                   clus
vv                                                                  EPB49 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  EPB49 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EPB49 MUTATED     8   0   0   4
  EPB49 WILD-TYPE 303  14  15  20
D72V10, multiclass
    clus
vv   EPB49 MUTATED EPB49 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EPB49 MUTATED       3                         0
  EPB49 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPB49 MUTATED                                           0     9
  EPB49 WILD-TYPE                                         1   234
D72V12, multiclass
                                           clus
vv                                          EPB49 MUTATED EPB49 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, binary
                 cls
clus                0   1
  EPB49 MUTATED     1  10
  EPB49 WILD-TYPE   3 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB49 MUTATED      1   10
  EPB49 WILD-TYPE    3  300
                        clus
vv                       EPB49 MUTATED EPB49 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(73) Variable = DDC MUTATION ANALYSIS
D73V1, survival
               sevent
clus2             0   1
  DDC MUTATED     8   2
  DDC WILD-TYPE 222 137
  DDC MUTATED DDC WILD-TYPE 
           10           359 
  DDC MUTATED DDC WILD-TYPE 
            2           137 
$`DDC MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8363 TCGA-CD-8531 TCGA-CG-4305 
        6.97        34.68        35.84         0.26        12.59        15.95 
TCGA-CG-4455 TCGA-CG-5721 TCGA-HU-A4GX TCGA-SW-A7EA 
       12.03         6.02        20.25        19.04 

$`DDC WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  DDC MUTATED DDC WILD-TYPE 
         0.26          0.00 
  DDC MUTATED DDC WILD-TYPE 
        35.84        122.30 
  DDC MUTATED DDC WILD-TYPE 
        14.27         14.27 
[1] "0.3 - 35.8 (14.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.7"
D73V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDC MUTATED         0        0        3        2         1         0
  DDC WILD-TYPE       2       15       37       28        36        52
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDC MUTATED           0          2          0          1        1
  DDC WILD-TYPE         3         68         53         31       37
D73V3, multiclass
            clus
vv           DDC MUTATED DDC WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             3            37
  STAGE II             2            28
  STAGE IIA            1            36
  STAGE IIB            0            52
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           0            53
  STAGE IIIC           1            31
  STAGE IV             1            37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  DDC MUTATED     0   5   3   2
  DDC WILD-TYPE  22  87 170  95
D73V4, multiclass
    clus
vv   DDC MUTATED DDC WILD-TYPE
  T1           0            22
  T2           5            87
  T3           3           170
  T4           2            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
  DDC MUTATED     4   5   1   0
  DDC WILD-TYPE 114  99  76  77
D73V5, multiclass
    clus
vv   DDC MUTATED DDC WILD-TYPE
  N0           4           114
  N1           5            99
  N2           1            76
  N3           0            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"
D73V6, binary
               cls
clus              0   1
  DDC MUTATED     9   0
  DDC WILD-TYPE 337  29
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDC MUTATED      9    0
  DDC WILD-TYPE  337   29
   clus
vv  DDC MUTATED DDC WILD-TYPE
  0           9           337
  1           0            29
[1] 2 2
[1] FALSE
D73V7, binary
               cls
clus              0   1
  DDC MUTATED     6   4
  DDC WILD-TYPE 139 244
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDC MUTATED      6    4
  DDC WILD-TYPE  139  244
        clus
vv       DDC MUTATED DDC WILD-TYPE
  FEMALE           6           139
  MALE             4           244
[1] 2 2
[1] FALSE
D73V8, binary
               cls
clus              0   1
  DDC MUTATED     9   1
  DDC WILD-TYPE 283  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDC MUTATED      9    1
  DDC WILD-TYPE  283   58
     clus
vv    DDC MUTATED DDC WILD-TYPE
  NO            9           283
  YES           1            58
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DDC MUTATED                                          0
  DDC WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DDC MUTATED                                       3
  DDC WILD-TYPE                                    67
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DDC MUTATED                                                        5
  DDC WILD-TYPE                                                    153
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DDC MUTATED                                                   1
  DDC WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DDC MUTATED                                                                   1
  DDC WILD-TYPE                                                                67
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DDC MUTATED                                                    0
  DDC WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DDC MUTATED                                                  0
  DDC WILD-TYPE                                               61
D73V9, multiclass
                                                                   clus
vv                                                                  DDC MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            0
                                                                   clus
vv                                                                  DDC WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  DDC MUTATED     9   0   0   1
  DDC WILD-TYPE 302  14  15  23
D73V10, multiclass
    clus
vv   DDC MUTATED DDC WILD-TYPE
  R0           9           302
  R1           0            14
  R2           0            15
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  DDC MUTATED       2                         0
  DDC WILD-TYPE    85                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDC MUTATED                                           0     5
  DDC WILD-TYPE                                         1   238
D73V12, multiclass
                                           clus
vv                                          DDC MUTATED DDC WILD-TYPE
  ASIAN                                               2            85
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               5           238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V13, binary
               cls
clus              0   1
  DDC MUTATED     0   7
  DDC WILD-TYPE   4 303
[1] "tbl2"
               cls
clus            [,1] [,2]
  DDC MUTATED      0    7
  DDC WILD-TYPE    4  303
                        clus
vv                       DDC MUTATED DDC WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           7           303
[1] 2 2
[1] FALSE

Clustering(74) Variable = IWS1 MUTATION ANALYSIS
D74V1, survival
                sevent
clus2              0   1
  IWS1 MUTATED    11   2
  IWS1 WILD-TYPE 219 137
  IWS1 MUTATED IWS1 WILD-TYPE 
            13            356 
  IWS1 MUTATED IWS1 WILD-TYPE 
             2            137 
$`IWS1 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8487 TCGA-CD-8534 
        6.97        34.68        29.59         6.18         1.12        12.07 
TCGA-CG-4465 TCGA-CG-5723 TCGA-D7-A4YX TCGA-D7-A6EV TCGA-HF-A5NB TCGA-HU-A4GU 
        9.01       105.07        36.43        11.24        30.51         6.58 
TCGA-HU-A4H3 
       29.00 

$`IWS1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  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          14.35 
[1] "1.1 - 105.1 (12.1)" "0.0 - 122.3 (14.3)"
[1] "hr=" "2.8"
D74V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IWS1 MUTATED         0        0        0        2         3         4
  IWS1 WILD-TYPE       2       15       40       28        34        48
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IWS1 MUTATED           0          2          0          2        1
  IWS1 WILD-TYPE         3         68         53         30       37
D74V3, multiclass
            clus
vv           IWS1 MUTATED IWS1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              2             28
  STAGE IIA             3             34
  STAGE IIB             4             48
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IWS1 MUTATED     0   2   7   5
  IWS1 WILD-TYPE  22  90 166  92
D74V4, multiclass
    clus
vv   IWS1 MUTATED IWS1 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            7            166
  T4            5             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
  IWS1 MUTATED     6   4   1   3
  IWS1 WILD-TYPE 112 100  76  74
D74V5, multiclass
    clus
vv   IWS1 MUTATED IWS1 WILD-TYPE
  N0            6            112
  N1            4            100
  N2            1             76
  N3            3             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"
D74V6, binary
                cls
clus               0   1
  IWS1 MUTATED    12   1
  IWS1 WILD-TYPE 334  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  IWS1 MUTATED     12    1
  IWS1 WILD-TYPE  334   28
   clus
vv  IWS1 MUTATED IWS1 WILD-TYPE
  0           12            334
  1            1             28
[1] 2 2
[1] FALSE
D74V7, binary
                cls
clus               0   1
  IWS1 MUTATED     8   6
  IWS1 WILD-TYPE 137 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  IWS1 MUTATED      8    6
  IWS1 WILD-TYPE  137  242
        clus
vv       IWS1 MUTATED IWS1 WILD-TYPE
  FEMALE            8            137
  MALE              6            242
[1] 2 2
[1] FALSE
D74V8, binary
                cls
clus               0   1
  IWS1 MUTATED    10   1
  IWS1 WILD-TYPE 282  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  IWS1 MUTATED     10    1
  IWS1 WILD-TYPE  282   58
     clus
vv    IWS1 MUTATED IWS1 WILD-TYPE
  NO            10            282
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IWS1 MUTATED                                          0
  IWS1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IWS1 MUTATED                                       4
  IWS1 WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IWS1 MUTATED                                                        8
  IWS1 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IWS1 MUTATED                                                   1
  IWS1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IWS1 MUTATED                                                                   1
  IWS1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IWS1 MUTATED                                                    0
  IWS1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IWS1 MUTATED                                                  0
  IWS1 WILD-TYPE                                               61
D74V9, multiclass
                                                                   clus
vv                                                                  IWS1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  IWS1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IWS1 MUTATED    10   1   1   2
  IWS1 WILD-TYPE 301  13  14  22
D74V10, multiclass
    clus
vv   IWS1 MUTATED IWS1 WILD-TYPE
  R0           10            301
  R1            1             13
  R2            1             14
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IWS1 MUTATED       3                         0
  IWS1 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IWS1 MUTATED                                           0     8
  IWS1 WILD-TYPE                                         1   235
D74V12, multiclass
                                           clus
vv                                          IWS1 MUTATED IWS1 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V13, binary
                cls
clus               0   1
  IWS1 MUTATED     0  11
  IWS1 WILD-TYPE   4 299
[1] "tbl2"
                cls
clus             [,1] [,2]
  IWS1 MUTATED      0   11
  IWS1 WILD-TYPE    4  299
                        clus
vv                       IWS1 MUTATED IWS1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           11            299
[1] 2 2
[1] FALSE

Clustering(75) Variable = LMAN1 MUTATION ANALYSIS
D75V1, survival
                 sevent
clus2               0   1
  LMAN1 MUTATED    10   0
  LMAN1 WILD-TYPE 220 139
  LMAN1 MUTATED LMAN1 WILD-TYPE 
             10             359 
  LMAN1 MUTATED LMAN1 WILD-TYPE 
              0             139 
$`LMAN1 MUTATED`
TCGA-BR-8078 TCGA-BR-8680 TCGA-CG-5728 TCGA-F1-A448 TCGA-HU-A4GN TCGA-HU-A4GT 
       29.59        31.96        65.10        21.27        29.98         6.51 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-R5-A7ZI 
       20.25        29.00        14.07        74.53 

$`LMAN1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A4GP 
        3.25        22.75        25.81        11.77        21.37         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-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 

  LMAN1 MUTATED LMAN1 WILD-TYPE 
           6.51            0.00 
  LMAN1 MUTATED LMAN1 WILD-TYPE 
          74.53          122.30 
  LMAN1 MUTATED LMAN1 WILD-TYPE 
         29.295          14.040 
[1] "6.5 - 74.5 (29.3)"  "0.0 - 122.3 (14.0)"
[1] "hr="     "2.6e+07"
D75V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LMAN1 MUTATED         0        0        3        0         2         1
  LMAN1 WILD-TYPE       2       15       37       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LMAN1 MUTATED           0          1          1          2        3
  LMAN1 WILD-TYPE         3         69         52         30       35
D75V3, multiclass
            clus
vv           LMAN1 MUTATED LMAN1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LMAN1 MUTATED     1   3   2   7
  LMAN1 WILD-TYPE  21  89 171  90
D75V4, multiclass
    clus
vv   LMAN1 MUTATED LMAN1 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             2             171
  T4             7              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
  LMAN1 MUTATED     5   3   3   2
  LMAN1 WILD-TYPE 113 101  74  75
D75V5, multiclass
    clus
vv   LMAN1 MUTATED LMAN1 WILD-TYPE
  N0             5             113
  N1             3             101
  N2             3              74
  N3             2              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"
D75V6, binary
                 cls
clus                0   1
  LMAN1 MUTATED    11   2
  LMAN1 WILD-TYPE 335  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMAN1 MUTATED     11    2
  LMAN1 WILD-TYPE  335   27
   clus
vv  LMAN1 MUTATED LMAN1 WILD-TYPE
  0            11             335
  1             2              27
[1] 2 2
[1] FALSE
D75V7, binary
                 cls
clus                0   1
  LMAN1 MUTATED     8   5
  LMAN1 WILD-TYPE 137 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMAN1 MUTATED      8    5
  LMAN1 WILD-TYPE  137  243
        clus
vv       LMAN1 MUTATED LMAN1 WILD-TYPE
  FEMALE             8             137
  MALE               5             243
[1] 2 2
[1] FALSE
D75V8, binary
                 cls
clus                0   1
  LMAN1 MUTATED     7   1
  LMAN1 WILD-TYPE 285  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMAN1 MUTATED      7    1
  LMAN1 WILD-TYPE  285   58
     clus
vv    LMAN1 MUTATED LMAN1 WILD-TYPE
  NO              7             285
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LMAN1 MUTATED                                          0
  LMAN1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LMAN1 MUTATED                                       3
  LMAN1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LMAN1 MUTATED                                                        3
  LMAN1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LMAN1 MUTATED                                                   1
  LMAN1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LMAN1 MUTATED                                                                   2
  LMAN1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LMAN1 MUTATED                                                    0
  LMAN1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LMAN1 MUTATED                                                  4
  LMAN1 WILD-TYPE                                               57
D75V9, multiclass
                                                                   clus
vv                                                                  LMAN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  LMAN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LMAN1 MUTATED    11   0   0   2
  LMAN1 WILD-TYPE 300  14  15  22
D75V10, multiclass
    clus
vv   LMAN1 MUTATED LMAN1 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LMAN1 MUTATED       6                         0
  LMAN1 WILD-TYPE    81                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LMAN1 MUTATED                                           0     5
  LMAN1 WILD-TYPE                                         1   238
D75V12, multiclass
                                           clus
vv                                          LMAN1 MUTATED LMAN1 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V13, binary
                 cls
clus                0   1
  LMAN1 MUTATED     2   9
  LMAN1 WILD-TYPE   2 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMAN1 MUTATED      2    9
  LMAN1 WILD-TYPE    2  301
                        clus
vv                       LMAN1 MUTATED LMAN1 WILD-TYPE
  HISPANIC OR LATINO                 2               2
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(76) Variable = FAM116A MUTATION ANALYSIS
D76V1, survival
                   sevent
clus2                 0   1
  FAM116A MUTATED     6   2
  FAM116A WILD-TYPE 224 137
  FAM116A MUTATED FAM116A WILD-TYPE 
                8               361 
  FAM116A MUTATED FAM116A WILD-TYPE 
                2               137 
$`FAM116A MUTATED`
TCGA-BR-4201 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-4305 TCGA-HF-A5NB TCGA-HU-A4GT 
       30.90        31.96        11.77        15.95        30.51         6.51 
TCGA-HU-A4GX TCGA-IN-A6RN 
       20.25        19.53 

$`FAM116A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  FAM116A MUTATED FAM116A WILD-TYPE 
             6.51              0.00 
  FAM116A MUTATED FAM116A WILD-TYPE 
            31.96            122.30 
  FAM116A MUTATED FAM116A WILD-TYPE 
            19.89             14.07 
[1] "6.5 - 32.0 (19.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D76V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM116A MUTATED         0        0        1        1         2         0
  FAM116A WILD-TYPE       2       15       39       29        35        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM116A MUTATED           0          1          0          2        1
  FAM116A WILD-TYPE         3         69         53         30       37
D76V3, multiclass
            clus
vv           FAM116A MUTATED FAM116A WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                2                35
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               2                30
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM116A MUTATED     1   3   2   3
  FAM116A WILD-TYPE  21  89 171  94
D76V4, multiclass
    clus
vv   FAM116A MUTATED FAM116A WILD-TYPE
  T1               1                21
  T2               3                89
  T3               2               171
  T4               3                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
  FAM116A MUTATED     2   2   3   1
  FAM116A WILD-TYPE 116 102  74  76
D76V5, multiclass
    clus
vv   FAM116A MUTATED FAM116A WILD-TYPE
  N0               2               116
  N1               2               102
  N2               3                74
  N3               1                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"
D76V6, binary
                   cls
clus                  0   1
  FAM116A MUTATED     8   1
  FAM116A WILD-TYPE 338  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM116A MUTATED      8    1
  FAM116A WILD-TYPE  338   28
   clus
vv  FAM116A MUTATED FAM116A WILD-TYPE
  0               8               338
  1               1                28
[1] 2 2
[1] FALSE
D76V7, binary
                   cls
clus                  0   1
  FAM116A MUTATED     5   4
  FAM116A WILD-TYPE 140 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM116A MUTATED      5    4
  FAM116A WILD-TYPE  140  244
        clus
vv       FAM116A MUTATED FAM116A WILD-TYPE
  FEMALE               5               140
  MALE                 4               244
[1] 2 2
[1] FALSE
D76V8, binary
                   cls
clus                  0   1
  FAM116A MUTATED     7   1
  FAM116A WILD-TYPE 285  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM116A MUTATED      7    1
  FAM116A WILD-TYPE  285   58
     clus
vv    FAM116A MUTATED FAM116A WILD-TYPE
  NO                7               285
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM116A MUTATED                                          0
  FAM116A WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM116A MUTATED                                       1
  FAM116A WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM116A MUTATED                                                        4
  FAM116A WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM116A MUTATED                                                   1
  FAM116A WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM116A MUTATED                                                                   1
  FAM116A WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM116A MUTATED                                                    0
  FAM116A WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM116A MUTATED                                                  2
  FAM116A WILD-TYPE                                               59
D76V9, multiclass
                                                                   clus
vv                                                                  FAM116A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  FAM116A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM116A MUTATED     6   1   0   1
  FAM116A WILD-TYPE 305  13  15  23
D76V10, multiclass
    clus
vv   FAM116A MUTATED FAM116A WILD-TYPE
  R0               6               305
  R1               1                13
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM116A MUTATED       4                         0
  FAM116A WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM116A MUTATED                                           0     2
  FAM116A WILD-TYPE                                         1   241
D76V12, multiclass
                                           clus
vv                                          FAM116A MUTATED FAM116A WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V13, binary
                   cls
clus                  0   1
  FAM116A MUTATED     0   6
  FAM116A WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM116A MUTATED      0    6
  FAM116A WILD-TYPE    4  304
                        clus
vv                       FAM116A MUTATED FAM116A WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(77) Variable = KIAA0664 MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  KIAA0664 MUTATED    12   7
  KIAA0664 WILD-TYPE 218 132
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                19                350 
  KIAA0664 MUTATED KIAA0664 WILD-TYPE 
                 7                132 
$`KIAA0664 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8363 
        6.97         6.61        34.68        29.59         6.18         0.26 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-A74A 
        6.58         6.02        12.03        28.96        65.10        19.96 
TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-MX-A5UJ TCGA-VQ-A8DT 
       30.51        22.32         0.10        20.25        19.73        48.79 
TCGA-VQ-A8P2 
       38.14 

$`KIAA0664 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  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              14.12 
[1] "0.1 - 65.1 (20.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0664 MUTATED         1        1        2        0         3         2
  KIAA0664 WILD-TYPE       1       14       38       30        34        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0664 MUTATED           1          5          1          4        3
  KIAA0664 WILD-TYPE         2         65         52         28       35
D77V3, multiclass
            clus
vv           KIAA0664 MUTATED KIAA0664 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  1                 14
  STAGE IB                  2                 38
  STAGE II                  0                 30
  STAGE IIA                 3                 34
  STAGE IIB                 2                 50
  STAGE III                 1                  2
  STAGE IIIA                5                 65
  STAGE IIIB                1                 52
  STAGE IIIC                4                 28
  STAGE IV                  3                 35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0664 MUTATED     2   3   8  10
  KIAA0664 WILD-TYPE  20  89 165  87
D77V4, multiclass
    clus
vv   KIAA0664 MUTATED KIAA0664 WILD-TYPE
  T1                2                 20
  T2                3                 89
  T3                8                165
  T4               10                 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
  KIAA0664 MUTATED     9   5   5   4
  KIAA0664 WILD-TYPE 109  99  72  73
D77V5, multiclass
    clus
vv   KIAA0664 MUTATED KIAA0664 WILD-TYPE
  N0                9                109
  N1                5                 99
  N2                5                 72
  N3                4                 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"
D77V6, binary
                    cls
clus                   0   1
  KIAA0664 MUTATED    20   1
  KIAA0664 WILD-TYPE 326  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0664 MUTATED     20    1
  KIAA0664 WILD-TYPE  326   28
   clus
vv  KIAA0664 MUTATED KIAA0664 WILD-TYPE
  0               20                326
  1                1                 28
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  KIAA0664 MUTATED    13  10
  KIAA0664 WILD-TYPE 132 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0664 MUTATED     13   10
  KIAA0664 WILD-TYPE  132  238
        clus
vv       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  FEMALE               13                132
  MALE                 10                238
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  KIAA0664 MUTATED    16   3
  KIAA0664 WILD-TYPE 276  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0664 MUTATED     16    3
  KIAA0664 WILD-TYPE  276   56
     clus
vv    KIAA0664 MUTATED KIAA0664 WILD-TYPE
  NO                16                276
  YES                3                 56
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA0664 MUTATED                                          0
  KIAA0664 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA0664 MUTATED                                       4
  KIAA0664 WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0664 MUTATED                                                        9
  KIAA0664 WILD-TYPE                                                    149
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA0664 MUTATED                                                   2
  KIAA0664 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0664 MUTATED                                                                   5
  KIAA0664 WILD-TYPE                                                                63
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA0664 MUTATED                                                    0
  KIAA0664 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA0664 MUTATED                                                  3
  KIAA0664 WILD-TYPE                                               58
D77V9, multiclass
                                                                   clus
vv                                                                  KIAA0664 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 3
                                                                   clus
vv                                                                  KIAA0664 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0664 MUTATED    16   1   1   4
  KIAA0664 WILD-TYPE 295  13  14  20
D77V10, multiclass
    clus
vv   KIAA0664 MUTATED KIAA0664 WILD-TYPE
  R0               16                295
  R1                1                 13
  R2                1                 14
  RX                4                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0664 MUTATED       4                         1
  KIAA0664 WILD-TYPE    83                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0664 MUTATED                                           0    12
  KIAA0664 WILD-TYPE                                         1   231
D77V12, multiclass
                                           clus
vv                                          KIAA0664 MUTATED KIAA0664 WILD-TYPE
  ASIAN                                                    4                 83
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   12                231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V13, binary
                    cls
clus                   0   1
  KIAA0664 MUTATED     0  16
  KIAA0664 WILD-TYPE   4 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0664 MUTATED      0   16
  KIAA0664 WILD-TYPE    4  294
                        clus
vv                       KIAA0664 MUTATED KIAA0664 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               16                294
[1] 2 2
[1] FALSE

Clustering(78) Variable = JARID2 MUTATION ANALYSIS
D78V1, survival
                  sevent
clus2                0   1
  JARID2 MUTATED    25   7
  JARID2 WILD-TYPE 205 132
  JARID2 MUTATED JARID2 WILD-TYPE 
              32              337 
  JARID2 MUTATED JARID2 WILD-TYPE 
               7              132 
$`JARID2 MUTATED`
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8368 
        9.67        34.68        44.94        14.43        29.59         4.31 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-8536 TCGA-CD-A4MG 
       25.05         1.12        28.14        31.96        12.43         6.58 
TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4455 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-5578 
       12.62         1.02        12.03       105.07        28.96        12.66 
TCGA-D7-A74A TCGA-F1-6874 TCGA-FP-A9TM TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GQ 
       19.96        14.47         6.21        22.68        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-R5-A7ZI 
        6.51         2.10        29.00        14.07        19.73        74.53 
TCGA-SW-A7EA TCGA-VQ-A8P2 
       19.04        38.14 

$`JARID2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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-D7-5579 
        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-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-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
        8.38         4.34         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-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-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-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-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-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 

  JARID2 MUTATED JARID2 WILD-TYPE 
             0.1              0.0 
  JARID2 MUTATED JARID2 WILD-TYPE 
          105.07           122.30 
  JARID2 MUTATED JARID2 WILD-TYPE 
          16.755           14.070 
[1] "0.1 - 105.1 (16.8)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2"  
D78V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  JARID2 MUTATED         0        1        6        3         6         2
  JARID2 WILD-TYPE       2       14       34       27        31        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  JARID2 MUTATED           1          5          0          5        3
  JARID2 WILD-TYPE         2         65         53         27       35
D78V3, multiclass
            clus
vv           JARID2 MUTATED JARID2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                6               34
  STAGE II                3               27
  STAGE IIA               6               31
  STAGE IIB               2               50
  STAGE III               1                2
  STAGE IIIA              5               65
  STAGE IIIB              0               53
  STAGE IIIC              5               27
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  JARID2 MUTATED     4   8  12  11
  JARID2 WILD-TYPE  18  84 161  86
D78V4, multiclass
    clus
vv   JARID2 MUTATED JARID2 WILD-TYPE
  T1              4               18
  T2              8               84
  T3             12              161
  T4             11               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
  JARID2 MUTATED    14   9   6   4
  JARID2 WILD-TYPE 104  95  71  73
D78V5, multiclass
    clus
vv   JARID2 MUTATED JARID2 WILD-TYPE
  N0             14              104
  N1              9               95
  N2              6               71
  N3              4               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"
D78V6, binary
                  cls
clus                 0   1
  JARID2 MUTATED    32   3
  JARID2 WILD-TYPE 314  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JARID2 MUTATED     32    3
  JARID2 WILD-TYPE  314   26
   clus
vv  JARID2 MUTATED JARID2 WILD-TYPE
  0             32              314
  1              3               26
[1] 2 2
[1] FALSE
D78V7, binary
                  cls
clus                 0   1
  JARID2 MUTATED    17  19
  JARID2 WILD-TYPE 128 229
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JARID2 MUTATED     17   19
  JARID2 WILD-TYPE  128  229
        clus
vv       JARID2 MUTATED JARID2 WILD-TYPE
  FEMALE             17              128
  MALE               19              229
[1] 2 2
[1] FALSE
D78V8, binary
                  cls
clus                 0   1
  JARID2 MUTATED    27   2
  JARID2 WILD-TYPE 265  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JARID2 MUTATED     27    2
  JARID2 WILD-TYPE  265   57
     clus
vv    JARID2 MUTATED JARID2 WILD-TYPE
  NO              27              265
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  JARID2 MUTATED                                          0
  JARID2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  JARID2 MUTATED                                       6
  JARID2 WILD-TYPE                                    64
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  JARID2 MUTATED                                                       16
  JARID2 WILD-TYPE                                                    142
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  JARID2 MUTATED                                                   2
  JARID2 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  JARID2 MUTATED                                                                   4
  JARID2 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  JARID2 MUTATED                                                    0
  JARID2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  JARID2 MUTATED                                                  8
  JARID2 WILD-TYPE                                               53
D78V9, multiclass
                                                                   clus
vv                                                                  JARID2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               8
                                                                   clus
vv                                                                  JARID2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                53
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  JARID2 MUTATED    28   0   1   4
  JARID2 WILD-TYPE 283  14  14  20
D78V10, multiclass
    clus
vv   JARID2 MUTATED JARID2 WILD-TYPE
  R0             28              283
  R1              0               14
  R2              1               14
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  JARID2 MUTATED      11                         0
  JARID2 WILD-TYPE    76                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  JARID2 MUTATED                                           0    20
  JARID2 WILD-TYPE                                         1   223
D78V12, multiclass
                                           clus
vv                                          JARID2 MUTATED JARID2 WILD-TYPE
  ASIAN                                                 11               76
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 20              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V13, binary
                  cls
clus                 0   1
  JARID2 MUTATED     1  29
  JARID2 WILD-TYPE   3 281
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JARID2 MUTATED      1   29
  JARID2 WILD-TYPE    3  281
                        clus
vv                       JARID2 MUTATED JARID2 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             29              281
[1] 2 2
[1] FALSE

Clustering(79) Variable = SLC9A10 MUTATION ANALYSIS
D79V1, survival
                   sevent
clus2                 0   1
  SLC9A10 MUTATED     9   3
  SLC9A10 WILD-TYPE 221 136
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               12               357 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
                3               136 
$`SLC9A10 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8680 TCGA-CG-5721 
       34.68        29.59         6.18         0.26        31.96         6.02 
TCGA-CG-5723 TCGA-D7-A6EY TCGA-HU-8602 TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-VQ-A8P2 
      105.07        11.44        22.32        19.73         8.61        38.14 

$`SLC9A10 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
             0.26              0.00 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
           105.07            122.30 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
           21.025            14.170 
[1] "0.3 - 105.1 (21.0)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.9"
D79V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC9A10 MUTATED         1        0        1        1         2         2
  SLC9A10 WILD-TYPE       1       15       39       29        35        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A10 MUTATED           0          2          1          0        3
  SLC9A10 WILD-TYPE         3         68         52         32       35
D79V3, multiclass
            clus
vv           SLC9A10 MUTATED SLC9A10 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                2                35
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 3                35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC9A10 MUTATED     1   2   5   5
  SLC9A10 WILD-TYPE  21  90 168  92
D79V4, multiclass
    clus
vv   SLC9A10 MUTATED SLC9A10 WILD-TYPE
  T1               1                21
  T2               2                90
  T3               5               168
  T4               5                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
  SLC9A10 MUTATED     5   4   2   2
  SLC9A10 WILD-TYPE 113 100  75  75
D79V5, multiclass
    clus
vv   SLC9A10 MUTATED SLC9A10 WILD-TYPE
  N0               5               113
  N1               4               100
  N2               2                75
  N3               2                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"
D79V6, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED    11   1
  SLC9A10 WILD-TYPE 335  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED     11    1
  SLC9A10 WILD-TYPE  335   28
   clus
vv  SLC9A10 MUTATED SLC9A10 WILD-TYPE
  0              11               335
  1               1                28
[1] 2 2
[1] FALSE
D79V7, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED     6   7
  SLC9A10 WILD-TYPE 139 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED      6    7
  SLC9A10 WILD-TYPE  139  241
        clus
vv       SLC9A10 MUTATED SLC9A10 WILD-TYPE
  FEMALE               6               139
  MALE                 7               241
[1] 2 2
[1] FALSE
D79V8, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED    12   1
  SLC9A10 WILD-TYPE 280  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED     12    1
  SLC9A10 WILD-TYPE  280   58
     clus
vv    SLC9A10 MUTATED SLC9A10 WILD-TYPE
  NO               12               280
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC9A10 MUTATED                                          0
  SLC9A10 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC9A10 MUTATED                                       1
  SLC9A10 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC9A10 MUTATED                                                        5
  SLC9A10 WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC9A10 MUTATED                                                   1
  SLC9A10 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC9A10 MUTATED                                                                   3
  SLC9A10 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC9A10 MUTATED                                                    0
  SLC9A10 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC9A10 MUTATED                                                  3
  SLC9A10 WILD-TYPE                                               58
D79V9, multiclass
                                                                   clus
vv                                                                  SLC9A10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  SLC9A10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC9A10 MUTATED    12   0   1   0
  SLC9A10 WILD-TYPE 299  14  14  24
D79V10, multiclass
    clus
vv   SLC9A10 MUTATED SLC9A10 WILD-TYPE
  R0              12               299
  R1               0                14
  R2               1                14
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC9A10 MUTATED       2                         1
  SLC9A10 WILD-TYPE    85                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC9A10 MUTATED                                           1     7
  SLC9A10 WILD-TYPE                                         0   236
D79V12, multiclass
                                           clus
vv                                          SLC9A10 MUTATED SLC9A10 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                   7               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V13, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED     0  10
  SLC9A10 WILD-TYPE   4 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED      0   10
  SLC9A10 WILD-TYPE    4  300
                        clus
vv                       SLC9A10 MUTATED SLC9A10 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              10               300
[1] 2 2
[1] FALSE

Clustering(80) Variable = ZFP36L2 MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  ZFP36L2 MUTATED    10   2
  ZFP36L2 WILD-TYPE 220 137
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               12               357 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                2               137 
$`ZFP36L2 MUTATED`
TCGA-BR-7716 TCGA-BR-8284 TCGA-BR-8361 TCGA-BR-8367 TCGA-BR-8487 TCGA-D7-6521 
       39.78         8.05        31.10        26.33         1.12        18.54 
TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4H8 TCGA-IP-7968 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       24.20         6.51        14.07         2.53        19.73        38.14 

$`ZFP36L2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-8368 
        6.18         0.26        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-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-D7-6522 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-D7-8576 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-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-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-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 

  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
             1.12              0.00 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
            39.78            122.30 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
           19.135            14.170 
[1] "1.1 - 39.8 (19.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.5"
D80V2, 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       2       14       38       30        35        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFP36L2 MUTATED           0          2          2          2        0
  ZFP36L2 WILD-TYPE         3         68         51         30       38
D80V3, multiclass
            clus
vv           ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               2                51
  STAGE IIIC               2                30
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZFP36L2 MUTATED     2   2   6   3
  ZFP36L2 WILD-TYPE  20  90 167  94
D80V4, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  T1               2                20
  T2               2                90
  T3               6               167
  T4               3                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
  ZFP36L2 MUTATED     4   3   4   2
  ZFP36L2 WILD-TYPE 114 101  73  75
D80V5, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  N0               4               114
  N1               3               101
  N2               4                73
  N3               2                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"
D80V6, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED    13   0
  ZFP36L2 WILD-TYPE 333  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED     13    0
  ZFP36L2 WILD-TYPE  333   29
   clus
vv  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  0              13               333
  1               0                29
[1] 2 2
[1] FALSE
D80V7, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     7   7
  ZFP36L2 WILD-TYPE 138 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      7    7
  ZFP36L2 WILD-TYPE  138  241
        clus
vv       ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  FEMALE               7               138
  MALE                 7               241
[1] 2 2
[1] FALSE
D80V8, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED    10   1
  ZFP36L2 WILD-TYPE 282  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED     10    1
  ZFP36L2 WILD-TYPE  282   58
     clus
vv    ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  NO               10               282
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZFP36L2 MUTATED                                          0
  ZFP36L2 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZFP36L2 MUTATED                                       1
  ZFP36L2 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZFP36L2 MUTATED                                                        6
  ZFP36L2 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZFP36L2 MUTATED                                                   1
  ZFP36L2 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZFP36L2 MUTATED                                                                   2
  ZFP36L2 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZFP36L2 MUTATED                                                    0
  ZFP36L2 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZFP36L2 MUTATED                                                  4
  ZFP36L2 WILD-TYPE                                               57
D80V9, multiclass
                                                                   clus
vv                                                                  ZFP36L2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                4
                                                                   clus
vv                                                                  ZFP36L2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZFP36L2 MUTATED    13   0   0   1
  ZFP36L2 WILD-TYPE 298  14  15  23
D80V10, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  R0              13               298
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ZFP36L2 MUTATED       3                         0
  ZFP36L2 WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZFP36L2 MUTATED                                           0    10
  ZFP36L2 WILD-TYPE                                         1   233
D80V12, multiclass
                                           clus
vv                                          ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V13, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     0  12
  ZFP36L2 WILD-TYPE   4 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      0   12
  ZFP36L2 WILD-TYPE    4  298
                        clus
vv                       ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              12               298
[1] 2 2
[1] FALSE

Clustering(81) Variable = CTCF MUTATION ANALYSIS
D81V1, survival
                sevent
clus2              0   1
  CTCF MUTATED     9   6
  CTCF WILD-TYPE 221 133
  CTCF MUTATED CTCF WILD-TYPE 
            15            354 
  CTCF MUTATED CTCF WILD-TYPE 
             6            133 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.24        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-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-8589 
        3.72         5.39        25.18         9.21        20.22        27.12 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34        28.14         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-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-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-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 

  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          14.22 
[1] "0.3 - 105.1 (16.1)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1"  
D81V2, 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       2       15       37       29        35        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTCF MUTATED           0          0          2          1        3
  CTCF WILD-TYPE         3         70         51         31       35
D81V3, multiclass
            clus
vv           CTCF MUTATED CTCF WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              3             37
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            2             51
  STAGE IIIC            1             31
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTCF MUTATED     0   4   3   8
  CTCF WILD-TYPE  22  88 170  89
D81V4, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  T1            0             22
  T2            4             88
  T3            3            170
  T4            8             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
  CTCF MUTATED     8   5   1   2
  CTCF WILD-TYPE 110  99  76  75
D81V5, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  N0            8            110
  N1            5             99
  N2            1             76
  N3            2             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"
D81V6, binary
                cls
clus               0   1
  CTCF MUTATED    14   1
  CTCF WILD-TYPE 332  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     14    1
  CTCF WILD-TYPE  332   28
   clus
vv  CTCF MUTATED CTCF WILD-TYPE
  0           14            332
  1            1             28
[1] 2 2
[1] FALSE
D81V7, binary
                cls
clus               0   1
  CTCF MUTATED    10   6
  CTCF WILD-TYPE 135 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     10    6
  CTCF WILD-TYPE  135  242
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  FEMALE           10            135
  MALE              6            242
[1] 2 2
[1] FALSE
D81V8, binary
                cls
clus               0   1
  CTCF MUTATED    15   1
  CTCF WILD-TYPE 277  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     15    1
  CTCF WILD-TYPE  277   58
     clus
vv    CTCF MUTATED CTCF WILD-TYPE
  NO            15            277
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CTCF MUTATED                                          1
  CTCF WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CTCF MUTATED                                       1
  CTCF WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTCF MUTATED                                                        9
  CTCF WILD-TYPE                                                    149
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CTCF MUTATED                                                   1
  CTCF WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTCF MUTATED                                                                   2
  CTCF WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CTCF MUTATED                                                    0
  CTCF WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CTCF MUTATED                                                  2
  CTCF WILD-TYPE                                               59
D81V9, multiclass
                                                                   clus
vv                                                                  CTCF MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  CTCF WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CTCF MUTATED    14   1   0   1
  CTCF WILD-TYPE 297  13  15  23
D81V10, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  R0           14            297
  R1            1             13
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CTCF MUTATED       2                         0
  CTCF WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTCF MUTATED                                           0    11
  CTCF WILD-TYPE                                         1   232
D81V12, multiclass
                                           clus
vv                                          CTCF MUTATED CTCF WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V13, binary
                cls
clus               0   1
  CTCF MUTATED     0  13
  CTCF WILD-TYPE   4 297
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED      0   13
  CTCF WILD-TYPE    4  297
                        clus
vv                       CTCF MUTATED CTCF WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           13            297
[1] 2 2
[1] FALSE

Clustering(82) Variable = HDAC4 MUTATION ANALYSIS
D82V1, survival
                 sevent
clus2               0   1
  HDAC4 MUTATED    17   6
  HDAC4 WILD-TYPE 213 133
  HDAC4 MUTATED HDAC4 WILD-TYPE 
             23             346 
  HDAC4 MUTATED HDAC4 WILD-TYPE 
              6             133 
$`HDAC4 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8487 
       26.70        34.68        31.10         4.31        31.27         1.12 
TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5725 TCGA-CG-5733 TCGA-D7-A4YY 
       28.14        16.14         6.58        15.02        21.07        13.78 
TCGA-F1-6874 TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GN 
       14.47        77.29        26.47        22.32        24.20        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-VQ-A8P2 
        0.10         6.51        20.25        29.00        38.14 

$`HDAC4 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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 
         22.320          14.025 
[1] "0.1 - 77.3 (22.3)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.9"
D82V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HDAC4 MUTATED         1        1        5        1         5         2
  HDAC4 WILD-TYPE       1       14       35       29        32        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HDAC4 MUTATED           0          3          2          6        0
  HDAC4 WILD-TYPE         3         67         51         26       38
D82V3, multiclass
            clus
vv           HDAC4 MUTATED HDAC4 WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               5              35
  STAGE II               1              29
  STAGE IIA              5              32
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             6              26
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HDAC4 MUTATED     2   8   6  10
  HDAC4 WILD-TYPE  20  84 167  87
D82V4, multiclass
    clus
vv   HDAC4 MUTATED HDAC4 WILD-TYPE
  T1             2              20
  T2             8              84
  T3             6             167
  T4            10              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
  HDAC4 MUTATED    13   4   4   5
  HDAC4 WILD-TYPE 105 100  73  72
D82V5, multiclass
    clus
vv   HDAC4 MUTATED HDAC4 WILD-TYPE
  N0            13             105
  N1             4             100
  N2             4              73
  N3             5              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"
D82V6, binary
                 cls
clus                0   1
  HDAC4 MUTATED    24   0
  HDAC4 WILD-TYPE 322  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC4 MUTATED     24    0
  HDAC4 WILD-TYPE  322   29
   clus
vv  HDAC4 MUTATED HDAC4 WILD-TYPE
  0            24             322
  1             0              29
[1] 2 2
[1] FALSE
D82V7, binary
                 cls
clus                0   1
  HDAC4 MUTATED    14  12
  HDAC4 WILD-TYPE 131 236
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC4 MUTATED     14   12
  HDAC4 WILD-TYPE  131  236
        clus
vv       HDAC4 MUTATED HDAC4 WILD-TYPE
  FEMALE            14             131
  MALE              12             236
[1] 2 2
[1] FALSE
D82V8, binary
                 cls
clus                0   1
  HDAC4 MUTATED    20   3
  HDAC4 WILD-TYPE 272  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC4 MUTATED     20    3
  HDAC4 WILD-TYPE  272   56
     clus
vv    HDAC4 MUTATED HDAC4 WILD-TYPE
  NO             20             272
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HDAC4 MUTATED                                          1
  HDAC4 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HDAC4 MUTATED                                       5
  HDAC4 WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HDAC4 MUTATED                                                       11
  HDAC4 WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HDAC4 MUTATED                                                   2
  HDAC4 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HDAC4 MUTATED                                                                   3
  HDAC4 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HDAC4 MUTATED                                                    0
  HDAC4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HDAC4 MUTATED                                                  4
  HDAC4 WILD-TYPE                                               57
D82V9, multiclass
                                                                   clus
vv                                                                  HDAC4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  HDAC4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HDAC4 MUTATED    24   0   0   1
  HDAC4 WILD-TYPE 287  14  15  23
D82V10, multiclass
    clus
vv   HDAC4 MUTATED HDAC4 WILD-TYPE
  R0            24             287
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HDAC4 MUTATED       8                         1
  HDAC4 WILD-TYPE    79                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HDAC4 MUTATED                                           0    13
  HDAC4 WILD-TYPE                                         1   230
D82V12, multiclass
                                           clus
vv                                          HDAC4 MUTATED HDAC4 WILD-TYPE
  ASIAN                                                 8              79
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V13, binary
                 cls
clus                0   1
  HDAC4 MUTATED     0  21
  HDAC4 WILD-TYPE   4 289
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC4 MUTATED      0   21
  HDAC4 WILD-TYPE    4  289
                        clus
vv                       HDAC4 MUTATED HDAC4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            21             289
[1] 2 2
[1] FALSE

Clustering(83) Variable = NAPEPLD MUTATION ANALYSIS
D83V1, survival
                   sevent
clus2                 0   1
  NAPEPLD MUTATED     6   4
  NAPEPLD WILD-TYPE 224 135
  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
               10               359 
  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
                4               135 
$`NAPEPLD MUTATED`
TCGA-BR-6452 TCGA-BR-8080 TCGA-BR-8372 TCGA-CG-4436 TCGA-CG-5723 TCGA-CG-5726 
       34.68         9.60        31.27         7.99       105.07        28.96 
TCGA-D7-A6EY TCGA-F1-6874 TCGA-HJ-7597 TCGA-VQ-A8P2 
       11.44        14.47        26.47        38.14 

$`NAPEPLD WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8081 TCGA-BR-8284 
       14.43        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-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-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-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-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-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 

  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
             7.99              0.00 
  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
           105.07            122.30 
  NAPEPLD MUTATED NAPEPLD WILD-TYPE 
           27.715            14.070 
[1] "8.0 - 105.1 (27.7)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D83V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NAPEPLD MUTATED         0        1        3        1         1         0
  NAPEPLD WILD-TYPE       2       14       37       29        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NAPEPLD MUTATED           0          1          1          2        0
  NAPEPLD WILD-TYPE         3         69         52         30       38
D83V3, multiclass
            clus
vv           NAPEPLD MUTATED NAPEPLD WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 3                37
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               2                30
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  NAPEPLD MUTATED     1   4   2   3
  NAPEPLD WILD-TYPE  21  88 171  94
D83V4, multiclass
    clus
vv   NAPEPLD MUTATED NAPEPLD WILD-TYPE
  T1               1                21
  T2               4                88
  T3               2               171
  T4               3                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
  NAPEPLD MUTATED     5   2   0   3
  NAPEPLD WILD-TYPE 113 102  77  74
D83V5, multiclass
    clus
vv   NAPEPLD MUTATED NAPEPLD WILD-TYPE
  N0               5               113
  N1               2               102
  N2               0                77
  N3               3                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"
D83V6, binary
                   cls
clus                  0   1
  NAPEPLD MUTATED     9   0
  NAPEPLD WILD-TYPE 337  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NAPEPLD MUTATED      9    0
  NAPEPLD WILD-TYPE  337   29
   clus
vv  NAPEPLD MUTATED NAPEPLD WILD-TYPE
  0               9               337
  1               0                29
[1] 2 2
[1] FALSE
D83V7, binary
                   cls
clus                  0   1
  NAPEPLD MUTATED     4   6
  NAPEPLD WILD-TYPE 141 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NAPEPLD MUTATED      4    6
  NAPEPLD WILD-TYPE  141  242
        clus
vv       NAPEPLD MUTATED NAPEPLD WILD-TYPE
  FEMALE               4               141
  MALE                 6               242
[1] 2 2
[1] FALSE
D83V8, binary
                   cls
clus                  0   1
  NAPEPLD MUTATED     8   1
  NAPEPLD WILD-TYPE 284  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NAPEPLD MUTATED      8    1
  NAPEPLD WILD-TYPE  284   58
     clus
vv    NAPEPLD MUTATED NAPEPLD WILD-TYPE
  NO                8               284
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NAPEPLD MUTATED                                          1
  NAPEPLD WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NAPEPLD MUTATED                                       0
  NAPEPLD WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NAPEPLD MUTATED                                                        3
  NAPEPLD WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NAPEPLD MUTATED                                                   2
  NAPEPLD WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NAPEPLD MUTATED                                                                   3
  NAPEPLD WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NAPEPLD MUTATED                                                    0
  NAPEPLD WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NAPEPLD MUTATED                                                  1
  NAPEPLD WILD-TYPE                                               60
D83V9, multiclass
                                                                   clus
vv                                                                  NAPEPLD MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  NAPEPLD WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  NAPEPLD MUTATED    10   0   0   0
  NAPEPLD WILD-TYPE 301  14  15  24
D83V10, multiclass
    clus
vv   NAPEPLD MUTATED NAPEPLD WILD-TYPE
  R0              10               301
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  NAPEPLD MUTATED       0                         0
  NAPEPLD WILD-TYPE    87                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NAPEPLD MUTATED                                           0     7
  NAPEPLD WILD-TYPE                                         1   236
D83V12, multiclass
                                           clus
vv                                          NAPEPLD MUTATED NAPEPLD WILD-TYPE
  ASIAN                                                   0                87
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V13, binary
                   cls
clus                  0   1
  NAPEPLD MUTATED     0   6
  NAPEPLD WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NAPEPLD MUTATED      0    6
  NAPEPLD WILD-TYPE    4  304
                        clus
vv                       NAPEPLD MUTATED NAPEPLD WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(84) Variable = RASA1 MUTATION ANALYSIS
D84V1, survival
                 sevent
clus2               0   1
  RASA1 MUTATED    10   6
  RASA1 WILD-TYPE 220 133
  RASA1 MUTATED RASA1 WILD-TYPE 
             16             353 
  RASA1 MUTATED RASA1 WILD-TYPE 
              6             133 
$`RASA1 MUTATED`
TCGA-CG-4460 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7958 TCGA-BR-8286 TCGA-BR-8680 
       21.99        32.78        44.94        29.56        29.42        31.96 
TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5726 TCGA-D7-6527 TCGA-D7-6815 
        3.02        15.95         1.02        28.96        10.26        15.98 
TCGA-D7-A6EY TCGA-HU-A4GX TCGA-R5-A7ZI TCGA-RD-A7BS 
       11.44        20.25        74.53        11.05 

$`RASA1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-4304 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       20.02        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-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-D7-6528 TCGA-D7-6817 
       18.61        17.85        13.35        17.19        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-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-A7BT TCGA-RD-A7BW 
        8.52         6.08         4.60         9.24         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 

  RASA1 MUTATED RASA1 WILD-TYPE 
           1.02            0.00 
  RASA1 MUTATED RASA1 WILD-TYPE 
          74.53          122.30 
  RASA1 MUTATED RASA1 WILD-TYPE 
          21.12           14.07 
[1] "1.0 - 74.5 (21.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D84V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RASA1 MUTATED         0        1        0        3         2         2
  RASA1 WILD-TYPE       2       14       40       27        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RASA1 MUTATED           0          1          2          1        5
  RASA1 WILD-TYPE         3         69         51         31       33
D84V3, multiclass
            clus
vv           RASA1 MUTATED RASA1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               3              27
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               5              33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RASA1 MUTATED     2   3   7   7
  RASA1 WILD-TYPE  20  89 166  90
D84V4, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  T1             2              20
  T2             3              89
  T3             7             166
  T4             7              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
  RASA1 MUTATED     6   6   4   1
  RASA1 WILD-TYPE 112  98  73  76
D84V5, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  N0             6             112
  N1             6              98
  N2             4              73
  N3             1              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"
D84V6, binary
                 cls
clus                0   1
  RASA1 MUTATED    13   5
  RASA1 WILD-TYPE 333  24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED     13    5
  RASA1 WILD-TYPE  333   24
   clus
vv  RASA1 MUTATED RASA1 WILD-TYPE
  0            13             333
  1             5              24
[1] 2 2
[1] FALSE
D84V7, binary
                 cls
clus                0   1
  RASA1 MUTATED    10   9
  RASA1 WILD-TYPE 135 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED     10    9
  RASA1 WILD-TYPE  135  239
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  FEMALE            10             135
  MALE               9             239
[1] 2 2
[1] FALSE
D84V8, binary
                 cls
clus                0   1
  RASA1 MUTATED    12   2
  RASA1 WILD-TYPE 280  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED     12    2
  RASA1 WILD-TYPE  280   57
     clus
vv    RASA1 MUTATED RASA1 WILD-TYPE
  NO             12             280
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RASA1 MUTATED                                          0
  RASA1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RASA1 MUTATED                                       3
  RASA1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RASA1 MUTATED                                                        9
  RASA1 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RASA1 MUTATED                                                   0
  RASA1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RASA1 MUTATED                                                                   3
  RASA1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RASA1 MUTATED                                                    1
  RASA1 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RASA1 MUTATED                                                  3
  RASA1 WILD-TYPE                                               58
D84V9, multiclass
                                                                   clus
vv                                                                  RASA1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  RASA1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RASA1 MUTATED    14   0   3   2
  RASA1 WILD-TYPE 297  14  12  22
D84V10, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  R0            14             297
  R1             0              14
  R2             3              12
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RASA1 MUTATED       2                         0
  RASA1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RASA1 MUTATED                                           0    12
  RASA1 WILD-TYPE                                         1   231
D84V12, multiclass
                                           clus
vv                                          RASA1 MUTATED RASA1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V13, binary
                 cls
clus                0   1
  RASA1 MUTATED     1  13
  RASA1 WILD-TYPE   3 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      1   13
  RASA1 WILD-TYPE    3  297
                        clus
vv                       RASA1 MUTATED RASA1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(85) Variable = RHOQ MUTATION ANALYSIS
D85V1, survival
                sevent
clus2              0   1
  RHOQ MUTATED     3   1
  RHOQ WILD-TYPE 227 138
  RHOQ MUTATED RHOQ WILD-TYPE 
             4            365 
  RHOQ MUTATED RHOQ WILD-TYPE 
             1            138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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         14.430 
[1] "1.0 - 22.3 (7.6)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D85V2, 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       2       15       39       30        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RHOQ MUTATED           0          0          0          0        2
  RHOQ WILD-TYPE         3         70         53         32       36
D85V3, multiclass
            clus
vv           RHOQ MUTATED RHOQ WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RHOQ MUTATED     1   0   2   2
  RHOQ WILD-TYPE  21  92 171  95
D85V4, multiclass
    clus
vv   RHOQ MUTATED RHOQ WILD-TYPE
  T1            1             21
  T2            0             92
  T3            2            171
  T4            2             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
  RHOQ MUTATED     2   1   2   0
  RHOQ WILD-TYPE 116 103  75  77
D85V5, multiclass
    clus
vv   RHOQ MUTATED RHOQ WILD-TYPE
  N0            2            116
  N1            1            103
  N2            2             75
  N3            0             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"
D85V6, binary
                cls
clus               0   1
  RHOQ MUTATED     4   1
  RHOQ WILD-TYPE 342  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOQ MUTATED      4    1
  RHOQ WILD-TYPE  342   28
   clus
vv  RHOQ MUTATED RHOQ WILD-TYPE
  0            4            342
  1            1             28
[1] 2 2
[1] FALSE
D85V7, binary
                cls
clus               0   1
  RHOQ MUTATED     3   2
  RHOQ WILD-TYPE 142 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOQ MUTATED      3    2
  RHOQ WILD-TYPE  142  246
        clus
vv       RHOQ MUTATED RHOQ WILD-TYPE
  FEMALE            3            142
  MALE              2            246
[1] 2 2
[1] FALSE
D85V8, binary
                cls
clus               0   1
  RHOQ MUTATED     3   0
  RHOQ WILD-TYPE 289  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOQ MUTATED      3    0
  RHOQ WILD-TYPE  289   59
     clus
vv    RHOQ MUTATED RHOQ WILD-TYPE
  NO             3            289
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RHOQ MUTATED                                          0
  RHOQ WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RHOQ MUTATED                                       1
  RHOQ WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RHOQ MUTATED                                                        3
  RHOQ WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RHOQ MUTATED                                                   0
  RHOQ WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RHOQ MUTATED                                                                   0
  RHOQ WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RHOQ MUTATED                                                    0
  RHOQ WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RHOQ MUTATED                                                  1
  RHOQ WILD-TYPE                                               60
D85V9, multiclass
                                                                   clus
vv                                                                  RHOQ MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  RHOQ WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RHOQ MUTATED     3   0   1   1
  RHOQ WILD-TYPE 308  14  14  23
D85V10, multiclass
    clus
vv   RHOQ MUTATED RHOQ WILD-TYPE
  R0            3            308
  R1            0             14
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RHOQ MUTATED       2                         0
  RHOQ WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RHOQ MUTATED                                           0     2
  RHOQ WILD-TYPE                                         1   241
D85V12, multiclass
                                           clus
vv                                          RHOQ MUTATED RHOQ WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V13, binary
                cls
clus               0   1
  RHOQ MUTATED     0   4
  RHOQ WILD-TYPE   4 306
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOQ MUTATED      0    4
  RHOQ WILD-TYPE    4  306
                        clus
vv                       RHOQ MUTATED RHOQ WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            4            306
[1] 2 2
[1] FALSE

Clustering(86) Variable = NT5M MUTATION ANALYSIS
D86V1, survival
                sevent
clus2              0   1
  NT5M MUTATED     3   1
  NT5M WILD-TYPE 227 138
  NT5M MUTATED NT5M WILD-TYPE 
             4            365 
  NT5M MUTATED NT5M WILD-TYPE 
             1            138 
$`NT5M MUTATED`
TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-A4QL TCGA-IN-A6RP 
       29.59         1.12        16.14         6.44 

$`NT5M WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  NT5M MUTATED NT5M WILD-TYPE 
          1.12           0.00 
  NT5M MUTATED NT5M WILD-TYPE 
         29.59         122.30 
  NT5M MUTATED NT5M WILD-TYPE 
         11.29          14.27 
[1] "1.1 - 29.6 (11.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D86V2, 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       2       15       40       30        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NT5M MUTATED           0          1          1          1        1
  NT5M WILD-TYPE         3         69         52         31       37
D86V3, multiclass
            clus
vv           NT5M MUTATED NT5M WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NT5M MUTATED     1   0   2   3
  NT5M WILD-TYPE  21  92 171  94
D86V4, multiclass
    clus
vv   NT5M MUTATED NT5M WILD-TYPE
  T1            1             21
  T2            0             92
  T3            2            171
  T4            3             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
  NT5M MUTATED     3   0   1   2
  NT5M WILD-TYPE 115 104  76  75
D86V5, multiclass
    clus
vv   NT5M MUTATED NT5M WILD-TYPE
  N0            3            115
  N1            0            104
  N2            1             76
  N3            2             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"
D86V6, binary
                cls
clus               0   1
  NT5M MUTATED     6   0
  NT5M WILD-TYPE 340  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  NT5M MUTATED      6    0
  NT5M WILD-TYPE  340   29
   clus
vv  NT5M MUTATED NT5M WILD-TYPE
  0            6            340
  1            0             29
[1] 2 2
[1] FALSE
D86V7, binary
                cls
clus               0   1
  NT5M MUTATED     5   1
  NT5M WILD-TYPE 140 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  NT5M MUTATED      5    1
  NT5M WILD-TYPE  140  247
        clus
vv       NT5M MUTATED NT5M WILD-TYPE
  FEMALE            5            140
  MALE              1            247
[1] 2 2
[1] FALSE
D86V8, binary
                cls
clus               0   1
  NT5M MUTATED     3   1
  NT5M WILD-TYPE 289  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  NT5M MUTATED      3    1
  NT5M WILD-TYPE  289   58
     clus
vv    NT5M MUTATED NT5M WILD-TYPE
  NO             3            289
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NT5M MUTATED                                          0
  NT5M WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NT5M MUTATED                                       0
  NT5M WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NT5M MUTATED                                                        6
  NT5M WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NT5M MUTATED                                                   0
  NT5M WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NT5M MUTATED                                                                   0
  NT5M WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NT5M MUTATED                                                    0
  NT5M WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NT5M MUTATED                                                  0
  NT5M WILD-TYPE                                               61
D86V9, multiclass
                                                                   clus
vv                                                                  NT5M MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  NT5M WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NT5M MUTATED     4   0   0   2
  NT5M WILD-TYPE 307  14  15  22
D86V10, multiclass
    clus
vv   NT5M MUTATED NT5M WILD-TYPE
  R0            4            307
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NT5M MUTATED       0                         0
  NT5M WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NT5M MUTATED                                           0     6
  NT5M WILD-TYPE                                         1   237
D86V12, multiclass
                                           clus
vv                                          NT5M MUTATED NT5M WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V13, binary
                cls
clus               0   1
  NT5M MUTATED     0   6
  NT5M WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  NT5M MUTATED      0    6
  NT5M WILD-TYPE    4  304
                        clus
vv                       NT5M MUTATED NT5M WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(87) Variable = CELSR1 MUTATION ANALYSIS
D87V1, survival
                  sevent
clus2                0   1
  CELSR1 MUTATED    19  12
  CELSR1 WILD-TYPE 211 127
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              31              338 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              12              127 
$`CELSR1 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8059 
       21.99        26.70        34.68        36.16        35.84        14.43 
TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8297 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8589 
       29.59         8.05         7.40         4.31         1.12        27.12 
TCGA-BR-8687 TCGA-BR-A4PD TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-4465 
        8.22        20.65         6.58        11.77         1.02         9.01 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-A6EY 
        6.02       105.07        28.96        65.10        21.07        11.44 
TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-8604 TCGA-HU-A4G9 TCGA-HU-A4GU TCGA-HU-A4GX 
       77.29        26.47        22.82        24.20         6.58        20.25 
TCGA-MX-A5UJ 
       19.73 

$`CELSR1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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-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-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-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-5734 TCGA-D7-5577 TCGA-D7-5578 
       15.02         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-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-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-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 

  CELSR1 MUTATED CELSR1 WILD-TYPE 
            1.02             0.00 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
          105.07           122.30 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
          20.650           14.055 
[1] "1.0 - 105.1 (20.6)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D87V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CELSR1 MUTATED         1        3        5        2         4         5
  CELSR1 WILD-TYPE       1       12       35       28        33        47
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CELSR1 MUTATED           1          4          2          4        4
  CELSR1 WILD-TYPE         2         66         51         28       34
D87V3, multiclass
            clus
vv           CELSR1 MUTATED CELSR1 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                3               12
  STAGE IB                5               35
  STAGE II                2               28
  STAGE IIA               4               33
  STAGE IIB               5               47
  STAGE III               1                2
  STAGE IIIA              4               66
  STAGE IIIB              2               51
  STAGE IIIC              4               28
  STAGE IV                4               34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CELSR1 MUTATED     5   8   9  14
  CELSR1 WILD-TYPE  17  84 164  83
D87V4, multiclass
    clus
vv   CELSR1 MUTATED CELSR1 WILD-TYPE
  T1              5               17
  T2              8               84
  T3              9              164
  T4             14               83
[1] 4 2
[1] TRUE
[1] "dimension of 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    17   9   5   4
  CELSR1 WILD-TYPE 101  95  72  73
D87V5, multiclass
    clus
vv   CELSR1 MUTATED CELSR1 WILD-TYPE
  N0             17              101
  N1              9               95
  N2              5               72
  N3              4               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"
D87V6, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    32   3
  CELSR1 WILD-TYPE 314  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     32    3
  CELSR1 WILD-TYPE  314   26
   clus
vv  CELSR1 MUTATED CELSR1 WILD-TYPE
  0             32              314
  1              3               26
[1] 2 2
[1] FALSE
D87V7, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    22  15
  CELSR1 WILD-TYPE 123 233
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     22   15
  CELSR1 WILD-TYPE  123  233
        clus
vv       CELSR1 MUTATED CELSR1 WILD-TYPE
  FEMALE             22              123
  MALE               15              233
[1] 2 2
[1] FALSE
D87V8, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    28   1
  CELSR1 WILD-TYPE 264  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     28    1
  CELSR1 WILD-TYPE  264   58
     clus
vv    CELSR1 MUTATED CELSR1 WILD-TYPE
  NO              28              264
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CELSR1 MUTATED                                          1
  CELSR1 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CELSR1 MUTATED                                       6
  CELSR1 WILD-TYPE                                    64
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CELSR1 MUTATED                                                       15
  CELSR1 WILD-TYPE                                                    143
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CELSR1 MUTATED                                                   1
  CELSR1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CELSR1 MUTATED                                                                   9
  CELSR1 WILD-TYPE                                                                59
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CELSR1 MUTATED                                                    1
  CELSR1 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CELSR1 MUTATED                                                  4
  CELSR1 WILD-TYPE                                               57
D87V9, multiclass
                                                                   clus
vv                                                                  CELSR1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              9
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  CELSR1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               59
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CELSR1 MUTATED    28   1   3   3
  CELSR1 WILD-TYPE 283  13  12  21
D87V10, multiclass
    clus
vv   CELSR1 MUTATED CELSR1 WILD-TYPE
  R0             28              283
  R1              1               13
  R2              3               12
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CELSR1 MUTATED       6                         1
  CELSR1 WILD-TYPE    81                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CELSR1 MUTATED                                           0    20
  CELSR1 WILD-TYPE                                         1   223
D87V12, multiclass
                                           clus
vv                                          CELSR1 MUTATED CELSR1 WILD-TYPE
  ASIAN                                                  6               81
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 20              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V13, binary
                  cls
clus                 0   1
  CELSR1 MUTATED     0  27
  CELSR1 WILD-TYPE   4 283
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED      0   27
  CELSR1 WILD-TYPE    4  283
                        clus
vv                       CELSR1 MUTATED CELSR1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             27              283
[1] 2 2
[1] FALSE

Clustering(88) Variable = YIPF2 MUTATION ANALYSIS
D88V1, survival
                 sevent
clus2               0   1
  YIPF2 MUTATED     5   2
  YIPF2 WILD-TYPE 225 137
  YIPF2 MUTATED YIPF2 WILD-TYPE 
              7             362 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
              2             137 
$`YIPF2 MUTATED`
TCGA-BR-4184 TCGA-BR-8059 TCGA-CG-4305 TCGA-HF-A5NB TCGA-HU-A4GP TCGA-VQ-A8E7 
        6.97        14.43        15.95        30.51         8.98        37.41 
TCGA-VQ-A8P2 
       38.14 

$`YIPF2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A8P3 
       48.79         5.46        13.25        13.02        43.36        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 

  YIPF2 MUTATED YIPF2 WILD-TYPE 
           6.97            0.00 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
          38.14          122.30 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
          15.95           14.12 
[1] "7.0 - 38.1 (15.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D88V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  YIPF2 MUTATED         0        0        0        1         1         0
  YIPF2 WILD-TYPE       2       15       40       29        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  YIPF2 MUTATED           1          2          0          1        1
  YIPF2 WILD-TYPE         2         68         53         31       37
D88V3, multiclass
            clus
vv           YIPF2 MUTATED YIPF2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              1               2
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  YIPF2 MUTATED     0   2   2   3
  YIPF2 WILD-TYPE  22  90 171  94
D88V4, multiclass
    clus
vv   YIPF2 MUTATED YIPF2 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             2             171
  T4             3              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
  YIPF2 MUTATED     0   6   0   1
  YIPF2 WILD-TYPE 118  98  77  76
D88V5, multiclass
    clus
vv   YIPF2 MUTATED YIPF2 WILD-TYPE
  N0             0             118
  N1             6              98
  N2             0              77
  N3             1              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"
D88V6, binary
                 cls
clus                0   1
  YIPF2 MUTATED     5   1
  YIPF2 WILD-TYPE 341  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      5    1
  YIPF2 WILD-TYPE  341   28
   clus
vv  YIPF2 MUTATED YIPF2 WILD-TYPE
  0             5             341
  1             1              28
[1] 2 2
[1] FALSE
D88V7, binary
                 cls
clus                0   1
  YIPF2 MUTATED     2   5
  YIPF2 WILD-TYPE 143 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      2    5
  YIPF2 WILD-TYPE  143  243
        clus
vv       YIPF2 MUTATED YIPF2 WILD-TYPE
  FEMALE             2             143
  MALE               5             243
[1] 2 2
[1] FALSE
D88V8, binary
                 cls
clus                0   1
  YIPF2 MUTATED     5   2
  YIPF2 WILD-TYPE 287  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      5    2
  YIPF2 WILD-TYPE  287   57
     clus
vv    YIPF2 MUTATED YIPF2 WILD-TYPE
  NO              5             287
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  YIPF2 MUTATED                                          0
  YIPF2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  YIPF2 MUTATED                                       1
  YIPF2 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  YIPF2 MUTATED                                                        2
  YIPF2 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  YIPF2 MUTATED                                                   2
  YIPF2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  YIPF2 MUTATED                                                                   1
  YIPF2 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  YIPF2 MUTATED                                                    0
  YIPF2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  YIPF2 MUTATED                                                  1
  YIPF2 WILD-TYPE                                               60
D88V9, multiclass
                                                                   clus
vv                                                                  YIPF2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  YIPF2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  YIPF2 MUTATED     5   1   0   1
  YIPF2 WILD-TYPE 306  13  15  23
D88V10, multiclass
    clus
vv   YIPF2 MUTATED YIPF2 WILD-TYPE
  R0             5             306
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  YIPF2 MUTATED       1                         0
  YIPF2 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  YIPF2 MUTATED                                           0     4
  YIPF2 WILD-TYPE                                         1   239
D88V12, multiclass
                                           clus
vv                                          YIPF2 MUTATED YIPF2 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V13, binary
                 cls
clus                0   1
  YIPF2 MUTATED     0   3
  YIPF2 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      0    3
  YIPF2 WILD-TYPE    4  307
                        clus
vv                       YIPF2 MUTATED YIPF2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(89) Variable = CR1 MUTATION ANALYSIS
D89V1, survival
               sevent
clus2             0   1
  CR1 MUTATED    19   9
  CR1 WILD-TYPE 211 130
  CR1 MUTATED CR1 WILD-TYPE 
           28           341 
  CR1 MUTATED CR1 WILD-TYPE 
            9           130 
$`CR1 MUTATED`
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7707 
        9.34         9.67         6.61        34.68        30.90        35.84 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8589 
       29.59        32.25         0.26        25.05         1.12        27.12 
TCGA-BR-8592 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 
        6.28        12.33        12.30         6.58        12.62        15.95 
TCGA-CG-4436 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-A4YU TCGA-D7-A4YY TCGA-HF-7132 
        7.99         6.02        65.10        16.44        13.78        77.29 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-IN-A6RL TCGA-VQ-AA64 
       20.25        29.00        13.35        18.41 

$`CR1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
       12.79         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-8530 
       12.39        12.76        12.59        12.53         7.17        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-4306 TCGA-CG-4437 
       11.77        20.02         3.02        27.02         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-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-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       21.14        20.91        14.27         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-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-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-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-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 

  CR1 MUTATED CR1 WILD-TYPE 
         0.26          0.00 
  CR1 MUTATED CR1 WILD-TYPE 
        77.29        122.30 
  CR1 MUTATED CR1 WILD-TYPE 
       14.865        14.270 
[1] "0.3 - 77.3 (14.9)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D89V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CR1 MUTATED         0        0        6        2         3         3
  CR1 WILD-TYPE       2       15       34       28        34        49
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CR1 MUTATED           1          3          5          3        2
  CR1 WILD-TYPE         2         67         48         29       36
D89V3, multiclass
            clus
vv           CR1 MUTATED CR1 WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             6            34
  STAGE II             2            28
  STAGE IIA            3            34
  STAGE IIB            3            49
  STAGE III            1             2
  STAGE IIIA           3            67
  STAGE IIIB           5            48
  STAGE IIIC           3            29
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CR1 MUTATED     0  10   7  11
  CR1 WILD-TYPE  22  82 166  86
D89V4, multiclass
    clus
vv   CR1 MUTATED CR1 WILD-TYPE
  T1           0            22
  T2          10            82
  T3           7           166
  T4          11            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
  CR1 MUTATED    14   8   3   4
  CR1 WILD-TYPE 104  96  74  73
D89V5, multiclass
    clus
vv   CR1 MUTATED CR1 WILD-TYPE
  N0          14           104
  N1           8            96
  N2           3            74
  N3           4            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"
D89V6, binary
               cls
clus              0   1
  CR1 MUTATED    29   1
  CR1 WILD-TYPE 317  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED     29    1
  CR1 WILD-TYPE  317   28
   clus
vv  CR1 MUTATED CR1 WILD-TYPE
  0          29           317
  1           1            28
[1] 2 2
[1] FALSE
D89V7, binary
               cls
clus              0   1
  CR1 MUTATED    14  16
  CR1 WILD-TYPE 131 232
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED     14   16
  CR1 WILD-TYPE  131  232
        clus
vv       CR1 MUTATED CR1 WILD-TYPE
  FEMALE          14           131
  MALE            16           232
[1] 2 2
[1] FALSE
D89V8, binary
               cls
clus              0   1
  CR1 MUTATED    22   5
  CR1 WILD-TYPE 270  54
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED     22    5
  CR1 WILD-TYPE  270   54
     clus
vv    CR1 MUTATED CR1 WILD-TYPE
  NO           22           270
  YES           5            54
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CR1 MUTATED                                          0
  CR1 WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CR1 MUTATED                                       4
  CR1 WILD-TYPE                                    66
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CR1 MUTATED                                                       17
  CR1 WILD-TYPE                                                    141
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CR1 MUTATED                                                   2
  CR1 WILD-TYPE                                                19
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CR1 MUTATED                                                                   6
  CR1 WILD-TYPE                                                                62
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CR1 MUTATED                                                    0
  CR1 WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CR1 MUTATED                                                  1
  CR1 WILD-TYPE                                               60
D89V9, multiclass
                                                                   clus
vv                                                                  CR1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                     17
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            1
                                                                   clus
vv                                                                  CR1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      141
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  CR1 MUTATED    25   0   0   3
  CR1 WILD-TYPE 286  14  15  21
D89V10, multiclass
    clus
vv   CR1 MUTATED CR1 WILD-TYPE
  R0          25           286
  R1           0            14
  R2           0            15
  RX           3            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CR1 MUTATED       6                         0
  CR1 WILD-TYPE    81                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CR1 MUTATED                                           0    18
  CR1 WILD-TYPE                                         1   225
D89V12, multiclass
                                           clus
vv                                          CR1 MUTATED CR1 WILD-TYPE
  ASIAN                                               6            81
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              18           225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V13, binary
               cls
clus              0   1
  CR1 MUTATED     0  23
  CR1 WILD-TYPE   4 287
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED      0   23
  CR1 WILD-TYPE    4  287
                        clus
vv                       CR1 MUTATED CR1 WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          23           287
[1] 2 2
[1] FALSE

Clustering(90) Variable = C19ORF40 MUTATION ANALYSIS
D90V1, survival
                    sevent
clus2                  0   1
  C19ORF40 MUTATED     4   2
  C19ORF40 WILD-TYPE 226 137
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
                 6                363 
  C19ORF40 MUTATED C19ORF40 WILD-TYPE 
                 2                137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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 

  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              14.43 
[1] "6.0 - 47.0 (10.5)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D90V2, 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       2       15       40       29        37        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C19ORF40 MUTATED           0          2          0          1        2
  C19ORF40 WILD-TYPE         3         68         53         31       36
D90V3, multiclass
            clus
vv           C19ORF40 MUTATED C19ORF40 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  1                 29
  STAGE IIA                 0                 37
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                0                 53
  STAGE IIIC                1                 31
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C19ORF40 MUTATED     0   1   3   2
  C19ORF40 WILD-TYPE  22  91 170  95
D90V4, multiclass
    clus
vv   C19ORF40 MUTATED C19ORF40 WILD-TYPE
  T1                0                 22
  T2                1                 91
  T3                3                170
  T4                2                 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
  C19ORF40 MUTATED     1   2   2   1
  C19ORF40 WILD-TYPE 117 102  75  76
D90V5, multiclass
    clus
vv   C19ORF40 MUTATED C19ORF40 WILD-TYPE
  N0                1                117
  N1                2                102
  N2                2                 75
  N3                1                 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"
D90V6, binary
                    cls
clus                   0   1
  C19ORF40 MUTATED     6   0
  C19ORF40 WILD-TYPE 340  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF40 MUTATED      6    0
  C19ORF40 WILD-TYPE  340   29
   clus
vv  C19ORF40 MUTATED C19ORF40 WILD-TYPE
  0                6                340
  1                0                 29
[1] 2 2
[1] FALSE
D90V7, binary
                    cls
clus                   0   1
  C19ORF40 MUTATED     2   5
  C19ORF40 WILD-TYPE 143 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF40 MUTATED      2    5
  C19ORF40 WILD-TYPE  143  243
        clus
vv       C19ORF40 MUTATED C19ORF40 WILD-TYPE
  FEMALE                2                143
  MALE                  5                243
[1] 2 2
[1] FALSE
D90V8, binary
                    cls
clus                   0   1
  C19ORF40 MUTATED     5   1
  C19ORF40 WILD-TYPE 287  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF40 MUTATED      5    1
  C19ORF40 WILD-TYPE  287   58
     clus
vv    C19ORF40 MUTATED C19ORF40 WILD-TYPE
  NO                 5                287
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C19ORF40 MUTATED                                          0
  C19ORF40 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C19ORF40 MUTATED                                       2
  C19ORF40 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C19ORF40 MUTATED                                                        3
  C19ORF40 WILD-TYPE                                                    155
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C19ORF40 MUTATED                                                   0
  C19ORF40 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C19ORF40 MUTATED                                                                   2
  C19ORF40 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C19ORF40 MUTATED                                                    0
  C19ORF40 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C19ORF40 MUTATED                                                  0
  C19ORF40 WILD-TYPE                                               61
D90V9, multiclass
                                                                   clus
vv                                                                  C19ORF40 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 0
                                                                   clus
vv                                                                  C19ORF40 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C19ORF40 MUTATED     4   0   1   2
  C19ORF40 WILD-TYPE 307  14  14  22
D90V10, multiclass
    clus
vv   C19ORF40 MUTATED C19ORF40 WILD-TYPE
  R0                4                307
  R1                0                 14
  R2                1                 14
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C19ORF40 MUTATED       2                         0
  C19ORF40 WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C19ORF40 MUTATED                                           1     2
  C19ORF40 WILD-TYPE                                         0   241
D90V12, multiclass
                                           clus
vv                                          C19ORF40 MUTATED C19ORF40 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                    2                241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V13, binary
                    cls
clus                   0   1
  C19ORF40 MUTATED     0   5
  C19ORF40 WILD-TYPE   4 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF40 MUTATED      0    5
  C19ORF40 WILD-TYPE    4  305
                        clus
vv                       C19ORF40 MUTATED C19ORF40 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                5                305
[1] 2 2
[1] FALSE

Clustering(91) Variable = WNT1 MUTATION ANALYSIS
D91V1, survival
                sevent
clus2              0   1
  WNT1 MUTATED     7   2
  WNT1 WILD-TYPE 223 137
  WNT1 MUTATED WNT1 WILD-TYPE 
             9            360 
  WNT1 MUTATED WNT1 WILD-TYPE 
             2            137 
$`WNT1 MUTATED`
TCGA-EQ-A4SO TCGA-BR-6565 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8487 TCGA-D7-A4YV 
       16.24         9.17        44.94        29.59         1.12         5.92 
TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-A4H8 
       11.08        77.29        14.07 

$`WNT1 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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 

  WNT1 MUTATED WNT1 WILD-TYPE 
          1.12           0.00 
  WNT1 MUTATED WNT1 WILD-TYPE 
         77.29         122.30 
  WNT1 MUTATED WNT1 WILD-TYPE 
         14.07          14.35 
[1] "1.1 - 77.3 (14.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.9"
D91V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WNT1 MUTATED         1        0        1        1         3         3
  WNT1 WILD-TYPE       1       15       39       29        34        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WNT1 MUTATED           0          0          1          0        0
  WNT1 WILD-TYPE         3         70         52         32       38
D91V3, multiclass
            clus
vv           WNT1 MUTATED WNT1 WILD-TYPE
  STAGE I               1              1
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             3             34
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WNT1 MUTATED     2   1   4   3
  WNT1 WILD-TYPE  20  91 169  94
D91V4, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  T1            2             20
  T2            1             91
  T3            4            169
  T4            3             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
  WNT1 MUTATED     5   5   0   0
  WNT1 WILD-TYPE 113  99  77  77
D91V5, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  N0            5            113
  N1            5             99
  N2            0             77
  N3            0             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"
D91V6, binary
                cls
clus               0   1
  WNT1 MUTATED     8   0
  WNT1 WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      8    0
  WNT1 WILD-TYPE  338   29
   clus
vv  WNT1 MUTATED WNT1 WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D91V7, binary
                cls
clus               0   1
  WNT1 MUTATED     4   6
  WNT1 WILD-TYPE 141 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      4    6
  WNT1 WILD-TYPE  141  242
        clus
vv       WNT1 MUTATED WNT1 WILD-TYPE
  FEMALE            4            141
  MALE              6            242
[1] 2 2
[1] FALSE
D91V8, binary
                cls
clus               0   1
  WNT1 MUTATED     7   3
  WNT1 WILD-TYPE 285  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      7    3
  WNT1 WILD-TYPE  285   56
     clus
vv    WNT1 MUTATED WNT1 WILD-TYPE
  NO             7            285
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  WNT1 MUTATED                                          0
  WNT1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  WNT1 MUTATED                                       0
  WNT1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WNT1 MUTATED                                                        6
  WNT1 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  WNT1 MUTATED                                                   1
  WNT1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WNT1 MUTATED                                                                   0
  WNT1 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  WNT1 MUTATED                                                    0
  WNT1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  WNT1 MUTATED                                                  2
  WNT1 WILD-TYPE                                               59
D91V9, multiclass
                                                                   clus
vv                                                                  WNT1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  WNT1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WNT1 MUTATED    10   0   0   0
  WNT1 WILD-TYPE 301  14  15  24
D91V10, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  R0           10            301
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  WNT1 MUTATED       1                         2
  WNT1 WILD-TYPE    86                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WNT1 MUTATED                                           0     6
  WNT1 WILD-TYPE                                         1   237
D91V12, multiclass
                                           clus
vv                                          WNT1 MUTATED WNT1 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V13, binary
                cls
clus               0   1
  WNT1 MUTATED     0   9
  WNT1 WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      0    9
  WNT1 WILD-TYPE    4  301
                        clus
vv                       WNT1 MUTATED WNT1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(92) Variable = IRF2 MUTATION ANALYSIS
D92V1, survival
                sevent
clus2              0   1
  IRF2 MUTATED     9   6
  IRF2 WILD-TYPE 221 133
  IRF2 MUTATED IRF2 WILD-TYPE 
            15            354 
  IRF2 MUTATED IRF2 WILD-TYPE 
             6            133 
$`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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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 

  IRF2 MUTATED IRF2 WILD-TYPE 
          0.56           0.00 
  IRF2 MUTATED IRF2 WILD-TYPE 
        122.30         116.38 
  IRF2 MUTATED IRF2 WILD-TYPE 
         28.96          14.12 
[1] "0.6 - 122.3 (29.0)" "0.0 - 116.4 (14.1)"
[1] "hr=" "1.3"
D92V2, 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       2       14       40       30        32        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IRF2 MUTATED           0          2          2          1        3
  IRF2 WILD-TYPE         3         68         51         31       35
D92V3, multiclass
            clus
vv           IRF2 MUTATED IRF2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             5             32
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            2             51
  STAGE IIIC            1             31
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IRF2 MUTATED     1   0   8   7
  IRF2 WILD-TYPE  21  92 165  90
D92V4, multiclass
    clus
vv   IRF2 MUTATED IRF2 WILD-TYPE
  T1            1             21
  T2            0             92
  T3            8            165
  T4            7             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
  IRF2 MUTATED     8   4   3   2
  IRF2 WILD-TYPE 110 100  74  75
D92V5, multiclass
    clus
vv   IRF2 MUTATED IRF2 WILD-TYPE
  N0            8            110
  N1            4            100
  N2            3             74
  N3            2             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"
D92V6, binary
                cls
clus               0   1
  IRF2 MUTATED    16   2
  IRF2 WILD-TYPE 330  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED     16    2
  IRF2 WILD-TYPE  330   27
   clus
vv  IRF2 MUTATED IRF2 WILD-TYPE
  0           16            330
  1            2             27
[1] 2 2
[1] FALSE
D92V7, binary
                cls
clus               0   1
  IRF2 MUTATED    11   8
  IRF2 WILD-TYPE 134 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED     11    8
  IRF2 WILD-TYPE  134  240
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  FEMALE           11            134
  MALE              8            240
[1] 2 2
[1] FALSE
D92V8, binary
                cls
clus               0   1
  IRF2 MUTATED    13   2
  IRF2 WILD-TYPE 279  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED     13    2
  IRF2 WILD-TYPE  279   57
     clus
vv    IRF2 MUTATED IRF2 WILD-TYPE
  NO            13            279
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IRF2 MUTATED                                          0
  IRF2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IRF2 MUTATED                                       2
  IRF2 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IRF2 MUTATED                                                        8
  IRF2 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IRF2 MUTATED                                                   1
  IRF2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IRF2 MUTATED                                                                   5
  IRF2 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IRF2 MUTATED                                                    0
  IRF2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IRF2 MUTATED                                                  3
  IRF2 WILD-TYPE                                               58
D92V9, multiclass
                                                                   clus
vv                                                                  IRF2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  IRF2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IRF2 MUTATED    14   0   0   5
  IRF2 WILD-TYPE 297  14  15  19
D92V10, multiclass
    clus
vv   IRF2 MUTATED IRF2 WILD-TYPE
  R0           14            297
  R1            0             14
  R2            0             15
  RX            5             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IRF2 MUTATED       1                         0
  IRF2 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IRF2 MUTATED                                           0    17
  IRF2 WILD-TYPE                                         1   226
D92V12, multiclass
                                           clus
vv                                          IRF2 MUTATED IRF2 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               17            226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V13, binary
                cls
clus               0   1
  IRF2 MUTATED     1  15
  IRF2 WILD-TYPE   3 295
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED      1   15
  IRF2 WILD-TYPE    3  295
                        clus
vv                       IRF2 MUTATED IRF2 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           15            295
[1] 2 2
[1] FALSE

Clustering(93) Variable = CR2 MUTATION ANALYSIS
D93V1, survival
               sevent
clus2             0   1
  CR2 MUTATED    19   4
  CR2 WILD-TYPE 211 135
  CR2 MUTATED CR2 WILD-TYPE 
           23           346 
  CR2 MUTATED CR2 WILD-TYPE 
            4           135 
$`CR2 MUTATED`
TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8368 
       26.70         9.67        34.68        29.59        32.25         4.31 
TCGA-BR-8382 TCGA-BR-8680 TCGA-CG-5721 TCGA-CG-5723 TCGA-EQ-8122 TCGA-HF-7132 
       25.05        31.96         6.02       105.07         7.99        77.29 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4GU 
       22.32        22.68        24.20        11.77         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-VQ-A8DL TCGA-VQ-A8P2 TCGA-VQ-A92D 
       20.25         2.10         0.92        38.14        66.81 

$`CR2 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-A4GJ TCGA-HU-A4GN 
       24.26         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        8.98         0.10         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-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-A94T TCGA-VQ-AA64 
       15.65        20.81         1.71        42.64        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 

  CR2 MUTATED CR2 WILD-TYPE 
         0.92          0.00 
  CR2 MUTATED CR2 WILD-TYPE 
       105.07        122.30 
  CR2 MUTATED CR2 WILD-TYPE 
        22.68         14.07 
[1] "0.9 - 105.1 (22.7)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.9"
D93V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CR2 MUTATED         0        2        2        2         3         7
  CR2 WILD-TYPE       2       13       38       28        34        45
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CR2 MUTATED           0          1          0          3        2
  CR2 WILD-TYPE         3         69         53         29       36
D93V3, multiclass
            clus
vv           CR2 MUTATED CR2 WILD-TYPE
  STAGE I              0             2
  STAGE IA             2            13
  STAGE IB             2            38
  STAGE II             2            28
  STAGE IIA            3            34
  STAGE IIB            7            45
  STAGE III            0             3
  STAGE IIIA           1            69
  STAGE IIIB           0            53
  STAGE IIIC           3            29
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CR2 MUTATED     2   4   6  10
  CR2 WILD-TYPE  20  88 167  87
D93V4, multiclass
    clus
vv   CR2 MUTATED CR2 WILD-TYPE
  T1           2            20
  T2           4            88
  T3           6           167
  T4          10            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
  CR2 MUTATED    11   7   2   2
  CR2 WILD-TYPE 107  97  75  75
D93V5, multiclass
    clus
vv   CR2 MUTATED CR2 WILD-TYPE
  N0          11           107
  N1           7            97
  N2           2            75
  N3           2            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"
D93V6, binary
               cls
clus              0   1
  CR2 MUTATED    21   1
  CR2 WILD-TYPE 325  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR2 MUTATED     21    1
  CR2 WILD-TYPE  325   28
   clus
vv  CR2 MUTATED CR2 WILD-TYPE
  0          21           325
  1           1            28
[1] 2 2
[1] FALSE
D93V7, binary
               cls
clus              0   1
  CR2 MUTATED    14   9
  CR2 WILD-TYPE 131 239
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR2 MUTATED     14    9
  CR2 WILD-TYPE  131  239
        clus
vv       CR2 MUTATED CR2 WILD-TYPE
  FEMALE          14           131
  MALE             9           239
[1] 2 2
[1] FALSE
D93V8, binary
               cls
clus              0   1
  CR2 MUTATED    20   3
  CR2 WILD-TYPE 272  56
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR2 MUTATED     20    3
  CR2 WILD-TYPE  272   56
     clus
vv    CR2 MUTATED CR2 WILD-TYPE
  NO           20           272
  YES           3            56
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CR2 MUTATED                                          0
  CR2 WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CR2 MUTATED                                       6
  CR2 WILD-TYPE                                    64
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CR2 MUTATED                                                        7
  CR2 WILD-TYPE                                                    151
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CR2 MUTATED                                                   2
  CR2 WILD-TYPE                                                19
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CR2 MUTATED                                                                   2
  CR2 WILD-TYPE                                                                66
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CR2 MUTATED                                                    0
  CR2 WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CR2 MUTATED                                                  6
  CR2 WILD-TYPE                                               55
D93V9, multiclass
                                                                   clus
vv                                                                  CR2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            6
                                                                   clus
vv                                                                  CR2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  CR2 MUTATED    20   0   0   1
  CR2 WILD-TYPE 291  14  15  23
D93V10, multiclass
    clus
vv   CR2 MUTATED CR2 WILD-TYPE
  R0          20           291
  R1           0            14
  R2           0            15
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CR2 MUTATED       9                         0
  CR2 WILD-TYPE    78                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CR2 MUTATED                                           0    11
  CR2 WILD-TYPE                                         1   232
D93V12, multiclass
                                           clus
vv                                          CR2 MUTATED CR2 WILD-TYPE
  ASIAN                                               9            78
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              11           232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V13, binary
               cls
clus              0   1
  CR2 MUTATED     0  17
  CR2 WILD-TYPE   4 293
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR2 MUTATED      0   17
  CR2 WILD-TYPE    4  293
                        clus
vv                       CR2 MUTATED CR2 WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          17           293
[1] 2 2
[1] FALSE

Clustering(94) Variable = LEMD1 MUTATION ANALYSIS
D94V1, survival
                 sevent
clus2               0   1
  LEMD1 MUTATED     3   1
  LEMD1 WILD-TYPE 227 138
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              4             365 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              1             138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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           14.43 
[1] "6.2 - 34.7 (8.8)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D94V2, 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       2       15       40       30        33        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LEMD1 MUTATED           0          0          0          0        0
  LEMD1 WILD-TYPE         3         70         53         32       38
D94V3, multiclass
            clus
vv           LEMD1 MUTATED LEMD1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              4              33
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LEMD1 MUTATED     0   0   4   0
  LEMD1 WILD-TYPE  22  92 169  97
D94V4, multiclass
    clus
vv   LEMD1 MUTATED LEMD1 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             4             169
  T4             0              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
  LEMD1 MUTATED     4   0   0   0
  LEMD1 WILD-TYPE 114 104  77  77
D94V5, multiclass
    clus
vv   LEMD1 MUTATED LEMD1 WILD-TYPE
  N0             4             114
  N1             0             104
  N2             0              77
  N3             0              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"
D94V6, binary
                 cls
clus                0   1
  LEMD1 MUTATED     4   0
  LEMD1 WILD-TYPE 342  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      4    0
  LEMD1 WILD-TYPE  342   29
   clus
vv  LEMD1 MUTATED LEMD1 WILD-TYPE
  0             4             342
  1             0              29
[1] 2 2
[1] FALSE
D94V7, binary
                 cls
clus                0   1
  LEMD1 MUTATED     1   3
  LEMD1 WILD-TYPE 144 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      1    3
  LEMD1 WILD-TYPE  144  245
        clus
vv       LEMD1 MUTATED LEMD1 WILD-TYPE
  FEMALE             1             144
  MALE               3             245
[1] 2 2
[1] FALSE
D94V8, binary
                 cls
clus                0   1
  LEMD1 MUTATED     3   1
  LEMD1 WILD-TYPE 289  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      3    1
  LEMD1 WILD-TYPE  289   58
     clus
vv    LEMD1 MUTATED LEMD1 WILD-TYPE
  NO              3             289
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LEMD1 MUTATED                                          0
  LEMD1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LEMD1 MUTATED                                       1
  LEMD1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LEMD1 MUTATED                                                        2
  LEMD1 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LEMD1 MUTATED                                                   0
  LEMD1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LEMD1 MUTATED                                                                   1
  LEMD1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LEMD1 MUTATED                                                    0
  LEMD1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LEMD1 MUTATED                                                  0
  LEMD1 WILD-TYPE                                               61
D94V9, multiclass
                                                                   clus
vv                                                                  LEMD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  LEMD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LEMD1 MUTATED     3   0   0   0
  LEMD1 WILD-TYPE 308  14  15  24
D94V10, multiclass
    clus
vv   LEMD1 MUTATED LEMD1 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LEMD1 MUTATED       1                         1
  LEMD1 WILD-TYPE    86                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LEMD1 MUTATED                                           0     2
  LEMD1 WILD-TYPE                                         1   241
D94V12, multiclass
                                           clus
vv                                          LEMD1 MUTATED LEMD1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V13, binary
                 cls
clus                0   1
  LEMD1 MUTATED     0   4
  LEMD1 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      0    4
  LEMD1 WILD-TYPE    4  306
                        clus
vv                       LEMD1 MUTATED LEMD1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(95) Variable = INF2 MUTATION ANALYSIS
D95V1, survival
                sevent
clus2              0   1
  INF2 MUTATED    11   7
  INF2 WILD-TYPE 219 132
  INF2 MUTATED INF2 WILD-TYPE 
            18            351 
  INF2 MUTATED INF2 WILD-TYPE 
             7            132 
$`INF2 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-7901 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-4465 
       21.99        26.70         3.45         1.12         6.58         9.01 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A6EX TCGA-FP-A4BF TCGA-HF-7132 
        6.02       105.07        28.96        11.31         5.52        77.29 
TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-MX-A5UJ 
       26.47        22.32        22.68         6.51        29.00        19.73 

$`INF2 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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-A9TM TCGA-HF-7133 
        5.03        13.58         0.56        11.08         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-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-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 

  INF2 MUTATED INF2 WILD-TYPE 
          1.12           0.00 
  INF2 MUTATED INF2 WILD-TYPE 
        105.07         122.30 
  INF2 MUTATED INF2 WILD-TYPE 
         20.86          14.17 
[1] "1.1 - 105.1 (20.9)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D95V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INF2 MUTATED         0        1        1        2         3         4
  INF2 WILD-TYPE       2       14       39       28        34        48
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INF2 MUTATED           0          4          0          1        3
  INF2 WILD-TYPE         3         66         53         31       35
D95V3, multiclass
            clus
vv           INF2 MUTATED INF2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              2             28
  STAGE IIA             3             34
  STAGE IIB             4             48
  STAGE III             0              3
  STAGE IIIA            4             66
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  INF2 MUTATED     1   3   8   7
  INF2 WILD-TYPE  21  89 165  90
D95V4, multiclass
    clus
vv   INF2 MUTATED INF2 WILD-TYPE
  T1            1             21
  T2            3             89
  T3            8            165
  T4            7             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
  INF2 MUTATED     8   6   3   2
  INF2 WILD-TYPE 110  98  74  75
D95V5, multiclass
    clus
vv   INF2 MUTATED INF2 WILD-TYPE
  N0            8            110
  N1            6             98
  N2            3             74
  N3            2             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"
D95V6, binary
                cls
clus               0   1
  INF2 MUTATED    16   2
  INF2 WILD-TYPE 330  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  INF2 MUTATED     16    2
  INF2 WILD-TYPE  330   27
   clus
vv  INF2 MUTATED INF2 WILD-TYPE
  0           16            330
  1            2             27
[1] 2 2
[1] FALSE
D95V7, binary
                cls
clus               0   1
  INF2 MUTATED    12   7
  INF2 WILD-TYPE 133 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  INF2 MUTATED     12    7
  INF2 WILD-TYPE  133  241
        clus
vv       INF2 MUTATED INF2 WILD-TYPE
  FEMALE           12            133
  MALE              7            241
[1] 2 2
[1] FALSE
D95V8, binary
                cls
clus               0   1
  INF2 MUTATED    14   1
  INF2 WILD-TYPE 278  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  INF2 MUTATED     14    1
  INF2 WILD-TYPE  278   58
     clus
vv    INF2 MUTATED INF2 WILD-TYPE
  NO            14            278
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  INF2 MUTATED                                          2
  INF2 WILD-TYPE                                        6
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  INF2 MUTATED                                       6
  INF2 WILD-TYPE                                    64
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  INF2 MUTATED                                                        4
  INF2 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  INF2 MUTATED                                                   1
  INF2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  INF2 MUTATED                                                                   3
  INF2 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  INF2 MUTATED                                                    0
  INF2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  INF2 MUTATED                                                  3
  INF2 WILD-TYPE                                               58
D95V9, multiclass
                                                                   clus
vv                                                                  INF2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  INF2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  INF2 MUTATED    13   1   2   1
  INF2 WILD-TYPE 298  13  13  23
D95V10, multiclass
    clus
vv   INF2 MUTATED INF2 WILD-TYPE
  R0           13            298
  R1            1             13
  R2            2             13
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  INF2 MUTATED       5                         0
  INF2 WILD-TYPE    82                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INF2 MUTATED                                           0     8
  INF2 WILD-TYPE                                         1   235
D95V12, multiclass
                                           clus
vv                                          INF2 MUTATED INF2 WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V13, binary
                cls
clus               0   1
  INF2 MUTATED     0  13
  INF2 WILD-TYPE   4 297
[1] "tbl2"
                cls
clus             [,1] [,2]
  INF2 MUTATED      0   13
  INF2 WILD-TYPE    4  297
                        clus
vv                       INF2 MUTATED INF2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           13            297
[1] 2 2
[1] FALSE

Clustering(96) Variable = CR1L MUTATION ANALYSIS
D96V1, survival
                sevent
clus2              0   1
  CR1L MUTATED     8   6
  CR1L WILD-TYPE 222 133
  CR1L MUTATED CR1L WILD-TYPE 
            14            355 
  CR1L MUTATED CR1L WILD-TYPE 
             6            133 
$`CR1L MUTATED`
TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-8363 TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-4437 
       26.70         9.67         0.26        11.77         1.02         8.05 
TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A6EY TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GU 
        6.02       105.07        11.44        24.20        11.77         6.58 
TCGA-HU-A4GY TCGA-RD-A8MW 
        0.26        37.91 

$`CR1L WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51        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-A8N0 
       11.05         8.61         5.13        16.67       122.30        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 

  CR1L MUTATED CR1L WILD-TYPE 
          0.26           0.00 
  CR1L MUTATED CR1L WILD-TYPE 
        105.07         122.30 
  CR1L MUTATED CR1L WILD-TYPE 
        10.555         14.660 
[1] "0.3 - 105.1 (10.6)" "0.0 - 122.3 (14.7)"
[1] "hr=" "1.4"
D96V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CR1L MUTATED         1        3        1        2         0         2
  CR1L WILD-TYPE       1       12       39       28        37        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CR1L MUTATED           0          2          2          0        2
  CR1L WILD-TYPE         3         68         51         32       36
D96V3, multiclass
            clus
vv           CR1L MUTATED CR1L WILD-TYPE
  STAGE I               1              1
  STAGE IA              3             12
  STAGE IB              1             39
  STAGE II              2             28
  STAGE IIA             0             37
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            2             51
  STAGE IIIC            0             32
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CR1L MUTATED     4   3   5   3
  CR1L WILD-TYPE  18  89 168  94
D96V4, multiclass
    clus
vv   CR1L MUTATED CR1L WILD-TYPE
  T1            4             18
  T2            3             89
  T3            5            168
  T4            3             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
  CR1L MUTATED     5   7   2   1
  CR1L WILD-TYPE 113  97  75  76
D96V5, multiclass
    clus
vv   CR1L MUTATED CR1L WILD-TYPE
  N0            5            113
  N1            7             97
  N2            2             75
  N3            1             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"
D96V6, binary
                cls
clus               0   1
  CR1L MUTATED    14   1
  CR1L WILD-TYPE 332  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED     14    1
  CR1L WILD-TYPE  332   28
   clus
vv  CR1L MUTATED CR1L WILD-TYPE
  0           14            332
  1            1             28
[1] 2 2
[1] FALSE
D96V7, binary
                cls
clus               0   1
  CR1L MUTATED     6  10
  CR1L WILD-TYPE 139 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED      6   10
  CR1L WILD-TYPE  139  238
        clus
vv       CR1L MUTATED CR1L WILD-TYPE
  FEMALE            6            139
  MALE             10            238
[1] 2 2
[1] FALSE
D96V8, binary
                cls
clus               0   1
  CR1L MUTATED    13   2
  CR1L WILD-TYPE 279  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED     13    2
  CR1L WILD-TYPE  279   57
     clus
vv    CR1L MUTATED CR1L WILD-TYPE
  NO            13            279
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CR1L MUTATED                                          0
  CR1L WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CR1L MUTATED                                       3
  CR1L WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CR1L MUTATED                                                        7
  CR1L WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CR1L MUTATED                                                   0
  CR1L WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CR1L MUTATED                                                                   3
  CR1L WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CR1L MUTATED                                                    0
  CR1L WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CR1L MUTATED                                                  3
  CR1L WILD-TYPE                                               58
D96V9, multiclass
                                                                   clus
vv                                                                  CR1L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  CR1L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CR1L MUTATED    13   0   1   1
  CR1L WILD-TYPE 298  14  14  23
D96V10, multiclass
    clus
vv   CR1L MUTATED CR1L WILD-TYPE
  R0           13            298
  R1            0             14
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CR1L MUTATED       6                         1
  CR1L WILD-TYPE    81                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CR1L MUTATED                                           0     5
  CR1L WILD-TYPE                                         1   238
D96V12, multiclass
                                           clus
vv                                          CR1L MUTATED CR1L WILD-TYPE
  ASIAN                                                6             81
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V13, binary
                cls
clus               0   1
  CR1L MUTATED     0  12
  CR1L WILD-TYPE   4 298
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED      0   12
  CR1L WILD-TYPE    4  298
                        clus
vv                       CR1L MUTATED CR1L WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           12            298
[1] 2 2
[1] FALSE

Clustering(97) Variable = NPHP1 MUTATION ANALYSIS
D97V1, survival
                 sevent
clus2               0   1
  NPHP1 MUTATED     6   3
  NPHP1 WILD-TYPE 224 136
  NPHP1 MUTATED NPHP1 WILD-TYPE 
              9             360 
  NPHP1 MUTATED NPHP1 WILD-TYPE 
              3             136 
$`NPHP1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8591 TCGA-CG-4306 
        6.97        30.90        29.59         1.12        28.14         1.02 
TCGA-HU-A4G6 TCGA-IN-A6RS TCGA-R5-A7ZI 
       24.26        12.59        74.53 

$`NPHP1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  NPHP1 MUTATED NPHP1 WILD-TYPE 
           1.02            0.00 
  NPHP1 MUTATED NPHP1 WILD-TYPE 
          74.53          122.30 
  NPHP1 MUTATED NPHP1 WILD-TYPE 
          24.26           14.22 
[1] "1.0 - 74.5 (24.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D97V2, 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       2       13       40       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NPHP1 MUTATED           0          2          0          1        2
  NPHP1 WILD-TYPE         3         68         53         31       36
D97V3, multiclass
            clus
vv           NPHP1 MUTATED NPHP1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NPHP1 MUTATED     2   1   3   4
  NPHP1 WILD-TYPE  20  91 170  93
D97V4, multiclass
    clus
vv   NPHP1 MUTATED NPHP1 WILD-TYPE
  T1             2              20
  T2             1              91
  T3             3             170
  T4             4              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
  NPHP1 MUTATED     5   2   1   1
  NPHP1 WILD-TYPE 113 102  76  76
D97V5, multiclass
    clus
vv   NPHP1 MUTATED NPHP1 WILD-TYPE
  N0             5             113
  N1             2             102
  N2             1              76
  N3             1              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"
D97V6, binary
                 cls
clus                0   1
  NPHP1 MUTATED     7   2
  NPHP1 WILD-TYPE 339  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHP1 MUTATED      7    2
  NPHP1 WILD-TYPE  339   27
   clus
vv  NPHP1 MUTATED NPHP1 WILD-TYPE
  0             7             339
  1             2              27
[1] 2 2
[1] FALSE
D97V7, binary
                 cls
clus                0   1
  NPHP1 MUTATED     5   5
  NPHP1 WILD-TYPE 140 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHP1 MUTATED      5    5
  NPHP1 WILD-TYPE  140  243
        clus
vv       NPHP1 MUTATED NPHP1 WILD-TYPE
  FEMALE             5             140
  MALE               5             243
[1] 2 2
[1] FALSE
D97V8, binary
                 cls
clus                0   1
  NPHP1 MUTATED     8   0
  NPHP1 WILD-TYPE 284  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHP1 MUTATED      8    0
  NPHP1 WILD-TYPE  284   59
     clus
vv    NPHP1 MUTATED NPHP1 WILD-TYPE
  NO              8             284
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NPHP1 MUTATED                                          0
  NPHP1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NPHP1 MUTATED                                       1
  NPHP1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NPHP1 MUTATED                                                        8
  NPHP1 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NPHP1 MUTATED                                                   0
  NPHP1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NPHP1 MUTATED                                                                   0
  NPHP1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NPHP1 MUTATED                                                    1
  NPHP1 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NPHP1 MUTATED                                                  0
  NPHP1 WILD-TYPE                                               61
D97V9, multiclass
                                                                   clus
vv                                                                  NPHP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  NPHP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NPHP1 MUTATED     6   0   1   3
  NPHP1 WILD-TYPE 305  14  14  21
D97V10, multiclass
    clus
vv   NPHP1 MUTATED NPHP1 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NPHP1 MUTATED       1                         0
  NPHP1 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NPHP1 MUTATED                                           0     8
  NPHP1 WILD-TYPE                                         1   235
D97V12, multiclass
                                           clus
vv                                          NPHP1 MUTATED NPHP1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V13, binary
                 cls
clus                0   1
  NPHP1 MUTATED     1   8
  NPHP1 WILD-TYPE   3 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHP1 MUTATED      1    8
  NPHP1 WILD-TYPE    3  302
                        clus
vv                       NPHP1 MUTATED NPHP1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(98) Variable = ADAMDEC1 MUTATION ANALYSIS
D98V1, survival
                    sevent
clus2                  0   1
  ADAMDEC1 MUTATED     8   2
  ADAMDEC1 WILD-TYPE 222 137
  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
                10                359 
  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
                 2                137 
$`ADAMDEC1 MUTATED`
TCGA-CG-4460 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-5721 
       21.99         4.31         1.12        31.96        11.77         6.02 
TCGA-CG-5728 TCGA-F1-A448 TCGA-HU-8602 TCGA-VQ-A8P2 
       65.10        21.27        22.32        38.14 

$`ADAMDEC1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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 

  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
              1.12               0.00 
  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
              65.1              122.3 
  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE 
             21.63              14.17 
[1] "1.1 - 65.1 (21.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.2"
D98V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADAMDEC1 MUTATED         0        0        2        0         1         1
  ADAMDEC1 WILD-TYPE       2       15       38       30        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAMDEC1 MUTATED           0          3          1          0        3
  ADAMDEC1 WILD-TYPE         3         67         52         32       35
D98V3, multiclass
            clus
vv           ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  2                 38
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                3                 67
  STAGE IIIB                1                 52
  STAGE IIIC                0                 32
  STAGE IV                  3                 35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ADAMDEC1 MUTATED     1   2   3   6
  ADAMDEC1 WILD-TYPE  21  90 170  91
D98V4, multiclass
    clus
vv   ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  T1                1                 21
  T2                2                 90
  T3                3                170
  T4                6                 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
  ADAMDEC1 MUTATED     5   4   1   1
  ADAMDEC1 WILD-TYPE 113 100  76  76
D98V5, multiclass
    clus
vv   ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  N0                5                113
  N1                4                100
  N2                1                 76
  N3                1                 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"
D98V6, binary
                    cls
clus                   0   1
  ADAMDEC1 MUTATED    10   2
  ADAMDEC1 WILD-TYPE 336  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMDEC1 MUTATED     10    2
  ADAMDEC1 WILD-TYPE  336   27
   clus
vv  ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  0               10                336
  1                2                 27
[1] 2 2
[1] FALSE
D98V7, binary
                    cls
clus                   0   1
  ADAMDEC1 MUTATED     7   5
  ADAMDEC1 WILD-TYPE 138 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMDEC1 MUTATED      7    5
  ADAMDEC1 WILD-TYPE  138  243
        clus
vv       ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  FEMALE                7                138
  MALE                  5                243
[1] 2 2
[1] FALSE
D98V8, binary
                    cls
clus                   0   1
  ADAMDEC1 MUTATED     7   2
  ADAMDEC1 WILD-TYPE 285  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMDEC1 MUTATED      7    2
  ADAMDEC1 WILD-TYPE  285   57
     clus
vv    ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  NO                 7                285
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ADAMDEC1 MUTATED                                          0
  ADAMDEC1 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ADAMDEC1 MUTATED                                       1
  ADAMDEC1 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ADAMDEC1 MUTATED                                                        5
  ADAMDEC1 WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ADAMDEC1 MUTATED                                                   2
  ADAMDEC1 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ADAMDEC1 MUTATED                                                                   3
  ADAMDEC1 WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ADAMDEC1 MUTATED                                                    0
  ADAMDEC1 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ADAMDEC1 MUTATED                                                  1
  ADAMDEC1 WILD-TYPE                                               60
D98V9, multiclass
                                                                   clus
vv                                                                  ADAMDEC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  ADAMDEC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ADAMDEC1 MUTATED     8   0   1   2
  ADAMDEC1 WILD-TYPE 303  14  14  22
D98V10, multiclass
    clus
vv   ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  R0                8                303
  R1                0                 14
  R2                1                 14
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ADAMDEC1 MUTATED       3                         0
  ADAMDEC1 WILD-TYPE    84                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ADAMDEC1 MUTATED                                           0     6
  ADAMDEC1 WILD-TYPE                                         1   237
D98V12, multiclass
                                           clus
vv                                          ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V13, binary
                    cls
clus                   0   1
  ADAMDEC1 MUTATED     1   7
  ADAMDEC1 WILD-TYPE   3 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMDEC1 MUTATED      1    7
  ADAMDEC1 WILD-TYPE    3  303
                        clus
vv                       ADAMDEC1 MUTATED ADAMDEC1 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO                7                303
[1] 2 2
[1] FALSE

Clustering(99) Variable = GXYLT1 MUTATION ANALYSIS
D99V1, survival
                  sevent
clus2                0   1
  GXYLT1 MUTATED     8   5
  GXYLT1 WILD-TYPE 222 134
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
              13              356 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
               5              134 
$`GXYLT1 MUTATED`
TCGA-B7-5816 TCGA-BR-6802 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8382 
       26.70        30.90        31.10         0.26        31.27        25.05 
TCGA-CD-8529 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-5733 TCGA-F1-6874 
       12.30         6.58        11.77        12.62        21.07        14.47 
TCGA-VQ-A8P2 
       38.14 

$`GXYLT1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-8384 
       14.04         3.32        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-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-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-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-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-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 

  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
            0.26             0.00 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
           38.14           122.30 
  GXYLT1 MUTATED GXYLT1 WILD-TYPE 
           21.07            14.12 
[1] "0.3 - 38.1 (21.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D99V2, 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       2       15       37       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GXYLT1 MUTATED           0          4          0          3        1
  GXYLT1 WILD-TYPE         3         66         53         29       37
D99V3, multiclass
            clus
vv           GXYLT1 MUTATED GXYLT1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              0               53
  STAGE IIIC              3               29
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GXYLT1 MUTATED     1   4   3   6
  GXYLT1 WILD-TYPE  21  88 170  91
D99V4, multiclass
    clus
vv   GXYLT1 MUTATED GXYLT1 WILD-TYPE
  T1              1               21
  T2              4               88
  T3              3              170
  T4              6               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
  GXYLT1 MUTATED     6   2   3   2
  GXYLT1 WILD-TYPE 112 102  74  75
D99V5, multiclass
    clus
vv   GXYLT1 MUTATED GXYLT1 WILD-TYPE
  N0              6              112
  N1              2              102
  N2              3               74
  N3              2               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"
D99V6, binary
                  cls
clus                 0   1
  GXYLT1 MUTATED    13   1
  GXYLT1 WILD-TYPE 333  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GXYLT1 MUTATED     13    1
  GXYLT1 WILD-TYPE  333   28
   clus
vv  GXYLT1 MUTATED GXYLT1 WILD-TYPE
  0             13              333
  1              1               28
[1] 2 2
[1] FALSE
D99V7, binary
                  cls
clus                 0   1
  GXYLT1 MUTATED     6   8
  GXYLT1 WILD-TYPE 139 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GXYLT1 MUTATED      6    8
  GXYLT1 WILD-TYPE  139  240
        clus
vv       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  FEMALE              6              139
  MALE                8              240
[1] 2 2
[1] FALSE
D99V8, binary
                  cls
clus                 0   1
  GXYLT1 MUTATED    11   2
  GXYLT1 WILD-TYPE 281  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GXYLT1 MUTATED     11    2
  GXYLT1 WILD-TYPE  281   57
     clus
vv    GXYLT1 MUTATED GXYLT1 WILD-TYPE
  NO              11              281
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GXYLT1 MUTATED                                          0
  GXYLT1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GXYLT1 MUTATED                                       2
  GXYLT1 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GXYLT1 MUTATED                                                        8
  GXYLT1 WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GXYLT1 MUTATED                                                   2
  GXYLT1 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GXYLT1 MUTATED                                                                   2
  GXYLT1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GXYLT1 MUTATED                                                    0
  GXYLT1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GXYLT1 MUTATED                                                  0
  GXYLT1 WILD-TYPE                                               61
D99V9, multiclass
                                                                   clus
vv                                                                  GXYLT1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  GXYLT1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GXYLT1 MUTATED    10   0   0   1
  GXYLT1 WILD-TYPE 301  14  15  23
D99V10, multiclass
    clus
vv   GXYLT1 MUTATED GXYLT1 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GXYLT1 MUTATED       4                         0
  GXYLT1 WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GXYLT1 MUTATED                                           0     9
  GXYLT1 WILD-TYPE                                         1   234
D99V12, multiclass
                                           clus
vv                                          GXYLT1 MUTATED GXYLT1 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V13, binary
                  cls
clus                 0   1
  GXYLT1 MUTATED     0  12
  GXYLT1 WILD-TYPE   4 298
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GXYLT1 MUTATED      0   12
  GXYLT1 WILD-TYPE    4  298
                        clus
vv                       GXYLT1 MUTATED GXYLT1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             12              298
[1] 2 2
[1] FALSE

Clustering(100) Variable = ENTPD2 MUTATION ANALYSIS
D100V1, survival
                  sevent
clus2                0   1
  ENTPD2 MUTATED     3   2
  ENTPD2 WILD-TYPE 227 137
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               5              364 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               2              137 
$`ENTPD2 MUTATED`
TCGA-B7-5816 TCGA-CD-A4MI TCGA-D7-A4YV TCGA-HU-A4G9 TCGA-VQ-A91V 
       26.70        11.77         5.92        24.20        42.64 

$`ENTPD2 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
            5.92             0.00 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
           42.64           122.30 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
           24.20            14.22 
[1] "5.9 - 42.6 (24.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D100V2, 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       2       14       40       30        37        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ENTPD2 MUTATED           0          2          0          0        0
  ENTPD2 WILD-TYPE         3         68         53         32       38
D100V3, multiclass
            clus
vv           ENTPD2 MUTATED ENTPD2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ENTPD2 MUTATED     1   0   3   1
  ENTPD2 WILD-TYPE  21  92 170  96
D100V4, multiclass
    clus
vv   ENTPD2 MUTATED ENTPD2 WILD-TYPE
  T1              1               21
  T2              0               92
  T3              3              170
  T4              1               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
  ENTPD2 MUTATED     2   3   1   0
  ENTPD2 WILD-TYPE 116 101  76  77
D100V5, multiclass
    clus
vv   ENTPD2 MUTATED ENTPD2 WILD-TYPE
  N0              2              116
  N1              3              101
  N2              1               76
  N3              0               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"
D100V6, binary
                  cls
clus                 0   1
  ENTPD2 MUTATED     6   0
  ENTPD2 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      6    0
  ENTPD2 WILD-TYPE  340   29
   clus
vv  ENTPD2 MUTATED ENTPD2 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D100V7, binary
                  cls
clus                 0   1
  ENTPD2 MUTATED     4   2
  ENTPD2 WILD-TYPE 141 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      4    2
  ENTPD2 WILD-TYPE  141  246
        clus
vv       ENTPD2 MUTATED ENTPD2 WILD-TYPE
  FEMALE              4              141
  MALE                2              246
[1] 2 2
[1] FALSE
D100V8, binary
                  cls
clus                 0   1
  ENTPD2 MUTATED     4   1
  ENTPD2 WILD-TYPE 288  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      4    1
  ENTPD2 WILD-TYPE  288   58
     clus
vv    ENTPD2 MUTATED ENTPD2 WILD-TYPE
  NO               4              288
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ENTPD2 MUTATED                                          0
  ENTPD2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ENTPD2 MUTATED                                       1
  ENTPD2 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ENTPD2 MUTATED                                                        2
  ENTPD2 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ENTPD2 MUTATED                                                   0
  ENTPD2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ENTPD2 MUTATED                                                                   0
  ENTPD2 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ENTPD2 MUTATED                                                    0
  ENTPD2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ENTPD2 MUTATED                                                  3
  ENTPD2 WILD-TYPE                                               58
D100V9, multiclass
                                                                   clus
vv                                                                  ENTPD2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  ENTPD2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ENTPD2 MUTATED     4   0   0   1
  ENTPD2 WILD-TYPE 307  14  15  23
D100V10, multiclass
    clus
vv   ENTPD2 MUTATED ENTPD2 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ENTPD2 MUTATED       2                         0
  ENTPD2 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ENTPD2 MUTATED                                           0     3
  ENTPD2 WILD-TYPE                                         1   240
D100V12, multiclass
                                           clus
vv                                          ENTPD2 MUTATED ENTPD2 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V13, binary
                  cls
clus                 0   1
  ENTPD2 MUTATED     0   5
  ENTPD2 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      0    5
  ENTPD2 WILD-TYPE    4  305
                        clus
vv                       ENTPD2 MUTATED ENTPD2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(101) Variable = EIF4G3 MUTATION ANALYSIS
D101V1, survival
                  sevent
clus2                0   1
  EIF4G3 MUTATED    12   8
  EIF4G3 WILD-TYPE 218 131
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
              20              349 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
               8              131 
$`EIF4G3 MUTATED`
TCGA-CG-4460 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8289 TCGA-BR-8363 
       21.99        11.70        34.68        29.59         2.66         0.26 
TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG 
       31.27         1.12        28.14        31.96        16.14         6.58 
TCGA-CG-4465 TCGA-D7-A6EY TCGA-F1-A448 TCGA-FP-A4BE TCGA-IN-A6RL TCGA-MX-A5UJ 
        9.01        11.44        21.27        11.08        13.35        19.73 
TCGA-R5-A7ZI TCGA-VQ-A8P2 
       74.53        38.14 

$`EIF4G3 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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-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-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-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-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 

  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
            0.26             0.00 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
           74.53           122.30 
  EIF4G3 MUTATED EIF4G3 WILD-TYPE 
          17.935           14.170 
[1] "0.3 - 74.5 (17.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D101V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EIF4G3 MUTATED         0        0        2        0         4         1
  EIF4G3 WILD-TYPE       2       15       38       30        33        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF4G3 MUTATED           0          3          3          2        5
  EIF4G3 WILD-TYPE         3         67         50         30       33
D101V3, multiclass
            clus
vv           EIF4G3 MUTATED EIF4G3 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               4               33
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              3               50
  STAGE IIIC              2               30
  STAGE IV                5               33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EIF4G3 MUTATED     0   3   8   9
  EIF4G3 WILD-TYPE  22  89 165  88
D101V4, multiclass
    clus
vv   EIF4G3 MUTATED EIF4G3 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              8              165
  T4              9               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
  EIF4G3 MUTATED     7   4   2   7
  EIF4G3 WILD-TYPE 111 100  75  70
D101V5, multiclass
    clus
vv   EIF4G3 MUTATED EIF4G3 WILD-TYPE
  N0              7              111
  N1              4              100
  N2              2               75
  N3              7               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"
D101V6, binary
                  cls
clus                 0   1
  EIF4G3 MUTATED    15   5
  EIF4G3 WILD-TYPE 331  24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED     15    5
  EIF4G3 WILD-TYPE  331   24
   clus
vv  EIF4G3 MUTATED EIF4G3 WILD-TYPE
  0             15              331
  1              5               24
[1] 2 2
[1] FALSE
D101V7, binary
                  cls
clus                 0   1
  EIF4G3 MUTATED    10  10
  EIF4G3 WILD-TYPE 135 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED     10   10
  EIF4G3 WILD-TYPE  135  238
        clus
vv       EIF4G3 MUTATED EIF4G3 WILD-TYPE
  FEMALE             10              135
  MALE               10              238
[1] 2 2
[1] FALSE
D101V8, binary
                  cls
clus                 0   1
  EIF4G3 MUTATED    16   3
  EIF4G3 WILD-TYPE 276  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED     16    3
  EIF4G3 WILD-TYPE  276   56
     clus
vv    EIF4G3 MUTATED EIF4G3 WILD-TYPE
  NO              16              276
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EIF4G3 MUTATED                                          0
  EIF4G3 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EIF4G3 MUTATED                                       4
  EIF4G3 WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EIF4G3 MUTATED                                                        9
  EIF4G3 WILD-TYPE                                                    149
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EIF4G3 MUTATED                                                   2
  EIF4G3 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EIF4G3 MUTATED                                                                   2
  EIF4G3 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EIF4G3 MUTATED                                                    0
  EIF4G3 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EIF4G3 MUTATED                                                  3
  EIF4G3 WILD-TYPE                                               58
D101V9, multiclass
                                                                   clus
vv                                                                  EIF4G3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  EIF4G3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EIF4G3 MUTATED    17   0   2   0
  EIF4G3 WILD-TYPE 294  14  13  24
D101V10, multiclass
    clus
vv   EIF4G3 MUTATED EIF4G3 WILD-TYPE
  R0             17              294
  R1              0               14
  R2              2               13
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  EIF4G3 MUTATED       2                         1
  EIF4G3 WILD-TYPE    85                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EIF4G3 MUTATED                                           0    15
  EIF4G3 WILD-TYPE                                         1   228
D101V12, multiclass
                                           clus
vv                                          EIF4G3 MUTATED EIF4G3 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 15              228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V13, binary
                  cls
clus                 0   1
  EIF4G3 MUTATED     2  15
  EIF4G3 WILD-TYPE   2 295
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G3 MUTATED      2   15
  EIF4G3 WILD-TYPE    2  295
                        clus
vv                       EIF4G3 MUTATED EIF4G3 WILD-TYPE
  HISPANIC OR LATINO                  2                2
  NOT HISPANIC OR LATINO             15              295
[1] 2 2
[1] FALSE

Clustering(102) Variable = PIGT MUTATION ANALYSIS
D102V1, survival
                sevent
clus2              0   1
  PIGT MUTATED     8   3
  PIGT WILD-TYPE 222 136
  PIGT MUTATED PIGT WILD-TYPE 
            11            358 
  PIGT MUTATED PIGT WILD-TYPE 
             3            136 
$`PIGT MUTATED`
TCGA-BR-8059 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MG TCGA-CG-5723 TCGA-CG-5726 
       14.43         1.12        28.14         6.58       105.07        28.96 
TCGA-CG-5728 TCGA-F1-6874 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GN 
       65.10        14.47        30.51        22.68        29.98 

$`PIGT WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-5730 TCGA-CG-5732 
        6.02         0.99        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-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-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 

  PIGT MUTATED PIGT WILD-TYPE 
          1.12           0.00 
  PIGT MUTATED PIGT WILD-TYPE 
        105.07         122.30 
  PIGT MUTATED PIGT WILD-TYPE 
        28.140         14.055 
[1] "1.1 - 105.1 (28.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2"  
D102V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIGT MUTATED         0        1        2        1         3         1
  PIGT WILD-TYPE       2       14       38       29        34        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIGT MUTATED           1          0          0          2        0
  PIGT WILD-TYPE         2         70         53         30       38
D102V3, multiclass
            clus
vv           PIGT MUTATED PIGT WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             3             34
  STAGE IIB             1             51
  STAGE III             1              2
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PIGT MUTATED     1   4   3   3
  PIGT WILD-TYPE  21  88 170  94
D102V4, multiclass
    clus
vv   PIGT MUTATED PIGT WILD-TYPE
  T1            1             21
  T2            4             88
  T3            3            170
  T4            3             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
  PIGT MUTATED     5   4   0   2
  PIGT WILD-TYPE 113 100  77  75
D102V5, multiclass
    clus
vv   PIGT MUTATED PIGT WILD-TYPE
  N0            5            113
  N1            4            100
  N2            0             77
  N3            2             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"
D102V6, binary
                cls
clus               0   1
  PIGT MUTATED    11   0
  PIGT WILD-TYPE 335  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGT MUTATED     11    0
  PIGT WILD-TYPE  335   29
   clus
vv  PIGT MUTATED PIGT WILD-TYPE
  0           11            335
  1            0             29
[1] 2 2
[1] FALSE
D102V7, binary
                cls
clus               0   1
  PIGT MUTATED     4   7
  PIGT WILD-TYPE 141 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGT MUTATED      4    7
  PIGT WILD-TYPE  141  241
        clus
vv       PIGT MUTATED PIGT WILD-TYPE
  FEMALE            4            141
  MALE              7            241
[1] 2 2
[1] FALSE
D102V8, binary
                cls
clus               0   1
  PIGT MUTATED     8   1
  PIGT WILD-TYPE 284  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGT MUTATED      8    1
  PIGT WILD-TYPE  284   58
     clus
vv    PIGT MUTATED PIGT WILD-TYPE
  NO             8            284
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PIGT MUTATED                                          0
  PIGT WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PIGT MUTATED                                       2
  PIGT WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIGT MUTATED                                                        3
  PIGT WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PIGT MUTATED                                                   1
  PIGT WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIGT MUTATED                                                                   4
  PIGT WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PIGT MUTATED                                                    0
  PIGT WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PIGT MUTATED                                                  1
  PIGT WILD-TYPE                                               60
D102V9, multiclass
                                                                   clus
vv                                                                  PIGT MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  PIGT WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PIGT MUTATED     8   1   0   0
  PIGT WILD-TYPE 303  13  15  24
D102V10, multiclass
    clus
vv   PIGT MUTATED PIGT WILD-TYPE
  R0            8            303
  R1            1             13
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PIGT MUTATED       3                         0
  PIGT WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIGT MUTATED                                           0     4
  PIGT WILD-TYPE                                         1   239
D102V12, multiclass
                                           clus
vv                                          PIGT MUTATED PIGT WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V13, binary
                cls
clus               0   1
  PIGT MUTATED     0   7
  PIGT WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGT MUTATED      0    7
  PIGT WILD-TYPE    4  303
                        clus
vv                       PIGT MUTATED PIGT WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(103) Variable = POLM MUTATION ANALYSIS
D103V1, survival
                sevent
clus2              0   1
  POLM MUTATED     7   2
  POLM WILD-TYPE 223 137
  POLM MUTATED POLM WILD-TYPE 
             9            360 
  POLM MUTATED POLM WILD-TYPE 
             2            137 
$`POLM MUTATED`
TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-A4MJ TCGA-CG-5723 TCGA-F1-6875 
       34.68         0.26         1.12        12.62       105.07        72.23 
TCGA-HU-A4G9 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       24.20        19.73        38.14 

$`POLM WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  POLM MUTATED POLM WILD-TYPE 
          0.26           0.00 
  POLM MUTATED POLM WILD-TYPE 
        105.07         122.30 
  POLM MUTATED POLM WILD-TYPE 
         24.20          14.12 
[1] "0.3 - 105.1 (24.2)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.5"
D103V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  POLM MUTATED         1        2        3        1         2         1
  POLM WILD-TYPE       1       13       37       29        35        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POLM MUTATED           0          2          0          0        0
  POLM WILD-TYPE         3         68         53         32       38
D103V3, multiclass
            clus
vv           POLM MUTATED POLM WILD-TYPE
  STAGE I               1              1
  STAGE IA              2             13
  STAGE IB              3             37
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  POLM MUTATED     2   5   3   2
  POLM WILD-TYPE  20  87 170  95
D103V4, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  T1            2             20
  T2            5             87
  T3            3            170
  T4            2             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
  POLM MUTATED     8   3   1   0
  POLM WILD-TYPE 110 101  76  77
D103V5, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  N0            8            110
  N1            3            101
  N2            1             76
  N3            0             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"
D103V6, binary
                cls
clus               0   1
  POLM MUTATED    12   0
  POLM WILD-TYPE 334  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED     12    0
  POLM WILD-TYPE  334   29
   clus
vv  POLM MUTATED POLM WILD-TYPE
  0           12            334
  1            0             29
[1] 2 2
[1] FALSE
D103V7, binary
                cls
clus               0   1
  POLM MUTATED     6   7
  POLM WILD-TYPE 139 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      6    7
  POLM WILD-TYPE  139  241
        clus
vv       POLM MUTATED POLM WILD-TYPE
  FEMALE            6            139
  MALE              7            241
[1] 2 2
[1] FALSE
D103V8, binary
                cls
clus               0   1
  POLM MUTATED    10   1
  POLM WILD-TYPE 282  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED     10    1
  POLM WILD-TYPE  282   58
     clus
vv    POLM MUTATED POLM WILD-TYPE
  NO            10            282
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  POLM MUTATED                                          0
  POLM WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  POLM MUTATED                                       0
  POLM WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  POLM MUTATED                                                        8
  POLM WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  POLM MUTATED                                                   1
  POLM WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  POLM MUTATED                                                                   2
  POLM WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  POLM MUTATED                                                    0
  POLM WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  POLM MUTATED                                                  2
  POLM WILD-TYPE                                               59
D103V9, multiclass
                                                                   clus
vv                                                                  POLM MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  POLM WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  POLM MUTATED    11   0   0   1
  POLM WILD-TYPE 300  14  15  23
D103V10, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  R0           11            300
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  POLM MUTATED       2                         2
  POLM WILD-TYPE    85                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  POLM MUTATED                                           0     7
  POLM WILD-TYPE                                         1   236
D103V12, multiclass
                                           clus
vv                                          POLM MUTATED POLM WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V13, binary
                cls
clus               0   1
  POLM MUTATED     0  10
  POLM WILD-TYPE   4 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      0   10
  POLM WILD-TYPE    4  300
                        clus
vv                       POLM MUTATED POLM WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           10            300
[1] 2 2
[1] FALSE

Clustering(104) Variable = CCDC108 MUTATION ANALYSIS
D104V1, survival
                   sevent
clus2                 0   1
  CCDC108 MUTATED    19   5
  CCDC108 WILD-TYPE 211 134
  CCDC108 MUTATED CCDC108 WILD-TYPE 
               24               345 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
                5               134 
$`CCDC108 MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8368 
       11.70         6.97        30.90        34.68        29.59         4.31 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4PE TCGA-CD-8527 TCGA-CD-8529 
       25.05         1.12        31.96        20.42         7.17        12.30 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CG-4465 TCGA-CG-5721 TCGA-FP-A4BE TCGA-HF-7132 
       12.43        12.30         9.01         6.02        11.08        77.29 
TCGA-HF-7134 TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H8 TCGA-VQ-A8P2 
       52.21        22.32        29.98         6.51        14.07        38.14 

$`CCDC108 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.53        12.33        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-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-D7-6519 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-7133 
        5.03        13.58         0.56         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-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-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-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 

  CCDC108 MUTATED CCDC108 WILD-TYPE 
             1.12              0.00 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
            77.29            122.30 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
            13.25             14.43 
[1] "1.1 - 77.3 (13.2)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "2"  
D104V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC108 MUTATED         0        1        5        3         5         3
  CCDC108 WILD-TYPE       2       14       35       27        32        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC108 MUTATED           0          2          0          1        4
  CCDC108 WILD-TYPE         3         68         53         31       34
D104V3, multiclass
            clus
vv           CCDC108 MUTATED CCDC108 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 5                35
  STAGE II                 3                27
  STAGE IIA                5                32
  STAGE IIB                3                49
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 4                34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC108 MUTATED     3   8   7   8
  CCDC108 WILD-TYPE  19  84 166  89
D104V4, multiclass
    clus
vv   CCDC108 MUTATED CCDC108 WILD-TYPE
  T1               3                19
  T2               8                84
  T3               7               166
  T4               8                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
  CCDC108 MUTATED    13   8   1   2
  CCDC108 WILD-TYPE 105  96  76  75
D104V5, multiclass
    clus
vv   CCDC108 MUTATED CCDC108 WILD-TYPE
  N0              13               105
  N1               8                96
  N2               1                76
  N3               2                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"
D104V6, binary
                   cls
clus                  0   1
  CCDC108 MUTATED    22   3
  CCDC108 WILD-TYPE 324  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED     22    3
  CCDC108 WILD-TYPE  324   26
   clus
vv  CCDC108 MUTATED CCDC108 WILD-TYPE
  0              22               324
  1               3                26
[1] 2 2
[1] FALSE
D104V7, binary
                   cls
clus                  0   1
  CCDC108 MUTATED    12  14
  CCDC108 WILD-TYPE 133 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED     12   14
  CCDC108 WILD-TYPE  133  234
        clus
vv       CCDC108 MUTATED CCDC108 WILD-TYPE
  FEMALE              12               133
  MALE                14               234
[1] 2 2
[1] FALSE
D104V8, binary
                   cls
clus                  0   1
  CCDC108 MUTATED    19   4
  CCDC108 WILD-TYPE 273  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED     19    4
  CCDC108 WILD-TYPE  273   55
     clus
vv    CCDC108 MUTATED CCDC108 WILD-TYPE
  NO               19               273
  YES               4                55
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CCDC108 MUTATED                                          0
  CCDC108 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CCDC108 MUTATED                                       4
  CCDC108 WILD-TYPE                                    66
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC108 MUTATED                                                       11
  CCDC108 WILD-TYPE                                                    147
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CCDC108 MUTATED                                                   3
  CCDC108 WILD-TYPE                                                18
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC108 MUTATED                                                                   4
  CCDC108 WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CCDC108 MUTATED                                                    0
  CCDC108 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CCDC108 MUTATED                                                  4
  CCDC108 WILD-TYPE                                               57
D104V9, multiclass
                                                                   clus
vv                                                                  CCDC108 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                4
                                                                   clus
vv                                                                  CCDC108 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC108 MUTATED    22   0   1   3
  CCDC108 WILD-TYPE 289  14  14  21
D104V10, multiclass
    clus
vv   CCDC108 MUTATED CCDC108 WILD-TYPE
  R0              22               289
  R1               0                14
  R2               1                14
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CCDC108 MUTATED       9                         1
  CCDC108 WILD-TYPE    78                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC108 MUTATED                                           0    11
  CCDC108 WILD-TYPE                                         1   232
D104V12, multiclass
                                           clus
vv                                          CCDC108 MUTATED CCDC108 WILD-TYPE
  ASIAN                                                   9                78
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V13, binary
                   cls
clus                  0   1
  CCDC108 MUTATED     0  20
  CCDC108 WILD-TYPE   4 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED      0   20
  CCDC108 WILD-TYPE    4  290
                        clus
vv                       CCDC108 MUTATED CCDC108 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              20               290
[1] 2 2
[1] FALSE

Clustering(105) Variable = KIAA0195 MUTATION ANALYSIS
D105V1, survival
                    sevent
clus2                  0   1
  KIAA0195 MUTATED    13   4
  KIAA0195 WILD-TYPE 217 135
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                17                352 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                 4                135 
$`KIAA0195 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-A4QL 
       26.70        34.68         4.31        31.27         1.12        16.14 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8602 
       12.43         6.58        11.08        30.51        26.47        22.32 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-VQ-A8DT TCGA-VQ-A8P2 
        0.10         6.51         6.58        48.79        38.14 

$`KIAA0195 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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 

  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
               0.1                0.0 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
             48.79             122.30 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
             16.14              14.22 
[1] "0.1 - 48.8 (16.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.7"
D105V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0195 MUTATED         1        0        2        1         5         3
  KIAA0195 WILD-TYPE       1       15       38       29        32        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0195 MUTATED           0          2          2          3        0
  KIAA0195 WILD-TYPE         3         68         51         29       38
D105V3, multiclass
            clus
vv           KIAA0195 MUTATED KIAA0195 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  0                 15
  STAGE IB                  2                 38
  STAGE II                  1                 29
  STAGE IIA                 5                 32
  STAGE IIB                 3                 49
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                2                 51
  STAGE IIIC                3                 29
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0195 MUTATED     1   2   9   7
  KIAA0195 WILD-TYPE  21  90 164  90
D105V4, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  T1                1                 21
  T2                2                 90
  T3                9                164
  T4                7                 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
  KIAA0195 MUTATED    11   3   1   4
  KIAA0195 WILD-TYPE 107 101  76  73
D105V5, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  N0               11                107
  N1                3                101
  N2                1                 76
  N3                4                 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"
D105V6, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    18   0
  KIAA0195 WILD-TYPE 328  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     18    0
  KIAA0195 WILD-TYPE  328   29
   clus
vv  KIAA0195 MUTATED KIAA0195 WILD-TYPE
  0               18                328
  1                0                 29
[1] 2 2
[1] FALSE
D105V7, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    11   9
  KIAA0195 WILD-TYPE 134 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     11    9
  KIAA0195 WILD-TYPE  134  239
        clus
vv       KIAA0195 MUTATED KIAA0195 WILD-TYPE
  FEMALE               11                134
  MALE                  9                239
[1] 2 2
[1] FALSE
D105V8, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    14   4
  KIAA0195 WILD-TYPE 278  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     14    4
  KIAA0195 WILD-TYPE  278   55
     clus
vv    KIAA0195 MUTATED KIAA0195 WILD-TYPE
  NO                14                278
  YES                4                 55
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA0195 MUTATED                                          1
  KIAA0195 WILD-TYPE                                        7
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA0195 MUTATED                                       4
  KIAA0195 WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0195 MUTATED                                                       10
  KIAA0195 WILD-TYPE                                                    148
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA0195 MUTATED                                                   2
  KIAA0195 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0195 MUTATED                                                                   1
  KIAA0195 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA0195 MUTATED                                                    0
  KIAA0195 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA0195 MUTATED                                                  2
  KIAA0195 WILD-TYPE                                               59
D105V9, multiclass
                                                                   clus
vv                                                                  KIAA0195 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  KIAA0195 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0195 MUTATED    16   1   0   2
  KIAA0195 WILD-TYPE 295  13  15  22
D105V10, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  R0               16                295
  R1                1                 13
  R2                0                 15
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0195 MUTATED       6                         2
  KIAA0195 WILD-TYPE    81                         7
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0195 MUTATED                                           0    10
  KIAA0195 WILD-TYPE                                         1   233
D105V12, multiclass
                                           clus
vv                                          KIAA0195 MUTATED KIAA0195 WILD-TYPE
  ASIAN                                                    6                 81
  BLACK OR AFRICAN AMERICAN                                2                  7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   10                233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V13, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED     0  17
  KIAA0195 WILD-TYPE   4 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED      0   17
  KIAA0195 WILD-TYPE    4  293
                        clus
vv                       KIAA0195 MUTATED KIAA0195 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               17                293
[1] 2 2
[1] FALSE

Clustering(106) Variable = CDH16 MUTATION ANALYSIS
D106V1, survival
                 sevent
clus2               0   1
  CDH16 MUTATED    10   5
  CDH16 WILD-TYPE 220 134
  CDH16 MUTATED CDH16 WILD-TYPE 
             15             354 
  CDH16 MUTATED CDH16 WILD-TYPE 
              5             134 
$`CDH16 MUTATED`
TCGA-BR-4201 TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8680 
       30.90        44.94         6.18         4.31        31.27        31.96 
TCGA-BR-A4QL TCGA-CG-4306 TCGA-D7-6815 TCGA-FP-7998 TCGA-HJ-7597 TCGA-HU-A4G9 
       16.14         1.02        15.98        22.29        26.47        24.20 
TCGA-HU-A4H3 TCGA-VQ-A8P2 TCGA-VQ-AA64 
       29.00        38.14        18.41 

$`CDH16 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-F1-6874 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-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-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-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-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 

  CDH16 MUTATED CDH16 WILD-TYPE 
           1.02            0.00 
  CDH16 MUTATED CDH16 WILD-TYPE 
          44.94          122.30 
  CDH16 MUTATED CDH16 WILD-TYPE 
          24.20           14.04 
[1] "1.0 - 44.9 (24.2)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.5"
D106V2, 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       2       13       38       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDH16 MUTATED           0          1          2          3        2
  CDH16 WILD-TYPE         3         69         51         29       36
D106V3, multiclass
            clus
vv           CDH16 MUTATED CDH16 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDH16 MUTATED     2   4   5   5
  CDH16 WILD-TYPE  20  88 168  92
D106V4, multiclass
    clus
vv   CDH16 MUTATED CDH16 WILD-TYPE
  T1             2              20
  T2             4              88
  T3             5             168
  T4             5              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
  CDH16 MUTATED     6   1   4   4
  CDH16 WILD-TYPE 112 103  73  73
D106V5, multiclass
    clus
vv   CDH16 MUTATED CDH16 WILD-TYPE
  N0             6             112
  N1             1             103
  N2             4              73
  N3             4              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"
D106V6, binary
                 cls
clus                0   1
  CDH16 MUTATED    12   2
  CDH16 WILD-TYPE 334  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH16 MUTATED     12    2
  CDH16 WILD-TYPE  334   27
   clus
vv  CDH16 MUTATED CDH16 WILD-TYPE
  0            12             334
  1             2              27
[1] 2 2
[1] FALSE
D106V7, binary
                 cls
clus                0   1
  CDH16 MUTATED     8   8
  CDH16 WILD-TYPE 137 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH16 MUTATED      8    8
  CDH16 WILD-TYPE  137  240
        clus
vv       CDH16 MUTATED CDH16 WILD-TYPE
  FEMALE             8             137
  MALE               8             240
[1] 2 2
[1] FALSE
D106V8, binary
                 cls
clus                0   1
  CDH16 MUTATED    11   3
  CDH16 WILD-TYPE 281  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH16 MUTATED     11    3
  CDH16 WILD-TYPE  281   56
     clus
vv    CDH16 MUTATED CDH16 WILD-TYPE
  NO             11             281
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CDH16 MUTATED                                          1
  CDH16 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CDH16 MUTATED                                       2
  CDH16 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDH16 MUTATED                                                        7
  CDH16 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CDH16 MUTATED                                                   1
  CDH16 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDH16 MUTATED                                                                   2
  CDH16 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CDH16 MUTATED                                                    0
  CDH16 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CDH16 MUTATED                                                  3
  CDH16 WILD-TYPE                                               58
D106V9, multiclass
                                                                   clus
vv                                                                  CDH16 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  CDH16 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDH16 MUTATED    14   0   1   1
  CDH16 WILD-TYPE 297  14  14  23
D106V10, multiclass
    clus
vv   CDH16 MUTATED CDH16 WILD-TYPE
  R0            14             297
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CDH16 MUTATED       4                         0
  CDH16 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDH16 MUTATED                                           0    11
  CDH16 WILD-TYPE                                         1   232
D106V12, multiclass
                                           clus
vv                                          CDH16 MUTATED CDH16 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V13, binary
                 cls
clus                0   1
  CDH16 MUTATED     1  12
  CDH16 WILD-TYPE   3 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH16 MUTATED      1   12
  CDH16 WILD-TYPE    3  298
                        clus
vv                       CDH16 MUTATED CDH16 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(107) Variable = ARHGAP5 MUTATION ANALYSIS
D107V1, survival
                   sevent
clus2                 0   1
  ARHGAP5 MUTATED    11   8
  ARHGAP5 WILD-TYPE 219 131
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               19               350 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
                8               131 
$`ARHGAP5 MUTATED`
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8487 
        9.34        34.68        14.43        32.25         4.31         1.12 
TCGA-BR-8589 TCGA-BR-A4J5 TCGA-CD-8529 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4465 
       27.12        28.34        12.30         6.58        15.95         9.01 
TCGA-D7-A6EZ TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-RD-A7C1 
       20.32        26.47        22.68        29.98         0.10        16.67 
TCGA-VQ-A8P2 
       38.14 

$`ARHGAP5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53         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-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-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-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-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-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-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-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 

  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
              0.1               0.0 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
            38.14            122.30 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
            16.67             14.07 
[1] "0.1 - 38.1 (16.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D107V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARHGAP5 MUTATED         0        0        5        1         4         3
  ARHGAP5 WILD-TYPE       2       15       35       29        33        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP5 MUTATED           1          3          1          1        2
  ARHGAP5 WILD-TYPE         2         67         52         31       36
D107V3, multiclass
            clus
vv           ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 5                35
  STAGE II                 1                29
  STAGE IIA                4                33
  STAGE IIB                3                49
  STAGE III                1                 2
  STAGE IIIA               3                67
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ARHGAP5 MUTATED     0   7   5   9
  ARHGAP5 WILD-TYPE  22  85 168  88
D107V4, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  T1               0                22
  T2               7                85
  T3               5               168
  T4               9                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
  ARHGAP5 MUTATED    11   8   2   1
  ARHGAP5 WILD-TYPE 107  96  75  76
D107V5, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  N0              11               107
  N1               8                96
  N2               2                75
  N3               1                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"
D107V6, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED    19   2
  ARHGAP5 WILD-TYPE 327  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED     19    2
  ARHGAP5 WILD-TYPE  327   27
   clus
vv  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  0              19               327
  1               2                27
[1] 2 2
[1] FALSE
D107V7, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED     8  14
  ARHGAP5 WILD-TYPE 137 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED      8   14
  ARHGAP5 WILD-TYPE  137  234
        clus
vv       ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  FEMALE               8               137
  MALE                14               234
[1] 2 2
[1] FALSE
D107V8, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED    18   2
  ARHGAP5 WILD-TYPE 274  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED     18    2
  ARHGAP5 WILD-TYPE  274   57
     clus
vv    ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  NO               18               274
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARHGAP5 MUTATED                                          1
  ARHGAP5 WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARHGAP5 MUTATED                                       4
  ARHGAP5 WILD-TYPE                                    66
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARHGAP5 MUTATED                                                        8
  ARHGAP5 WILD-TYPE                                                    150
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARHGAP5 MUTATED                                                   3
  ARHGAP5 WILD-TYPE                                                18
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARHGAP5 MUTATED                                                                   4
  ARHGAP5 WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARHGAP5 MUTATED                                                    0
  ARHGAP5 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARHGAP5 MUTATED                                                  2
  ARHGAP5 WILD-TYPE                                               59
D107V9, multiclass
                                                                   clus
vv                                                                  ARHGAP5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  ARHGAP5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ARHGAP5 MUTATED    18   0   1   1
  ARHGAP5 WILD-TYPE 293  14  14  23
D107V10, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  R0              18               293
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ARHGAP5 MUTATED       6                         0
  ARHGAP5 WILD-TYPE    81                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARHGAP5 MUTATED                                           0    13
  ARHGAP5 WILD-TYPE                                         1   230
D107V12, multiclass
                                           clus
vv                                          ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  ASIAN                                                   6                81
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V13, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED     0  18
  ARHGAP5 WILD-TYPE   4 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED      0   18
  ARHGAP5 WILD-TYPE    4  292
                        clus
vv                       ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              18               292
[1] 2 2
[1] FALSE

Clustering(108) Variable = STK38 MUTATION ANALYSIS
D108V1, survival
                 sevent
clus2               0   1
  STK38 MUTATED     5   0
  STK38 WILD-TYPE 225 139
  STK38 MUTATED STK38 WILD-TYPE 
              5             364 
  STK38 MUTATED STK38 WILD-TYPE 
              0             139 
$`STK38 MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8361 TCGA-CG-5721 TCGA-HU-A4GT 
       34.68        36.16        31.10         6.02         6.51 

$`STK38 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  STK38 MUTATED STK38 WILD-TYPE 
           6.02            0.00 
  STK38 MUTATED STK38 WILD-TYPE 
          36.16          122.30 
  STK38 MUTATED STK38 WILD-TYPE 
          31.10           14.22 
[1] "6.0 - 36.2 (31.1)"  "0.0 - 122.3 (14.2)"
[1] "hr="     "9200000"
D108V2, 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       2       14       39       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STK38 MUTATED           0          0          0          1        1
  STK38 WILD-TYPE         3         70         53         31       37
D108V3, multiclass
            clus
vv           STK38 MUTATED STK38 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK38 MUTATED     1   1   2   2
  STK38 WILD-TYPE  21  91 171  95
D108V4, multiclass
    clus
vv   STK38 MUTATED STK38 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             2             171
  T4             2              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
  STK38 MUTATED     4   1   1   0
  STK38 WILD-TYPE 114 103  76  77
D108V5, multiclass
    clus
vv   STK38 MUTATED STK38 WILD-TYPE
  N0             4             114
  N1             1             103
  N2             1              76
  N3             0              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"
D108V6, binary
                 cls
clus                0   1
  STK38 MUTATED     6   0
  STK38 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      6    0
  STK38 WILD-TYPE  340   29
   clus
vv  STK38 MUTATED STK38 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D108V7, binary
                 cls
clus                0   1
  STK38 MUTATED     3   3
  STK38 WILD-TYPE 142 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      3    3
  STK38 WILD-TYPE  142  245
        clus
vv       STK38 MUTATED STK38 WILD-TYPE
  FEMALE             3             142
  MALE               3             245
[1] 2 2
[1] FALSE
D108V8, binary
                 cls
clus                0   1
  STK38 MUTATED     5   0
  STK38 WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      5    0
  STK38 WILD-TYPE  287   59
     clus
vv    STK38 MUTATED STK38 WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  STK38 MUTATED                                          0
  STK38 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  STK38 MUTATED                                       0
  STK38 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  STK38 MUTATED                                                        2
  STK38 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  STK38 MUTATED                                                   0
  STK38 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  STK38 MUTATED                                                                   2
  STK38 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  STK38 MUTATED                                                    1
  STK38 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  STK38 MUTATED                                                  1
  STK38 WILD-TYPE                                               60
D108V9, multiclass
                                                                   clus
vv                                                                  STK38 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  STK38 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STK38 MUTATED     6   0   0   0
  STK38 WILD-TYPE 305  14  15  24
D108V10, multiclass
    clus
vv   STK38 MUTATED STK38 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  STK38 MUTATED       1                         0
  STK38 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  STK38 MUTATED                                           0     3
  STK38 WILD-TYPE                                         1   240
D108V12, multiclass
                                           clus
vv                                          STK38 MUTATED STK38 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V13, binary
                 cls
clus                0   1
  STK38 MUTATED     0   4
  STK38 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      0    4
  STK38 WILD-TYPE    4  306
                        clus
vv                       STK38 MUTATED STK38 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(109) Variable = CST1 MUTATION ANALYSIS
D109V1, survival
                sevent
clus2              0   1
  CST1 MUTATED     5   2
  CST1 WILD-TYPE 225 137
  CST1 MUTATED CST1 WILD-TYPE 
             7            362 
  CST1 MUTATED CST1 WILD-TYPE 
             2            137 
$`CST1 MUTATED`
TCGA-CG-4460 TCGA-BR-7704 TCGA-CD-8530 TCGA-CG-5721 TCGA-D7-A6EY TCGA-HU-A4G9 
       21.99        35.24        12.39         6.02        11.44        24.20 
TCGA-HU-A4GX 
       20.25 

$`CST1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  CST1 MUTATED CST1 WILD-TYPE 
          6.02           0.00 
  CST1 MUTATED CST1 WILD-TYPE 
         35.24         122.30 
  CST1 MUTATED CST1 WILD-TYPE 
         20.25          14.22 
[1] "6.0 - 35.2 (20.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D109V2, 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       2       14       40       28        37        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CST1 MUTATED           0          0          1          1        2
  CST1 WILD-TYPE         3         70         52         31       36
D109V3, multiclass
            clus
vv           CST1 MUTATED CST1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              0             40
  STAGE II              2             28
  STAGE IIA             0             37
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CST1 MUTATED     1   0   3   3
  CST1 WILD-TYPE  21  92 170  94
D109V4, multiclass
    clus
vv   CST1 MUTATED CST1 WILD-TYPE
  T1            1             21
  T2            0             92
  T3            3            170
  T4            3             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
  CST1 MUTATED     3   2   1   1
  CST1 WILD-TYPE 115 102  76  76
D109V5, multiclass
    clus
vv   CST1 MUTATED CST1 WILD-TYPE
  N0            3            115
  N1            2            102
  N2            1             76
  N3            1             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"
D109V6, binary
                cls
clus               0   1
  CST1 MUTATED     6   1
  CST1 WILD-TYPE 340  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  CST1 MUTATED      6    1
  CST1 WILD-TYPE  340   28
   clus
vv  CST1 MUTATED CST1 WILD-TYPE
  0            6            340
  1            1             28
[1] 2 2
[1] FALSE
D109V7, binary
                cls
clus               0   1
  CST1 MUTATED     5   2
  CST1 WILD-TYPE 140 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  CST1 MUTATED      5    2
  CST1 WILD-TYPE  140  246
        clus
vv       CST1 MUTATED CST1 WILD-TYPE
  FEMALE            5            140
  MALE              2            246
[1] 2 2
[1] FALSE
D109V8, binary
                cls
clus               0   1
  CST1 MUTATED     6   1
  CST1 WILD-TYPE 286  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  CST1 MUTATED      6    1
  CST1 WILD-TYPE  286   58
     clus
vv    CST1 MUTATED CST1 WILD-TYPE
  NO             6            286
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CST1 MUTATED                                          0
  CST1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CST1 MUTATED                                       2
  CST1 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CST1 MUTATED                                                        0
  CST1 WILD-TYPE                                                    158
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CST1 MUTATED                                                   0
  CST1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CST1 MUTATED                                                                   3
  CST1 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CST1 MUTATED                                                    0
  CST1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CST1 MUTATED                                                  2
  CST1 WILD-TYPE                                               59
D109V9, multiclass
                                                                   clus
vv                                                                  CST1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       0
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  CST1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       158
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CST1 MUTATED     6   0   1   0
  CST1 WILD-TYPE 305  14  14  24
D109V10, multiclass
    clus
vv   CST1 MUTATED CST1 WILD-TYPE
  R0            6            305
  R1            0             14
  R2            1             14
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CST1 MUTATED       3                         0
  CST1 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CST1 MUTATED                                           0     2
  CST1 WILD-TYPE                                         1   241
D109V12, multiclass
                                           clus
vv                                          CST1 MUTATED CST1 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V13, binary
                cls
clus               0   1
  CST1 MUTATED     0   5
  CST1 WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  CST1 MUTATED      0    5
  CST1 WILD-TYPE    4  305
                        clus
vv                       CST1 MUTATED CST1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(110) Variable = PTCHD3 MUTATION ANALYSIS
D110V1, survival
                  sevent
clus2                0   1
  PTCHD3 MUTATED     9   8
  PTCHD3 WILD-TYPE 221 131
  PTCHD3 MUTATED PTCHD3 WILD-TYPE 
              17              352 
  PTCHD3 MUTATED PTCHD3 WILD-TYPE 
               8              131 
$`PTCHD3 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 TCGA-BR-8680 
        6.97        30.90        34.68        35.84         1.12        31.96 
TCGA-BR-A4QL TCGA-CD-8536 TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4465 TCGA-CG-5721 
       16.14        12.43        20.02        15.95         9.01         6.02 
TCGA-D7-A4YV TCGA-D7-A6EZ TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-RD-A8N9 
        5.92        20.32        24.20         0.10        35.61 

$`PTCHD3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-4301 TCGA-CG-4304 
        6.58        12.20        11.77        12.62         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-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-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-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-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-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 

  PTCHD3 MUTATED PTCHD3 WILD-TYPE 
             0.1              0.0 
  PTCHD3 MUTATED PTCHD3 WILD-TYPE 
           35.84           122.30 
  PTCHD3 MUTATED PTCHD3 WILD-TYPE 
           16.14            14.12 
[1] "0.1 - 35.8 (16.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D110V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTCHD3 MUTATED         1        1        2        3         2         1
  PTCHD3 WILD-TYPE       1       14       38       27        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTCHD3 MUTATED           0          2          2          1        3
  PTCHD3 WILD-TYPE         3         68         51         31       35
D110V3, multiclass
            clus
vv           PTCHD3 MUTATED PTCHD3 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                3               27
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              2               51
  STAGE IIIC              1               31
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTCHD3 MUTATED     2   5   8   4
  PTCHD3 WILD-TYPE  20  87 165  93
D110V4, multiclass
    clus
vv   PTCHD3 MUTATED PTCHD3 WILD-TYPE
  T1              2               20
  T2              5               87
  T3              8              165
  T4              4               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
  PTCHD3 MUTATED     6   6   4   2
  PTCHD3 WILD-TYPE 112  98  73  75
D110V5, multiclass
    clus
vv   PTCHD3 MUTATED PTCHD3 WILD-TYPE
  N0              6              112
  N1              6               98
  N2              4               73
  N3              2               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"
D110V6, binary
                  cls
clus                 0   1
  PTCHD3 MUTATED    15   2
  PTCHD3 WILD-TYPE 331  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTCHD3 MUTATED     15    2
  PTCHD3 WILD-TYPE  331   27
   clus
vv  PTCHD3 MUTATED PTCHD3 WILD-TYPE
  0             15              331
  1              2               27
[1] 2 2
[1] FALSE
D110V7, binary
                  cls
clus                 0   1
  PTCHD3 MUTATED     9  10
  PTCHD3 WILD-TYPE 136 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTCHD3 MUTATED      9   10
  PTCHD3 WILD-TYPE  136  238
        clus
vv       PTCHD3 MUTATED PTCHD3 WILD-TYPE
  FEMALE              9              136
  MALE               10              238
[1] 2 2
[1] FALSE
D110V8, binary
                  cls
clus                 0   1
  PTCHD3 MUTATED    15   1
  PTCHD3 WILD-TYPE 277  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTCHD3 MUTATED     15    1
  PTCHD3 WILD-TYPE  277   58
     clus
vv    PTCHD3 MUTATED PTCHD3 WILD-TYPE
  NO              15              277
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PTCHD3 MUTATED                                          0
  PTCHD3 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PTCHD3 MUTATED                                       2
  PTCHD3 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTCHD3 MUTATED                                                       10
  PTCHD3 WILD-TYPE                                                    148
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PTCHD3 MUTATED                                                   0
  PTCHD3 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTCHD3 MUTATED                                                                   3
  PTCHD3 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PTCHD3 MUTATED                                                    0
  PTCHD3 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PTCHD3 MUTATED                                                  4
  PTCHD3 WILD-TYPE                                               57
D110V9, multiclass
                                                                   clus
vv                                                                  PTCHD3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  PTCHD3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PTCHD3 MUTATED    16   0   1   2
  PTCHD3 WILD-TYPE 295  14  14  22
D110V10, multiclass
    clus
vv   PTCHD3 MUTATED PTCHD3 WILD-TYPE
  R0             16              295
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PTCHD3 MUTATED       5                         1
  PTCHD3 WILD-TYPE    82                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTCHD3 MUTATED                                           0     8
  PTCHD3 WILD-TYPE                                         1   235
D110V12, multiclass
                                           clus
vv                                          PTCHD3 MUTATED PTCHD3 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V13, binary
                  cls
clus                 0   1
  PTCHD3 MUTATED     0  14
  PTCHD3 WILD-TYPE   4 296
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTCHD3 MUTATED      0   14
  PTCHD3 WILD-TYPE    4  296
                        clus
vv                       PTCHD3 MUTATED PTCHD3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             14              296
[1] 2 2
[1] FALSE

Clustering(111) Variable = TBX4 MUTATION ANALYSIS
D111V1, survival
                sevent
clus2              0   1
  TBX4 MUTATED     9   4
  TBX4 WILD-TYPE 221 135
  TBX4 MUTATED TBX4 WILD-TYPE 
            13            356 
  TBX4 MUTATED TBX4 WILD-TYPE 
             4            135 
$`TBX4 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8078 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MJ 
        6.97        30.90        29.59        28.14        16.14        12.62 
TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5728 TCGA-F1-6874 TCGA-FP-A9TM TCGA-HU-A4GU 
        9.01         6.02        65.10        14.47         6.21         6.58 
TCGA-HU-A4H8 
       14.07 

$`TBX4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-F1-6875 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-HF-7132 
        5.03        13.58         0.56        11.08         5.52        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 

  TBX4 MUTATED TBX4 WILD-TYPE 
          6.02           0.00 
  TBX4 MUTATED TBX4 WILD-TYPE 
          65.1          122.3 
  TBX4 MUTATED TBX4 WILD-TYPE 
         14.07          14.35 
[1] "6.0 - 65.1 (14.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D111V2, 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       2       15       36       30        37        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBX4 MUTATED           0          1          1          1        3
  TBX4 WILD-TYPE         3         69         52         31       35
D111V3, multiclass
            clus
vv           TBX4 MUTATED TBX4 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              4             36
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TBX4 MUTATED     2   4   3   5
  TBX4 WILD-TYPE  20  88 170  92
D111V4, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  T1            2             20
  T2            4             88
  T3            3            170
  T4            5             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
  TBX4 MUTATED     4   5   1   3
  TBX4 WILD-TYPE 114  99  76  74
D111V5, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  N0            4            114
  N1            5             99
  N2            1             76
  N3            3             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"
D111V6, binary
                cls
clus               0   1
  TBX4 MUTATED    12   1
  TBX4 WILD-TYPE 334  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED     12    1
  TBX4 WILD-TYPE  334   28
   clus
vv  TBX4 MUTATED TBX4 WILD-TYPE
  0           12            334
  1            1             28
[1] 2 2
[1] FALSE
D111V7, binary
                cls
clus               0   1
  TBX4 MUTATED     6   8
  TBX4 WILD-TYPE 139 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED      6    8
  TBX4 WILD-TYPE  139  240
        clus
vv       TBX4 MUTATED TBX4 WILD-TYPE
  FEMALE            6            139
  MALE              8            240
[1] 2 2
[1] FALSE
D111V8, binary
                cls
clus               0   1
  TBX4 MUTATED    10   1
  TBX4 WILD-TYPE 282  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED     10    1
  TBX4 WILD-TYPE  282   58
     clus
vv    TBX4 MUTATED TBX4 WILD-TYPE
  NO            10            282
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TBX4 MUTATED                                          0
  TBX4 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TBX4 MUTATED                                       2
  TBX4 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TBX4 MUTATED                                                        8
  TBX4 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TBX4 MUTATED                                                   0
  TBX4 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TBX4 MUTATED                                                                   3
  TBX4 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TBX4 MUTATED                                                    0
  TBX4 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TBX4 MUTATED                                                  1
  TBX4 WILD-TYPE                                               60
D111V9, multiclass
                                                                   clus
vv                                                                  TBX4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  TBX4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TBX4 MUTATED     9   0   1   3
  TBX4 WILD-TYPE 302  14  14  21
D111V10, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  R0            9            302
  R1            0             14
  R2            1             14
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TBX4 MUTATED       3                         0
  TBX4 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TBX4 MUTATED                                           0     8
  TBX4 WILD-TYPE                                         1   235
D111V12, multiclass
                                           clus
vv                                          TBX4 MUTATED TBX4 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V13, binary
                cls
clus               0   1
  TBX4 MUTATED     0  11
  TBX4 WILD-TYPE   4 299
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED      0   11
  TBX4 WILD-TYPE    4  299
                        clus
vv                       TBX4 MUTATED TBX4 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           11            299
[1] 2 2
[1] FALSE

Clustering(112) Variable = ZMYM4 MUTATION ANALYSIS
D112V1, survival
                 sevent
clus2               0   1
  ZMYM4 MUTATED    11   5
  ZMYM4 WILD-TYPE 219 134
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
             16             353 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
              5             134 
$`ZMYM4 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-8382 
       21.99        26.70        11.01         6.97        35.84        25.05 
TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4466 
       27.12        28.14        31.96         6.58        15.95        18.97 
TCGA-CG-5721 TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-VQ-A8P2 
        6.02         0.10        20.25        38.14 

$`ZMYM4 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
        9.86        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 
          38.14          122.30 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
          21.12           14.07 
[1] "0.1 - 38.1 (21.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D112V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZMYM4 MUTATED         0        0        2        1         1         3
  ZMYM4 WILD-TYPE       2       15       38       29        36        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZMYM4 MUTATED           0          3          1          4        4
  ZMYM4 WILD-TYPE         3         67         52         28       34
D112V3, multiclass
            clus
vv           ZMYM4 MUTATED ZMYM4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             4              28
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZMYM4 MUTATED     0   3   2  14
  ZMYM4 WILD-TYPE  22  89 171  83
D112V4, multiclass
    clus
vv   ZMYM4 MUTATED ZMYM4 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             2             171
  T4            14              83
[1] 4 2
[1] TRUE
[1] "dimension of 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     6   6   4   2
  ZMYM4 WILD-TYPE 112  98  73  75
D112V5, multiclass
    clus
vv   ZMYM4 MUTATED ZMYM4 WILD-TYPE
  N0             6             112
  N1             6              98
  N2             4              73
  N3             2              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"
D112V6, binary
                 cls
clus                0   1
  ZMYM4 MUTATED    16   2
  ZMYM4 WILD-TYPE 330  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED     16    2
  ZMYM4 WILD-TYPE  330   27
   clus
vv  ZMYM4 MUTATED ZMYM4 WILD-TYPE
  0            16             330
  1             2              27
[1] 2 2
[1] FALSE
D112V7, binary
                 cls
clus                0   1
  ZMYM4 MUTATED     8  11
  ZMYM4 WILD-TYPE 137 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED      8   11
  ZMYM4 WILD-TYPE  137  237
        clus
vv       ZMYM4 MUTATED ZMYM4 WILD-TYPE
  FEMALE             8             137
  MALE              11             237
[1] 2 2
[1] FALSE
D112V8, binary
                 cls
clus                0   1
  ZMYM4 MUTATED    16   1
  ZMYM4 WILD-TYPE 276  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED     16    1
  ZMYM4 WILD-TYPE  276   58
     clus
vv    ZMYM4 MUTATED ZMYM4 WILD-TYPE
  NO             16             276
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZMYM4 MUTATED                                          0
  ZMYM4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZMYM4 MUTATED                                       3
  ZMYM4 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZMYM4 MUTATED                                                        8
  ZMYM4 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZMYM4 MUTATED                                                   1
  ZMYM4 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZMYM4 MUTATED                                                                   5
  ZMYM4 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZMYM4 MUTATED                                                    0
  ZMYM4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZMYM4 MUTATED                                                  2
  ZMYM4 WILD-TYPE                                               59
D112V9, multiclass
                                                                   clus
vv                                                                  ZMYM4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  ZMYM4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZMYM4 MUTATED    13   0   1   3
  ZMYM4 WILD-TYPE 298  14  14  21
D112V10, multiclass
    clus
vv   ZMYM4 MUTATED ZMYM4 WILD-TYPE
  R0            13             298
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZMYM4 MUTATED       4                         0
  ZMYM4 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZMYM4 MUTATED                                           0    11
  ZMYM4 WILD-TYPE                                         1   232
D112V12, multiclass
                                           clus
vv                                          ZMYM4 MUTATED ZMYM4 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V13, binary
                 cls
clus                0   1
  ZMYM4 MUTATED     0  14
  ZMYM4 WILD-TYPE   4 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED      0   14
  ZMYM4 WILD-TYPE    4  296
                        clus
vv                       ZMYM4 MUTATED ZMYM4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(113) Variable = SPTY2D1 MUTATION ANALYSIS
D113V1, survival
                   sevent
clus2                 0   1
  SPTY2D1 MUTATED    11   5
  SPTY2D1 WILD-TYPE 219 134
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
               16               353 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
                5               134 
$`SPTY2D1 MUTATED`
TCGA-BR-4184 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 TCGA-CD-5800 TCGA-CD-8525 
        6.97        31.10         4.31        31.27        13.15        12.59 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-A4YV TCGA-HF-A5NB 
        6.58         6.02        28.96        65.10         5.92        30.51 
TCGA-HU-8243 TCGA-HU-8602 TCGA-MX-A5UJ TCGA-VQ-A8P2 
        5.92        22.32        19.73        38.14 

$`SPTY2D1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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 

  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
             4.31              0.00 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
             65.1             122.3 
  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE 
            16.44             14.27 
[1] "4.3 - 65.1 (16.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D113V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPTY2D1 MUTATED         0        1        2        1         1         3
  SPTY2D1 WILD-TYPE       2       14       38       29        36        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPTY2D1 MUTATED           0          4          0          4        1
  SPTY2D1 WILD-TYPE         3         66         53         28       37
D113V3, multiclass
            clus
vv           SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 2                38
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                3                49
  STAGE III                0                 3
  STAGE IIIA               4                66
  STAGE IIIB               0                53
  STAGE IIIC               4                28
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SPTY2D1 MUTATED     2   2   6   8
  SPTY2D1 WILD-TYPE  20  90 167  89
D113V4, multiclass
    clus
vv   SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  T1               2                20
  T2               2                90
  T3               6               167
  T4               8                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
  SPTY2D1 MUTATED     7   6   2   3
  SPTY2D1 WILD-TYPE 111  98  75  74
D113V5, multiclass
    clus
vv   SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  N0               7               111
  N1               6                98
  N2               2                75
  N3               3                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"
D113V6, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED    18   0
  SPTY2D1 WILD-TYPE 328  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED     18    0
  SPTY2D1 WILD-TYPE  328   29
   clus
vv  SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  0              18               328
  1               0                29
[1] 2 2
[1] FALSE
D113V7, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED    11   8
  SPTY2D1 WILD-TYPE 134 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED     11    8
  SPTY2D1 WILD-TYPE  134  240
        clus
vv       SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  FEMALE              11               134
  MALE                 8               240
[1] 2 2
[1] FALSE
D113V8, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED    12   3
  SPTY2D1 WILD-TYPE 280  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED     12    3
  SPTY2D1 WILD-TYPE  280   56
     clus
vv    SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  NO               12               280
  YES               3                56
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SPTY2D1 MUTATED                                          0
  SPTY2D1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SPTY2D1 MUTATED                                       2
  SPTY2D1 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPTY2D1 MUTATED                                                        6
  SPTY2D1 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SPTY2D1 MUTATED                                                   3
  SPTY2D1 WILD-TYPE                                                18
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPTY2D1 MUTATED                                                                   4
  SPTY2D1 WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SPTY2D1 MUTATED                                                    1
  SPTY2D1 WILD-TYPE                                                  4
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SPTY2D1 MUTATED                                                  3
  SPTY2D1 WILD-TYPE                                               58
D113V9, multiclass
                                                                   clus
vv                                                                  SPTY2D1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  SPTY2D1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SPTY2D1 MUTATED    14   1   0   3
  SPTY2D1 WILD-TYPE 297  13  15  21
D113V10, multiclass
    clus
vv   SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  R0              14               297
  R1               1                13
  R2               0                15
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SPTY2D1 MUTATED       5                         0
  SPTY2D1 WILD-TYPE    82                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPTY2D1 MUTATED                                           0    10
  SPTY2D1 WILD-TYPE                                         1   233
D113V12, multiclass
                                           clus
vv                                          SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  ASIAN                                                   5                82
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V13, binary
                   cls
clus                  0   1
  SPTY2D1 MUTATED     0  14
  SPTY2D1 WILD-TYPE   4 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPTY2D1 MUTATED      0   14
  SPTY2D1 WILD-TYPE    4  296
                        clus
vv                       SPTY2D1 MUTATED SPTY2D1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              14               296
[1] 2 2
[1] FALSE

Clustering(114) Variable = SLC12A9 MUTATION ANALYSIS
D114V1, survival
                   sevent
clus2                 0   1
  SLC12A9 MUTATED     8   8
  SLC12A9 WILD-TYPE 222 131
  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
               16               353 
  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
                8               131 
$`SLC12A9 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-8289 TCGA-BR-8368 TCGA-CD-A4MG 
       21.99         6.97         9.34         2.66         4.31         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-A4YV 
       11.77        12.62        15.95         6.02        65.10         5.92 
TCGA-HF-7132 TCGA-HU-A4GX TCGA-VQ-A8P2 TCGA-VQ-AA6I 
       77.29        20.25        38.14        16.14 

$`SLC12A9 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-A4MH TCGA-CG-4300 TCGA-CG-4301 
       11.31        12.43        11.61        12.20        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-D7-5578 
        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-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-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 

  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
             2.66              0.00 
  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
            77.29            122.30 
  SLC12A9 MUTATED SLC12A9 WILD-TYPE 
           12.195            14.430 
[1] "2.7 - 77.3 (12.2)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.4"
D114V2, 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       1       15       37       28        36        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC12A9 MUTATED           0          3          1          1        4
  SLC12A9 WILD-TYPE         3         67         52         31       34
D114V3, multiclass
            clus
vv           SLC12A9 MUTATED SLC12A9 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 3                37
  STAGE II                 2                28
  STAGE IIA                1                36
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               3                67
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 4                34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC12A9 MUTATED     1   5   6   7
  SLC12A9 WILD-TYPE  21  87 167  90
D114V4, multiclass
    clus
vv   SLC12A9 MUTATED SLC12A9 WILD-TYPE
  T1               1                21
  T2               5                87
  T3               6               167
  T4               7                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
  SLC12A9 MUTATED     5  10   2   2
  SLC12A9 WILD-TYPE 113  94  75  75
D114V5, multiclass
    clus
vv   SLC12A9 MUTATED SLC12A9 WILD-TYPE
  N0               5               113
  N1              10                94
  N2               2                75
  N3               2                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"
D114V6, binary
                   cls
clus                  0   1
  SLC12A9 MUTATED    15   2
  SLC12A9 WILD-TYPE 331  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A9 MUTATED     15    2
  SLC12A9 WILD-TYPE  331   27
   clus
vv  SLC12A9 MUTATED SLC12A9 WILD-TYPE
  0              15               331
  1               2                27
[1] 2 2
[1] FALSE
D114V7, binary
                   cls
clus                  0   1
  SLC12A9 MUTATED     7  13
  SLC12A9 WILD-TYPE 138 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A9 MUTATED      7   13
  SLC12A9 WILD-TYPE  138  235
        clus
vv       SLC12A9 MUTATED SLC12A9 WILD-TYPE
  FEMALE               7               138
  MALE                13               235
[1] 2 2
[1] FALSE
D114V8, binary
                   cls
clus                  0   1
  SLC12A9 MUTATED    15   2
  SLC12A9 WILD-TYPE 277  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A9 MUTATED     15    2
  SLC12A9 WILD-TYPE  277   57
     clus
vv    SLC12A9 MUTATED SLC12A9 WILD-TYPE
  NO               15               277
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC12A9 MUTATED                                          0
  SLC12A9 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC12A9 MUTATED                                       2
  SLC12A9 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC12A9 MUTATED                                                        9
  SLC12A9 WILD-TYPE                                                    149
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC12A9 MUTATED                                                   2
  SLC12A9 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC12A9 MUTATED                                                                   6
  SLC12A9 WILD-TYPE                                                                62
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC12A9 MUTATED                                                    0
  SLC12A9 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC12A9 MUTATED                                                  1
  SLC12A9 WILD-TYPE                                               60
D114V9, multiclass
                                                                   clus
vv                                                                  SLC12A9 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  SLC12A9 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC12A9 MUTATED    12   0   1   4
  SLC12A9 WILD-TYPE 299  14  14  20
D114V10, multiclass
    clus
vv   SLC12A9 MUTATED SLC12A9 WILD-TYPE
  R0              12               299
  R1               0                14
  R2               1                14
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC12A9 MUTATED       4                         1
  SLC12A9 WILD-TYPE    83                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC12A9 MUTATED                                           0    10
  SLC12A9 WILD-TYPE                                         1   233
D114V12, multiclass
                                           clus
vv                                          SLC12A9 MUTATED SLC12A9 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V13, binary
                   cls
clus                  0   1
  SLC12A9 MUTATED     0  13
  SLC12A9 WILD-TYPE   4 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A9 MUTATED      0   13
  SLC12A9 WILD-TYPE    4  297
                        clus
vv                       SLC12A9 MUTATED SLC12A9 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              13               297
[1] 2 2
[1] FALSE

Clustering(115) Variable = ALPK2 MUTATION ANALYSIS
D115V1, survival
                 sevent
clus2               0   1
  ALPK2 MUTATED    15   7
  ALPK2 WILD-TYPE 215 132
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             22             347 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
              7             132 
$`ALPK2 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6852 
       21.99         6.97         9.34         6.61        34.68        44.94 
TCGA-BR-7707 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A453 
       35.84        25.05         1.12        28.14        31.96         6.08 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-F1-A448 TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GN 
        6.58         6.02        21.27        22.32        24.20        29.98 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-VQ-A8P2 
        6.51        20.25        14.07        38.14 

$`ALPK2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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 
          21.63           14.07 
[1] "1.1 - 44.9 (21.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D115V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ALPK2 MUTATED         0        1        2        0         6         1
  ALPK2 WILD-TYPE       2       14       38       30        31        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ALPK2 MUTATED           1          2          1          3        4
  ALPK2 WILD-TYPE         2         68         52         29       34
D115V3, multiclass
            clus
vv           ALPK2 MUTATED ALPK2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              6              31
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             3              29
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALPK2 MUTATED     3   3   7   9
  ALPK2 WILD-TYPE  19  89 166  88
D115V4, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  T1             3              19
  T2             3              89
  T3             7             166
  T4             9              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
  ALPK2 MUTATED     8   8   2   4
  ALPK2 WILD-TYPE 110  96  75  73
D115V5, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  N0             8             110
  N1             8              96
  N2             2              75
  N3             4              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"
D115V6, binary
                 cls
clus                0   1
  ALPK2 MUTATED    20   3
  ALPK2 WILD-TYPE 326  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     20    3
  ALPK2 WILD-TYPE  326   26
   clus
vv  ALPK2 MUTATED ALPK2 WILD-TYPE
  0            20             326
  1             3              26
[1] 2 2
[1] FALSE
D115V7, binary
                 cls
clus                0   1
  ALPK2 MUTATED    13  11
  ALPK2 WILD-TYPE 132 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     13   11
  ALPK2 WILD-TYPE  132  237
        clus
vv       ALPK2 MUTATED ALPK2 WILD-TYPE
  FEMALE            13             132
  MALE              11             237
[1] 2 2
[1] FALSE
D115V8, binary
                 cls
clus                0   1
  ALPK2 MUTATED    20   2
  ALPK2 WILD-TYPE 272  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     20    2
  ALPK2 WILD-TYPE  272   57
     clus
vv    ALPK2 MUTATED ALPK2 WILD-TYPE
  NO             20             272
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ALPK2 MUTATED                                          1
  ALPK2 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ALPK2 MUTATED                                       3
  ALPK2 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ALPK2 MUTATED                                                       11
  ALPK2 WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ALPK2 MUTATED                                                   2
  ALPK2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ALPK2 MUTATED                                                                   2
  ALPK2 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ALPK2 MUTATED                                                    0
  ALPK2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ALPK2 MUTATED                                                  5
  ALPK2 WILD-TYPE                                               56
D115V9, multiclass
                                                                   clus
vv                                                                  ALPK2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              5
                                                                   clus
vv                                                                  ALPK2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ALPK2 MUTATED    17   0   1   5
  ALPK2 WILD-TYPE 294  14  14  19
D115V10, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  R0            17             294
  R1             0              14
  R2             1              14
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ALPK2 MUTATED       9                         0
  ALPK2 WILD-TYPE    78                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ALPK2 MUTATED                                           0    13
  ALPK2 WILD-TYPE                                         1   230
D115V12, multiclass
                                           clus
vv                                          ALPK2 MUTATED ALPK2 WILD-TYPE
  ASIAN                                                 9              78
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V13, binary
                 cls
clus                0   1
  ALPK2 MUTATED     1  20
  ALPK2 WILD-TYPE   3 290
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED      1   20
  ALPK2 WILD-TYPE    3  290
                        clus
vv                       ALPK2 MUTATED ALPK2 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            20             290
[1] 2 2
[1] FALSE

Clustering(116) Variable = CABP5 MUTATION ANALYSIS
D116V1, survival
                 sevent
clus2               0   1
  CABP5 MUTATED     4   1
  CABP5 WILD-TYPE 226 138
  CABP5 MUTATED CABP5 WILD-TYPE 
              5             364 
  CABP5 MUTATED CABP5 WILD-TYPE 
              1             138 
$`CABP5 MUTATED`
TCGA-BR-6452 TCGA-FP-A4BE TCGA-HU-8238 TCGA-HU-A4GQ TCGA-VQ-A8P2 
       34.68        11.08         1.51         0.10        38.14 

$`CABP5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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           14.35 
[1] "0.1 - 38.1 (11.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.7"
D116V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CABP5 MUTATED         0        0        1        0         2         0
  CABP5 WILD-TYPE       2       15       39       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CABP5 MUTATED           0          1          0          1        0
  CABP5 WILD-TYPE         3         69         53         31       38
D116V3, multiclass
            clus
vv           CABP5 MUTATED CABP5 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CABP5 MUTATED     0   1   3   2
  CABP5 WILD-TYPE  22  91 170  95
D116V4, multiclass
    clus
vv   CABP5 MUTATED CABP5 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             3             170
  T4             2              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
  CABP5 MUTATED     3   1   2   0
  CABP5 WILD-TYPE 115 103  75  77
D116V5, multiclass
    clus
vv   CABP5 MUTATED CABP5 WILD-TYPE
  N0             3             115
  N1             1             103
  N2             2              75
  N3             0              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"
D116V6, binary
                 cls
clus                0   1
  CABP5 MUTATED     6   0
  CABP5 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CABP5 MUTATED      6    0
  CABP5 WILD-TYPE  340   29
   clus
vv  CABP5 MUTATED CABP5 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D116V7, binary
                 cls
clus                0   1
  CABP5 MUTATED     1   5
  CABP5 WILD-TYPE 144 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CABP5 MUTATED      1    5
  CABP5 WILD-TYPE  144  243
        clus
vv       CABP5 MUTATED CABP5 WILD-TYPE
  FEMALE             1             144
  MALE               5             243
[1] 2 2
[1] FALSE
D116V8, binary
                 cls
clus                0   1
  CABP5 MUTATED     3   2
  CABP5 WILD-TYPE 289  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CABP5 MUTATED      3    2
  CABP5 WILD-TYPE  289   57
     clus
vv    CABP5 MUTATED CABP5 WILD-TYPE
  NO              3             289
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CABP5 MUTATED                                          0
  CABP5 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CABP5 MUTATED                                       0
  CABP5 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CABP5 MUTATED                                                        2
  CABP5 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CABP5 MUTATED                                                   1
  CABP5 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CABP5 MUTATED                                                                   1
  CABP5 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CABP5 MUTATED                                                    0
  CABP5 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CABP5 MUTATED                                                  2
  CABP5 WILD-TYPE                                               59
D116V9, multiclass
                                                                   clus
vv                                                                  CABP5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  CABP5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CABP5 MUTATED     6   0   0   0
  CABP5 WILD-TYPE 305  14  15  24
D116V10, multiclass
    clus
vv   CABP5 MUTATED CABP5 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CABP5 MUTATED       2                         1
  CABP5 WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CABP5 MUTATED                                           0     2
  CABP5 WILD-TYPE                                         1   241
D116V12, multiclass
                                           clus
vv                                          CABP5 MUTATED CABP5 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V13, binary
                 cls
clus                0   1
  CABP5 MUTATED     0   4
  CABP5 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CABP5 MUTATED      0    4
  CABP5 WILD-TYPE    4  306
                        clus
vv                       CABP5 MUTATED CABP5 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(117) Variable = MED15 MUTATION ANALYSIS
D117V1, survival
                 sevent
clus2               0   1
  MED15 MUTATED    13   4
  MED15 WILD-TYPE 217 135
  MED15 MUTATED MED15 WILD-TYPE 
             17             352 
  MED15 MUTATED MED15 WILD-TYPE 
              4             135 
$`MED15 MUTATED`
TCGA-BR-4201 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8589 TCGA-CD-A4MI 
       30.90        30.90        44.94        29.59        27.12        11.77 
TCGA-CG-5728 TCGA-D7-A6EY TCGA-F1-A72C TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4GN 
       65.10        11.44        11.38        77.29        30.51        29.98 
TCGA-HU-A4GX TCGA-MX-A5UG TCGA-SW-A7EA TCGA-VQ-AA6J TCGA-ZA-A8F6 
       20.25         3.72        19.04        27.55        17.26 

$`MED15 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         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-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-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       63.62        36.95        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-AA6K 
       54.12        26.04        16.14        12.43 

  MED15 MUTATED MED15 WILD-TYPE 
           3.72            0.00 
  MED15 MUTATED MED15 WILD-TYPE 
          77.29          122.30 
  MED15 MUTATED MED15 WILD-TYPE 
          27.55           14.04 
[1] "3.7 - 77.3 (27.6)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "2.5"
D117V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MED15 MUTATED         1        0        3        1         3         1
  MED15 WILD-TYPE       1       15       37       29        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MED15 MUTATED           0          3          3          2        0
  MED15 WILD-TYPE         3         67         50         30       38
D117V3, multiclass
            clus
vv           MED15 MUTATED MED15 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             3              50
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MED15 MUTATED     1   6   6   5
  MED15 WILD-TYPE  21  86 167  92
D117V4, multiclass
    clus
vv   MED15 MUTATED MED15 WILD-TYPE
  T1             1              21
  T2             6              86
  T3             6             167
  T4             5              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
  MED15 MUTATED     6   6   3   2
  MED15 WILD-TYPE 112  98  74  75
D117V5, multiclass
    clus
vv   MED15 MUTATED MED15 WILD-TYPE
  N0             6             112
  N1             6              98
  N2             3              74
  N3             2              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"
D117V6, binary
                 cls
clus                0   1
  MED15 MUTATED    16   0
  MED15 WILD-TYPE 330  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED     16    0
  MED15 WILD-TYPE  330   29
   clus
vv  MED15 MUTATED MED15 WILD-TYPE
  0            16             330
  1             0              29
[1] 2 2
[1] FALSE
D117V7, binary
                 cls
clus                0   1
  MED15 MUTATED     8  10
  MED15 WILD-TYPE 137 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      8   10
  MED15 WILD-TYPE  137  238
        clus
vv       MED15 MUTATED MED15 WILD-TYPE
  FEMALE             8             137
  MALE              10             238
[1] 2 2
[1] FALSE
D117V8, binary
                 cls
clus                0   1
  MED15 MUTATED    15   2
  MED15 WILD-TYPE 277  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED     15    2
  MED15 WILD-TYPE  277   57
     clus
vv    MED15 MUTATED MED15 WILD-TYPE
  NO             15             277
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MED15 MUTATED                                          0
  MED15 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MED15 MUTATED                                       3
  MED15 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MED15 MUTATED                                                        7
  MED15 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MED15 MUTATED                                                   2
  MED15 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MED15 MUTATED                                                                   4
  MED15 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MED15 MUTATED                                                    0
  MED15 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MED15 MUTATED                                                  2
  MED15 WILD-TYPE                                               59
D117V9, multiclass
                                                                   clus
vv                                                                  MED15 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  MED15 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MED15 MUTATED    15   1   0   1
  MED15 WILD-TYPE 296  13  15  23
D117V10, multiclass
    clus
vv   MED15 MUTATED MED15 WILD-TYPE
  R0            15             296
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MED15 MUTATED       5                         2
  MED15 WILD-TYPE    82                         7
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MED15 MUTATED                                           0     8
  MED15 WILD-TYPE                                         1   235
D117V12, multiclass
                                           clus
vv                                          MED15 MUTATED MED15 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             2               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V13, binary
                 cls
clus                0   1
  MED15 MUTATED     0  14
  MED15 WILD-TYPE   4 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      0   14
  MED15 WILD-TYPE    4  296
                        clus
vv                       MED15 MUTATED MED15 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(118) Variable = GYLTL1B MUTATION ANALYSIS
D118V1, survival
                   sevent
clus2                 0   1
  GYLTL1B MUTATED    13   3
  GYLTL1B WILD-TYPE 217 136
  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
               16               353 
  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
                3               136 
$`GYLTL1B MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-A453 
        6.97        34.68        32.78        29.59         1.12         6.08 
TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5723 TCGA-FP-A4BE TCGA-HF-A5NB 
       12.62         1.02         6.02       105.07        11.08        30.51 
TCGA-HU-A4G9 TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       24.20        14.07        19.73        38.14 

$`GYLTL1B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
             1.02              0.00 
  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
           105.07            122.30 
  GYLTL1B MUTATED GYLTL1B WILD-TYPE 
            16.90             14.27 
[1] "1.0 - 105.1 (16.9)" "0.0 - 122.3 (14.3)"
[1] "hr=" "2.3"
D118V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GYLTL1B MUTATED         0        1        2        1         4         2
  GYLTL1B WILD-TYPE       2       14       38       29        33        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GYLTL1B MUTATED           0          3          0          1        3
  GYLTL1B WILD-TYPE         3         67         53         31       35
D118V3, multiclass
            clus
vv           GYLTL1B MUTATED GYLTL1B WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 2                38
  STAGE II                 1                29
  STAGE IIA                4                33
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               3                67
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 3                35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GYLTL1B MUTATED     2   2   7   6
  GYLTL1B WILD-TYPE  20  90 166  91
D118V4, multiclass
    clus
vv   GYLTL1B MUTATED GYLTL1B WILD-TYPE
  T1               2                20
  T2               2                90
  T3               7               166
  T4               6                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
  GYLTL1B MUTATED     8   5   2   2
  GYLTL1B WILD-TYPE 110  99  75  75
D118V5, multiclass
    clus
vv   GYLTL1B MUTATED GYLTL1B WILD-TYPE
  N0               8               110
  N1               5                99
  N2               2                75
  N3               2                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
  GYLTL1B MUTATED    14   2
  GYLTL1B WILD-TYPE 332  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GYLTL1B MUTATED     14    2
  GYLTL1B WILD-TYPE  332   27
   clus
vv  GYLTL1B MUTATED GYLTL1B WILD-TYPE
  0              14               332
  1               2                27
[1] 2 2
[1] FALSE
D118V7, binary
                   cls
clus                  0   1
  GYLTL1B MUTATED     7  10
  GYLTL1B WILD-TYPE 138 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GYLTL1B MUTATED      7   10
  GYLTL1B WILD-TYPE  138  238
        clus
vv       GYLTL1B MUTATED GYLTL1B WILD-TYPE
  FEMALE               7               138
  MALE                10               238
[1] 2 2
[1] FALSE
D118V8, binary
                   cls
clus                  0   1
  GYLTL1B MUTATED    13   3
  GYLTL1B WILD-TYPE 279  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GYLTL1B MUTATED     13    3
  GYLTL1B WILD-TYPE  279   56
     clus
vv    GYLTL1B MUTATED GYLTL1B WILD-TYPE
  NO               13               279
  YES               3                56
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GYLTL1B MUTATED                                          1
  GYLTL1B WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GYLTL1B MUTATED                                       0
  GYLTL1B WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GYLTL1B MUTATED                                                        9
  GYLTL1B WILD-TYPE                                                    149
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GYLTL1B MUTATED                                                   2
  GYLTL1B WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GYLTL1B MUTATED                                                                   2
  GYLTL1B WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GYLTL1B MUTATED                                                    0
  GYLTL1B WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GYLTL1B MUTATED                                                  3
  GYLTL1B WILD-TYPE                                               58
D118V9, multiclass
                                                                   clus
vv                                                                  GYLTL1B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  GYLTL1B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GYLTL1B MUTATED    13   1   1   1
  GYLTL1B WILD-TYPE 298  13  14  23
D118V10, multiclass
    clus
vv   GYLTL1B MUTATED GYLTL1B WILD-TYPE
  R0              13               298
  R1               1                13
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  GYLTL1B MUTATED       4                         1
  GYLTL1B WILD-TYPE    83                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GYLTL1B MUTATED                                           0     8
  GYLTL1B WILD-TYPE                                         1   235
D118V12, multiclass
                                           clus
vv                                          GYLTL1B MUTATED GYLTL1B WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V13, binary
                   cls
clus                  0   1
  GYLTL1B MUTATED     0  12
  GYLTL1B WILD-TYPE   4 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GYLTL1B MUTATED      0   12
  GYLTL1B WILD-TYPE    4  298
                        clus
vv                       GYLTL1B MUTATED GYLTL1B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              12               298
[1] 2 2
[1] FALSE

Clustering(119) Variable = IL2RG MUTATION ANALYSIS
D119V1, survival
                 sevent
clus2               0   1
  IL2RG MUTATED     7   1
  IL2RG WILD-TYPE 223 138
  IL2RG MUTATED IL2RG WILD-TYPE 
              8             361 
  IL2RG MUTATED IL2RG WILD-TYPE 
              1             138 
$`IL2RG MUTATED`
TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5728 TCGA-HF-7132 
       34.68         6.18         1.12        31.96        65.10        77.29 
TCGA-HJ-7597 TCGA-IN-A7NT 
       26.47        10.62 

$`IL2RG WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  IL2RG MUTATED IL2RG WILD-TYPE 
           1.12            0.00 
  IL2RG MUTATED IL2RG WILD-TYPE 
          77.29          122.30 
  IL2RG MUTATED IL2RG WILD-TYPE 
         29.215          14.170 
[1] "1.1 - 77.3 (29.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "4.4"
D119V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IL2RG MUTATED         0        0        2        1         3         1
  IL2RG WILD-TYPE       2       15       38       29        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL2RG MUTATED           0          0          0          0        2
  IL2RG WILD-TYPE         3         70         53         32       36
D119V3, multiclass
            clus
vv           IL2RG MUTATED IL2RG WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IL2RG MUTATED     0   3   5   2
  IL2RG WILD-TYPE  22  89 168  95
D119V4, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  T1             0              22
  T2             3              89
  T3             5             168
  T4             2              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
  IL2RG MUTATED     5   2   2   0
  IL2RG WILD-TYPE 113 102  75  77
D119V5, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  N0             5             113
  N1             2             102
  N2             2              75
  N3             0              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"
D119V6, binary
                 cls
clus                0   1
  IL2RG MUTATED     7   1
  IL2RG WILD-TYPE 339  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      7    1
  IL2RG WILD-TYPE  339   28
   clus
vv  IL2RG MUTATED IL2RG WILD-TYPE
  0             7             339
  1             1              28
[1] 2 2
[1] FALSE
D119V7, binary
                 cls
clus                0   1
  IL2RG MUTATED     7   3
  IL2RG WILD-TYPE 138 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      7    3
  IL2RG WILD-TYPE  138  245
        clus
vv       IL2RG MUTATED IL2RG WILD-TYPE
  FEMALE             7             138
  MALE               3             245
[1] 2 2
[1] FALSE
D119V8, binary
                 cls
clus                0   1
  IL2RG MUTATED     6   1
  IL2RG WILD-TYPE 286  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      6    1
  IL2RG WILD-TYPE  286   58
     clus
vv    IL2RG MUTATED IL2RG WILD-TYPE
  NO              6             286
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IL2RG MUTATED                                          1
  IL2RG WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IL2RG MUTATED                                       0
  IL2RG WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IL2RG MUTATED                                                        5
  IL2RG WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IL2RG MUTATED                                                   1
  IL2RG WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IL2RG MUTATED                                                                   2
  IL2RG WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IL2RG MUTATED                                                    0
  IL2RG WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IL2RG MUTATED                                                  1
  IL2RG WILD-TYPE                                               60
D119V9, multiclass
                                                                   clus
vv                                                                  IL2RG MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  IL2RG WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IL2RG MUTATED     8   0   0   2
  IL2RG WILD-TYPE 303  14  15  22
D119V10, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  R0             8             303
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IL2RG MUTATED       1                         0
  IL2RG WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IL2RG MUTATED                                           0     7
  IL2RG WILD-TYPE                                         1   236
D119V12, multiclass
                                           clus
vv                                          IL2RG MUTATED IL2RG WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V13, binary
                 cls
clus                0   1
  IL2RG MUTATED     0   8
  IL2RG WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      0    8
  IL2RG WILD-TYPE    4  302
                        clus
vv                       IL2RG MUTATED IL2RG WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(120) Variable = CCDC88A MUTATION ANALYSIS
D120V1, survival
                   sevent
clus2                 0   1
  CCDC88A MUTATED    12   6
  CCDC88A WILD-TYPE 218 133
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               18               351 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
                6               133 
$`CCDC88A MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6707 TCGA-BR-8363 TCGA-BR-8382 
       26.70        30.90        34.68        19.89         0.26        25.05 
TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-5721 TCGA-D7-6528 
        1.12        31.96         1.02         8.05         6.02        15.22 
TCGA-F1-6874 TCGA-FP-A4BE TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-VQ-A8P2 
       14.47        11.08        22.68         0.10        29.00        38.14 

$`CCDC88A WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         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-D7-6815 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-F1-6875 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-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 

  CCDC88A MUTATED CCDC88A WILD-TYPE 
              0.1               0.0 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
            38.14            122.30 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
           17.555            14.070 
[1] "0.1 - 38.1 (17.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D120V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC88A MUTATED         0        0        4        1         4         2
  CCDC88A WILD-TYPE       2       15       36       29        33        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC88A MUTATED           0          2          0          3        4
  CCDC88A WILD-TYPE         3         68         53         29       34
D120V3, multiclass
            clus
vv           CCDC88A MUTATED CCDC88A WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 4                36
  STAGE II                 1                29
  STAGE IIA                4                33
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               3                29
  STAGE IV                 4                34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC88A MUTATED     0   6   6   9
  CCDC88A WILD-TYPE  22  86 167  88
D120V4, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  T1               0                22
  T2               6                86
  T3               6               167
  T4               9                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
  CCDC88A MUTATED    10   4   4   2
  CCDC88A WILD-TYPE 108 100  73  75
D120V5, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  N0              10               108
  N1               4               100
  N2               4                73
  N3               2                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"
D120V6, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    20   2
  CCDC88A WILD-TYPE 326  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     20    2
  CCDC88A WILD-TYPE  326   27
   clus
vv  CCDC88A MUTATED CCDC88A WILD-TYPE
  0              20               326
  1               2                27
[1] 2 2
[1] FALSE
D120V7, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    12  10
  CCDC88A WILD-TYPE 133 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     12   10
  CCDC88A WILD-TYPE  133  238
        clus
vv       CCDC88A MUTATED CCDC88A WILD-TYPE
  FEMALE              12               133
  MALE                10               238
[1] 2 2
[1] FALSE
D120V8, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    14   2
  CCDC88A WILD-TYPE 278  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     14    2
  CCDC88A WILD-TYPE  278   57
     clus
vv    CCDC88A MUTATED CCDC88A WILD-TYPE
  NO               14               278
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CCDC88A MUTATED                                          0
  CCDC88A WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CCDC88A MUTATED                                       3
  CCDC88A WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC88A MUTATED                                                       11
  CCDC88A WILD-TYPE                                                    147
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CCDC88A MUTATED                                                   1
  CCDC88A WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC88A MUTATED                                                                   4
  CCDC88A WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CCDC88A MUTATED                                                    0
  CCDC88A WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CCDC88A MUTATED                                                  3
  CCDC88A WILD-TYPE                                               58
D120V9, multiclass
                                                                   clus
vv                                                                  CCDC88A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  CCDC88A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC88A MUTATED    16   0   1   4
  CCDC88A WILD-TYPE 295  14  14  20
D120V10, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  R0              16               295
  R1               0                14
  R2               1                14
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CCDC88A MUTATED       4                         1
  CCDC88A WILD-TYPE    83                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC88A MUTATED                                           0    13
  CCDC88A WILD-TYPE                                         1   230
D120V12, multiclass
                                           clus
vv                                          CCDC88A MUTATED CCDC88A WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V13, binary
                   cls
clus                  0   1
  CCDC88A MUTATED     0  17
  CCDC88A WILD-TYPE   4 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED      0   17
  CCDC88A WILD-TYPE    4  293
                        clus
vv                       CCDC88A MUTATED CCDC88A WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              17               293
[1] 2 2
[1] FALSE

Clustering(121) Variable = PIGB MUTATION ANALYSIS
D121V1, survival
                sevent
clus2              0   1
  PIGB MUTATED     6   1
  PIGB WILD-TYPE 224 138
  PIGB MUTATED PIGB WILD-TYPE 
             7            362 
  PIGB MUTATED PIGB WILD-TYPE 
             1            138 
$`PIGB MUTATED`
TCGA-B7-5816 TCGA-BR-7707 TCGA-BR-8487 TCGA-BR-8589 TCGA-CG-5721 TCGA-HF-7132 
       26.70        35.84         1.12        27.12         6.02        77.29 
TCGA-HU-A4GQ 
        0.10 

$`PIGB WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  PIGB MUTATED PIGB WILD-TYPE 
           0.1            0.0 
  PIGB MUTATED PIGB WILD-TYPE 
         77.29         122.30 
  PIGB MUTATED PIGB WILD-TYPE 
         26.70          14.22 
[1] "0.1 - 77.3 (26.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3.2"
D121V2, 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       2       15       38       29        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIGB MUTATED           0          0          1          1        1
  PIGB WILD-TYPE         3         70         52         31       37
D121V3, multiclass
            clus
vv           PIGB MUTATED PIGB WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PIGB MUTATED     1   3   1   4
  PIGB WILD-TYPE  21  89 172  93
D121V4, multiclass
    clus
vv   PIGB MUTATED PIGB WILD-TYPE
  T1            1             21
  T2            3             89
  T3            1            172
  T4            4             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
  PIGB MUTATED     4   3   1   0
  PIGB WILD-TYPE 114 101  76  77
D121V5, multiclass
    clus
vv   PIGB MUTATED PIGB WILD-TYPE
  N0            4            114
  N1            3            101
  N2            1             76
  N3            0             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"
D121V6, binary
                cls
clus               0   1
  PIGB MUTATED    10   0
  PIGB WILD-TYPE 336  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGB MUTATED     10    0
  PIGB WILD-TYPE  336   29
   clus
vv  PIGB MUTATED PIGB WILD-TYPE
  0           10            336
  1            0             29
[1] 2 2
[1] FALSE
D121V7, binary
                cls
clus               0   1
  PIGB MUTATED     5   5
  PIGB WILD-TYPE 140 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGB MUTATED      5    5
  PIGB WILD-TYPE  140  243
        clus
vv       PIGB MUTATED PIGB WILD-TYPE
  FEMALE            5            140
  MALE              5            243
[1] 2 2
[1] FALSE
D121V8, binary
                cls
clus               0   1
  PIGB MUTATED     6   1
  PIGB WILD-TYPE 286  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGB MUTATED      6    1
  PIGB WILD-TYPE  286   58
     clus
vv    PIGB MUTATED PIGB WILD-TYPE
  NO             6            286
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PIGB MUTATED                                          0
  PIGB WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PIGB MUTATED                                       1
  PIGB WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIGB MUTATED                                                        5
  PIGB WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PIGB MUTATED                                                   1
  PIGB WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIGB MUTATED                                                                   2
  PIGB WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PIGB MUTATED                                                    0
  PIGB WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PIGB MUTATED                                                  1
  PIGB WILD-TYPE                                               60
D121V9, multiclass
                                                                   clus
vv                                                                  PIGB MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  PIGB WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PIGB MUTATED     8   0   0   2
  PIGB WILD-TYPE 303  14  15  22
D121V10, multiclass
    clus
vv   PIGB MUTATED PIGB WILD-TYPE
  R0            8            303
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PIGB MUTATED       1                         0
  PIGB WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIGB MUTATED                                           0     6
  PIGB WILD-TYPE                                         1   237
D121V12, multiclass
                                           clus
vv                                          PIGB MUTATED PIGB WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V13, binary
                cls
clus               0   1
  PIGB MUTATED     0   7
  PIGB WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGB MUTATED      0    7
  PIGB WILD-TYPE    4  303
                        clus
vv                       PIGB MUTATED PIGB WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(122) Variable = PIK3CA MUTATION ANALYSIS
D122V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    41  17
  PIK3CA WILD-TYPE 189 122
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              58              311 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              17              122 
$`PIK3CA MUTATED`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-4253 TCGA-BR-6452 TCGA-BR-6455 
       26.70        11.70         9.47         4.08        34.68        13.87 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-8081 
       18.05        19.89        30.90        44.94        21.90        32.25 
TCGA-BR-8284 TCGA-BR-8360 TCGA-BR-8366 TCGA-BR-8381 TCGA-BR-8487 TCGA-BR-8588 
        8.05         6.18         0.95         7.36         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A4PF 
       27.12        28.14         7.53        31.96        20.88         1.15 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-5721 
       13.15        13.18        12.43        11.77        15.95         6.02 
TCGA-CG-5722 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6815 
        0.99        65.10        21.07        25.71        12.66        15.98 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6EZ TCGA-D7-A747 TCGA-FP-7735 TCGA-FP-7916 
        5.92        36.43        20.32         8.38         3.48        14.07 
TCGA-FP-7998 TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8602 TCGA-HU-8608 
       22.29        77.29        30.51         1.51        22.32        21.07 
TCGA-HU-A4G2 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H3 
       24.30         0.10         6.58        20.25         2.10        29.00 
TCGA-HU-A4H4 TCGA-VQ-A8P2 TCGA-VQ-AA69 TCGA-VQ-AA6K 
       23.84        38.14        28.41        12.43 

$`PIK3CA WILD-TYPE`
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-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       20.15         9.86        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-4255 
        6.97         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-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-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       32.78        25.61        12.16         8.98        40.21        31.20 
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-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-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
        7.40        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-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-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 
        9.34         6.28        26.73        24.79        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-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       13.51        20.65        20.42        21.44        16.14         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.41        13.02        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-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-5723 
       30.97         6.97        36.00         1.02         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-D7-5579 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-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-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-7829 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       19.53        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-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G3 
        5.92        24.39        28.96        22.82         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-A4GT TCGA-HU-A4GY 
       11.77        21.37        29.98         8.98         6.51         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        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-AA6A TCGA-VQ-AA6B 
       66.81        11.24        18.41        43.66        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 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
             0.1              0.0 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           77.29           122.30 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          15.965           14.170 
[1] "0.1 - 77.3 (16.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D122V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIK3CA MUTATED         1        0        4        4         7        14
  PIK3CA WILD-TYPE       1       15       36       26        30        38
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3CA MUTATED           0         13          5         10        5
  PIK3CA WILD-TYPE         3         57         48         22       33
D122V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                4               36
  STAGE II                4               26
  STAGE IIA               7               30
  STAGE IIB              14               38
  STAGE III               0                3
  STAGE IIIA             13               57
  STAGE IIIB              5               48
  STAGE IIIC             10               22
  STAGE IV                5               33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3CA MUTATED     1  11  28  25
  PIK3CA WILD-TYPE  21  81 145  72
D122V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              1               21
  T2             11               81
  T3             28              145
  T4             25               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"
                  vv
clus               N0 N1 N2 N3
  PIK3CA MUTATED   19 18 15 11
  PIK3CA WILD-TYPE 99 86 62 66
D122V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             19               99
  N1             18               86
  N2             15               62
  N3             11               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"
D122V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    57   4
  PIK3CA WILD-TYPE 289  25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     57    4
  PIK3CA WILD-TYPE  289   25
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             57              289
  1              4               25
[1] 2 2
[1] FALSE
D122V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    24  41
  PIK3CA WILD-TYPE 121 207
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     24   41
  PIK3CA WILD-TYPE  121  207
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             24              121
  MALE               41              207
[1] 2 2
[1] FALSE
D122V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    51   6
  PIK3CA WILD-TYPE 241  53
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     51    6
  PIK3CA WILD-TYPE  241   53
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              51              241
  YES              6               53
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PIK3CA MUTATED                                          1
  PIK3CA WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PIK3CA MUTATED                                      13
  PIK3CA WILD-TYPE                                    57
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIK3CA MUTATED                                                       26
  PIK3CA WILD-TYPE                                                    132
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PIK3CA MUTATED                                                   3
  PIK3CA WILD-TYPE                                                18
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIK3CA MUTATED                                                                  12
  PIK3CA WILD-TYPE                                                                56
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PIK3CA MUTATED                                                    1
  PIK3CA WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PIK3CA MUTATED                                                  9
  PIK3CA WILD-TYPE                                               52
D122V9, multiclass
                                                                   clus
vv                                                                  PIK3CA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         13
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        26
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               9
                                                                   clus
vv                                                                  PIK3CA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           57
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         132
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               56
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                52
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED    55   2   2   3
  PIK3CA WILD-TYPE 256  12  13  21
D122V10, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             55              256
  R1              2               12
  R2              2               13
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PIK3CA MUTATED      17                         2
  PIK3CA WILD-TYPE    70                         7
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIK3CA MUTATED                                           0    37
  PIK3CA WILD-TYPE                                         1   206
D122V12, multiclass
                                           clus
vv                                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                                 17               70
  BLACK OR AFRICAN AMERICAN                              2                7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 37              206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V13, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1  52
  PIK3CA WILD-TYPE   3 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   52
  PIK3CA WILD-TYPE    3  258
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             52              258
[1] 2 2
[1] FALSE

Clustering(123) Variable = PPIG MUTATION ANALYSIS
D123V1, survival
                sevent
clus2              0   1
  PPIG MUTATED    12   3
  PPIG WILD-TYPE 218 136
  PPIG MUTATED PPIG WILD-TYPE 
            15            354 
  PPIG MUTATED PPIG WILD-TYPE 
             3            136 
$`PPIG MUTATED`
TCGA-B7-5818 TCGA-BR-4256 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8486 
       11.70         9.34        31.10         4.31        31.27        20.22 
TCGA-CD-A4MI TCGA-CG-5723 TCGA-F1-6874 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-KB-A6F7 
       11.77       105.07        14.47         6.51         6.58        63.62 
TCGA-MX-A5UJ TCGA-R5-A804 TCGA-VQ-A8P2 
       19.73         4.60        38.14 

$`PPIG WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-A93J TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 
        2.53         5.56        36.95         3.72        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-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 

  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          14.22 
[1] "4.3 - 105.1 (14.5)" "0.0 - 122.3 (14.2)"
[1] "hr=" "2.2"
D123V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPIG MUTATED         1        1        5        1         1         1
  PPIG WILD-TYPE       1       14       35       29        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPIG MUTATED           0          3          0          2        2
  PPIG WILD-TYPE         3         67         53         30       36
D123V3, multiclass
            clus
vv           PPIG MUTATED PPIG WILD-TYPE
  STAGE I               1              1
  STAGE IA              1             14
  STAGE IB              5             35
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PPIG MUTATED     3   5   5   4
  PPIG WILD-TYPE  19  87 168  93
D123V4, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  T1            3             19
  T2            5             87
  T3            5            168
  T4            4             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
  PPIG MUTATED     6   7   4   1
  PPIG WILD-TYPE 112  97  73  76
D123V5, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  N0            6            112
  N1            7             97
  N2            4             73
  N3            1             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"
D123V6, binary
                cls
clus               0   1
  PPIG MUTATED    16   1
  PPIG WILD-TYPE 330  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED     16    1
  PPIG WILD-TYPE  330   28
   clus
vv  PPIG MUTATED PPIG WILD-TYPE
  0           16            330
  1            1             28
[1] 2 2
[1] FALSE
D123V7, binary
                cls
clus               0   1
  PPIG MUTATED     7  11
  PPIG WILD-TYPE 138 237
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      7   11
  PPIG WILD-TYPE  138  237
        clus
vv       PPIG MUTATED PPIG WILD-TYPE
  FEMALE            7            138
  MALE             11            237
[1] 2 2
[1] FALSE
D123V8, binary
                cls
clus               0   1
  PPIG MUTATED    14   2
  PPIG WILD-TYPE 278  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED     14    2
  PPIG WILD-TYPE  278   57
     clus
vv    PPIG MUTATED PPIG WILD-TYPE
  NO            14            278
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PPIG MUTATED                                          0
  PPIG WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PPIG MUTATED                                       3
  PPIG WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPIG MUTATED                                                        9
  PPIG WILD-TYPE                                                    149
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PPIG MUTATED                                                   1
  PPIG WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPIG MUTATED                                                                   3
  PPIG WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PPIG MUTATED                                                    0
  PPIG WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PPIG MUTATED                                                  2
  PPIG WILD-TYPE                                               59
D123V9, multiclass
                                                                   clus
vv                                                                  PPIG MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  PPIG WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PPIG MUTATED    14   0   0   2
  PPIG WILD-TYPE 297  14  15  22
D123V10, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  R0           14            297
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PPIG MUTATED       3                         2
  PPIG WILD-TYPE    84                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPIG MUTATED                                           0    10
  PPIG WILD-TYPE                                         1   233
D123V12, multiclass
                                           clus
vv                                          PPIG MUTATED PPIG WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V13, binary
                cls
clus               0   1
  PPIG MUTATED     0  14
  PPIG WILD-TYPE   4 296
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      0   14
  PPIG WILD-TYPE    4  296
                        clus
vv                       PPIG MUTATED PPIG WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           14            296
[1] 2 2
[1] FALSE

Clustering(124) Variable = ATP6V1B1 MUTATION ANALYSIS
D124V1, survival
                    sevent
clus2                  0   1
  ATP6V1B1 MUTATED     9  10
  ATP6V1B1 WILD-TYPE 221 129
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                19                350 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                10                129 
$`ATP6V1B1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8081 
       26.70         6.97        18.35        35.84        29.59        32.25 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 
       31.96        16.14         6.58         1.02         6.02        28.96 
TCGA-CG-5733 TCGA-D7-A4YV TCGA-D7-A6EY TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H4 
       21.07         5.92        11.44        29.98         0.10        23.84 
TCGA-HU-A4H8 
       14.07 

$`ATP6V1B1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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 

  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
               0.1                0.0 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
             35.84             122.30 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
             18.35              14.12 
[1] "0.1 - 35.8 (18.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D124V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP6V1B1 MUTATED         0        1        2        0         2         5
  ATP6V1B1 WILD-TYPE       2       14       38       30        35        47
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1B1 MUTATED           0          2          2          1        3
  ATP6V1B1 WILD-TYPE         3         68         51         31       35
D124V3, multiclass
            clus
vv           ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  2                 38
  STAGE II                  0                 30
  STAGE IIA                 2                 35
  STAGE IIB                 5                 47
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                2                 51
  STAGE IIIC                1                 31
  STAGE IV                  3                 35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ATP6V1B1 MUTATED     2   4   6   6
  ATP6V1B1 WILD-TYPE  20  88 167  91
D124V4, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  T1                2                 20
  T2                4                 88
  T3                6                167
  T4                6                 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
  ATP6V1B1 MUTATED     6   7   5   2
  ATP6V1B1 WILD-TYPE 112  97  72  75
D124V5, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  N0                6                112
  N1                7                 97
  N2                5                 72
  N3                2                 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"
D124V6, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    18   2
  ATP6V1B1 WILD-TYPE 328  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     18    2
  ATP6V1B1 WILD-TYPE  328   27
   clus
vv  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  0               18                328
  1                2                 27
[1] 2 2
[1] FALSE
D124V7, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    11  10
  ATP6V1B1 WILD-TYPE 134 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     11   10
  ATP6V1B1 WILD-TYPE  134  238
        clus
vv       ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  FEMALE               11                134
  MALE                 10                238
[1] 2 2
[1] FALSE
D124V8, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    17   0
  ATP6V1B1 WILD-TYPE 275  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     17    0
  ATP6V1B1 WILD-TYPE  275   59
     clus
vv    ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  NO                17                275
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ATP6V1B1 MUTATED                                          0
  ATP6V1B1 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ATP6V1B1 MUTATED                                       2
  ATP6V1B1 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATP6V1B1 MUTATED                                                        9
  ATP6V1B1 WILD-TYPE                                                    149
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ATP6V1B1 MUTATED                                                   0
  ATP6V1B1 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATP6V1B1 MUTATED                                                                   3
  ATP6V1B1 WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ATP6V1B1 MUTATED                                                    0
  ATP6V1B1 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ATP6V1B1 MUTATED                                                  7
  ATP6V1B1 WILD-TYPE                                               54
D124V9, multiclass
                                                                   clus
vv                                                                  ATP6V1B1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 7
                                                                   clus
vv                                                                  ATP6V1B1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ATP6V1B1 MUTATED    15   0   1   4
  ATP6V1B1 WILD-TYPE 296  14  14  20
D124V10, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  R0               15                296
  R1                0                 14
  R2                1                 14
  RX                4                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ATP6V1B1 MUTATED       6                         0
  ATP6V1B1 WILD-TYPE    81                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATP6V1B1 MUTATED                                           0    11
  ATP6V1B1 WILD-TYPE                                         1   232
D124V12, multiclass
                                           clus
vv                                          ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  ASIAN                                                    6                 81
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   11                232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V13, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED     0  17
  ATP6V1B1 WILD-TYPE   4 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED      0   17
  ATP6V1B1 WILD-TYPE    4  293
                        clus
vv                       ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               17                293
[1] 2 2
[1] FALSE

Clustering(125) Variable = PLEKHA6 MUTATION ANALYSIS
D125V1, survival
                   sevent
clus2                 0   1
  PLEKHA6 MUTATED    10  10
  PLEKHA6 WILD-TYPE 220 129
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               20               349 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               10               129 
$`PLEKHA6 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7715 TCGA-BR-8059 TCGA-BR-8361 
        6.97        34.68        32.78        33.63        14.43        31.10 
TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-A4QL TCGA-CD-A4MI TCGA-CG-4306 
        0.26         4.31        25.05        16.14        11.77         1.02 
TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HU-A4GT TCGA-IN-A6RR 
        6.02        21.07         5.92        11.08         6.51         6.74 
TCGA-R5-A7ZI TCGA-VQ-A8P2 
       74.53        38.14 

$`PLEKHA6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
            13.10             14.27 
[1] "0.3 - 74.5 (13.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D125V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLEKHA6 MUTATED         0        0        2        0         5         2
  PLEKHA6 WILD-TYPE       2       15       38       30        32        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHA6 MUTATED           1          6          1          2        4
  PLEKHA6 WILD-TYPE         2         64         52         30       34
D125V3, multiclass
            clus
vv           PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                5                32
  STAGE IIB                2                50
  STAGE III                1                 2
  STAGE IIIA               6                64
  STAGE IIIB               1                52
  STAGE IIIC               2                30
  STAGE IV                 4                34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHA6 MUTATED     0   3  11   9
  PLEKHA6 WILD-TYPE  22  89 162  88
D125V4, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  T1               0                22
  T2               3                89
  T3              11               162
  T4               9                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
  PLEKHA6 MUTATED     9   8   4   2
  PLEKHA6 WILD-TYPE 109  96  73  75
D125V5, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  N0               9               109
  N1               8                96
  N2               4                73
  N3               2                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"
D125V6, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    20   2
  PLEKHA6 WILD-TYPE 326  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     20    2
  PLEKHA6 WILD-TYPE  326   27
   clus
vv  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  0              20               326
  1               2                27
[1] 2 2
[1] FALSE
D125V7, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    13  10
  PLEKHA6 WILD-TYPE 132 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     13   10
  PLEKHA6 WILD-TYPE  132  238
        clus
vv       PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  FEMALE              13               132
  MALE                10               238
[1] 2 2
[1] FALSE
D125V8, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    18   2
  PLEKHA6 WILD-TYPE 274  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     18    2
  PLEKHA6 WILD-TYPE  274   57
     clus
vv    PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  NO               18               274
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PLEKHA6 MUTATED                                          0
  PLEKHA6 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PLEKHA6 MUTATED                                       1
  PLEKHA6 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLEKHA6 MUTATED                                                       15
  PLEKHA6 WILD-TYPE                                                    143
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PLEKHA6 MUTATED                                                   1
  PLEKHA6 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLEKHA6 MUTATED                                                                   4
  PLEKHA6 WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PLEKHA6 MUTATED                                                    0
  PLEKHA6 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PLEKHA6 MUTATED                                                  2
  PLEKHA6 WILD-TYPE                                               59
D125V9, multiclass
                                                                   clus
vv                                                                  PLEKHA6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  PLEKHA6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PLEKHA6 MUTATED    18   0   1   3
  PLEKHA6 WILD-TYPE 293  14  14  21
D125V10, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  R0              18               293
  R1               0                14
  R2               1                14
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PLEKHA6 MUTATED       2                         1
  PLEKHA6 WILD-TYPE    85                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLEKHA6 MUTATED                                           0    17
  PLEKHA6 WILD-TYPE                                         1   226
D125V12, multiclass
                                           clus
vv                                          PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  17               226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V13, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED     1  18
  PLEKHA6 WILD-TYPE   3 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED      1   18
  PLEKHA6 WILD-TYPE    3  292
                        clus
vv                       PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              18               292
[1] 2 2
[1] FALSE

Clustering(126) Variable = PLA2G1B MUTATION ANALYSIS
D126V1, survival
                   sevent
clus2                 0   1
  PLA2G1B MUTATED     5   1
  PLA2G1B WILD-TYPE 225 138
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
                6               363 
  PLA2G1B MUTATED PLA2G1B WILD-TYPE 
                1               138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
       12.39        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-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-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        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-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 

  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            14.470 
[1] "11.8 - 19.5 (12.7)" "0.0 - 122.3 (14.5)"
[1] "hr=" "1.9"
D126V2, 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       2       15       40       29        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLA2G1B MUTATED           0          2          1          0        0
  PLA2G1B WILD-TYPE         3         68         52         32       38
D126V3, multiclass
            clus
vv           PLA2G1B MUTATED PLA2G1B WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLA2G1B MUTATED     0   0   6   0
  PLA2G1B WILD-TYPE  22  92 167  97
D126V4, multiclass
    clus
vv   PLA2G1B MUTATED PLA2G1B WILD-TYPE
  T1               0                22
  T2               0                92
  T3               6               167
  T4               0                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
  PLA2G1B MUTATED     2   3   0   1
  PLA2G1B WILD-TYPE 116 101  77  76
D126V5, multiclass
    clus
vv   PLA2G1B MUTATED PLA2G1B WILD-TYPE
  N0               2               116
  N1               3               101
  N2               0                77
  N3               1                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"
D126V6, binary
                   cls
clus                  0   1
  PLA2G1B MUTATED     5   0
  PLA2G1B WILD-TYPE 341  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G1B MUTATED      5    0
  PLA2G1B WILD-TYPE  341   29
   clus
vv  PLA2G1B MUTATED PLA2G1B WILD-TYPE
  0               5               341
  1               0                29
[1] 2 2
[1] FALSE
D126V7, binary
                   cls
clus                  0   1
  PLA2G1B MUTATED     3   3
  PLA2G1B WILD-TYPE 142 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G1B MUTATED      3    3
  PLA2G1B WILD-TYPE  142  245
        clus
vv       PLA2G1B MUTATED PLA2G1B WILD-TYPE
  FEMALE               3               142
  MALE                 3               245
[1] 2 2
[1] FALSE
D126V8, binary
                   cls
clus                  0   1
  PLA2G1B MUTATED     3   3
  PLA2G1B WILD-TYPE 289  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G1B MUTATED      3    3
  PLA2G1B WILD-TYPE  289   56
     clus
vv    PLA2G1B MUTATED PLA2G1B WILD-TYPE
  NO                3               289
  YES               3                56
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PLA2G1B MUTATED                                          0
  PLA2G1B WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PLA2G1B MUTATED                                       1
  PLA2G1B WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLA2G1B MUTATED                                                        2
  PLA2G1B WILD-TYPE                                                    156
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PLA2G1B MUTATED                                                   1
  PLA2G1B WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLA2G1B MUTATED                                                                   1
  PLA2G1B WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PLA2G1B MUTATED                                                    0
  PLA2G1B WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PLA2G1B MUTATED                                                  1
  PLA2G1B WILD-TYPE                                               60
D126V9, multiclass
                                                                   clus
vv                                                                  PLA2G1B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  PLA2G1B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PLA2G1B MUTATED     5   1   0   0
  PLA2G1B WILD-TYPE 306  13  15  24
D126V10, multiclass
    clus
vv   PLA2G1B MUTATED PLA2G1B WILD-TYPE
  R0               5               306
  R1               1                13
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PLA2G1B MUTATED       3                         0
  PLA2G1B WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLA2G1B MUTATED                                           0     3
  PLA2G1B WILD-TYPE                                         1   240
D126V12, multiclass
                                           clus
vv                                          PLA2G1B MUTATED PLA2G1B WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V13, binary
                   cls
clus                  0   1
  PLA2G1B MUTATED     0   6
  PLA2G1B WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G1B MUTATED      0    6
  PLA2G1B WILD-TYPE    4  304
                        clus
vv                       PLA2G1B MUTATED PLA2G1B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(127) Variable = RTKN2 MUTATION ANALYSIS
D127V1, survival
                 sevent
clus2               0   1
  RTKN2 MUTATED     7   3
  RTKN2 WILD-TYPE 223 136
  RTKN2 MUTATED RTKN2 WILD-TYPE 
             10             359 
  RTKN2 MUTATED RTKN2 WILD-TYPE 
              3             136 
$`RTKN2 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8372 TCGA-BR-8590 TCGA-CG-5721 
       30.90        34.68        29.59        31.27         9.34         6.02 
TCGA-D7-A4YV TCGA-HF-A5NB TCGA-HU-8602 TCGA-R5-A7ZI 
        5.92        30.51        22.32        74.53 

$`RTKN2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  RTKN2 MUTATED RTKN2 WILD-TYPE 
           5.92            0.00 
  RTKN2 MUTATED RTKN2 WILD-TYPE 
          74.53          122.30 
  RTKN2 MUTATED RTKN2 WILD-TYPE 
          30.05           14.07 
[1] "5.9 - 74.5 (30.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D127V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RTKN2 MUTATED         0        0        0        0         1         3
  RTKN2 WILD-TYPE       2       15       40       30        36        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RTKN2 MUTATED           0          0          0          3        3
  RTKN2 WILD-TYPE         3         70         53         29       35
D127V3, multiclass
            clus
vv           RTKN2 MUTATED RTKN2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RTKN2 MUTATED     0   1   2   8
  RTKN2 WILD-TYPE  22  91 171  89
D127V4, multiclass
    clus
vv   RTKN2 MUTATED RTKN2 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             2             171
  T4             8              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
  RTKN2 MUTATED     3   3   2   2
  RTKN2 WILD-TYPE 115 101  75  75
D127V5, multiclass
    clus
vv   RTKN2 MUTATED RTKN2 WILD-TYPE
  N0             3             115
  N1             3             101
  N2             2              75
  N3             2              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"
D127V6, binary
                 cls
clus                0   1
  RTKN2 MUTATED    10   1
  RTKN2 WILD-TYPE 336  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTKN2 MUTATED     10    1
  RTKN2 WILD-TYPE  336   28
   clus
vv  RTKN2 MUTATED RTKN2 WILD-TYPE
  0            10             336
  1             1              28
[1] 2 2
[1] FALSE
D127V7, binary
                 cls
clus                0   1
  RTKN2 MUTATED     8   3
  RTKN2 WILD-TYPE 137 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTKN2 MUTATED      8    3
  RTKN2 WILD-TYPE  137  245
        clus
vv       RTKN2 MUTATED RTKN2 WILD-TYPE
  FEMALE             8             137
  MALE               3             245
[1] 2 2
[1] FALSE
D127V8, binary
                 cls
clus                0   1
  RTKN2 MUTATED     9   1
  RTKN2 WILD-TYPE 283  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTKN2 MUTATED      9    1
  RTKN2 WILD-TYPE  283   58
     clus
vv    RTKN2 MUTATED RTKN2 WILD-TYPE
  NO              9             283
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RTKN2 MUTATED                                          0
  RTKN2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RTKN2 MUTATED                                       2
  RTKN2 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RTKN2 MUTATED                                                        6
  RTKN2 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RTKN2 MUTATED                                                   1
  RTKN2 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RTKN2 MUTATED                                                                   1
  RTKN2 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RTKN2 MUTATED                                                    0
  RTKN2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RTKN2 MUTATED                                                  1
  RTKN2 WILD-TYPE                                               60
D127V9, multiclass
                                                                   clus
vv                                                                  RTKN2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  RTKN2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RTKN2 MUTATED     8   1   0   2
  RTKN2 WILD-TYPE 303  13  15  22
D127V10, multiclass
    clus
vv   RTKN2 MUTATED RTKN2 WILD-TYPE
  R0             8             303
  R1             1              13
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RTKN2 MUTATED       1                         0
  RTKN2 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RTKN2 MUTATED                                           0     8
  RTKN2 WILD-TYPE                                         1   235
D127V12, multiclass
                                           clus
vv                                          RTKN2 MUTATED RTKN2 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V13, binary
                 cls
clus                0   1
  RTKN2 MUTATED     1   8
  RTKN2 WILD-TYPE   3 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTKN2 MUTATED      1    8
  RTKN2 WILD-TYPE    3  302
                        clus
vv                       RTKN2 MUTATED RTKN2 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(128) Variable = PAX2 MUTATION ANALYSIS
D128V1, survival
                sevent
clus2              0   1
  PAX2 MUTATED     8   3
  PAX2 WILD-TYPE 222 136
  PAX2 MUTATED PAX2 WILD-TYPE 
            11            358 
  PAX2 MUTATED PAX2 WILD-TYPE 
             3            136 
$`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-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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        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-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-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-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-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-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-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         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 

  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          14.22 
[1] "0.1 - 105.1 (19.6)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.7"
D128V2, 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       2       15       39       29        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAX2 MUTATED           0          2          0          4        0
  PAX2 WILD-TYPE         3         68         53         28       38
D128V3, multiclass
            clus
vv           PAX2 MUTATED PAX2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            4             28
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAX2 MUTATED     0   2   4   6
  PAX2 WILD-TYPE  22  90 169  91
D128V4, multiclass
    clus
vv   PAX2 MUTATED PAX2 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            4            169
  T4            6             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
  PAX2 MUTATED     5   3   1   3
  PAX2 WILD-TYPE 113 101  76  74
D128V5, multiclass
    clus
vv   PAX2 MUTATED PAX2 WILD-TYPE
  N0            5            113
  N1            3            101
  N2            1             76
  N3            3             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"
D128V6, binary
                cls
clus               0   1
  PAX2 MUTATED    12   0
  PAX2 WILD-TYPE 334  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED     12    0
  PAX2 WILD-TYPE  334   29
   clus
vv  PAX2 MUTATED PAX2 WILD-TYPE
  0           12            334
  1            0             29
[1] 2 2
[1] FALSE
D128V7, binary
                cls
clus               0   1
  PAX2 MUTATED     5   7
  PAX2 WILD-TYPE 140 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED      5    7
  PAX2 WILD-TYPE  140  241
        clus
vv       PAX2 MUTATED PAX2 WILD-TYPE
  FEMALE            5            140
  MALE              7            241
[1] 2 2
[1] FALSE
D128V8, binary
                cls
clus               0   1
  PAX2 MUTATED    11   0
  PAX2 WILD-TYPE 281  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED     11    0
  PAX2 WILD-TYPE  281   59
     clus
vv    PAX2 MUTATED PAX2 WILD-TYPE
  NO            11            281
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PAX2 MUTATED                                          0
  PAX2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PAX2 MUTATED                                       3
  PAX2 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAX2 MUTATED                                                        7
  PAX2 WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PAX2 MUTATED                                                   0
  PAX2 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAX2 MUTATED                                                                   1
  PAX2 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PAX2 MUTATED                                                    0
  PAX2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PAX2 MUTATED                                                  1
  PAX2 WILD-TYPE                                               60
D128V9, multiclass
                                                                   clus
vv                                                                  PAX2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  PAX2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PAX2 MUTATED     8   0   0   1
  PAX2 WILD-TYPE 303  14  15  23
D128V10, multiclass
    clus
vv   PAX2 MUTATED PAX2 WILD-TYPE
  R0            8            303
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PAX2 MUTATED       4                         0
  PAX2 WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAX2 MUTATED                                           0     7
  PAX2 WILD-TYPE                                         1   236
D128V12, multiclass
                                           clus
vv                                          PAX2 MUTATED PAX2 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V13, binary
                cls
clus               0   1
  PAX2 MUTATED     0  11
  PAX2 WILD-TYPE   4 299
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED      0   11
  PAX2 WILD-TYPE    4  299
                        clus
vv                       PAX2 MUTATED PAX2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           11            299
[1] 2 2
[1] FALSE

Clustering(129) Variable = SERPINI1 MUTATION ANALYSIS
D129V1, survival
                    sevent
clus2                  0   1
  SERPINI1 MUTATED     6   2
  SERPINI1 WILD-TYPE 224 137
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
                 8                361 
  SERPINI1 MUTATED SERPINI1 WILD-TYPE 
                 2                137 
$`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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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 

  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              14.07 
[1] "1.0 - 31.3 (23.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D129V2, 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       2       15       40       30        36        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINI1 MUTATED           0          0          1          1        2
  SERPINI1 WILD-TYPE         3         70         52         31       36
D129V3, multiclass
            clus
vv           SERPINI1 MUTATED SERPINI1 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 3                 49
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                1                 52
  STAGE IIIC                1                 31
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SERPINI1 MUTATED     1   1   2   5
  SERPINI1 WILD-TYPE  21  91 171  92
D129V4, multiclass
    clus
vv   SERPINI1 MUTATED SERPINI1 WILD-TYPE
  T1                1                 21
  T2                1                 91
  T3                2                171
  T4                5                 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
  SERPINI1 MUTATED     3   2   2   1
  SERPINI1 WILD-TYPE 115 102  75  76
D129V5, multiclass
    clus
vv   SERPINI1 MUTATED SERPINI1 WILD-TYPE
  N0                3                115
  N1                2                102
  N2                2                 75
  N3                1                 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"
D129V6, binary
                    cls
clus                   0   1
  SERPINI1 MUTATED     7   2
  SERPINI1 WILD-TYPE 339  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINI1 MUTATED      7    2
  SERPINI1 WILD-TYPE  339   27
   clus
vv  SERPINI1 MUTATED SERPINI1 WILD-TYPE
  0                7                339
  1                2                 27
[1] 2 2
[1] FALSE
D129V7, binary
                    cls
clus                   0   1
  SERPINI1 MUTATED     5   4
  SERPINI1 WILD-TYPE 140 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINI1 MUTATED      5    4
  SERPINI1 WILD-TYPE  140  244
        clus
vv       SERPINI1 MUTATED SERPINI1 WILD-TYPE
  FEMALE                5                140
  MALE                  4                244
[1] 2 2
[1] FALSE
D129V8, binary
                    cls
clus                   0   1
  SERPINI1 MUTATED     7   0
  SERPINI1 WILD-TYPE 285  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINI1 MUTATED      7    0
  SERPINI1 WILD-TYPE  285   59
     clus
vv    SERPINI1 MUTATED SERPINI1 WILD-TYPE
  NO                 7                285
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SERPINI1 MUTATED                                          0
  SERPINI1 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SERPINI1 MUTATED                                       2
  SERPINI1 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SERPINI1 MUTATED                                                        4
  SERPINI1 WILD-TYPE                                                    154
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SERPINI1 MUTATED                                                   0
  SERPINI1 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SERPINI1 MUTATED                                                                   2
  SERPINI1 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SERPINI1 MUTATED                                                    0
  SERPINI1 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SERPINI1 MUTATED                                                  1
  SERPINI1 WILD-TYPE                                               60
D129V9, multiclass
                                                                   clus
vv                                                                  SERPINI1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  SERPINI1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SERPINI1 MUTATED     6   0   2   1
  SERPINI1 WILD-TYPE 305  14  13  23
D129V10, multiclass
    clus
vv   SERPINI1 MUTATED SERPINI1 WILD-TYPE
  R0                6                305
  R1                0                 14
  R2                2                 13
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SERPINI1 MUTATED       2                         0
  SERPINI1 WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SERPINI1 MUTATED                                           0     5
  SERPINI1 WILD-TYPE                                         1   238
D129V12, multiclass
                                           clus
vv                                          SERPINI1 MUTATED SERPINI1 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V13, binary
                    cls
clus                   0   1
  SERPINI1 MUTATED     0   7
  SERPINI1 WILD-TYPE   4 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINI1 MUTATED      0    7
  SERPINI1 WILD-TYPE    4  303
                        clus
vv                       SERPINI1 MUTATED SERPINI1 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                7                303
[1] 2 2
[1] FALSE

Clustering(130) Variable = TMEM41A MUTATION ANALYSIS
D130V1, survival
                   sevent
clus2                 0   1
  TMEM41A MUTATED     5   3
  TMEM41A WILD-TYPE 225 136
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                8               361 
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                3               136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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            14.170 
[1] "1.1 - 38.1 (29.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D130V2, 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       2       14       40       30        34        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM41A MUTATED           0          3          0          1        0
  TMEM41A WILD-TYPE         3         67         53         31       38
D130V3, multiclass
            clus
vv           TMEM41A MUTATED TMEM41A WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                3                34
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               3                67
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM41A MUTATED     1   0   4   4
  TMEM41A WILD-TYPE  21  92 169  93
D130V4, multiclass
    clus
vv   TMEM41A MUTATED TMEM41A WILD-TYPE
  T1               1                21
  T2               0                92
  T3               4               169
  T4               4                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
  TMEM41A MUTATED     6   2   0   1
  TMEM41A WILD-TYPE 112 102  77  76
D130V5, multiclass
    clus
vv   TMEM41A MUTATED TMEM41A WILD-TYPE
  N0               6               112
  N1               2               102
  N2               0                77
  N3               1                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"
D130V6, binary
                   cls
clus                  0   1
  TMEM41A MUTATED     9   0
  TMEM41A WILD-TYPE 337  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      9    0
  TMEM41A WILD-TYPE  337   29
   clus
vv  TMEM41A MUTATED TMEM41A WILD-TYPE
  0               9               337
  1               0                29
[1] 2 2
[1] FALSE
D130V7, binary
                   cls
clus                  0   1
  TMEM41A MUTATED     5   4
  TMEM41A WILD-TYPE 140 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      5    4
  TMEM41A WILD-TYPE  140  244
        clus
vv       TMEM41A MUTATED TMEM41A WILD-TYPE
  FEMALE               5               140
  MALE                 4               244
[1] 2 2
[1] FALSE
D130V8, binary
                   cls
clus                  0   1
  TMEM41A MUTATED     5   2
  TMEM41A WILD-TYPE 287  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      5    2
  TMEM41A WILD-TYPE  287   57
     clus
vv    TMEM41A MUTATED TMEM41A WILD-TYPE
  NO                5               287
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TMEM41A MUTATED                                          0
  TMEM41A WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TMEM41A MUTATED                                       1
  TMEM41A WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM41A MUTATED                                                        5
  TMEM41A WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TMEM41A MUTATED                                                   2
  TMEM41A WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM41A MUTATED                                                                   1
  TMEM41A WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TMEM41A MUTATED                                                    0
  TMEM41A WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TMEM41A MUTATED                                                  0
  TMEM41A WILD-TYPE                                               61
D130V9, multiclass
                                                                   clus
vv                                                                  TMEM41A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  TMEM41A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM41A MUTATED     5   1   0   1
  TMEM41A WILD-TYPE 306  13  15  23
D130V10, multiclass
    clus
vv   TMEM41A MUTATED TMEM41A WILD-TYPE
  R0               5               306
  R1               1                13
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM41A MUTATED       2                         0
  TMEM41A WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM41A MUTATED                                           0     5
  TMEM41A WILD-TYPE                                         1   238
D130V12, multiclass
                                           clus
vv                                          TMEM41A MUTATED TMEM41A WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V13, binary
                   cls
clus                  0   1
  TMEM41A MUTATED     0   6
  TMEM41A WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      0    6
  TMEM41A WILD-TYPE    4  304
                        clus
vv                       TMEM41A MUTATED TMEM41A WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(131) Variable = ADAM30 MUTATION ANALYSIS
D131V1, survival
                  sevent
clus2                0   1
  ADAM30 MUTATED     7   7
  ADAM30 WILD-TYPE 223 132
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              14              355 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               7              132 
$`ADAM30 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8059 TCGA-BR-8284 TCGA-BR-8382 TCGA-CD-8525 
        6.97        30.90        14.43         8.05        25.05        12.59 
TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-5734 TCGA-F1-6874 TCGA-HF-A5NB TCGA-HU-A4GT 
       12.62         1.02         7.99        14.47        30.51         6.51 
TCGA-HU-A4GU TCGA-VQ-A8P2 
        6.58        38.14 

$`ADAM30 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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-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-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 

  ADAM30 MUTATED ADAM30 WILD-TYPE 
            1.02             0.00 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
           38.14           122.30 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
          12.605           14.660 
[1] "1.0 - 38.1 (12.6)"  "0.0 - 122.3 (14.7)"
[1] "hr=" "1.6"
D131V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADAM30 MUTATED         0        0        2        0         1         1
  ADAM30 WILD-TYPE       2       15       38       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM30 MUTATED           1          4          0          3        2
  ADAM30 WILD-TYPE         2         66         53         29       36
D131V3, multiclass
            clus
vv           ADAM30 MUTATED ADAM30 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               1                2
  STAGE IIIA              4               66
  STAGE IIIB              0               53
  STAGE IIIC              3               29
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM30 MUTATED     1   3   6   6
  ADAM30 WILD-TYPE  21  89 167  91
D131V4, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              6              167
  T4              6               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
  ADAM30 MUTATED     3   6   2   3
  ADAM30 WILD-TYPE 115  98  75  74
D131V5, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  N0              3              115
  N1              6               98
  N2              2               75
  N3              3               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"
D131V6, binary
                  cls
clus                 0   1
  ADAM30 MUTATED    14   1
  ADAM30 WILD-TYPE 332  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED     14    1
  ADAM30 WILD-TYPE  332   28
   clus
vv  ADAM30 MUTATED ADAM30 WILD-TYPE
  0             14              332
  1              1               28
[1] 2 2
[1] FALSE
D131V7, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     8   8
  ADAM30 WILD-TYPE 137 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      8    8
  ADAM30 WILD-TYPE  137  240
        clus
vv       ADAM30 MUTATED ADAM30 WILD-TYPE
  FEMALE              8              137
  MALE                8              240
[1] 2 2
[1] FALSE
D131V8, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     9   3
  ADAM30 WILD-TYPE 283  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      9    3
  ADAM30 WILD-TYPE  283   56
     clus
vv    ADAM30 MUTATED ADAM30 WILD-TYPE
  NO               9              283
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ADAM30 MUTATED                                          0
  ADAM30 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ADAM30 MUTATED                                       1
  ADAM30 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ADAM30 MUTATED                                                        7
  ADAM30 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ADAM30 MUTATED                                                   3
  ADAM30 WILD-TYPE                                                18
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ADAM30 MUTATED                                                                   4
  ADAM30 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ADAM30 MUTATED                                                    0
  ADAM30 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ADAM30 MUTATED                                                  1
  ADAM30 WILD-TYPE                                               60
D131V9, multiclass
                                                                   clus
vv                                                                  ADAM30 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ADAM30 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ADAM30 MUTATED     9   1   1   4
  ADAM30 WILD-TYPE 302  13  14  20
D131V10, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  R0              9              302
  R1              1               13
  R2              1               14
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ADAM30 MUTATED       4                         0
  ADAM30 WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ADAM30 MUTATED                                           0     9
  ADAM30 WILD-TYPE                                         1   234
D131V12, multiclass
                                           clus
vv                                          ADAM30 MUTATED ADAM30 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V13, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     0  12
  ADAM30 WILD-TYPE   4 298
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      0   12
  ADAM30 WILD-TYPE    4  298
                        clus
vv                       ADAM30 MUTATED ADAM30 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             12              298
[1] 2 2
[1] FALSE

Clustering(132) Variable = B3GNT5 MUTATION ANALYSIS
D132V1, survival
                  sevent
clus2                0   1
  B3GNT5 MUTATED     8   1
  B3GNT5 WILD-TYPE 222 138
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
               9              360 
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
               1              138 
$`B3GNT5 MUTATED`
TCGA-BR-4257 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 TCGA-CG-5723 
        9.67         4.31         1.12        31.96         6.02       105.07 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-VQ-A8P2 
        6.58        20.25        38.14 

$`B3GNT5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         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 

  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
            1.12             0.00 
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
          105.07           122.30 
  B3GNT5 MUTATED B3GNT5 WILD-TYPE 
            9.67            14.35 
[1] "1.1 - 105.1 (9.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "3.6"
D132V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  B3GNT5 MUTATED         0        0        1        1         1         2
  B3GNT5 WILD-TYPE       2       15       39       29        36        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B3GNT5 MUTATED           0          1          0          1        3
  B3GNT5 WILD-TYPE         3         69         53         31       35
D132V3, multiclass
            clus
vv           B3GNT5 MUTATED B3GNT5 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  B3GNT5 MUTATED     0   2   2   6
  B3GNT5 WILD-TYPE  22  90 171  91
D132V4, multiclass
    clus
vv   B3GNT5 MUTATED B3GNT5 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              2              171
  T4              6               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
  B3GNT5 MUTATED     3   4   3   0
  B3GNT5 WILD-TYPE 115 100  74  77
D132V5, multiclass
    clus
vv   B3GNT5 MUTATED B3GNT5 WILD-TYPE
  N0              3              115
  N1              4              100
  N2              3               74
  N3              0               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"
D132V6, binary
                  cls
clus                 0   1
  B3GNT5 MUTATED    10   1
  B3GNT5 WILD-TYPE 336  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  B3GNT5 MUTATED     10    1
  B3GNT5 WILD-TYPE  336   28
   clus
vv  B3GNT5 MUTATED B3GNT5 WILD-TYPE
  0             10              336
  1              1               28
[1] 2 2
[1] FALSE
D132V7, binary
                  cls
clus                 0   1
  B3GNT5 MUTATED     5   6
  B3GNT5 WILD-TYPE 140 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  B3GNT5 MUTATED      5    6
  B3GNT5 WILD-TYPE  140  242
        clus
vv       B3GNT5 MUTATED B3GNT5 WILD-TYPE
  FEMALE              5              140
  MALE                6              242
[1] 2 2
[1] FALSE
D132V8, binary
                  cls
clus                 0   1
  B3GNT5 MUTATED     9   1
  B3GNT5 WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  B3GNT5 MUTATED      9    1
  B3GNT5 WILD-TYPE  283   58
     clus
vv    B3GNT5 MUTATED B3GNT5 WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  B3GNT5 MUTATED                                          0
  B3GNT5 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  B3GNT5 MUTATED                                       2
  B3GNT5 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  B3GNT5 MUTATED                                                        5
  B3GNT5 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  B3GNT5 MUTATED                                                   1
  B3GNT5 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  B3GNT5 MUTATED                                                                   2
  B3GNT5 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  B3GNT5 MUTATED                                                    0
  B3GNT5 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  B3GNT5 MUTATED                                                  1
  B3GNT5 WILD-TYPE                                               60
D132V9, multiclass
                                                                   clus
vv                                                                  B3GNT5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  B3GNT5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  B3GNT5 MUTATED     9   0   0   2
  B3GNT5 WILD-TYPE 302  14  15  22
D132V10, multiclass
    clus
vv   B3GNT5 MUTATED B3GNT5 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  B3GNT5 MUTATED       3                         0
  B3GNT5 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  B3GNT5 MUTATED                                           0     6
  B3GNT5 WILD-TYPE                                         1   237
D132V12, multiclass
                                           clus
vv                                          B3GNT5 MUTATED B3GNT5 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V13, binary
                  cls
clus                 0   1
  B3GNT5 MUTATED     0   8
  B3GNT5 WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  B3GNT5 MUTATED      0    8
  B3GNT5 WILD-TYPE    4  302
                        clus
vv                       B3GNT5 MUTATED B3GNT5 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(133) Variable = PAPD4 MUTATION ANALYSIS
D133V1, survival
                 sevent
clus2               0   1
  PAPD4 MUTATED     7   3
  PAPD4 WILD-TYPE 223 136
  PAPD4 MUTATED PAPD4 WILD-TYPE 
             10             359 
  PAPD4 MUTATED PAPD4 WILD-TYPE 
              3             136 
$`PAPD4 MUTATED`
TCGA-BR-8372 TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-5725 TCGA-CG-5726 TCGA-D7-A6EV 
       31.27        31.96        15.95        15.02        28.96        11.24 
TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H3 
       22.68         0.10        20.25        29.00 

$`PAPD4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-5728 
        0.99         6.02         0.99       105.07        12.03        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-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-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-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 

  PAPD4 MUTATED PAPD4 WILD-TYPE 
            0.1             0.0 
  PAPD4 MUTATED PAPD4 WILD-TYPE 
          31.96          122.30 
  PAPD4 MUTATED PAPD4 WILD-TYPE 
         21.465          14.070 
[1] "0.1 - 32.0 (21.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D133V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAPD4 MUTATED         0        1        1        1         0         3
  PAPD4 WILD-TYPE       2       14       39       29        37        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAPD4 MUTATED           0          0          0          4        1
  PAPD4 WILD-TYPE         3         70         53         28       37
D133V3, multiclass
            clus
vv           PAPD4 MUTATED PAPD4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             4              28
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PAPD4 MUTATED     1   3   1   6
  PAPD4 WILD-TYPE  21  89 172  91
D133V4, multiclass
    clus
vv   PAPD4 MUTATED PAPD4 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             1             172
  T4             6              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
  PAPD4 MUTATED     3   2   4   2
  PAPD4 WILD-TYPE 115 102  73  75
D133V5, multiclass
    clus
vv   PAPD4 MUTATED PAPD4 WILD-TYPE
  N0             3             115
  N1             2             102
  N2             4              73
  N3             2              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"
D133V6, binary
                 cls
clus                0   1
  PAPD4 MUTATED    10   1
  PAPD4 WILD-TYPE 336  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAPD4 MUTATED     10    1
  PAPD4 WILD-TYPE  336   28
   clus
vv  PAPD4 MUTATED PAPD4 WILD-TYPE
  0            10             336
  1             1              28
[1] 2 2
[1] FALSE
D133V7, binary
                 cls
clus                0   1
  PAPD4 MUTATED     4   7
  PAPD4 WILD-TYPE 141 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAPD4 MUTATED      4    7
  PAPD4 WILD-TYPE  141  241
        clus
vv       PAPD4 MUTATED PAPD4 WILD-TYPE
  FEMALE             4             141
  MALE               7             241
[1] 2 2
[1] FALSE
D133V8, binary
                 cls
clus                0   1
  PAPD4 MUTATED     9   0
  PAPD4 WILD-TYPE 283  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAPD4 MUTATED      9    0
  PAPD4 WILD-TYPE  283   59
     clus
vv    PAPD4 MUTATED PAPD4 WILD-TYPE
  NO              9             283
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PAPD4 MUTATED                                          0
  PAPD4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PAPD4 MUTATED                                       3
  PAPD4 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAPD4 MUTATED                                                        4
  PAPD4 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PAPD4 MUTATED                                                   0
  PAPD4 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAPD4 MUTATED                                                                   2
  PAPD4 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PAPD4 MUTATED                                                    0
  PAPD4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PAPD4 MUTATED                                                  2
  PAPD4 WILD-TYPE                                               59
D133V9, multiclass
                                                                   clus
vv                                                                  PAPD4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  PAPD4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PAPD4 MUTATED    10   0   0   0
  PAPD4 WILD-TYPE 301  14  15  24
D133V10, multiclass
    clus
vv   PAPD4 MUTATED PAPD4 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PAPD4 MUTATED       5                         0
  PAPD4 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAPD4 MUTATED                                           0     3
  PAPD4 WILD-TYPE                                         1   240
D133V12, multiclass
                                           clus
vv                                          PAPD4 MUTATED PAPD4 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V13, binary
                 cls
clus                0   1
  PAPD4 MUTATED     0   8
  PAPD4 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAPD4 MUTATED      0    8
  PAPD4 WILD-TYPE    4  302
                        clus
vv                       PAPD4 MUTATED PAPD4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(134) Variable = DTX3 MUTATION ANALYSIS
D134V1, survival
                sevent
clus2              0   1
  DTX3 MUTATED     5   2
  DTX3 WILD-TYPE 225 137
  DTX3 MUTATED DTX3 WILD-TYPE 
             7            362 
  DTX3 MUTATED DTX3 WILD-TYPE 
             2            137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  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          14.12 
[1] "6.5 - 65.1 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D134V2, 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       2       15       37       30        35        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DTX3 MUTATED           0          0          0          0        0
  DTX3 WILD-TYPE         3         70         53         32       38
D134V3, multiclass
            clus
vv           DTX3 MUTATED DTX3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              3             37
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DTX3 MUTATED     0   4   2   1
  DTX3 WILD-TYPE  22  88 171  96
D134V4, multiclass
    clus
vv   DTX3 MUTATED DTX3 WILD-TYPE
  T1            0             22
  T2            4             88
  T3            2            171
  T4            1             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
  DTX3 MUTATED     6   0   0   0
  DTX3 WILD-TYPE 112 104  77  77
D134V5, multiclass
    clus
vv   DTX3 MUTATED DTX3 WILD-TYPE
  N0            6            112
  N1            0            104
  N2            0             77
  N3            0             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"
D134V6, binary
                cls
clus               0   1
  DTX3 MUTATED     7   0
  DTX3 WILD-TYPE 339  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  DTX3 MUTATED      7    0
  DTX3 WILD-TYPE  339   29
   clus
vv  DTX3 MUTATED DTX3 WILD-TYPE
  0            7            339
  1            0             29
[1] 2 2
[1] FALSE
D134V7, binary
                cls
clus               0   1
  DTX3 MUTATED     5   2
  DTX3 WILD-TYPE 140 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  DTX3 MUTATED      5    2
  DTX3 WILD-TYPE  140  246
        clus
vv       DTX3 MUTATED DTX3 WILD-TYPE
  FEMALE            5            140
  MALE              2            246
[1] 2 2
[1] FALSE
D134V8, binary
                cls
clus               0   1
  DTX3 MUTATED     5   1
  DTX3 WILD-TYPE 287  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  DTX3 MUTATED      5    1
  DTX3 WILD-TYPE  287   58
     clus
vv    DTX3 MUTATED DTX3 WILD-TYPE
  NO             5            287
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DTX3 MUTATED                                          0
  DTX3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DTX3 MUTATED                                       1
  DTX3 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DTX3 MUTATED                                                        3
  DTX3 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DTX3 MUTATED                                                   0
  DTX3 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DTX3 MUTATED                                                                   2
  DTX3 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DTX3 MUTATED                                                    0
  DTX3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DTX3 MUTATED                                                  1
  DTX3 WILD-TYPE                                               60
D134V9, multiclass
                                                                   clus
vv                                                                  DTX3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  DTX3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DTX3 MUTATED     6   0   0   1
  DTX3 WILD-TYPE 305  14  15  23
D134V10, multiclass
    clus
vv   DTX3 MUTATED DTX3 WILD-TYPE
  R0            6            305
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DTX3 MUTATED       1                         1
  DTX3 WILD-TYPE    86                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DTX3 MUTATED                                           0     4
  DTX3 WILD-TYPE                                         1   239
D134V12, multiclass
                                           clus
vv                                          DTX3 MUTATED DTX3 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V13, binary
                cls
clus               0   1
  DTX3 MUTATED     0   6
  DTX3 WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  DTX3 MUTATED      0    6
  DTX3 WILD-TYPE    4  304
                        clus
vv                       DTX3 MUTATED DTX3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(135) Variable = BTBD11 MUTATION ANALYSIS
D135V1, survival
                  sevent
clus2                0   1
  BTBD11 MUTATED    19   6
  BTBD11 WILD-TYPE 211 133
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              25              344 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               6              133 
$`BTBD11 MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 
       26.70        19.56        18.35         6.18         6.61        34.68 
TCGA-BR-6852 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-A4IY TCGA-BR-A4QM TCGA-CD-A4MG 
       44.94        25.05         1.12        12.89         5.13         6.58 
TCGA-CG-4305 TCGA-CG-4443 TCGA-CG-5721 TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-F1-A448 
       15.95        29.98         6.02         5.92        14.76        21.27 
TCGA-HU-8238 TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-MX-A5UJ TCGA-SW-A7EA 
        1.51        22.82        22.68        20.25        19.73        19.04 
TCGA-VQ-A8P2 
       38.14 

$`BTBD11 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        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 
          19.040           14.055 
[1] "1.1 - 44.9 (19.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D135V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BTBD11 MUTATED         0        1        2        1         5         5
  BTBD11 WILD-TYPE       2       14       38       29        32        47
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTBD11 MUTATED           1          3          1          3        1
  BTBD11 WILD-TYPE         2         67         52         29       37
D135V3, multiclass
            clus
vv           BTBD11 MUTATED BTBD11 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               5               32
  STAGE IIB               5               47
  STAGE III               1                2
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              3               29
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BTBD11 MUTATED     1   6  11   7
  BTBD11 WILD-TYPE  21  86 162  90
D135V4, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  T1              1               21
  T2              6               86
  T3             11              162
  T4              7               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
  BTBD11 MUTATED    10   7   5   3
  BTBD11 WILD-TYPE 108  97  72  74
D135V5, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  N0             10              108
  N1              7               97
  N2              5               72
  N3              3               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"
D135V6, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    26   0
  BTBD11 WILD-TYPE 320  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     26    0
  BTBD11 WILD-TYPE  320   29
   clus
vv  BTBD11 MUTATED BTBD11 WILD-TYPE
  0             26              320
  1              0               29
[1] 2 2
[1] FALSE
D135V7, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    13  13
  BTBD11 WILD-TYPE 132 235
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     13   13
  BTBD11 WILD-TYPE  132  235
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  FEMALE             13              132
  MALE               13              235
[1] 2 2
[1] FALSE
D135V8, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    21   3
  BTBD11 WILD-TYPE 271  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     21    3
  BTBD11 WILD-TYPE  271   56
     clus
vv    BTBD11 MUTATED BTBD11 WILD-TYPE
  NO              21              271
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BTBD11 MUTATED                                          0
  BTBD11 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BTBD11 MUTATED                                       6
  BTBD11 WILD-TYPE                                    64
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BTBD11 MUTATED                                                       10
  BTBD11 WILD-TYPE                                                    148
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BTBD11 MUTATED                                                   3
  BTBD11 WILD-TYPE                                                18
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BTBD11 MUTATED                                                                   2
  BTBD11 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BTBD11 MUTATED                                                    0
  BTBD11 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BTBD11 MUTATED                                                  5
  BTBD11 WILD-TYPE                                               56
D135V9, multiclass
                                                                   clus
vv                                                                  BTBD11 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               5
                                                                   clus
vv                                                                  BTBD11 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BTBD11 MUTATED    19   0   0   4
  BTBD11 WILD-TYPE 292  14  15  20
D135V10, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  R0             19              292
  R1              0               14
  R2              0               15
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  BTBD11 MUTATED       6                         0
  BTBD11 WILD-TYPE    81                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BTBD11 MUTATED                                           0    17
  BTBD11 WILD-TYPE                                         1   226
D135V12, multiclass
                                           clus
vv                                          BTBD11 MUTATED BTBD11 WILD-TYPE
  ASIAN                                                  6               81
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 17              226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V13, binary
                  cls
clus                 0   1
  BTBD11 MUTATED     1  21
  BTBD11 WILD-TYPE   3 289
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      1   21
  BTBD11 WILD-TYPE    3  289
                        clus
vv                       BTBD11 MUTATED BTBD11 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             21              289
[1] 2 2
[1] FALSE

Clustering(136) Variable = ART1 MUTATION ANALYSIS
D136V1, survival
                sevent
clus2              0   1
  ART1 MUTATED     6   1
  ART1 WILD-TYPE 224 138
  ART1 MUTATED ART1 WILD-TYPE 
             7            362 
  ART1 MUTATED ART1 WILD-TYPE 
             1            138 
$`ART1 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8078 TCGA-CD-5800 TCGA-F1-6874 
        6.61        34.68        30.90        29.59        13.15        14.47 
TCGA-HU-A4H8 
       14.07 

$`ART1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  ART1 MUTATED ART1 WILD-TYPE 
          6.61           0.00 
  ART1 MUTATED ART1 WILD-TYPE 
         34.68         122.30 
  ART1 MUTATED ART1 WILD-TYPE 
         14.47          14.22 
[1] "6.6 - 34.7 (14.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3.1"
D136V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ART1 MUTATED         0        0        3        1         1         1
  ART1 WILD-TYPE       2       15       37       29        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ART1 MUTATED           1          1          0          0        0
  ART1 WILD-TYPE         2         69         53         32       38
D136V3, multiclass
            clus
vv           ART1 MUTATED ART1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              3             37
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             1              2
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ART1 MUTATED     1   3   3   1
  ART1 WILD-TYPE  21  89 170  96
D136V4, multiclass
    clus
vv   ART1 MUTATED ART1 WILD-TYPE
  T1            1             21
  T2            3             89
  T3            3            170
  T4            1             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
  ART1 MUTATED     5   2   1   0
  ART1 WILD-TYPE 113 102  76  77
D136V5, multiclass
    clus
vv   ART1 MUTATED ART1 WILD-TYPE
  N0            5            113
  N1            2            102
  N2            1             76
  N3            0             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"
D136V6, binary
                cls
clus               0   1
  ART1 MUTATED     8   0
  ART1 WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART1 MUTATED      8    0
  ART1 WILD-TYPE  338   29
   clus
vv  ART1 MUTATED ART1 WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D136V7, binary
                cls
clus               0   1
  ART1 MUTATED     4   4
  ART1 WILD-TYPE 141 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART1 MUTATED      4    4
  ART1 WILD-TYPE  141  244
        clus
vv       ART1 MUTATED ART1 WILD-TYPE
  FEMALE            4            141
  MALE              4            244
[1] 2 2
[1] FALSE
D136V8, binary
                cls
clus               0   1
  ART1 MUTATED     7   0
  ART1 WILD-TYPE 285  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART1 MUTATED      7    0
  ART1 WILD-TYPE  285   59
     clus
vv    ART1 MUTATED ART1 WILD-TYPE
  NO             7            285
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ART1 MUTATED                                          0
  ART1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ART1 MUTATED                                       0
  ART1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ART1 MUTATED                                                        4
  ART1 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ART1 MUTATED                                                   0
  ART1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ART1 MUTATED                                                                   2
  ART1 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ART1 MUTATED                                                    1
  ART1 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ART1 MUTATED                                                  1
  ART1 WILD-TYPE                                               60
D136V9, multiclass
                                                                   clus
vv                                                                  ART1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  ART1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ART1 MUTATED     7   0   0   1
  ART1 WILD-TYPE 304  14  15  23
D136V10, multiclass
    clus
vv   ART1 MUTATED ART1 WILD-TYPE
  R0            7            304
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ART1 MUTATED       2                         0
  ART1 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ART1 MUTATED                                           0     5
  ART1 WILD-TYPE                                         1   238
D136V12, multiclass
                                           clus
vv                                          ART1 MUTATED ART1 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V13, binary
                cls
clus               0   1
  ART1 MUTATED     0   7
  ART1 WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART1 MUTATED      0    7
  ART1 WILD-TYPE    4  303
                        clus
vv                       ART1 MUTATED ART1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(137) Variable = BRD8 MUTATION ANALYSIS
D137V1, survival
                sevent
clus2              0   1
  BRD8 MUTATED    19  12
  BRD8 WILD-TYPE 211 127
  BRD8 MUTATED BRD8 WILD-TYPE 
            31            338 
  BRD8 MUTATED BRD8 WILD-TYPE 
            12            127 
$`BRD8 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6564 TCGA-BR-8077 TCGA-BR-8078 
       21.99        34.68        13.87        26.10         0.69        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8370 TCGA-BR-8591 TCGA-BR-A44U 
       32.25         8.05         2.20         3.32        28.14        13.87 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
       12.59        12.53        12.30        12.39        12.59        11.64 
TCGA-CG-5733 TCGA-D7-8572 TCGA-D7-8576 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8211 
       21.07        16.80        14.66        17.06        59.54        13.58 
TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        5.92         0.76        11.77        29.98         8.98         0.10 
TCGA-VQ-A8P2 
       38.14 

$`BRD8 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57         6.61        15.95        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         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-8080 
       29.56        33.21        37.25        14.43        11.44         9.60 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8360 
        0.56        29.42         2.66        19.96         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-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-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-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-8527 TCGA-CD-8528 TCGA-CD-8533 
       12.10        12.39        12.76         7.17        12.33        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-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        24.72        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-8210 
       11.38         3.48        19.53        14.07        22.29         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-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        22.82        21.07        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-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 

  BRD8 MUTATED BRD8 WILD-TYPE 
           0.1            0.0 
  BRD8 MUTATED BRD8 WILD-TYPE 
         59.54         122.30 
  BRD8 MUTATED BRD8 WILD-TYPE 
        13.580         14.615 
[1] "0.1 - 59.5 (13.6)"  "0.0 - 122.3 (14.6)"
[1] "hr=" "1.1"
D137V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRD8 MUTATED         0        2        1        2         4         6
  BRD8 WILD-TYPE       2       13       39       28        33        46
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BRD8 MUTATED           0          7          4          4        2
  BRD8 WILD-TYPE         3         63         49         28       36
D137V3, multiclass
            clus
vv           BRD8 MUTATED BRD8 WILD-TYPE
  STAGE I               0              2
  STAGE IA              2             13
  STAGE IB              1             39
  STAGE II              2             28
  STAGE IIA             4             33
  STAGE IIB             6             46
  STAGE III             0              3
  STAGE IIIA            7             63
  STAGE IIIB            4             49
  STAGE IIIC            4             28
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BRD8 MUTATED     2   5  13  12
  BRD8 WILD-TYPE  20  87 160  85
D137V4, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  T1            2             20
  T2            5             87
  T3           13            160
  T4           12             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
  BRD8 MUTATED    12  10   4   6
  BRD8 WILD-TYPE 106  94  73  71
D137V5, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  N0           12            106
  N1           10             94
  N2            4             73
  N3            6             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"
D137V6, binary
                cls
clus               0   1
  BRD8 MUTATED    28   2
  BRD8 WILD-TYPE 318  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED     28    2
  BRD8 WILD-TYPE  318   27
   clus
vv  BRD8 MUTATED BRD8 WILD-TYPE
  0           28            318
  1            2             27
[1] 2 2
[1] FALSE
D137V7, binary
                cls
clus               0   1
  BRD8 MUTATED    15  17
  BRD8 WILD-TYPE 130 231
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED     15   17
  BRD8 WILD-TYPE  130  231
        clus
vv       BRD8 MUTATED BRD8 WILD-TYPE
  FEMALE           15            130
  MALE             17            231
[1] 2 2
[1] FALSE
D137V8, binary
                cls
clus               0   1
  BRD8 MUTATED    23   7
  BRD8 WILD-TYPE 269  52
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED     23    7
  BRD8 WILD-TYPE  269   52
     clus
vv    BRD8 MUTATED BRD8 WILD-TYPE
  NO            23            269
  YES            7             52
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BRD8 MUTATED                                          0
  BRD8 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BRD8 MUTATED                                       6
  BRD8 WILD-TYPE                                    64
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BRD8 MUTATED                                                       12
  BRD8 WILD-TYPE                                                    146
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BRD8 MUTATED                                                   3
  BRD8 WILD-TYPE                                                18
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BRD8 MUTATED                                                                   5
  BRD8 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BRD8 MUTATED                                                    0
  BRD8 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BRD8 MUTATED                                                  6
  BRD8 WILD-TYPE                                               55
D137V9, multiclass
                                                                   clus
vv                                                                  BRD8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             6
                                                                   clus
vv                                                                  BRD8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BRD8 MUTATED    29   1   1   1
  BRD8 WILD-TYPE 282  13  14  23
D137V10, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  R0           29            282
  R1            1             13
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BRD8 MUTATED      12                         0
  BRD8 WILD-TYPE    75                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRD8 MUTATED                                           0    18
  BRD8 WILD-TYPE                                         1   225
D137V12, multiclass
                                           clus
vv                                          BRD8 MUTATED BRD8 WILD-TYPE
  ASIAN                                               12             75
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               18            225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V13, binary
                cls
clus               0   1
  BRD8 MUTATED     0  29
  BRD8 WILD-TYPE   4 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED      0   29
  BRD8 WILD-TYPE    4  281
                        clus
vv                       BRD8 MUTATED BRD8 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           29            281
[1] 2 2
[1] FALSE

Clustering(138) Variable = FOXN3 MUTATION ANALYSIS
D138V1, survival
                 sevent
clus2               0   1
  FOXN3 MUTATED     8   3
  FOXN3 WILD-TYPE 222 136
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             11             358 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
              3             136 
$`FOXN3 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8360 
       26.70         6.97        34.68        32.78        35.84         6.18 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-A4YV TCGA-HU-A4GT TCGA-MX-A5UJ 
        6.58         6.02         5.92         6.51        19.73 

$`FOXN3 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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 

  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           14.35 
[1] "5.9 - 35.8 (7.0)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D138V2, 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       2       15       39       30        32        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FOXN3 MUTATED           0          2          0          0        1
  FOXN3 WILD-TYPE         3         68         53         32       37
D138V3, multiclass
            clus
vv           FOXN3 MUTATED FOXN3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              5              32
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOXN3 MUTATED     0   1   8   3
  FOXN3 WILD-TYPE  22  91 165  94
D138V4, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             8             165
  T4             3              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
  FOXN3 MUTATED     8   3   1   0
  FOXN3 WILD-TYPE 110 101  76  77
D138V5, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  N0             8             110
  N1             3             101
  N2             1              76
  N3             0              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"
D138V6, binary
                 cls
clus                0   1
  FOXN3 MUTATED    12   0
  FOXN3 WILD-TYPE 334  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED     12    0
  FOXN3 WILD-TYPE  334   29
   clus
vv  FOXN3 MUTATED FOXN3 WILD-TYPE
  0            12             334
  1             0              29
[1] 2 2
[1] FALSE
D138V7, binary
                 cls
clus                0   1
  FOXN3 MUTATED     8   5
  FOXN3 WILD-TYPE 137 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED      8    5
  FOXN3 WILD-TYPE  137  243
        clus
vv       FOXN3 MUTATED FOXN3 WILD-TYPE
  FEMALE             8             137
  MALE               5             243
[1] 2 2
[1] FALSE
D138V8, binary
                 cls
clus                0   1
  FOXN3 MUTATED    12   0
  FOXN3 WILD-TYPE 280  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED     12    0
  FOXN3 WILD-TYPE  280   59
     clus
vv    FOXN3 MUTATED FOXN3 WILD-TYPE
  NO             12             280
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FOXN3 MUTATED                                          0
  FOXN3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FOXN3 MUTATED                                       2
  FOXN3 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FOXN3 MUTATED                                                        5
  FOXN3 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FOXN3 MUTATED                                                   0
  FOXN3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FOXN3 MUTATED                                                                   3
  FOXN3 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FOXN3 MUTATED                                                    0
  FOXN3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FOXN3 MUTATED                                                  3
  FOXN3 WILD-TYPE                                               58
D138V9, multiclass
                                                                   clus
vv                                                                  FOXN3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  FOXN3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FOXN3 MUTATED    10   0   0   2
  FOXN3 WILD-TYPE 301  14  15  22
D138V10, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FOXN3 MUTATED       2                         0
  FOXN3 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FOXN3 MUTATED                                           0    10
  FOXN3 WILD-TYPE                                         1   233
D138V12, multiclass
                                           clus
vv                                          FOXN3 MUTATED FOXN3 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V13, binary
                 cls
clus                0   1
  FOXN3 MUTATED     0  12
  FOXN3 WILD-TYPE   4 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED      0   12
  FOXN3 WILD-TYPE    4  298
                        clus
vv                       FOXN3 MUTATED FOXN3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(139) Variable = SPG20 MUTATION ANALYSIS
D139V1, survival
                 sevent
clus2               0   1
  SPG20 MUTATED    14   6
  SPG20 WILD-TYPE 216 133
  SPG20 MUTATED SPG20 WILD-TYPE 
             20             349 
  SPG20 MUTATED SPG20 WILD-TYPE 
              6             133 
$`SPG20 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 
       26.70         6.97        30.90         9.34         9.67        34.68 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-8591 
       13.68        19.33        29.59        32.25         1.12        28.14 
TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-5723 TCGA-HU-8602 TCGA-HU-A4G2 TCGA-HU-A4GT 
       16.14        15.95       105.07        22.32        24.30         6.51 
TCGA-HU-A4H3 TCGA-VQ-A8P2 
       29.00        38.14 

$`SPG20 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       17.29        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-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-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-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-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         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-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 

  SPG20 MUTATED SPG20 WILD-TYPE 
           1.12            0.00 
  SPG20 MUTATED SPG20 WILD-TYPE 
         105.07          122.30 
  SPG20 MUTATED SPG20 WILD-TYPE 
          23.31           14.04 
[1] "1.1 - 105.1 (23.3)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.7"
D139V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPG20 MUTATED         0        0        0        2         4         6
  SPG20 WILD-TYPE       2       15       40       28        33        46
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPG20 MUTATED           0          2          1          2        0
  SPG20 WILD-TYPE         3         68         52         30       38
D139V3, multiclass
            clus
vv           SPG20 MUTATED SPG20 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               2              28
  STAGE IIA              4              33
  STAGE IIB              6              46
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPG20 MUTATED     0   3   8   7
  SPG20 WILD-TYPE  22  89 165  90
D139V4, multiclass
    clus
vv   SPG20 MUTATED SPG20 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             8             165
  T4             7              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
  SPG20 MUTATED     8   8   0   3
  SPG20 WILD-TYPE 110  96  77  74
D139V5, multiclass
    clus
vv   SPG20 MUTATED SPG20 WILD-TYPE
  N0             8             110
  N1             8              96
  N2             0              77
  N3             3              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"
D139V6, binary
                 cls
clus                0   1
  SPG20 MUTATED    21   0
  SPG20 WILD-TYPE 325  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG20 MUTATED     21    0
  SPG20 WILD-TYPE  325   29
   clus
vv  SPG20 MUTATED SPG20 WILD-TYPE
  0            21             325
  1             0              29
[1] 2 2
[1] FALSE
D139V7, binary
                 cls
clus                0   1
  SPG20 MUTATED    13   9
  SPG20 WILD-TYPE 132 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG20 MUTATED     13    9
  SPG20 WILD-TYPE  132  239
        clus
vv       SPG20 MUTATED SPG20 WILD-TYPE
  FEMALE            13             132
  MALE               9             239
[1] 2 2
[1] FALSE
D139V8, binary
                 cls
clus                0   1
  SPG20 MUTATED    18   1
  SPG20 WILD-TYPE 274  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG20 MUTATED     18    1
  SPG20 WILD-TYPE  274   58
     clus
vv    SPG20 MUTATED SPG20 WILD-TYPE
  NO             18             274
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SPG20 MUTATED                                          0
  SPG20 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SPG20 MUTATED                                       4
  SPG20 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPG20 MUTATED                                                       16
  SPG20 WILD-TYPE                                                    142
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SPG20 MUTATED                                                   1
  SPG20 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPG20 MUTATED                                                                   0
  SPG20 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SPG20 MUTATED                                                    0
  SPG20 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SPG20 MUTATED                                                  1
  SPG20 WILD-TYPE                                               60
D139V9, multiclass
                                                                   clus
vv                                                                  SPG20 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  SPG20 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SPG20 MUTATED    16   0   0   6
  SPG20 WILD-TYPE 295  14  15  18
D139V10, multiclass
    clus
vv   SPG20 MUTATED SPG20 WILD-TYPE
  R0            16             295
  R1             0              14
  R2             0              15
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SPG20 MUTATED       4                         0
  SPG20 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPG20 MUTATED                                           0    16
  SPG20 WILD-TYPE                                         1   227
D139V12, multiclass
                                           clus
vv                                          SPG20 MUTATED SPG20 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                16             227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V13, binary
                 cls
clus                0   1
  SPG20 MUTATED     0  19
  SPG20 WILD-TYPE   4 291
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPG20 MUTATED      0   19
  SPG20 WILD-TYPE    4  291
                        clus
vv                       SPG20 MUTATED SPG20 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            19             291
[1] 2 2
[1] FALSE

Clustering(140) Variable = WNK4 MUTATION ANALYSIS
D140V1, survival
                sevent
clus2              0   1
  WNK4 MUTATED    12   8
  WNK4 WILD-TYPE 218 131
  WNK4 MUTATED WNK4 WILD-TYPE 
            20            349 
  WNK4 MUTATED WNK4 WILD-TYPE 
             8            131 
$`WNK4 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-7723 TCGA-BR-8487 
       21.99         6.97        34.68        35.84        28.73         1.12 
TCGA-BR-A4QL TCGA-CD-8527 TCGA-CD-8533 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
       16.14         7.17        15.39         6.02       105.07        28.96 
TCGA-D7-A4YV TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN 
        5.92        77.29        30.51        22.32        22.68        29.98 
TCGA-HU-A4GQ TCGA-HU-A4H3 
        0.10        29.00 

$`WNK4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-5730 
        0.99         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-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-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-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-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-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 

  WNK4 MUTATED WNK4 WILD-TYPE 
           0.1            0.0 
  WNK4 MUTATED WNK4 WILD-TYPE 
        105.07         122.30 
  WNK4 MUTATED WNK4 WILD-TYPE 
         22.50          14.04 
[1] "0.1 - 105.1 (22.5)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.2"
D140V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WNK4 MUTATED         0        1        1        4         3         4
  WNK4 WILD-TYPE       2       14       39       26        34        48
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WNK4 MUTATED           0          2          2          3        2
  WNK4 WILD-TYPE         3         68         51         29       36
D140V3, multiclass
            clus
vv           WNK4 MUTATED WNK4 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              4             26
  STAGE IIA             3             34
  STAGE IIB             4             48
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            2             51
  STAGE IIIC            3             29
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WNK4 MUTATED     1   5   9   8
  WNK4 WILD-TYPE  21  87 164  89
D140V4, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  T1            1             21
  T2            5             87
  T3            9            164
  T4            8             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
  WNK4 MUTATED     8   9   1   4
  WNK4 WILD-TYPE 110  95  76  73
D140V5, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  N0            8            110
  N1            9             95
  N2            1             76
  N3            4             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"
D140V6, binary
                cls
clus               0   1
  WNK4 MUTATED    21   1
  WNK4 WILD-TYPE 325  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED     21    1
  WNK4 WILD-TYPE  325   28
   clus
vv  WNK4 MUTATED WNK4 WILD-TYPE
  0           21            325
  1            1             28
[1] 2 2
[1] FALSE
D140V7, binary
                cls
clus               0   1
  WNK4 MUTATED    14  10
  WNK4 WILD-TYPE 131 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED     14   10
  WNK4 WILD-TYPE  131  238
        clus
vv       WNK4 MUTATED WNK4 WILD-TYPE
  FEMALE           14            131
  MALE             10            238
[1] 2 2
[1] FALSE
D140V8, binary
                cls
clus               0   1
  WNK4 MUTATED    17   2
  WNK4 WILD-TYPE 275  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED     17    2
  WNK4 WILD-TYPE  275   57
     clus
vv    WNK4 MUTATED WNK4 WILD-TYPE
  NO            17            275
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  WNK4 MUTATED                                          0
  WNK4 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  WNK4 MUTATED                                       3
  WNK4 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WNK4 MUTATED                                                       11
  WNK4 WILD-TYPE                                                    147
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  WNK4 MUTATED                                                   2
  WNK4 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WNK4 MUTATED                                                                   5
  WNK4 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  WNK4 MUTATED                                                    0
  WNK4 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  WNK4 MUTATED                                                  3
  WNK4 WILD-TYPE                                               58
D140V9, multiclass
                                                                   clus
vv                                                                  WNK4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  WNK4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WNK4 MUTATED    17   1   1   4
  WNK4 WILD-TYPE 294  13  14  20
D140V10, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  R0           17            294
  R1            1             13
  R2            1             14
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  WNK4 MUTATED       7                         0
  WNK4 WILD-TYPE    80                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WNK4 MUTATED                                           0    11
  WNK4 WILD-TYPE                                         1   232
D140V12, multiclass
                                           clus
vv                                          WNK4 MUTATED WNK4 WILD-TYPE
  ASIAN                                                7             80
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V13, binary
                cls
clus               0   1
  WNK4 MUTATED     0  18
  WNK4 WILD-TYPE   4 292
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED      0   18
  WNK4 WILD-TYPE    4  292
                        clus
vv                       WNK4 MUTATED WNK4 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           18            292
[1] 2 2
[1] FALSE

Clustering(141) Variable = CBLL1 MUTATION ANALYSIS
D141V1, survival
                 sevent
clus2               0   1
  CBLL1 MUTATED     3   4
  CBLL1 WILD-TYPE 227 135
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              7             362 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              4             135 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  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           14.22 
[1] "2.7 - 36.2 (15.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D141V2, 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       1       14       40       29        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CBLL1 MUTATED           0          1          2          0        1
  CBLL1 WILD-TYPE         3         69         51         32       37
D141V3, multiclass
            clus
vv           CBLL1 MUTATED CBLL1 WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CBLL1 MUTATED     2   1   2   2
  CBLL1 WILD-TYPE  20  91 171  95
D141V4, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  T1             2              20
  T2             1              91
  T3             2             171
  T4             2              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
  CBLL1 MUTATED     1   4   1   2
  CBLL1 WILD-TYPE 117 100  76  75
D141V5, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  N0             1             117
  N1             4             100
  N2             1              76
  N3             2              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"
D141V6, binary
                 cls
clus                0   1
  CBLL1 MUTATED     6   1
  CBLL1 WILD-TYPE 340  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      6    1
  CBLL1 WILD-TYPE  340   28
   clus
vv  CBLL1 MUTATED CBLL1 WILD-TYPE
  0             6             340
  1             1              28
[1] 2 2
[1] FALSE
D141V7, binary
                 cls
clus                0   1
  CBLL1 MUTATED     2   6
  CBLL1 WILD-TYPE 143 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      2    6
  CBLL1 WILD-TYPE  143  242
        clus
vv       CBLL1 MUTATED CBLL1 WILD-TYPE
  FEMALE             2             143
  MALE               6             242
[1] 2 2
[1] FALSE
D141V8, binary
                 cls
clus                0   1
  CBLL1 MUTATED     8   0
  CBLL1 WILD-TYPE 284  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      8    0
  CBLL1 WILD-TYPE  284   59
     clus
vv    CBLL1 MUTATED CBLL1 WILD-TYPE
  NO              8             284
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CBLL1 MUTATED                                          0
  CBLL1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CBLL1 MUTATED                                       0
  CBLL1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CBLL1 MUTATED                                                        3
  CBLL1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CBLL1 MUTATED                                                   0
  CBLL1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CBLL1 MUTATED                                                                   1
  CBLL1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CBLL1 MUTATED                                                    1
  CBLL1 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CBLL1 MUTATED                                                  3
  CBLL1 WILD-TYPE                                               58
D141V9, multiclass
                                                                   clus
vv                                                                  CBLL1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  CBLL1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CBLL1 MUTATED     7   0   0   1
  CBLL1 WILD-TYPE 304  14  15  23
D141V10, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CBLL1 MUTATED       1                         1
  CBLL1 WILD-TYPE    86                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CBLL1 MUTATED                                           0     5
  CBLL1 WILD-TYPE                                         1   238
D141V12, multiclass
                                           clus
vv                                          CBLL1 MUTATED CBLL1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V13, binary
                 cls
clus                0   1
  CBLL1 MUTATED     0   7
  CBLL1 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      0    7
  CBLL1 WILD-TYPE    4  303
                        clus
vv                       CBLL1 MUTATED CBLL1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(142) Variable = TTF1 MUTATION ANALYSIS
D142V1, survival
                sevent
clus2              0   1
  TTF1 MUTATED    11   3
  TTF1 WILD-TYPE 219 136
  TTF1 MUTATED TTF1 WILD-TYPE 
            14            355 
  TTF1 MUTATED TTF1 WILD-TYPE 
             3            136 
$`TTF1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7196 TCGA-BR-7707 TCGA-BR-8360 
        6.97        30.90        34.68        21.90        35.84         6.18 
TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-CG-4305 
        4.31        25.05         1.12        27.12        31.96        15.95 
TCGA-D7-6822 TCGA-HU-A4GH 
       12.33        11.77 

$`TTF1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-D7-8570 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-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-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 

  TTF1 MUTATED TTF1 WILD-TYPE 
          1.12           0.00 
  TTF1 MUTATED TTF1 WILD-TYPE 
         35.84         122.30 
  TTF1 MUTATED TTF1 WILD-TYPE 
        18.925         14.170 
[1] "1.1 - 35.8 (18.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.9"
D142V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TTF1 MUTATED         0        1        3        1         3         0
  TTF1 WILD-TYPE       2       14       37       29        34        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TTF1 MUTATED           0          1          1          1        3
  TTF1 WILD-TYPE         3         69         52         31       35
D142V3, multiclass
            clus
vv           TTF1 MUTATED TTF1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              3             37
  STAGE II              1             29
  STAGE IIA             3             34
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TTF1 MUTATED     1   5   6   4
  TTF1 WILD-TYPE  21  87 167  93
D142V4, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  T1            1             21
  T2            5             87
  T3            6            167
  T4            4             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
  TTF1 MUTATED     7   3   2   2
  TTF1 WILD-TYPE 111 101  75  75
D142V5, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  N0            7            111
  N1            3            101
  N2            2             75
  N3            2             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"
D142V6, binary
                cls
clus               0   1
  TTF1 MUTATED    12   2
  TTF1 WILD-TYPE 334  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED     12    2
  TTF1 WILD-TYPE  334   27
   clus
vv  TTF1 MUTATED TTF1 WILD-TYPE
  0           12            334
  1            2             27
[1] 2 2
[1] FALSE
D142V7, binary
                cls
clus               0   1
  TTF1 MUTATED     7   9
  TTF1 WILD-TYPE 138 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      7    9
  TTF1 WILD-TYPE  138  239
        clus
vv       TTF1 MUTATED TTF1 WILD-TYPE
  FEMALE            7            138
  MALE              9            239
[1] 2 2
[1] FALSE
D142V8, binary
                cls
clus               0   1
  TTF1 MUTATED    14   0
  TTF1 WILD-TYPE 278  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED     14    0
  TTF1 WILD-TYPE  278   59
     clus
vv    TTF1 MUTATED TTF1 WILD-TYPE
  NO            14            278
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TTF1 MUTATED                                          0
  TTF1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TTF1 MUTATED                                       0
  TTF1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TTF1 MUTATED                                                       12
  TTF1 WILD-TYPE                                                    146
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TTF1 MUTATED                                                   0
  TTF1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TTF1 MUTATED                                                                   1
  TTF1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TTF1 MUTATED                                                    0
  TTF1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TTF1 MUTATED                                                  3
  TTF1 WILD-TYPE                                               58
D142V9, multiclass
                                                                   clus
vv                                                                  TTF1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  TTF1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TTF1 MUTATED    12   0   0   4
  TTF1 WILD-TYPE 299  14  15  20
D142V10, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  R0           12            299
  R1            0             14
  R2            0             15
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TTF1 MUTATED       2                         0
  TTF1 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TTF1 MUTATED                                           0    13
  TTF1 WILD-TYPE                                         1   230
D142V12, multiclass
                                           clus
vv                                          TTF1 MUTATED TTF1 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V13, binary
                cls
clus               0   1
  TTF1 MUTATED     0  15
  TTF1 WILD-TYPE   4 295
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      0   15
  TTF1 WILD-TYPE    4  295
                        clus
vv                       TTF1 MUTATED TTF1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           15            295
[1] 2 2
[1] FALSE

Clustering(143) Variable = SCLT1 MUTATION ANALYSIS
D143V1, survival
                 sevent
clus2               0   1
  SCLT1 MUTATED     9   6
  SCLT1 WILD-TYPE 221 133
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             15             354 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
              6             133 
$`SCLT1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-A4QL 
        6.97        30.90        34.68        25.18         1.12        16.14 
TCGA-CD-A48A TCGA-CG-4306 TCGA-CG-5728 TCGA-D7-A6EY TCGA-HF-7132 TCGA-HU-8602 
       12.43         1.02        65.10        11.44        77.29        22.32 
TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-HU-A4GX 
       22.68         6.58        20.25 

$`SCLT1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8485 TCGA-BR-8486 
        7.36        25.05         3.72         5.39         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-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-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-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-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 

  SCLT1 MUTATED SCLT1 WILD-TYPE 
           1.02            0.00 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
          77.29          122.30 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
          20.25           14.12 
[1] "1.0 - 77.3 (20.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D143V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCLT1 MUTATED         0        0        2        1         3         3
  SCLT1 WILD-TYPE       2       15       38       29        34        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SCLT1 MUTATED           0          2          2          1        2
  SCLT1 WILD-TYPE         3         68         51         31       36
D143V3, multiclass
            clus
vv           SCLT1 MUTATED SCLT1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SCLT1 MUTATED     0   4   9   4
  SCLT1 WILD-TYPE  22  88 164  93
D143V4, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  T1             0              22
  T2             4              88
  T3             9             164
  T4             4              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
  SCLT1 MUTATED     6   5   3   2
  SCLT1 WILD-TYPE 112  99  74  75
D143V5, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  N0             6             112
  N1             5              99
  N2             3              74
  N3             2              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"
D143V6, binary
                 cls
clus                0   1
  SCLT1 MUTATED    15   1
  SCLT1 WILD-TYPE 331  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     15    1
  SCLT1 WILD-TYPE  331   28
   clus
vv  SCLT1 MUTATED SCLT1 WILD-TYPE
  0            15             331
  1             1              28
[1] 2 2
[1] FALSE
D143V7, binary
                 cls
clus                0   1
  SCLT1 MUTATED    10   7
  SCLT1 WILD-TYPE 135 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     10    7
  SCLT1 WILD-TYPE  135  241
        clus
vv       SCLT1 MUTATED SCLT1 WILD-TYPE
  FEMALE            10             135
  MALE               7             241
[1] 2 2
[1] FALSE
D143V8, binary
                 cls
clus                0   1
  SCLT1 MUTATED    11   2
  SCLT1 WILD-TYPE 281  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     11    2
  SCLT1 WILD-TYPE  281   57
     clus
vv    SCLT1 MUTATED SCLT1 WILD-TYPE
  NO             11             281
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SCLT1 MUTATED                                          0
  SCLT1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SCLT1 MUTATED                                       4
  SCLT1 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SCLT1 MUTATED                                                        9
  SCLT1 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SCLT1 MUTATED                                                   1
  SCLT1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SCLT1 MUTATED                                                                   2
  SCLT1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SCLT1 MUTATED                                                    0
  SCLT1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SCLT1 MUTATED                                                  1
  SCLT1 WILD-TYPE                                               60
D143V9, multiclass
                                                                   clus
vv                                                                  SCLT1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  SCLT1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SCLT1 MUTATED    11   0   1   3
  SCLT1 WILD-TYPE 300  14  14  21
D143V10, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SCLT1 MUTATED       5                         0
  SCLT1 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SCLT1 MUTATED                                           0     8
  SCLT1 WILD-TYPE                                         1   235
D143V12, multiclass
                                           clus
vv                                          SCLT1 MUTATED SCLT1 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V13, binary
                 cls
clus                0   1
  SCLT1 MUTATED     0  13
  SCLT1 WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED      0   13
  SCLT1 WILD-TYPE    4  297
                        clus
vv                       SCLT1 MUTATED SCLT1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(144) Variable = PALB2 MUTATION ANALYSIS
D144V1, survival
                 sevent
clus2               0   1
  PALB2 MUTATED     7   4
  PALB2 WILD-TYPE 223 135
  PALB2 MUTATED PALB2 WILD-TYPE 
             11             358 
  PALB2 MUTATED PALB2 WILD-TYPE 
              4             135 
$`PALB2 MUTATED`
TCGA-CG-4460 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8361 TCGA-BR-8591 TCGA-BR-A4QL 
       21.99        32.78        44.94        31.10        28.14        16.14 
TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-A4GQ TCGA-VQ-A8P2 TCGA-VQ-AA64 
        6.02       105.07         0.10        38.14        18.41 

$`PALB2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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 

  PALB2 MUTATED PALB2 WILD-TYPE 
            0.1             0.0 
  PALB2 MUTATED PALB2 WILD-TYPE 
         105.07          122.30 
  PALB2 MUTATED PALB2 WILD-TYPE 
         28.140          14.055 
[1] "0.1 - 105.1 (28.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D144V2, 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       2       15       40       29        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PALB2 MUTATED           0          1          2          3        2
  PALB2 WILD-TYPE         3         69         51         29       36
D144V3, multiclass
            clus
vv           PALB2 MUTATED PALB2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PALB2 MUTATED     0   1   4   6
  PALB2 WILD-TYPE  22  91 169  91
D144V4, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             4             169
  T4             6              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
  PALB2 MUTATED     2   4   3   2
  PALB2 WILD-TYPE 116 100  74  75
D144V5, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  N0             2             116
  N1             4             100
  N2             3              74
  N3             2              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"
D144V6, binary
                 cls
clus                0   1
  PALB2 MUTATED    10   1
  PALB2 WILD-TYPE 336  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED     10    1
  PALB2 WILD-TYPE  336   28
   clus
vv  PALB2 MUTATED PALB2 WILD-TYPE
  0            10             336
  1             1              28
[1] 2 2
[1] FALSE
D144V7, binary
                 cls
clus                0   1
  PALB2 MUTATED     5   6
  PALB2 WILD-TYPE 140 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED      5    6
  PALB2 WILD-TYPE  140  242
        clus
vv       PALB2 MUTATED PALB2 WILD-TYPE
  FEMALE             5             140
  MALE               6             242
[1] 2 2
[1] FALSE
D144V8, binary
                 cls
clus                0   1
  PALB2 MUTATED     9   2
  PALB2 WILD-TYPE 283  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED      9    2
  PALB2 WILD-TYPE  283   57
     clus
vv    PALB2 MUTATED PALB2 WILD-TYPE
  NO              9             283
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PALB2 MUTATED                                          0
  PALB2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PALB2 MUTATED                                       0
  PALB2 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PALB2 MUTATED                                                        6
  PALB2 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PALB2 MUTATED                                                   1
  PALB2 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PALB2 MUTATED                                                                   3
  PALB2 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PALB2 MUTATED                                                    0
  PALB2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PALB2 MUTATED                                                  1
  PALB2 WILD-TYPE                                               60
D144V9, multiclass
                                                                   clus
vv                                                                  PALB2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  PALB2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PALB2 MUTATED    10   0   1   0
  PALB2 WILD-TYPE 301  14  14  24
D144V10, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PALB2 MUTATED       1                         0
  PALB2 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PALB2 MUTATED                                           0     7
  PALB2 WILD-TYPE                                         1   236
D144V12, multiclass
                                           clus
vv                                          PALB2 MUTATED PALB2 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V13, binary
                 cls
clus                0   1
  PALB2 MUTATED     0   6
  PALB2 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED      0    6
  PALB2 WILD-TYPE    4  304
                        clus
vv                       PALB2 MUTATED PALB2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(145) Variable = ABCC4 MUTATION ANALYSIS
D145V1, survival
                 sevent
clus2               0   1
  ABCC4 MUTATED    12   5
  ABCC4 WILD-TYPE 218 134
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             17             352 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
              5             134 
$`ABCC4 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15         9.86        26.70        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-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-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-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-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-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-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-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5577 
       12.03        15.02         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-D7-6818 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-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 

  ABCC4 MUTATED ABCC4 WILD-TYPE 
           0.95            0.00 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
         105.07          122.30 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
          13.78           14.37 
[1] "0.9 - 105.1 (13.8)" "0.0 - 122.3 (14.4)"
[1] "hr=" "1.3"
D145V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCC4 MUTATED         0        1        2        2         3         2
  ABCC4 WILD-TYPE       2       14       38       28        34        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABCC4 MUTATED           1          2          1          0        4
  ABCC4 WILD-TYPE         2         68         52         32       34
D145V3, multiclass
            clus
vv           ABCC4 MUTATED ABCC4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               2              28
  STAGE IIA              3              34
  STAGE IIB              2              50
  STAGE III              1               2
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCC4 MUTATED     1   4   7   7
  ABCC4 WILD-TYPE  21  88 166  90
D145V4, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             7             166
  T4             7              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
  ABCC4 MUTATED     8   5   2   2
  ABCC4 WILD-TYPE 110  99  75  75
D145V5, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  N0             8             110
  N1             5              99
  N2             2              75
  N3             2              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"
D145V6, binary
                 cls
clus                0   1
  ABCC4 MUTATED    15   3
  ABCC4 WILD-TYPE 331  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     15    3
  ABCC4 WILD-TYPE  331   26
   clus
vv  ABCC4 MUTATED ABCC4 WILD-TYPE
  0            15             331
  1             3              26
[1] 2 2
[1] FALSE
D145V7, binary
                 cls
clus                0   1
  ABCC4 MUTATED     8  11
  ABCC4 WILD-TYPE 137 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED      8   11
  ABCC4 WILD-TYPE  137  237
        clus
vv       ABCC4 MUTATED ABCC4 WILD-TYPE
  FEMALE             8             137
  MALE              11             237
[1] 2 2
[1] FALSE
D145V8, binary
                 cls
clus                0   1
  ABCC4 MUTATED    11   1
  ABCC4 WILD-TYPE 281  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     11    1
  ABCC4 WILD-TYPE  281   58
     clus
vv    ABCC4 MUTATED ABCC4 WILD-TYPE
  NO             11             281
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ABCC4 MUTATED                                          0
  ABCC4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ABCC4 MUTATED                                       1
  ABCC4 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCC4 MUTATED                                                       11
  ABCC4 WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ABCC4 MUTATED                                                   0
  ABCC4 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCC4 MUTATED                                                                   6
  ABCC4 WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ABCC4 MUTATED                                                    0
  ABCC4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ABCC4 MUTATED                                                  1
  ABCC4 WILD-TYPE                                               60
D145V9, multiclass
                                                                   clus
vv                                                                  ABCC4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  ABCC4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCC4 MUTATED    14   0   2   2
  ABCC4 WILD-TYPE 297  14  13  22
D145V10, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  R0            14             297
  R1             0              14
  R2             2              13
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCC4 MUTATED       1                         0
  ABCC4 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCC4 MUTATED                                           0    10
  ABCC4 WILD-TYPE                                         1   233
D145V12, multiclass
                                           clus
vv                                          ABCC4 MUTATED ABCC4 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V13, binary
                 cls
clus                0   1
  ABCC4 MUTATED     0  11
  ABCC4 WILD-TYPE   4 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED      0   11
  ABCC4 WILD-TYPE    4  299
                        clus
vv                       ABCC4 MUTATED ABCC4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(146) Variable = EAF2 MUTATION ANALYSIS
D146V1, survival
                sevent
clus2              0   1
  EAF2 MUTATED     5   3
  EAF2 WILD-TYPE 225 136
  EAF2 MUTATED EAF2 WILD-TYPE 
             8            361 
  EAF2 MUTATED EAF2 WILD-TYPE 
             3            136 
$`EAF2 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4305 TCGA-D7-A6EY 
       21.99        34.68        28.14        16.14        15.95        11.44 
TCGA-HU-A4G9 TCGA-HU-A4GN 
       24.20        29.98 

$`EAF2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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 

  EAF2 MUTATED EAF2 WILD-TYPE 
         11.44           0.00 
  EAF2 MUTATED EAF2 WILD-TYPE 
         34.68         122.30 
  EAF2 MUTATED EAF2 WILD-TYPE 
        23.095         14.070 
[1] "11.4 - 34.7 (23.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D146V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EAF2 MUTATED         0        1        0        1         2         0
  EAF2 WILD-TYPE       2       14       40       29        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EAF2 MUTATED           0          0          2          1        2
  EAF2 WILD-TYPE         3         70         51         31       36
D146V3, multiclass
            clus
vv           EAF2 MUTATED EAF2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            2             51
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EAF2 MUTATED     1   2   3   3
  EAF2 WILD-TYPE  21  90 170  94
D146V4, multiclass
    clus
vv   EAF2 MUTATED EAF2 WILD-TYPE
  T1            1             21
  T2            2             90
  T3            3            170
  T4            3             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
  EAF2 MUTATED     2   3   1   3
  EAF2 WILD-TYPE 116 101  76  74
D146V5, multiclass
    clus
vv   EAF2 MUTATED EAF2 WILD-TYPE
  N0            2            116
  N1            3            101
  N2            1             76
  N3            3             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"
D146V6, binary
                cls
clus               0   1
  EAF2 MUTATED     8   1
  EAF2 WILD-TYPE 338  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      8    1
  EAF2 WILD-TYPE  338   28
   clus
vv  EAF2 MUTATED EAF2 WILD-TYPE
  0            8            338
  1            1             28
[1] 2 2
[1] FALSE
D146V7, binary
                cls
clus               0   1
  EAF2 MUTATED     6   3
  EAF2 WILD-TYPE 139 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      6    3
  EAF2 WILD-TYPE  139  245
        clus
vv       EAF2 MUTATED EAF2 WILD-TYPE
  FEMALE            6            139
  MALE              3            245
[1] 2 2
[1] FALSE
D146V8, binary
                cls
clus               0   1
  EAF2 MUTATED     8   0
  EAF2 WILD-TYPE 284  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      8    0
  EAF2 WILD-TYPE  284   59
     clus
vv    EAF2 MUTATED EAF2 WILD-TYPE
  NO             8            284
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EAF2 MUTATED                                          0
  EAF2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EAF2 MUTATED                                       0
  EAF2 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EAF2 MUTATED                                                        5
  EAF2 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EAF2 MUTATED                                                   0
  EAF2 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EAF2 MUTATED                                                                   1
  EAF2 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EAF2 MUTATED                                                    0
  EAF2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EAF2 MUTATED                                                  3
  EAF2 WILD-TYPE                                               58
D146V9, multiclass
                                                                   clus
vv                                                                  EAF2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  EAF2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EAF2 MUTATED     7   0   1   1
  EAF2 WILD-TYPE 304  14  14  23
D146V10, multiclass
    clus
vv   EAF2 MUTATED EAF2 WILD-TYPE
  R0            7            304
  R1            0             14
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  EAF2 MUTATED       2                         0
  EAF2 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EAF2 MUTATED                                           0     5
  EAF2 WILD-TYPE                                         1   238
D146V12, multiclass
                                           clus
vv                                          EAF2 MUTATED EAF2 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V13, binary
                cls
clus               0   1
  EAF2 MUTATED     0   7
  EAF2 WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      0    7
  EAF2 WILD-TYPE    4  303
                        clus
vv                       EAF2 MUTATED EAF2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(147) Variable = FAAH MUTATION ANALYSIS
D147V1, survival
                sevent
clus2              0   1
  FAAH MUTATED     2   3
  FAAH WILD-TYPE 228 136
  FAAH MUTATED FAAH WILD-TYPE 
             5            364 
  FAAH MUTATED FAAH WILD-TYPE 
             3            136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  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          14.12 
[1] "9.3 - 32.2 (16.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D147V2, 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       2       15       40       30        37        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAAH MUTATED           1          0          1          1        0
  FAAH WILD-TYPE         2         70         52         31       38
D147V3, multiclass
            clus
vv           FAAH MUTATED FAAH WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             1             51
  STAGE III             1              2
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FAAH MUTATED     0   0   1   3
  FAAH WILD-TYPE  22  92 172  94
D147V4, multiclass
    clus
vv   FAAH MUTATED FAAH WILD-TYPE
  T1            0             22
  T2            0             92
  T3            1            172
  T4            3             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
  FAAH MUTATED     1   2   0   2
  FAAH WILD-TYPE 117 102  77  75
D147V5, multiclass
    clus
vv   FAAH MUTATED FAAH WILD-TYPE
  N0            1            117
  N1            2            102
  N2            0             77
  N3            2             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"
D147V6, binary
                cls
clus               0   1
  FAAH MUTATED     5   0
  FAAH WILD-TYPE 341  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAAH MUTATED      5    0
  FAAH WILD-TYPE  341   29
   clus
vv  FAAH MUTATED FAAH WILD-TYPE
  0            5            341
  1            0             29
[1] 2 2
[1] FALSE
D147V7, binary
                cls
clus               0   1
  FAAH MUTATED     2   3
  FAAH WILD-TYPE 143 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAAH MUTATED      2    3
  FAAH WILD-TYPE  143  245
        clus
vv       FAAH MUTATED FAAH WILD-TYPE
  FEMALE            2            143
  MALE              3            245
[1] 2 2
[1] FALSE
D147V8, binary
                cls
clus               0   1
  FAAH MUTATED     5   0
  FAAH WILD-TYPE 287  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAAH MUTATED      5    0
  FAAH WILD-TYPE  287   59
     clus
vv    FAAH MUTATED FAAH WILD-TYPE
  NO             5            287
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAAH MUTATED                                          0
  FAAH WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAAH MUTATED                                       1
  FAAH WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAAH MUTATED                                                        3
  FAAH WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAAH MUTATED                                                   0
  FAAH WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAAH MUTATED                                                                   1
  FAAH WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAAH MUTATED                                                    0
  FAAH WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAAH MUTATED                                                  0
  FAAH WILD-TYPE                                               61
D147V9, multiclass
                                                                   clus
vv                                                                  FAAH MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  FAAH WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FAAH MUTATED     3   0   0   1
  FAAH WILD-TYPE 308  14  15  23
D147V10, multiclass
    clus
vv   FAAH MUTATED FAAH WILD-TYPE
  R0            3            308
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FAAH MUTATED       0                         0
  FAAH WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAAH MUTATED                                           0     5
  FAAH WILD-TYPE                                         1   238
D147V12, multiclass
                                           clus
vv                                          FAAH MUTATED FAAH WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V13, binary
                cls
clus               0   1
  FAAH MUTATED     0   5
  FAAH WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAAH MUTATED      0    5
  FAAH WILD-TYPE    4  305
                        clus
vv                       FAAH MUTATED FAAH WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(148) Variable = BTBD7 MUTATION ANALYSIS
D148V1, survival
                 sevent
clus2               0   1
  BTBD7 MUTATED    13   6
  BTBD7 WILD-TYPE 217 133
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             19             350 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
              6             133 
$`BTBD7 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8372 
        6.97        30.90        34.68        35.84        29.59        31.27 
TCGA-CD-A4MI TCGA-CG-4469 TCGA-CG-5726 TCGA-F1-6874 TCGA-HF-7132 TCGA-HJ-7597 
       11.77         7.07        28.96        14.47        77.29        26.47 
TCGA-HU-8602 TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-MX-A5UJ TCGA-SW-A7EA 
       22.32         6.58        20.25        23.84        19.73        19.04 
TCGA-VQ-A8P2 
       38.14 

$`BTBD7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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-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 

  BTBD7 MUTATED BTBD7 WILD-TYPE 
           6.58            0.00 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
          77.29          122.30 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
         23.840          14.025 
[1] "6.6 - 77.3 (23.8)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.7"
D148V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BTBD7 MUTATED         0        1        4        1         1         4
  BTBD7 WILD-TYPE       2       14       36       29        36        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTBD7 MUTATED           0          5          0          2        1
  BTBD7 WILD-TYPE         3         65         53         30       37
D148V3, multiclass
            clus
vv           BTBD7 MUTATED BTBD7 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               4              36
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             5              65
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BTBD7 MUTATED     1   7   6   6
  BTBD7 WILD-TYPE  21  85 167  91
D148V4, multiclass
    clus
vv   BTBD7 MUTATED BTBD7 WILD-TYPE
  T1             1              21
  T2             7              85
  T3             6             167
  T4             6              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
  BTBD7 MUTATED     9   5   3   2
  BTBD7 WILD-TYPE 109  99  74  75
D148V5, multiclass
    clus
vv   BTBD7 MUTATED BTBD7 WILD-TYPE
  N0             9             109
  N1             5              99
  N2             3              74
  N3             2              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"
D148V6, binary
                 cls
clus                0   1
  BTBD7 MUTATED    18   0
  BTBD7 WILD-TYPE 328  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED     18    0
  BTBD7 WILD-TYPE  328   29
   clus
vv  BTBD7 MUTATED BTBD7 WILD-TYPE
  0            18             328
  1             0              29
[1] 2 2
[1] FALSE
D148V7, binary
                 cls
clus                0   1
  BTBD7 MUTATED    11   9
  BTBD7 WILD-TYPE 134 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED     11    9
  BTBD7 WILD-TYPE  134  239
        clus
vv       BTBD7 MUTATED BTBD7 WILD-TYPE
  FEMALE            11             134
  MALE               9             239
[1] 2 2
[1] FALSE
D148V8, binary
                 cls
clus                0   1
  BTBD7 MUTATED    15   2
  BTBD7 WILD-TYPE 277  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED     15    2
  BTBD7 WILD-TYPE  277   57
     clus
vv    BTBD7 MUTATED BTBD7 WILD-TYPE
  NO             15             277
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BTBD7 MUTATED                                          1
  BTBD7 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BTBD7 MUTATED                                       4
  BTBD7 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BTBD7 MUTATED                                                        8
  BTBD7 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BTBD7 MUTATED                                                   2
  BTBD7 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BTBD7 MUTATED                                                                   3
  BTBD7 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BTBD7 MUTATED                                                    0
  BTBD7 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BTBD7 MUTATED                                                  2
  BTBD7 WILD-TYPE                                               59
D148V9, multiclass
                                                                   clus
vv                                                                  BTBD7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  BTBD7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BTBD7 MUTATED    15   1   0   3
  BTBD7 WILD-TYPE 296  13  15  21
D148V10, multiclass
    clus
vv   BTBD7 MUTATED BTBD7 WILD-TYPE
  R0            15             296
  R1             1              13
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BTBD7 MUTATED       5                         0
  BTBD7 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BTBD7 MUTATED                                           0    12
  BTBD7 WILD-TYPE                                         1   231
D148V12, multiclass
                                           clus
vv                                          BTBD7 MUTATED BTBD7 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V13, binary
                 cls
clus                0   1
  BTBD7 MUTATED     0  16
  BTBD7 WILD-TYPE   4 294
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED      0   16
  BTBD7 WILD-TYPE    4  294
                        clus
vv                       BTBD7 MUTATED BTBD7 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            16             294
[1] 2 2
[1] FALSE

Clustering(149) Variable = MAGEE2 MUTATION ANALYSIS
D149V1, survival
                  sevent
clus2                0   1
  MAGEE2 MUTATED     8   3
  MAGEE2 WILD-TYPE 222 136
  MAGEE2 MUTATED MAGEE2 WILD-TYPE 
              11              358 
  MAGEE2 MUTATED MAGEE2 WILD-TYPE 
               3              136 
$`MAGEE2 MUTATED`
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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-8363 
        0.56        29.42         2.66        19.96         2.20         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-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-D7-6522 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-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-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 

  MAGEE2 MUTATED MAGEE2 WILD-TYPE 
            3.39             0.00 
  MAGEE2 MUTATED MAGEE2 WILD-TYPE 
           38.14           122.30 
  MAGEE2 MUTATED MAGEE2 WILD-TYPE 
           19.04            14.12 
[1] "3.4 - 38.1 (19.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D149V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAGEE2 MUTATED         0        1        1        0         1         3
  MAGEE2 WILD-TYPE       2       14       39       30        36        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGEE2 MUTATED           0          2          0          2        0
  MAGEE2 WILD-TYPE         3         68         53         30       38
D149V3, multiclass
            clus
vv           MAGEE2 MUTATED MAGEE2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAGEE2 MUTATED     1   3   2   5
  MAGEE2 WILD-TYPE  21  89 171  92
D149V4, multiclass
    clus
vv   MAGEE2 MUTATED MAGEE2 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              2              171
  T4              5               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
  MAGEE2 MUTATED     5   2   3   1
  MAGEE2 WILD-TYPE 113 102  74  76
D149V5, multiclass
    clus
vv   MAGEE2 MUTATED MAGEE2 WILD-TYPE
  N0              5              113
  N1              2              102
  N2              3               74
  N3              1               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"
D149V6, binary
                  cls
clus                 0   1
  MAGEE2 MUTATED    11   0
  MAGEE2 WILD-TYPE 335  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEE2 MUTATED     11    0
  MAGEE2 WILD-TYPE  335   29
   clus
vv  MAGEE2 MUTATED MAGEE2 WILD-TYPE
  0             11              335
  1              0               29
[1] 2 2
[1] FALSE
D149V7, binary
                  cls
clus                 0   1
  MAGEE2 MUTATED     4   7
  MAGEE2 WILD-TYPE 141 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEE2 MUTATED      4    7
  MAGEE2 WILD-TYPE  141  241
        clus
vv       MAGEE2 MUTATED MAGEE2 WILD-TYPE
  FEMALE              4              141
  MALE                7              241
[1] 2 2
[1] FALSE
D149V8, binary
                  cls
clus                 0   1
  MAGEE2 MUTATED     9   1
  MAGEE2 WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEE2 MUTATED      9    1
  MAGEE2 WILD-TYPE  283   58
     clus
vv    MAGEE2 MUTATED MAGEE2 WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MAGEE2 MUTATED                                          0
  MAGEE2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MAGEE2 MUTATED                                       4
  MAGEE2 WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAGEE2 MUTATED                                                        4
  MAGEE2 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MAGEE2 MUTATED                                                   1
  MAGEE2 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAGEE2 MUTATED                                                                   2
  MAGEE2 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MAGEE2 MUTATED                                                    0
  MAGEE2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MAGEE2 MUTATED                                                  0
  MAGEE2 WILD-TYPE                                               61
D149V9, multiclass
                                                                   clus
vv                                                                  MAGEE2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  MAGEE2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAGEE2 MUTATED    10   0   0   0
  MAGEE2 WILD-TYPE 301  14  15  24
D149V10, multiclass
    clus
vv   MAGEE2 MUTATED MAGEE2 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAGEE2 MUTATED       1                         0
  MAGEE2 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAGEE2 MUTATED                                           0     9
  MAGEE2 WILD-TYPE                                         1   234
D149V12, multiclass
                                           clus
vv                                          MAGEE2 MUTATED MAGEE2 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V13, binary
                  cls
clus                 0   1
  MAGEE2 MUTATED     0   9
  MAGEE2 WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEE2 MUTATED      0    9
  MAGEE2 WILD-TYPE    4  301
                        clus
vv                       MAGEE2 MUTATED MAGEE2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(150) Variable = DOCK5 MUTATION ANALYSIS
D150V1, survival
                 sevent
clus2               0   1
  DOCK5 MUTATED    16   4
  DOCK5 WILD-TYPE 214 135
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             20             349 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
              4             135 
$`DOCK5 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8285 TCGA-BR-8372 
       21.99         6.97        34.68        29.59         0.56        31.27 
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-8531 TCGA-CD-8536 TCGA-CG-5733 
        1.12        28.14        31.96        12.59        12.43        21.07 
TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GX 
       30.51        22.32         0.76        22.68        29.98        20.25 
TCGA-MX-A5UJ TCGA-VQ-A8P2 
       19.73        38.14 

$`DOCK5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-8286 TCGA-BR-8289 
        0.69         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-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-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-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-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-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-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       22.82        21.07        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-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-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 

  DOCK5 MUTATED DOCK5 WILD-TYPE 
           0.56            0.00 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
          38.14          122.30 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
         22.155          14.040 
[1] "0.6 - 38.1 (22.2)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "2.4"
D150V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DOCK5 MUTATED         1        1        1        1         3         4
  DOCK5 WILD-TYPE       1       14       39       29        34        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DOCK5 MUTATED           0          5          0          5        2
  DOCK5 WILD-TYPE         3         65         53         27       36
D150V3, multiclass
            clus
vv           DOCK5 MUTATED DOCK5 WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             5              65
  STAGE IIIB             0              53
  STAGE IIIC             5              27
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DOCK5 MUTATED     2   3   8  11
  DOCK5 WILD-TYPE  20  89 165  86
D150V4, multiclass
    clus
vv   DOCK5 MUTATED DOCK5 WILD-TYPE
  T1             2              20
  T2             3              89
  T3             8             165
  T4            11              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
  DOCK5 MUTATED     8   8   4   4
  DOCK5 WILD-TYPE 110  96  73  73
D150V5, multiclass
    clus
vv   DOCK5 MUTATED DOCK5 WILD-TYPE
  N0             8             110
  N1             8              96
  N2             4              73
  N3             4              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"
D150V6, binary
                 cls
clus                0   1
  DOCK5 MUTATED    20   2
  DOCK5 WILD-TYPE 326  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     20    2
  DOCK5 WILD-TYPE  326   27
   clus
vv  DOCK5 MUTATED DOCK5 WILD-TYPE
  0            20             326
  1             2              27
[1] 2 2
[1] FALSE
D150V7, binary
                 cls
clus                0   1
  DOCK5 MUTATED    14  11
  DOCK5 WILD-TYPE 131 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     14   11
  DOCK5 WILD-TYPE  131  237
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  FEMALE            14             131
  MALE              11             237
[1] 2 2
[1] FALSE
D150V8, binary
                 cls
clus                0   1
  DOCK5 MUTATED    19   3
  DOCK5 WILD-TYPE 273  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     19    3
  DOCK5 WILD-TYPE  273   56
     clus
vv    DOCK5 MUTATED DOCK5 WILD-TYPE
  NO             19             273
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DOCK5 MUTATED                                          0
  DOCK5 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DOCK5 MUTATED                                       4
  DOCK5 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DOCK5 MUTATED                                                       10
  DOCK5 WILD-TYPE                                                    148
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DOCK5 MUTATED                                                   2
  DOCK5 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DOCK5 MUTATED                                                                   5
  DOCK5 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DOCK5 MUTATED                                                    0
  DOCK5 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DOCK5 MUTATED                                                  4
  DOCK5 WILD-TYPE                                               57
D150V9, multiclass
                                                                   clus
vv                                                                  DOCK5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  DOCK5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DOCK5 MUTATED    19   1   1   3
  DOCK5 WILD-TYPE 292  13  14  21
D150V10, multiclass
    clus
vv   DOCK5 MUTATED DOCK5 WILD-TYPE
  R0            19             292
  R1             1              13
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DOCK5 MUTATED       8                         1
  DOCK5 WILD-TYPE    79                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DOCK5 MUTATED                                           0    12
  DOCK5 WILD-TYPE                                         1   231
D150V12, multiclass
                                           clus
vv                                          DOCK5 MUTATED DOCK5 WILD-TYPE
  ASIAN                                                 8              79
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V13, binary
                 cls
clus                0   1
  DOCK5 MUTATED     0  20
  DOCK5 WILD-TYPE   4 290
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED      0   20
  DOCK5 WILD-TYPE    4  290
                        clus
vv                       DOCK5 MUTATED DOCK5 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            20             290
[1] 2 2
[1] FALSE

Clustering(151) Variable = ZFHX4 MUTATION ANALYSIS
D151V1, survival
                 sevent
clus2               0   1
  ZFHX4 MUTATED    39  21
  ZFHX4 WILD-TYPE 191 118
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
             60             309 
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
             21             118 
$`ZFHX4 MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4257 
       26.70        19.56         6.97        30.90         9.34         9.67 
TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-8059 
       34.68        18.05        44.94        36.16        35.24        14.43 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8483 
       29.59        32.25        31.10         4.31        25.05         5.39 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL 
        9.21         1.12        27.12        28.14        31.96        16.14 
TCGA-CD-5800 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 
       13.15        11.61         6.58        11.77        12.62        15.95 
TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 
       19.07         9.01         6.02       105.07        65.10        21.07 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-A4YY TCGA-D7-A6EY TCGA-D7-A6EZ 
       10.26        12.79        12.36        13.78        11.44        20.32 
TCGA-FP-A4BE TCGA-HF-7134 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G8 
       11.08        52.21        22.32        22.82        21.07        22.68 
TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-A7NR TCGA-IN-A7NT 
        8.98         6.51        14.07        33.40         6.51        10.62 
TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-RD-A7BW TCGA-VQ-A8DU TCGA-VQ-A8P2 TCGA-VQ-A8PE 
       19.73         8.61         5.13         5.46        38.14        22.19 

$`ZFHX4 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        11.70        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-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-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-7707 TCGA-BR-7715 TCGA-BR-7716 
       31.20        21.90         9.21        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-8284 
       33.21        37.25        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-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-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 
        3.72        25.18        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-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-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-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
       12.20        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-4455 
        8.05        54.08         4.01        14.01        29.98        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-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-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 
       13.35        17.19        15.22        15.98        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-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-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-A5NB 
        0.56         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-8610 
       26.47         1.51         5.92        24.39        28.96         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-A4GQ TCGA-HU-A4GU 
       25.81        11.77        21.37        29.98         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-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       23.80        21.17        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-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
        6.74        12.59        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-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05        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-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       37.41        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 

  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
           1.12            0.00 
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
         105.07          122.30 
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
         16.045          14.070 
[1] "1.1 - 105.1 (16.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D151V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZFHX4 MUTATED         1        2        7        6         8         8
  ZFHX4 WILD-TYPE       1       13       33       24        29        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFHX4 MUTATED           1         13          6          5        6
  ZFHX4 WILD-TYPE         2         57         47         27       32
D151V3, multiclass
            clus
vv           ZFHX4 MUTATED ZFHX4 WILD-TYPE
  STAGE I                1               1
  STAGE IA               2              13
  STAGE IB               7              33
  STAGE II               6              24
  STAGE IIA              8              29
  STAGE IIB              8              44
  STAGE III              1               2
  STAGE IIIA            13              57
  STAGE IIIB             6              47
  STAGE IIIC             5              27
  STAGE IV               6              32
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZFHX4 MUTATED     4  15  27  19
  ZFHX4 WILD-TYPE  18  77 146  78
D151V4, multiclass
    clus
vv   ZFHX4 MUTATED ZFHX4 WILD-TYPE
  T1             4              18
  T2            15              77
  T3            27             146
  T4            19              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"
                 vv
clus              N0 N1 N2 N3
  ZFHX4 MUTATED   23 18 10 13
  ZFHX4 WILD-TYPE 95 86 67 64
D151V5, multiclass
    clus
vv   ZFHX4 MUTATED ZFHX4 WILD-TYPE
  N0            23              95
  N1            18              86
  N2            10              67
  N3            13              64
[1] 4 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
  ZFHX4 MUTATED    62   3
  ZFHX4 WILD-TYPE 284  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX4 MUTATED     62    3
  ZFHX4 WILD-TYPE  284   26
   clus
vv  ZFHX4 MUTATED ZFHX4 WILD-TYPE
  0            62             284
  1             3              26
[1] 2 2
[1] FALSE
D151V7, binary
                 cls
clus                0   1
  ZFHX4 MUTATED    34  34
  ZFHX4 WILD-TYPE 111 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX4 MUTATED     34   34
  ZFHX4 WILD-TYPE  111  214
        clus
vv       ZFHX4 MUTATED ZFHX4 WILD-TYPE
  FEMALE            34             111
  MALE              34             214
[1] 2 2
[1] FALSE
D151V8, binary
                 cls
clus                0   1
  ZFHX4 MUTATED    53   8
  ZFHX4 WILD-TYPE 239  51
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX4 MUTATED     53    8
  ZFHX4 WILD-TYPE  239   51
     clus
vv    ZFHX4 MUTATED ZFHX4 WILD-TYPE
  NO             53             239
  YES             8              51
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZFHX4 MUTATED                                          0
  ZFHX4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZFHX4 MUTATED                                      10
  ZFHX4 WILD-TYPE                                    60
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZFHX4 MUTATED                                                       32
  ZFHX4 WILD-TYPE                                                    126
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZFHX4 MUTATED                                                   2
  ZFHX4 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZFHX4 MUTATED                                                                  11
  ZFHX4 WILD-TYPE                                                                57
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZFHX4 MUTATED                                                    3
  ZFHX4 WILD-TYPE                                                  2
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZFHX4 MUTATED                                                 10
  ZFHX4 WILD-TYPE                                               51
D151V9, multiclass
                                                                   clus
vv                                                                  ZFHX4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        10
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       32
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            11
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             10
                                                                   clus
vv                                                                  ZFHX4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        126
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              57
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               51
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZFHX4 MUTATED    52   0   2   8
  ZFHX4 WILD-TYPE 259  14  13  16
D151V10, multiclass
    clus
vv   ZFHX4 MUTATED ZFHX4 WILD-TYPE
  R0            52             259
  R1             0              14
  R2             2              13
  RX             8              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZFHX4 MUTATED      14                         2
  ZFHX4 WILD-TYPE    73                         7
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZFHX4 MUTATED                                           1    42
  ZFHX4 WILD-TYPE                                         0   201
D151V12, multiclass
                                           clus
vv                                          ZFHX4 MUTATED ZFHX4 WILD-TYPE
  ASIAN                                                14              73
  BLACK OR AFRICAN AMERICAN                             2               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               0
  WHITE                                                42             201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V13, binary
                 cls
clus                0   1
  ZFHX4 MUTATED     0  56
  ZFHX4 WILD-TYPE   4 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX4 MUTATED      0   56
  ZFHX4 WILD-TYPE    4  254
                        clus
vv                       ZFHX4 MUTATED ZFHX4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            56             254
[1] 2 2
[1] FALSE

Clustering(152) Variable = FHDC1 MUTATION ANALYSIS
D152V1, survival
                 sevent
clus2               0   1
  FHDC1 MUTATED     5  10
  FHDC1 WILD-TYPE 225 129
  FHDC1 MUTATED FHDC1 WILD-TYPE 
             15             354 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
             10             129 
$`FHDC1 MUTATED`
TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8382 
       30.90         9.34         9.67        14.43        32.25        25.05 
TCGA-BR-8591 TCGA-CD-A4MG TCGA-CG-4306 TCGA-D7-5577 TCGA-D7-A6EY TCGA-F1-6874 
       28.14         6.58         1.02        25.71        11.44        14.47 
TCGA-F1-A448 TCGA-HU-A4G8 TCGA-VQ-AA6G 
       21.27        22.68        26.04 

$`FHDC1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-4267 TCGA-BR-4279 TCGA-BR-4280 
       18.35         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-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-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-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-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-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-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-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-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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        54.12        16.14        27.55        12.43        17.26 

  FHDC1 MUTATED FHDC1 WILD-TYPE 
           1.02            0.00 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
          32.25          122.30 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
          21.27           14.07 
[1] "1.0 - 32.2 (21.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D152V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FHDC1 MUTATED         0        0        1        0         2         2
  FHDC1 WILD-TYPE       2       15       39       30        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FHDC1 MUTATED           1          3          2          2        1
  FHDC1 WILD-TYPE         2         67         51         30       37
D152V3, multiclass
            clus
vv           FHDC1 MUTATED FHDC1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              1               2
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FHDC1 MUTATED     0   3   7   5
  FHDC1 WILD-TYPE  22  89 166  92
D152V4, multiclass
    clus
vv   FHDC1 MUTATED FHDC1 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             7             166
  T4             5              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
  FHDC1 MUTATED     5   4   1   5
  FHDC1 WILD-TYPE 113 100  76  72
D152V5, multiclass
    clus
vv   FHDC1 MUTATED FHDC1 WILD-TYPE
  N0             5             113
  N1             4             100
  N2             1              76
  N3             5              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"
D152V6, binary
                 cls
clus                0   1
  FHDC1 MUTATED    16   1
  FHDC1 WILD-TYPE 330  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED     16    1
  FHDC1 WILD-TYPE  330   28
   clus
vv  FHDC1 MUTATED FHDC1 WILD-TYPE
  0            16             330
  1             1              28
[1] 2 2
[1] FALSE
D152V7, binary
                 cls
clus                0   1
  FHDC1 MUTATED     8   9
  FHDC1 WILD-TYPE 137 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED      8    9
  FHDC1 WILD-TYPE  137  239
        clus
vv       FHDC1 MUTATED FHDC1 WILD-TYPE
  FEMALE             8             137
  MALE               9             239
[1] 2 2
[1] FALSE
D152V8, binary
                 cls
clus                0   1
  FHDC1 MUTATED    13   2
  FHDC1 WILD-TYPE 279  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED     13    2
  FHDC1 WILD-TYPE  279   57
     clus
vv    FHDC1 MUTATED FHDC1 WILD-TYPE
  NO             13             279
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FHDC1 MUTATED                                          0
  FHDC1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FHDC1 MUTATED                                       2
  FHDC1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FHDC1 MUTATED                                                        9
  FHDC1 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FHDC1 MUTATED                                                   1
  FHDC1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FHDC1 MUTATED                                                                   3
  FHDC1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FHDC1 MUTATED                                                    0
  FHDC1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FHDC1 MUTATED                                                  2
  FHDC1 WILD-TYPE                                               59
D152V9, multiclass
                                                                   clus
vv                                                                  FHDC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  FHDC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FHDC1 MUTATED     9   1   1   4
  FHDC1 WILD-TYPE 302  13  14  20
D152V10, multiclass
    clus
vv   FHDC1 MUTATED FHDC1 WILD-TYPE
  R0             9             302
  R1             1              13
  R2             1              14
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FHDC1 MUTATED       2                         0
  FHDC1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FHDC1 MUTATED                                           0    13
  FHDC1 WILD-TYPE                                         1   230
D152V12, multiclass
                                           clus
vv                                          FHDC1 MUTATED FHDC1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V13, binary
                 cls
clus                0   1
  FHDC1 MUTATED     1  13
  FHDC1 WILD-TYPE   3 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED      1   13
  FHDC1 WILD-TYPE    3  297
                        clus
vv                       FHDC1 MUTATED FHDC1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(153) Variable = RB1CC1 MUTATION ANALYSIS
D153V1, survival
                  sevent
clus2                0   1
  RB1CC1 MUTATED    11   3
  RB1CC1 WILD-TYPE 219 136
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
              14              355 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
               3              136 
$`RB1CC1 MUTATED`
TCGA-FP-A8CX TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4305 
        0.23        31.10        31.27        28.14        16.14        15.95 
TCGA-CG-5723 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4H3 TCGA-HU-A4H8 
      105.07         5.92        11.08        30.51        29.00        14.07 
TCGA-IN-A6RL TCGA-VQ-A8P2 
       13.35        38.14 

$`RB1CC1 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       47.05        21.99        22.98        79.07        16.24        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB 
        2.10        12.95        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-A6RS TCGA-IN-A7NR 
       12.46        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 

  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
            0.23             0.00 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
          105.07           122.30 
  RB1CC1 MUTATED RB1CC1 WILD-TYPE 
           22.14            14.07 
[1] "0.2 - 105.1 (22.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.3"
D153V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RB1CC1 MUTATED         0        0        1        2         1         1
  RB1CC1 WILD-TYPE       2       15       39       28        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RB1CC1 MUTATED           0          2          1          6        0
  RB1CC1 WILD-TYPE         3         68         52         26       38
D153V3, multiclass
            clus
vv           RB1CC1 MUTATED RB1CC1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              6               26
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RB1CC1 MUTATED     1   3   3   7
  RB1CC1 WILD-TYPE  21  89 170  90
D153V4, multiclass
    clus
vv   RB1CC1 MUTATED RB1CC1 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              3              170
  T4              7               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
  RB1CC1 MUTATED     1   7   1   6
  RB1CC1 WILD-TYPE 117  97  76  71
D153V5, multiclass
    clus
vv   RB1CC1 MUTATED RB1CC1 WILD-TYPE
  N0              1              117
  N1              7               97
  N2              1               76
  N3              6               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"
D153V6, binary
                  cls
clus                 0   1
  RB1CC1 MUTATED    14   0
  RB1CC1 WILD-TYPE 332  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RB1CC1 MUTATED     14    0
  RB1CC1 WILD-TYPE  332   29
   clus
vv  RB1CC1 MUTATED RB1CC1 WILD-TYPE
  0             14              332
  1              0               29
[1] 2 2
[1] FALSE
D153V7, binary
                  cls
clus                 0   1
  RB1CC1 MUTATED     6   9
  RB1CC1 WILD-TYPE 139 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RB1CC1 MUTATED      6    9
  RB1CC1 WILD-TYPE  139  239
        clus
vv       RB1CC1 MUTATED RB1CC1 WILD-TYPE
  FEMALE              6              139
  MALE                9              239
[1] 2 2
[1] FALSE
D153V8, binary
                  cls
clus                 0   1
  RB1CC1 MUTATED     9   3
  RB1CC1 WILD-TYPE 283  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RB1CC1 MUTATED      9    3
  RB1CC1 WILD-TYPE  283   56
     clus
vv    RB1CC1 MUTATED RB1CC1 WILD-TYPE
  NO               9              283
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RB1CC1 MUTATED                                          1
  RB1CC1 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RB1CC1 MUTATED                                       1
  RB1CC1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RB1CC1 MUTATED                                                        9
  RB1CC1 WILD-TYPE                                                    149
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RB1CC1 MUTATED                                                   2
  RB1CC1 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RB1CC1 MUTATED                                                                   0
  RB1CC1 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RB1CC1 MUTATED                                                    0
  RB1CC1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RB1CC1 MUTATED                                                  2
  RB1CC1 WILD-TYPE                                               59
D153V9, multiclass
                                                                   clus
vv                                                                  RB1CC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  RB1CC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RB1CC1 MUTATED    13   1   0   1
  RB1CC1 WILD-TYPE 298  13  15  23
D153V10, multiclass
    clus
vv   RB1CC1 MUTATED RB1CC1 WILD-TYPE
  R0             13              298
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RB1CC1 MUTATED       2                         1
  RB1CC1 WILD-TYPE    85                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RB1CC1 MUTATED                                           0     9
  RB1CC1 WILD-TYPE                                         1   234
D153V12, multiclass
                                           clus
vv                                          RB1CC1 MUTATED RB1CC1 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V13, binary
                  cls
clus                 0   1
  RB1CC1 MUTATED     0  11
  RB1CC1 WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RB1CC1 MUTATED      0   11
  RB1CC1 WILD-TYPE    4  299
                        clus
vv                       RB1CC1 MUTATED RB1CC1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(154) Variable = PRRG3 MUTATION ANALYSIS
D154V1, survival
                 sevent
clus2               0   1
  PRRG3 MUTATED     4   3
  PRRG3 WILD-TYPE 226 136
  PRRG3 MUTATED PRRG3 WILD-TYPE 
              7             362 
  PRRG3 MUTATED PRRG3 WILD-TYPE 
              3             136 
$`PRRG3 MUTATED`
TCGA-BR-4280 TCGA-BR-8078 TCGA-BR-8360 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-5577 
        6.61        29.59         6.18         6.02       105.07        25.71 
TCGA-HJ-7597 
       26.47 

$`PRRG3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-8576 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 

  PRRG3 MUTATED PRRG3 WILD-TYPE 
           6.02            0.00 
  PRRG3 MUTATED PRRG3 WILD-TYPE 
         105.07          122.30 
  PRRG3 MUTATED PRRG3 WILD-TYPE 
          25.71           14.22 
[1] "6.0 - 105.1 (25.7)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D154V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRRG3 MUTATED         0        0        1        1         1         1
  PRRG3 WILD-TYPE       2       15       39       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRRG3 MUTATED           1          1          0          0        1
  PRRG3 WILD-TYPE         2         69         53         32       37
D154V3, multiclass
            clus
vv           PRRG3 MUTATED PRRG3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRRG3 MUTATED     1   4   1   2
  PRRG3 WILD-TYPE  21  88 172  95
D154V4, multiclass
    clus
vv   PRRG3 MUTATED PRRG3 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             1             172
  T4             2              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
  PRRG3 MUTATED     3   3   0   1
  PRRG3 WILD-TYPE 115 101  77  76
D154V5, multiclass
    clus
vv   PRRG3 MUTATED PRRG3 WILD-TYPE
  N0             3             115
  N1             3             101
  N2             0              77
  N3             1              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"
D154V6, binary
                 cls
clus                0   1
  PRRG3 MUTATED     7   0
  PRRG3 WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG3 MUTATED      7    0
  PRRG3 WILD-TYPE  339   29
   clus
vv  PRRG3 MUTATED PRRG3 WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D154V7, binary
                 cls
clus                0   1
  PRRG3 MUTATED     5   3
  PRRG3 WILD-TYPE 140 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG3 MUTATED      5    3
  PRRG3 WILD-TYPE  140  245
        clus
vv       PRRG3 MUTATED PRRG3 WILD-TYPE
  FEMALE             5             140
  MALE               3             245
[1] 2 2
[1] FALSE
D154V8, binary
                 cls
clus                0   1
  PRRG3 MUTATED     7   0
  PRRG3 WILD-TYPE 285  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG3 MUTATED      7    0
  PRRG3 WILD-TYPE  285   59
     clus
vv    PRRG3 MUTATED PRRG3 WILD-TYPE
  NO              7             285
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PRRG3 MUTATED                                          1
  PRRG3 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PRRG3 MUTATED                                       0
  PRRG3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRRG3 MUTATED                                                        4
  PRRG3 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PRRG3 MUTATED                                                   0
  PRRG3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRRG3 MUTATED                                                                   2
  PRRG3 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PRRG3 MUTATED                                                    0
  PRRG3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PRRG3 MUTATED                                                  1
  PRRG3 WILD-TYPE                                               60
D154V9, multiclass
                                                                   clus
vv                                                                  PRRG3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  PRRG3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRRG3 MUTATED     6   0   0   2
  PRRG3 WILD-TYPE 305  14  15  22
D154V10, multiclass
    clus
vv   PRRG3 MUTATED PRRG3 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PRRG3 MUTATED       0                         0
  PRRG3 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRRG3 MUTATED                                           0     6
  PRRG3 WILD-TYPE                                         1   237
D154V12, multiclass
                                           clus
vv                                          PRRG3 MUTATED PRRG3 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V13, binary
                 cls
clus                0   1
  PRRG3 MUTATED     0   6
  PRRG3 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG3 MUTATED      0    6
  PRRG3 WILD-TYPE    4  304
                        clus
vv                       PRRG3 MUTATED PRRG3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(155) Variable = KIAA1462 MUTATION ANALYSIS
D155V1, survival
                    sevent
clus2                  0   1
  KIAA1462 MUTATED    12   9
  KIAA1462 WILD-TYPE 218 130
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
                21                348 
  KIAA1462 MUTATED KIAA1462 WILD-TYPE 
                 9                130 
$`KIAA1462 MUTATED`
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-A4J1 TCGA-BR-A4QL 
        9.67        34.68         6.18        31.10         0.72        16.14 
TCGA-CD-8527 TCGA-CD-A489 TCGA-CG-4436 TCGA-CG-5721 TCGA-CG-5733 TCGA-EQ-8122 
        7.17        11.31         7.99         6.02        21.07         7.99 
TCGA-F1-A448 TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GF 
       21.27        77.29        26.47        22.32        22.68        25.81 
TCGA-HU-A4H8 TCGA-IN-8663 TCGA-VQ-A8P2 
       14.07         3.39        38.14 

$`KIAA1462 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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-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-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        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-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 

  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              14.22 
[1] "0.7 - 77.3 (16.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D155V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1462 MUTATED         0        0        3        2         4         5
  KIAA1462 WILD-TYPE       2       15       37       28        33        47
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1462 MUTATED           0          4          2          1        1
  KIAA1462 WILD-TYPE         3         66         51         31       37
D155V3, multiclass
            clus
vv           KIAA1462 MUTATED KIAA1462 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  3                 37
  STAGE II                  2                 28
  STAGE IIA                 4                 33
  STAGE IIB                 5                 47
  STAGE III                 0                  3
  STAGE IIIA                4                 66
  STAGE IIIB                2                 51
  STAGE IIIC                1                 31
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1462 MUTATED     1   6   8   7
  KIAA1462 WILD-TYPE  21  86 165  90
D155V4, multiclass
    clus
vv   KIAA1462 MUTATED KIAA1462 WILD-TYPE
  T1                1                 21
  T2                6                 86
  T3                8                165
  T4                7                 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
  KIAA1462 MUTATED     9   9   3   2
  KIAA1462 WILD-TYPE 109  95  74  75
D155V5, multiclass
    clus
vv   KIAA1462 MUTATED KIAA1462 WILD-TYPE
  N0                9                109
  N1                9                 95
  N2                3                 74
  N3                2                 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"
D155V6, binary
                    cls
clus                   0   1
  KIAA1462 MUTATED    22   0
  KIAA1462 WILD-TYPE 324  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1462 MUTATED     22    0
  KIAA1462 WILD-TYPE  324   29
   clus
vv  KIAA1462 MUTATED KIAA1462 WILD-TYPE
  0               22                324
  1                0                 29
[1] 2 2
[1] FALSE
D155V7, binary
                    cls
clus                   0   1
  KIAA1462 MUTATED    12  12
  KIAA1462 WILD-TYPE 133 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1462 MUTATED     12   12
  KIAA1462 WILD-TYPE  133  236
        clus
vv       KIAA1462 MUTATED KIAA1462 WILD-TYPE
  FEMALE               12                133
  MALE                 12                236
[1] 2 2
[1] FALSE
D155V8, binary
                    cls
clus                   0   1
  KIAA1462 MUTATED    17   4
  KIAA1462 WILD-TYPE 275  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1462 MUTATED     17    4
  KIAA1462 WILD-TYPE  275   55
     clus
vv    KIAA1462 MUTATED KIAA1462 WILD-TYPE
  NO                17                275
  YES                4                 55
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA1462 MUTATED                                          1
  KIAA1462 WILD-TYPE                                        7
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA1462 MUTATED                                       3
  KIAA1462 WILD-TYPE                                    67
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1462 MUTATED                                                        8
  KIAA1462 WILD-TYPE                                                    150
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA1462 MUTATED                                                   3
  KIAA1462 WILD-TYPE                                                18
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1462 MUTATED                                                                   7
  KIAA1462 WILD-TYPE                                                                61
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA1462 MUTATED                                                    0
  KIAA1462 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA1462 MUTATED                                                  2
  KIAA1462 WILD-TYPE                                               59
D155V9, multiclass
                                                                   clus
vv                                                                  KIAA1462 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                7
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  KIAA1462 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 61
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1462 MUTATED    18   0   0   3
  KIAA1462 WILD-TYPE 293  14  15  21
D155V10, multiclass
    clus
vv   KIAA1462 MUTATED KIAA1462 WILD-TYPE
  R0               18                293
  R1                0                 14
  R2                0                 15
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1462 MUTATED       7                         0
  KIAA1462 WILD-TYPE    80                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1462 MUTATED                                           0    13
  KIAA1462 WILD-TYPE                                         1   230
D155V12, multiclass
                                           clus
vv                                          KIAA1462 MUTATED KIAA1462 WILD-TYPE
  ASIAN                                                    7                 80
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   13                230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V13, binary
                    cls
clus                   0   1
  KIAA1462 MUTATED     1  18
  KIAA1462 WILD-TYPE   3 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1462 MUTATED      1   18
  KIAA1462 WILD-TYPE    3  292
                        clus
vv                       KIAA1462 MUTATED KIAA1462 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               18                292
[1] 2 2
[1] FALSE

Clustering(156) Variable = KCNJ10 MUTATION ANALYSIS
D156V1, survival
                  sevent
clus2                0   1
  KCNJ10 MUTATED     7   4
  KCNJ10 WILD-TYPE 223 135
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
              11              358 
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
               4              135 
$`KCNJ10 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8487 TCGA-CD-A4MG 
       26.70         6.97        34.68        36.16         1.12         6.58 
TCGA-CG-5733 TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4GT TCGA-VQ-A8P2 
       21.07        11.44        22.32         6.51        38.14 

$`KCNJ10 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
            1.12             0.00 
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
           38.14           122.30 
  KCNJ10 MUTATED KCNJ10 WILD-TYPE 
           21.07            14.22 
[1] "1.1 - 38.1 (21.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D156V2, 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       1       14       40       30        33        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNJ10 MUTATED           0          4          1          0        0
  KCNJ10 WILD-TYPE         3         66         52         32       38
D156V3, multiclass
            clus
vv           KCNJ10 MUTATED KCNJ10 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               4               33
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KCNJ10 MUTATED     2   1   6   4
  KCNJ10 WILD-TYPE  20  91 167  93
D156V4, multiclass
    clus
vv   KCNJ10 MUTATED KCNJ10 WILD-TYPE
  T1              2               20
  T2              1               91
  T3              6              167
  T4              4               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
  KCNJ10 MUTATED     8   4   1   1
  KCNJ10 WILD-TYPE 110 100  76  76
D156V5, multiclass
    clus
vv   KCNJ10 MUTATED KCNJ10 WILD-TYPE
  N0              8              110
  N1              4              100
  N2              1               76
  N3              1               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"
D156V6, binary
                  cls
clus                 0   1
  KCNJ10 MUTATED    12   0
  KCNJ10 WILD-TYPE 334  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ10 MUTATED     12    0
  KCNJ10 WILD-TYPE  334   29
   clus
vv  KCNJ10 MUTATED KCNJ10 WILD-TYPE
  0             12              334
  1              0               29
[1] 2 2
[1] FALSE
D156V7, binary
                  cls
clus                 0   1
  KCNJ10 MUTATED     9   5
  KCNJ10 WILD-TYPE 136 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ10 MUTATED      9    5
  KCNJ10 WILD-TYPE  136  243
        clus
vv       KCNJ10 MUTATED KCNJ10 WILD-TYPE
  FEMALE              9              136
  MALE                5              243
[1] 2 2
[1] FALSE
D156V8, binary
                  cls
clus                 0   1
  KCNJ10 MUTATED    11   1
  KCNJ10 WILD-TYPE 281  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ10 MUTATED     11    1
  KCNJ10 WILD-TYPE  281   58
     clus
vv    KCNJ10 MUTATED KCNJ10 WILD-TYPE
  NO              11              281
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KCNJ10 MUTATED                                          0
  KCNJ10 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KCNJ10 MUTATED                                       3
  KCNJ10 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNJ10 MUTATED                                                        6
  KCNJ10 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KCNJ10 MUTATED                                                   1
  KCNJ10 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNJ10 MUTATED                                                                   1
  KCNJ10 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KCNJ10 MUTATED                                                    1
  KCNJ10 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KCNJ10 MUTATED                                                  2
  KCNJ10 WILD-TYPE                                               59
D156V9, multiclass
                                                                   clus
vv                                                                  KCNJ10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  KCNJ10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KCNJ10 MUTATED    10   0   0   3
  KCNJ10 WILD-TYPE 301  14  15  21
D156V10, multiclass
    clus
vv   KCNJ10 MUTATED KCNJ10 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KCNJ10 MUTATED       3                         1
  KCNJ10 WILD-TYPE    84                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNJ10 MUTATED                                           0     9
  KCNJ10 WILD-TYPE                                         1   234
D156V12, multiclass
                                           clus
vv                                          KCNJ10 MUTATED KCNJ10 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V13, binary
                  cls
clus                 0   1
  KCNJ10 MUTATED     0  12
  KCNJ10 WILD-TYPE   4 298
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNJ10 MUTATED      0   12
  KCNJ10 WILD-TYPE    4  298
                        clus
vv                       KCNJ10 MUTATED KCNJ10 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             12              298
[1] 2 2
[1] FALSE

Clustering(157) Variable = GANAB MUTATION ANALYSIS
D157V1, survival
                 sevent
clus2               0   1
  GANAB MUTATED    12   6
  GANAB WILD-TYPE 218 133
  GANAB MUTATED GANAB WILD-TYPE 
             18             351 
  GANAB MUTATED GANAB WILD-TYPE 
              6             133 
$`GANAB MUTATED`
TCGA-B7-5816 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8284 TCGA-BR-8372 TCGA-BR-8680 
       26.70         9.34        34.68         8.05        31.27        31.96 
TCGA-CD-8534 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5721 TCGA-D7-8573 TCGA-D7-A4YY 
       12.07         6.58        11.77         6.02        19.50        13.78 
TCGA-F1-A448 TCGA-FP-7735 TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GP 
       21.27         3.48         5.92        22.32        29.98         8.98 

$`GANAB WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        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-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        72.23        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-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-8604 TCGA-HU-8608 
       26.47         1.51        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-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-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 

  GANAB MUTATED GANAB WILD-TYPE 
           3.48            0.00 
  GANAB MUTATED GANAB WILD-TYPE 
          34.68          122.30 
  GANAB MUTATED GANAB WILD-TYPE 
         12.925          14.430 
[1] "3.5 - 34.7 (12.9)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D157V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GANAB MUTATED         0        0        1        1         5         2
  GANAB WILD-TYPE       2       15       39       29        32        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GANAB MUTATED           0          1          2          3        2
  GANAB WILD-TYPE         3         69         51         29       36
D157V3, multiclass
            clus
vv           GANAB MUTATED GANAB WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              5              32
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GANAB MUTATED     0   3   7   7
  GANAB WILD-TYPE  22  89 166  90
D157V4, multiclass
    clus
vv   GANAB MUTATED GANAB WILD-TYPE
  T1             0              22
  T2             3              89
  T3             7             166
  T4             7              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
  GANAB MUTATED     7   5   1   5
  GANAB WILD-TYPE 111  99  76  72
D157V5, multiclass
    clus
vv   GANAB MUTATED GANAB WILD-TYPE
  N0             7             111
  N1             5              99
  N2             1              76
  N3             5              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"
D157V6, binary
                 cls
clus                0   1
  GANAB MUTATED    16   1
  GANAB WILD-TYPE 330  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED     16    1
  GANAB WILD-TYPE  330   28
   clus
vv  GANAB MUTATED GANAB WILD-TYPE
  0            16             330
  1             1              28
[1] 2 2
[1] FALSE
D157V7, binary
                 cls
clus                0   1
  GANAB MUTATED     5  13
  GANAB WILD-TYPE 140 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED      5   13
  GANAB WILD-TYPE  140  235
        clus
vv       GANAB MUTATED GANAB WILD-TYPE
  FEMALE             5             140
  MALE              13             235
[1] 2 2
[1] FALSE
D157V8, binary
                 cls
clus                0   1
  GANAB MUTATED    16   2
  GANAB WILD-TYPE 276  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED     16    2
  GANAB WILD-TYPE  276   57
     clus
vv    GANAB MUTATED GANAB WILD-TYPE
  NO             16             276
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GANAB MUTATED                                          0
  GANAB WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GANAB MUTATED                                       5
  GANAB WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GANAB MUTATED                                                        6
  GANAB WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GANAB MUTATED                                                   1
  GANAB WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GANAB MUTATED                                                                   2
  GANAB WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GANAB MUTATED                                                    0
  GANAB WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GANAB MUTATED                                                  4
  GANAB WILD-TYPE                                               57
D157V9, multiclass
                                                                   clus
vv                                                                  GANAB MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  GANAB WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GANAB MUTATED    15   0   0   1
  GANAB WILD-TYPE 296  14  15  23
D157V10, multiclass
    clus
vv   GANAB MUTATED GANAB WILD-TYPE
  R0            15             296
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GANAB MUTATED       8                         1
  GANAB WILD-TYPE    79                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GANAB MUTATED                                           0     8
  GANAB WILD-TYPE                                         1   235
D157V12, multiclass
                                           clus
vv                                          GANAB MUTATED GANAB WILD-TYPE
  ASIAN                                                 8              79
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V13, binary
                 cls
clus                0   1
  GANAB MUTATED     1  16
  GANAB WILD-TYPE   3 294
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED      1   16
  GANAB WILD-TYPE    3  294
                        clus
vv                       GANAB MUTATED GANAB WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            16             294
[1] 2 2
[1] FALSE

Clustering(158) Variable = GPSM3 MUTATION ANALYSIS
D158V1, survival
                 sevent
clus2               0   1
  GPSM3 MUTATED     7   3
  GPSM3 WILD-TYPE 223 136
  GPSM3 MUTATED GPSM3 WILD-TYPE 
             10             359 
  GPSM3 MUTATED GPSM3 WILD-TYPE 
              3             136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        21.37        29.98         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-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 

  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          14.270 
[1] "1.0 - 35.8 (17.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D158V2, 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       2       13       39       29        35        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPSM3 MUTATED           0          1          0          0        1
  GPSM3 WILD-TYPE         3         69         53         32       37
D158V3, multiclass
            clus
vv           GPSM3 MUTATED GPSM3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPSM3 MUTATED     2   4   4   2
  GPSM3 WILD-TYPE  20  88 169  95
D158V4, multiclass
    clus
vv   GPSM3 MUTATED GPSM3 WILD-TYPE
  T1             2              20
  T2             4              88
  T3             4             169
  T4             2              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
  GPSM3 MUTATED     7   2   2   0
  GPSM3 WILD-TYPE 111 102  75  77
D158V5, multiclass
    clus
vv   GPSM3 MUTATED GPSM3 WILD-TYPE
  N0             7             111
  N1             2             102
  N2             2              75
  N3             0              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"
D158V6, binary
                 cls
clus                0   1
  GPSM3 MUTATED    11   1
  GPSM3 WILD-TYPE 335  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM3 MUTATED     11    1
  GPSM3 WILD-TYPE  335   28
   clus
vv  GPSM3 MUTATED GPSM3 WILD-TYPE
  0            11             335
  1             1              28
[1] 2 2
[1] FALSE
D158V7, binary
                 cls
clus                0   1
  GPSM3 MUTATED     7   5
  GPSM3 WILD-TYPE 138 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM3 MUTATED      7    5
  GPSM3 WILD-TYPE  138  243
        clus
vv       GPSM3 MUTATED GPSM3 WILD-TYPE
  FEMALE             7             138
  MALE               5             243
[1] 2 2
[1] FALSE
D158V8, binary
                 cls
clus                0   1
  GPSM3 MUTATED    10   0
  GPSM3 WILD-TYPE 282  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM3 MUTATED     10    0
  GPSM3 WILD-TYPE  282   59
     clus
vv    GPSM3 MUTATED GPSM3 WILD-TYPE
  NO             10             282
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GPSM3 MUTATED                                          0
  GPSM3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GPSM3 MUTATED                                       3
  GPSM3 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPSM3 MUTATED                                                        4
  GPSM3 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GPSM3 MUTATED                                                   0
  GPSM3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPSM3 MUTATED                                                                   2
  GPSM3 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GPSM3 MUTATED                                                    0
  GPSM3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GPSM3 MUTATED                                                  3
  GPSM3 WILD-TYPE                                               58
D158V9, multiclass
                                                                   clus
vv                                                                  GPSM3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  GPSM3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GPSM3 MUTATED     8   0   1   2
  GPSM3 WILD-TYPE 303  14  14  22
D158V10, multiclass
    clus
vv   GPSM3 MUTATED GPSM3 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GPSM3 MUTATED       6                         0
  GPSM3 WILD-TYPE    81                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPSM3 MUTATED                                           0     5
  GPSM3 WILD-TYPE                                         1   238
D158V12, multiclass
                                           clus
vv                                          GPSM3 MUTATED GPSM3 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V13, binary
                 cls
clus                0   1
  GPSM3 MUTATED     0  11
  GPSM3 WILD-TYPE   4 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM3 MUTATED      0   11
  GPSM3 WILD-TYPE    4  299
                        clus
vv                       GPSM3 MUTATED GPSM3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(159) Variable = WNT16 MUTATION ANALYSIS
D159V1, survival
                 sevent
clus2               0   1
  WNT16 MUTATED     8   2
  WNT16 WILD-TYPE 222 137
  WNT16 MUTATED WNT16 WILD-TYPE 
             10             359 
  WNT16 MUTATED WNT16 WILD-TYPE 
              2             137 
$`WNT16 MUTATED`
TCGA-BR-8081 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-5721 TCGA-D7-A6EY 
       32.25        28.14        16.14        12.62         6.02        11.44 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-MX-A5UJ TCGA-R5-A7ZI 
       22.68        29.98        19.73        74.53 

$`WNT16 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  WNT16 MUTATED WNT16 WILD-TYPE 
           6.02            0.00 
  WNT16 MUTATED WNT16 WILD-TYPE 
          74.53          122.30 
  WNT16 MUTATED WNT16 WILD-TYPE 
         21.205          14.070 
[1] "6.0 - 74.5 (21.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.6"
D159V2, 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       2       15       38       30        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WNT16 MUTATED           0          1          2          1        2
  WNT16 WILD-TYPE         3         69         51         31       36
D159V3, multiclass
            clus
vv           WNT16 MUTATED WNT16 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WNT16 MUTATED     0   3   4   4
  WNT16 WILD-TYPE  22  89 169  93
D159V4, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             4             169
  T4             4              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
  WNT16 MUTATED     3   5   1   3
  WNT16 WILD-TYPE 115  99  76  74
D159V5, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  N0             3             115
  N1             5              99
  N2             1              76
  N3             3              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"
D159V6, binary
                 cls
clus                0   1
  WNT16 MUTATED    11   1
  WNT16 WILD-TYPE 335  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED     11    1
  WNT16 WILD-TYPE  335   28
   clus
vv  WNT16 MUTATED WNT16 WILD-TYPE
  0            11             335
  1             1              28
[1] 2 2
[1] FALSE
D159V7, binary
                 cls
clus                0   1
  WNT16 MUTATED     7   5
  WNT16 WILD-TYPE 138 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      7    5
  WNT16 WILD-TYPE  138  243
        clus
vv       WNT16 MUTATED WNT16 WILD-TYPE
  FEMALE             7             138
  MALE               5             243
[1] 2 2
[1] FALSE
D159V8, binary
                 cls
clus                0   1
  WNT16 MUTATED    10   0
  WNT16 WILD-TYPE 282  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED     10    0
  WNT16 WILD-TYPE  282   59
     clus
vv    WNT16 MUTATED WNT16 WILD-TYPE
  NO             10             282
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  WNT16 MUTATED                                          0
  WNT16 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  WNT16 MUTATED                                       2
  WNT16 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WNT16 MUTATED                                                        5
  WNT16 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  WNT16 MUTATED                                                   0
  WNT16 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WNT16 MUTATED                                                                   2
  WNT16 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  WNT16 MUTATED                                                    0
  WNT16 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  WNT16 MUTATED                                                  3
  WNT16 WILD-TYPE                                               58
D159V9, multiclass
                                                                   clus
vv                                                                  WNT16 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  WNT16 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WNT16 MUTATED     9   0   0   1
  WNT16 WILD-TYPE 302  14  15  23
D159V10, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  R0             9             302
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  WNT16 MUTATED       3                         0
  WNT16 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WNT16 MUTATED                                           0     7
  WNT16 WILD-TYPE                                         1   236
D159V12, multiclass
                                           clus
vv                                          WNT16 MUTATED WNT16 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V13, binary
                 cls
clus                0   1
  WNT16 MUTATED     1   9
  WNT16 WILD-TYPE   3 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      1    9
  WNT16 WILD-TYPE    3  301
                        clus
vv                       WNT16 MUTATED WNT16 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(160) Variable = KIRREL MUTATION ANALYSIS
D160V1, survival
                  sevent
clus2                0   1
  KIRREL MUTATED    10  10
  KIRREL WILD-TYPE 220 129
  KIRREL MUTATED KIRREL WILD-TYPE 
              20              349 
  KIRREL MUTATED KIRREL WILD-TYPE 
              10              129 
$`KIRREL MUTATED`
TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8361 TCGA-BR-A4CS 
        9.34         6.18        35.84        14.43        31.10         1.48 
TCGA-CG-5728 TCGA-D7-6525 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-HJ-7597 TCGA-HU-8243 
       65.10        13.35        11.31        11.44        26.47         5.92 
TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-HU-A4H4 TCGA-IN-8663 TCGA-IN-A6RL TCGA-MX-A5UJ 
       22.68        11.77        23.84         3.39        13.35        19.73 
TCGA-R5-A7ZI TCGA-VQ-A8P2 
       74.53        38.14 

$`KIRREL WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-4279 
       18.35        30.90         4.08         4.08         9.67         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-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-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-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-D7-6526 
       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-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-HU-8238 TCGA-HU-8244 
       77.29        63.06        52.21        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-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-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-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.81        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-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 

  KIRREL MUTATED KIRREL WILD-TYPE 
            1.48             0.00 
  KIRREL MUTATED KIRREL WILD-TYPE 
           74.53           122.30 
  KIRREL MUTATED KIRREL WILD-TYPE 
           13.89            14.27 
[1] "1.5 - 74.5 (13.9)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D160V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIRREL MUTATED         0        1        4        0         0         3
  KIRREL WILD-TYPE       2       14       36       30        37        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIRREL MUTATED           1          5          1          3        1
  KIRREL WILD-TYPE         2         65         52         29       37
D160V3, multiclass
            clus
vv           KIRREL MUTATED KIRREL WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                4               36
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               3               49
  STAGE III               1                2
  STAGE IIIA              5               65
  STAGE IIIB              1               52
  STAGE IIIC              3               29
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIRREL MUTATED     1   8   4   6
  KIRREL WILD-TYPE  21  84 169  91
D160V4, multiclass
    clus
vv   KIRREL MUTATED KIRREL WILD-TYPE
  T1              1               21
  T2              8               84
  T3              4              169
  T4              6               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
  KIRREL MUTATED     5   6   6   3
  KIRREL WILD-TYPE 113  98  71  74
D160V5, multiclass
    clus
vv   KIRREL MUTATED KIRREL WILD-TYPE
  N0              5              113
  N1              6               98
  N2              6               71
  N3              3               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"
D160V6, binary
                  cls
clus                 0   1
  KIRREL MUTATED    18   1
  KIRREL WILD-TYPE 328  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED     18    1
  KIRREL WILD-TYPE  328   28
   clus
vv  KIRREL MUTATED KIRREL WILD-TYPE
  0             18              328
  1              1               28
[1] 2 2
[1] FALSE
D160V7, binary
                  cls
clus                 0   1
  KIRREL MUTATED    10  10
  KIRREL WILD-TYPE 135 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED     10   10
  KIRREL WILD-TYPE  135  238
        clus
vv       KIRREL MUTATED KIRREL WILD-TYPE
  FEMALE             10              135
  MALE               10              238
[1] 2 2
[1] FALSE
D160V8, binary
                  cls
clus                 0   1
  KIRREL MUTATED    18   1
  KIRREL WILD-TYPE 274  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED     18    1
  KIRREL WILD-TYPE  274   58
     clus
vv    KIRREL MUTATED KIRREL WILD-TYPE
  NO              18              274
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIRREL MUTATED                                          1
  KIRREL WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIRREL MUTATED                                       3
  KIRREL WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIRREL MUTATED                                                        7
  KIRREL WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIRREL MUTATED                                                   1
  KIRREL WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIRREL MUTATED                                                                   2
  KIRREL WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIRREL MUTATED                                                    0
  KIRREL WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIRREL MUTATED                                                  6
  KIRREL WILD-TYPE                                               55
D160V9, multiclass
                                                                   clus
vv                                                                  KIRREL MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               6
                                                                   clus
vv                                                                  KIRREL WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KIRREL MUTATED    17   0   0   2
  KIRREL WILD-TYPE 294  14  15  22
D160V10, multiclass
    clus
vv   KIRREL MUTATED KIRREL WILD-TYPE
  R0             17              294
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KIRREL MUTATED       4                         0
  KIRREL WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIRREL MUTATED                                           0    15
  KIRREL WILD-TYPE                                         1   228
D160V12, multiclass
                                           clus
vv                                          KIRREL MUTATED KIRREL WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 15              228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V13, binary
                  cls
clus                 0   1
  KIRREL MUTATED     1  17
  KIRREL WILD-TYPE   3 293
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED      1   17
  KIRREL WILD-TYPE    3  293
                        clus
vv                       KIRREL MUTATED KIRREL WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             17              293
[1] 2 2
[1] FALSE

Clustering(161) Variable = MTMR9 MUTATION ANALYSIS
D161V1, survival
                 sevent
clus2               0   1
  MTMR9 MUTATED     6   3
  MTMR9 WILD-TYPE 224 136
  MTMR9 MUTATED MTMR9 WILD-TYPE 
              9             360 
  MTMR9 MUTATED MTMR9 WILD-TYPE 
              3             136 
$`MTMR9 MUTATED`
TCGA-BR-6452 TCGA-BR-7704 TCGA-BR-8360 TCGA-CG-4305 TCGA-CG-4465 TCGA-D7-A4YV 
       34.68        35.24         6.18        15.95         9.01         5.92 
TCGA-HU-8602 TCGA-HU-A4GQ TCGA-VQ-A8P2 
       22.32         0.10        38.14 

$`MTMR9 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
          15.95           14.22 
[1] "0.1 - 38.1 (15.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D161V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTMR9 MUTATED         0        0        1        2         2         2
  MTMR9 WILD-TYPE       2       15       39       28        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MTMR9 MUTATED           0          1          0          1        1
  MTMR9 WILD-TYPE         3         69         53         31       37
D161V3, multiclass
            clus
vv           MTMR9 MUTATED MTMR9 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MTMR9 MUTATED     1   2   5   4
  MTMR9 WILD-TYPE  21  90 168  93
D161V4, multiclass
    clus
vv   MTMR9 MUTATED MTMR9 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             5             168
  T4             4              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
  MTMR9 MUTATED     5   4   1   1
  MTMR9 WILD-TYPE 113 100  76  76
D161V5, multiclass
    clus
vv   MTMR9 MUTATED MTMR9 WILD-TYPE
  N0             5             113
  N1             4             100
  N2             1              76
  N3             1              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"
D161V6, binary
                 cls
clus                0   1
  MTMR9 MUTATED    11   1
  MTMR9 WILD-TYPE 335  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR9 MUTATED     11    1
  MTMR9 WILD-TYPE  335   28
   clus
vv  MTMR9 MUTATED MTMR9 WILD-TYPE
  0            11             335
  1             1              28
[1] 2 2
[1] FALSE
D161V7, binary
                 cls
clus                0   1
  MTMR9 MUTATED     8   5
  MTMR9 WILD-TYPE 137 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR9 MUTATED      8    5
  MTMR9 WILD-TYPE  137  243
        clus
vv       MTMR9 MUTATED MTMR9 WILD-TYPE
  FEMALE             8             137
  MALE               5             243
[1] 2 2
[1] FALSE
D161V8, binary
                 cls
clus                0   1
  MTMR9 MUTATED     7   1
  MTMR9 WILD-TYPE 285  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR9 MUTATED      7    1
  MTMR9 WILD-TYPE  285   58
     clus
vv    MTMR9 MUTATED MTMR9 WILD-TYPE
  NO              7             285
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MTMR9 MUTATED                                          0
  MTMR9 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MTMR9 MUTATED                                       2
  MTMR9 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MTMR9 MUTATED                                                        5
  MTMR9 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MTMR9 MUTATED                                                   1
  MTMR9 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MTMR9 MUTATED                                                                   3
  MTMR9 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MTMR9 MUTATED                                                    0
  MTMR9 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MTMR9 MUTATED                                                  2
  MTMR9 WILD-TYPE                                               59
D161V9, multiclass
                                                                   clus
vv                                                                  MTMR9 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  MTMR9 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MTMR9 MUTATED     9   0   1   3
  MTMR9 WILD-TYPE 302  14  14  21
D161V10, multiclass
    clus
vv   MTMR9 MUTATED MTMR9 WILD-TYPE
  R0             9             302
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MTMR9 MUTATED       2                         0
  MTMR9 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MTMR9 MUTATED                                           0     8
  MTMR9 WILD-TYPE                                         1   235
D161V12, multiclass
                                           clus
vv                                          MTMR9 MUTATED MTMR9 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V13, binary
                 cls
clus                0   1
  MTMR9 MUTATED     0   9
  MTMR9 WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR9 MUTATED      0    9
  MTMR9 WILD-TYPE    4  301
                        clus
vv                       MTMR9 MUTATED MTMR9 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(162) Variable = FAHD2B MUTATION ANALYSIS
D162V1, survival
                  sevent
clus2                0   1
  FAHD2B MUTATED     5   3
  FAHD2B WILD-TYPE 225 136
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               8              361 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               3              136 
$`FAHD2B MUTATED`
TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-8360 TCGA-BR-8382 TCGA-BR-8680 TCGA-CD-8536 
       30.90        32.78         6.18        25.05        31.96        12.43 
TCGA-CD-A4MJ TCGA-CG-4306 
       12.62         1.02 

$`FAHD2B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  FAHD2B MUTATED FAHD2B WILD-TYPE 
            1.02             0.00 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
           32.78           122.30 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
          18.835           14.270 
[1] "1.0 - 32.8 (18.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D162V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAHD2B MUTATED         0        0        1        1         2         1
  FAHD2B WILD-TYPE       2       15       39       29        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAHD2B MUTATED           0          0          0          1        2
  FAHD2B WILD-TYPE         3         70         53         31       36
D162V3, multiclass
            clus
vv           FAHD2B MUTATED FAHD2B WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAHD2B MUTATED     0   2   4   3
  FAHD2B WILD-TYPE  22  90 169  94
D162V4, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  T1              0               22
  T2              2               90
  T3              4              169
  T4              3               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
  FAHD2B MUTATED     5   0   2   1
  FAHD2B WILD-TYPE 113 104  75  76
D162V5, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  N0              5              113
  N1              0              104
  N2              2               75
  N3              1               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"
D162V6, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     7   2
  FAHD2B WILD-TYPE 339  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      7    2
  FAHD2B WILD-TYPE  339   27
   clus
vv  FAHD2B MUTATED FAHD2B WILD-TYPE
  0              7              339
  1              2               27
[1] 2 2
[1] FALSE
D162V7, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     3   6
  FAHD2B WILD-TYPE 142 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      3    6
  FAHD2B WILD-TYPE  142  242
        clus
vv       FAHD2B MUTATED FAHD2B WILD-TYPE
  FEMALE              3              142
  MALE                6              242
[1] 2 2
[1] FALSE
D162V8, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     8   0
  FAHD2B WILD-TYPE 284  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      8    0
  FAHD2B WILD-TYPE  284   59
     clus
vv    FAHD2B MUTATED FAHD2B WILD-TYPE
  NO               8              284
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAHD2B MUTATED                                          0
  FAHD2B WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAHD2B MUTATED                                       0
  FAHD2B WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAHD2B MUTATED                                                        6
  FAHD2B WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAHD2B MUTATED                                                   0
  FAHD2B WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAHD2B MUTATED                                                                   2
  FAHD2B WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAHD2B MUTATED                                                    0
  FAHD2B WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAHD2B MUTATED                                                  1
  FAHD2B WILD-TYPE                                               60
D162V9, multiclass
                                                                   clus
vv                                                                  FAHD2B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  FAHD2B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAHD2B MUTATED     6   0   1   1
  FAHD2B WILD-TYPE 305  14  14  23
D162V10, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  R0              6              305
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAHD2B MUTATED       3                         0
  FAHD2B WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAHD2B MUTATED                                           0     5
  FAHD2B WILD-TYPE                                         1   238
D162V12, multiclass
                                           clus
vv                                          FAHD2B MUTATED FAHD2B WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V13, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     0   8
  FAHD2B WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      0    8
  FAHD2B WILD-TYPE    4  302
                        clus
vv                       FAHD2B MUTATED FAHD2B WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(163) Variable = KLRK1 MUTATION ANALYSIS
D163V1, survival
                 sevent
clus2               0   1
  KLRK1 MUTATED     2   2
  KLRK1 WILD-TYPE 228 137
  KLRK1 MUTATED KLRK1 WILD-TYPE 
              4             365 
  KLRK1 MUTATED KLRK1 WILD-TYPE 
              2             137 
$`KLRK1 MUTATED`
TCGA-BR-8487 TCGA-BR-A4QL TCGA-D7-A6EY TCGA-HU-A4GT 
        1.12        16.14        11.44         6.51 

$`KLRK1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  KLRK1 MUTATED KLRK1 WILD-TYPE 
           1.12            0.00 
  KLRK1 MUTATED KLRK1 WILD-TYPE 
          16.14          122.30 
  KLRK1 MUTATED KLRK1 WILD-TYPE 
          8.975          14.430 
[1] "1.1 - 16.1 (9.0)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "2.7"
D163V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLRK1 MUTATED         0        0        0        0         2         0
  KLRK1 WILD-TYPE       2       15       40       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLRK1 MUTATED           0          0          2          0        1
  KLRK1 WILD-TYPE         3         70         51         32       37
D163V3, multiclass
            clus
vv           KLRK1 MUTATED KLRK1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             2              51
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLRK1 MUTATED     0   0   4   1
  KLRK1 WILD-TYPE  22  92 169  96
D163V4, multiclass
    clus
vv   KLRK1 MUTATED KLRK1 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             4             169
  T4             1              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
  KLRK1 MUTATED     2   0   1   2
  KLRK1 WILD-TYPE 116 104  76  75
D163V5, multiclass
    clus
vv   KLRK1 MUTATED KLRK1 WILD-TYPE
  N0             2             116
  N1             0             104
  N2             1              76
  N3             2              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"
D163V6, binary
                 cls
clus                0   1
  KLRK1 MUTATED     5   0
  KLRK1 WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRK1 MUTATED      5    0
  KLRK1 WILD-TYPE  341   29
   clus
vv  KLRK1 MUTATED KLRK1 WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D163V7, binary
                 cls
clus                0   1
  KLRK1 MUTATED     5   0
  KLRK1 WILD-TYPE 140 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRK1 MUTATED      5    0
  KLRK1 WILD-TYPE  140  248
        clus
vv       KLRK1 MUTATED KLRK1 WILD-TYPE
  FEMALE             5             140
  MALE               0             248
[1] 2 2
[1] FALSE
D163V8, binary
                 cls
clus                0   1
  KLRK1 MUTATED     4   0
  KLRK1 WILD-TYPE 288  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRK1 MUTATED      4    0
  KLRK1 WILD-TYPE  288   59
     clus
vv    KLRK1 MUTATED KLRK1 WILD-TYPE
  NO              4             288
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KLRK1 MUTATED                                          0
  KLRK1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KLRK1 MUTATED                                       0
  KLRK1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KLRK1 MUTATED                                                        3
  KLRK1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KLRK1 MUTATED                                                   0
  KLRK1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KLRK1 MUTATED                                                                   0
  KLRK1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KLRK1 MUTATED                                                    0
  KLRK1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KLRK1 MUTATED                                                  2
  KLRK1 WILD-TYPE                                               59
D163V9, multiclass
                                                                   clus
vv                                                                  KLRK1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  KLRK1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KLRK1 MUTATED     4   0   0   1
  KLRK1 WILD-TYPE 307  14  15  23
D163V10, multiclass
    clus
vv   KLRK1 MUTATED KLRK1 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KLRK1 MUTATED       1                         0
  KLRK1 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLRK1 MUTATED                                           0     4
  KLRK1 WILD-TYPE                                         1   239
D163V12, multiclass
                                           clus
vv                                          KLRK1 MUTATED KLRK1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V13, binary
                 cls
clus                0   1
  KLRK1 MUTATED     0   5
  KLRK1 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRK1 MUTATED      0    5
  KLRK1 WILD-TYPE    4  305
                        clus
vv                       KLRK1 MUTATED KLRK1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(164) Variable = KLC2 MUTATION ANALYSIS
D164V1, survival
                sevent
clus2              0   1
  KLC2 MUTATED     8   6
  KLC2 WILD-TYPE 222 133
  KLC2 MUTATED KLC2 WILD-TYPE 
            14            355 
  KLC2 MUTATED KLC2 WILD-TYPE 
             6            133 
$`KLC2 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8487 
       21.99         6.97        44.94        35.84        32.25         1.12 
TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-A6EY TCGA-EQ-5647 TCGA-FP-8211 TCGA-HJ-7597 
      105.07        21.07        11.44         0.62        13.58        26.47 
TCGA-HU-A4GX TCGA-VQ-A8P2 
       20.25        38.14 

$`KLC2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-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-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 

  KLC2 MUTATED KLC2 WILD-TYPE 
          0.62           0.00 
  KLC2 MUTATED KLC2 WILD-TYPE 
        105.07         122.30 
  KLC2 MUTATED KLC2 WILD-TYPE 
         21.53          14.07 
[1] "0.6 - 105.1 (21.5)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D164V2, 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       2       15       38       29        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLC2 MUTATED           0          3          1          1        2
  KLC2 WILD-TYPE         3         67         52         31       36
D164V3, multiclass
            clus
vv           KLC2 MUTATED KLC2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KLC2 MUTATED     0   4   5   5
  KLC2 WILD-TYPE  22  88 168  92
D164V4, multiclass
    clus
vv   KLC2 MUTATED KLC2 WILD-TYPE
  T1            0             22
  T2            4             88
  T3            5            168
  T4            5             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
  KLC2 MUTATED     5   5   2   2
  KLC2 WILD-TYPE 113  99  75  75
D164V5, multiclass
    clus
vv   KLC2 MUTATED KLC2 WILD-TYPE
  N0            5            113
  N1            5             99
  N2            2             75
  N3            2             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"
D164V6, binary
                cls
clus               0   1
  KLC2 MUTATED     9   2
  KLC2 WILD-TYPE 337  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC2 MUTATED      9    2
  KLC2 WILD-TYPE  337   27
   clus
vv  KLC2 MUTATED KLC2 WILD-TYPE
  0            9            337
  1            2             27
[1] 2 2
[1] FALSE
D164V7, binary
                cls
clus               0   1
  KLC2 MUTATED    10   4
  KLC2 WILD-TYPE 135 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC2 MUTATED     10    4
  KLC2 WILD-TYPE  135  244
        clus
vv       KLC2 MUTATED KLC2 WILD-TYPE
  FEMALE           10            135
  MALE              4            244
[1] 2 2
[1] FALSE
D164V8, binary
                cls
clus               0   1
  KLC2 MUTATED    12   2
  KLC2 WILD-TYPE 280  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC2 MUTATED     12    2
  KLC2 WILD-TYPE  280   57
     clus
vv    KLC2 MUTATED KLC2 WILD-TYPE
  NO            12            280
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KLC2 MUTATED                                          1
  KLC2 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KLC2 MUTATED                                       1
  KLC2 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KLC2 MUTATED                                                        8
  KLC2 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KLC2 MUTATED                                                   1
  KLC2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KLC2 MUTATED                                                                   2
  KLC2 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KLC2 MUTATED                                                    0
  KLC2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KLC2 MUTATED                                                  1
  KLC2 WILD-TYPE                                               60
D164V9, multiclass
                                                                   clus
vv                                                                  KLC2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  KLC2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KLC2 MUTATED    10   1   2   1
  KLC2 WILD-TYPE 301  13  13  23
D164V10, multiclass
    clus
vv   KLC2 MUTATED KLC2 WILD-TYPE
  R0           10            301
  R1            1             13
  R2            2             13
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  KLC2 MUTATED       1                         0
  KLC2 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLC2 MUTATED                                           0    10
  KLC2 WILD-TYPE                                         1   233
D164V12, multiclass
                                           clus
vv                                          KLC2 MUTATED KLC2 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V13, binary
                cls
clus               0   1
  KLC2 MUTATED     0  10
  KLC2 WILD-TYPE   4 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC2 MUTATED      0   10
  KLC2 WILD-TYPE    4  300
                        clus
vv                       KLC2 MUTATED KLC2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           10            300
[1] 2 2
[1] FALSE

Clustering(165) Variable = WDR7 MUTATION ANALYSIS
D165V1, survival
                sevent
clus2              0   1
  WDR7 MUTATED    12   4
  WDR7 WILD-TYPE 218 135
  WDR7 MUTATED WDR7 WILD-TYPE 
            16            353 
  WDR7 MUTATED WDR7 WILD-TYPE 
             4            135 
$`WDR7 MUTATED`
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8372 TCGA-CD-A4MI 
        9.34        34.68        44.94        36.16        31.27        11.77 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-F1-A448 TCGA-FP-A4BE 
        6.02       105.07        65.10        21.07        21.27        11.08 
TCGA-HF-A5NB TCGA-HU-A4GT TCGA-HU-A4GX TCGA-R5-A7ZR 
       30.51         6.51        20.25         6.08 

$`WDR7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-7196 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       31.20        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-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-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-5724 
        6.97        36.00         1.02         0.99         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-D7-8573 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-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-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-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       74.53         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 

  WDR7 MUTATED WDR7 WILD-TYPE 
          6.02           0.00 
  WDR7 MUTATED WDR7 WILD-TYPE 
        105.07         122.30 
  WDR7 MUTATED WDR7 WILD-TYPE 
         21.17          14.07 
[1] "6.0 - 105.1 (21.2)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2"  
D165V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WDR7 MUTATED         1        1        2        1         4         1
  WDR7 WILD-TYPE       1       14       38       29        33        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WDR7 MUTATED           1          3          1          3        2
  WDR7 WILD-TYPE         2         67         52         29       36
D165V3, multiclass
            clus
vv           WDR7 MUTATED WDR7 WILD-TYPE
  STAGE I               1              1
  STAGE IA              1             14
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             4             33
  STAGE IIB             1             51
  STAGE III             1              2
  STAGE IIIA            3             67
  STAGE IIIB            1             52
  STAGE IIIC            3             29
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WDR7 MUTATED     3   4   7   7
  WDR7 WILD-TYPE  19  88 166  90
D165V4, multiclass
    clus
vv   WDR7 MUTATED WDR7 WILD-TYPE
  T1            3             19
  T2            4             88
  T3            7            166
  T4            7             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
  WDR7 MUTATED     9   5   3   3
  WDR7 WILD-TYPE 109  99  74  74
D165V5, multiclass
    clus
vv   WDR7 MUTATED WDR7 WILD-TYPE
  N0            9            109
  N1            5             99
  N2            3             74
  N3            3             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"
D165V6, binary
                cls
clus               0   1
  WDR7 MUTATED    21   0
  WDR7 WILD-TYPE 325  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR7 MUTATED     21    0
  WDR7 WILD-TYPE  325   29
   clus
vv  WDR7 MUTATED WDR7 WILD-TYPE
  0           21            325
  1            0             29
[1] 2 2
[1] FALSE
D165V7, binary
                cls
clus               0   1
  WDR7 MUTATED    11  11
  WDR7 WILD-TYPE 134 237
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR7 MUTATED     11   11
  WDR7 WILD-TYPE  134  237
        clus
vv       WDR7 MUTATED WDR7 WILD-TYPE
  FEMALE           11            134
  MALE             11            237
[1] 2 2
[1] FALSE
D165V8, binary
                cls
clus               0   1
  WDR7 MUTATED    14   3
  WDR7 WILD-TYPE 278  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR7 MUTATED     14    3
  WDR7 WILD-TYPE  278   56
     clus
vv    WDR7 MUTATED WDR7 WILD-TYPE
  NO            14            278
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  WDR7 MUTATED                                          0
  WDR7 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  WDR7 MUTATED                                       1
  WDR7 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WDR7 MUTATED                                                       11
  WDR7 WILD-TYPE                                                    147
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  WDR7 MUTATED                                                   2
  WDR7 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WDR7 MUTATED                                                                   5
  WDR7 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  WDR7 MUTATED                                                    1
  WDR7 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  WDR7 MUTATED                                                  2
  WDR7 WILD-TYPE                                               59
D165V9, multiclass
                                                                   clus
vv                                                                  WDR7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  WDR7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WDR7 MUTATED    15   1   0   4
  WDR7 WILD-TYPE 296  13  15  20
D165V10, multiclass
    clus
vv   WDR7 MUTATED WDR7 WILD-TYPE
  R0           15            296
  R1            1             13
  R2            0             15
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  WDR7 MUTATED       3                         3
  WDR7 WILD-TYPE    84                         6
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WDR7 MUTATED                                           0    10
  WDR7 WILD-TYPE                                         1   233
D165V12, multiclass
                                           clus
vv                                          WDR7 MUTATED WDR7 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            3              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V13, binary
                cls
clus               0   1
  WDR7 MUTATED     1  15
  WDR7 WILD-TYPE   3 295
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR7 MUTATED      1   15
  WDR7 WILD-TYPE    3  295
                        clus
vv                       WDR7 MUTATED WDR7 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           15            295
[1] 2 2
[1] FALSE

Clustering(166) Variable = TCHP MUTATION ANALYSIS
D166V1, survival
                sevent
clus2              0   1
  TCHP MUTATED     9   3
  TCHP WILD-TYPE 221 136
  TCHP MUTATED TCHP WILD-TYPE 
            12            357 
  TCHP MUTATED TCHP WILD-TYPE 
             3            136 
$`TCHP MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-8078 TCGA-BR-8372 TCGA-CD-A4MG 
       26.70         6.97         6.61        29.59        31.27         6.58 
TCGA-D7-8572 TCGA-D7-A4YT TCGA-HU-A4GX TCGA-KB-A6F5 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       16.80        14.27        20.25         5.56        19.73        38.14 

$`TCHP WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-D7-8573 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-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-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-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-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 

  TCHP MUTATED TCHP WILD-TYPE 
          5.56           0.00 
  TCHP MUTATED TCHP WILD-TYPE 
         38.14         122.30 
  TCHP MUTATED TCHP WILD-TYPE 
        18.265         14.070 
[1] "5.6 - 38.1 (18.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D166V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TCHP MUTATED         0        0        0        0         1         3
  TCHP WILD-TYPE       2       15       40       30        36        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TCHP MUTATED           1          5          0          2        0
  TCHP WILD-TYPE         2         65         53         30       38
D166V3, multiclass
            clus
vv           TCHP MUTATED TCHP WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             3             49
  STAGE III             1              2
  STAGE IIIA            5             65
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TCHP MUTATED     0   3   4   5
  TCHP WILD-TYPE  22  89 169  92
D166V4, multiclass
    clus
vv   TCHP MUTATED TCHP WILD-TYPE
  T1            0             22
  T2            3             89
  T3            4            169
  T4            5             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
  TCHP MUTATED     3   3   4   2
  TCHP WILD-TYPE 115 101  73  75
D166V5, multiclass
    clus
vv   TCHP MUTATED TCHP WILD-TYPE
  N0            3            115
  N1            3            101
  N2            4             73
  N3            2             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"
D166V6, binary
                cls
clus               0   1
  TCHP MUTATED    11   0
  TCHP WILD-TYPE 335  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHP MUTATED     11    0
  TCHP WILD-TYPE  335   29
   clus
vv  TCHP MUTATED TCHP WILD-TYPE
  0           11            335
  1            0             29
[1] 2 2
[1] FALSE
D166V7, binary
                cls
clus               0   1
  TCHP MUTATED     5   7
  TCHP WILD-TYPE 140 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHP MUTATED      5    7
  TCHP WILD-TYPE  140  241
        clus
vv       TCHP MUTATED TCHP WILD-TYPE
  FEMALE            5            140
  MALE              7            241
[1] 2 2
[1] FALSE
D166V8, binary
                cls
clus               0   1
  TCHP MUTATED    11   1
  TCHP WILD-TYPE 281  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHP MUTATED     11    1
  TCHP WILD-TYPE  281   58
     clus
vv    TCHP MUTATED TCHP WILD-TYPE
  NO            11            281
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TCHP MUTATED                                          0
  TCHP WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TCHP MUTATED                                       3
  TCHP WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TCHP MUTATED                                                        5
  TCHP WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TCHP MUTATED                                                   1
  TCHP WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TCHP MUTATED                                                                   1
  TCHP WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TCHP MUTATED                                                    0
  TCHP WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TCHP MUTATED                                                  2
  TCHP WILD-TYPE                                               59
D166V9, multiclass
                                                                   clus
vv                                                                  TCHP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  TCHP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TCHP MUTATED     9   0   0   2
  TCHP WILD-TYPE 302  14  15  22
D166V10, multiclass
    clus
vv   TCHP MUTATED TCHP WILD-TYPE
  R0            9            302
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TCHP MUTATED       2                         0
  TCHP WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TCHP MUTATED                                           0     9
  TCHP WILD-TYPE                                         1   234
D166V12, multiclass
                                           clus
vv                                          TCHP MUTATED TCHP WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V13, binary
                cls
clus               0   1
  TCHP MUTATED     0  10
  TCHP WILD-TYPE   4 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHP MUTATED      0   10
  TCHP WILD-TYPE    4  300
                        clus
vv                       TCHP MUTATED TCHP WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           10            300
[1] 2 2
[1] FALSE

Clustering(167) Variable = SNRK MUTATION ANALYSIS
D167V1, survival
                sevent
clus2              0   1
  SNRK MUTATED     8   6
  SNRK WILD-TYPE 222 133
  SNRK MUTATED SNRK WILD-TYPE 
            14            355 
  SNRK MUTATED SNRK WILD-TYPE 
             6            133 
$`SNRK MUTATED`
TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-8284 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8367 
        6.97         9.67         8.05         6.18         0.26        26.33 
TCGA-BR-8371 TCGA-CD-8524 TCGA-CD-8530 TCGA-CG-5721 TCGA-D7-8572 TCGA-D7-8574 
       11.80        12.76        12.39         6.02        16.80        17.19 
TCGA-HU-A4G8 TCGA-VQ-A8P2 
       22.68        38.14 

$`SNRK WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-D7-8573 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-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-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 

  SNRK MUTATED SNRK WILD-TYPE 
          0.26           0.00 
  SNRK MUTATED SNRK WILD-TYPE 
         38.14         122.30 
  SNRK MUTATED SNRK WILD-TYPE 
        12.095         14.470 
[1] "0.3 - 38.1 (12.1)"  "0.0 - 122.3 (14.5)"
[1] "hr=" "1.5"
D167V2, 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       2       15       39       28        36        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNRK MUTATED           0          4          2          1        1
  SNRK WILD-TYPE         3         66         51         31       37
D167V3, multiclass
            clus
vv           SNRK MUTATED SNRK WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              2             28
  STAGE IIA             1             36
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            4             66
  STAGE IIIB            2             51
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SNRK MUTATED     0   3   7   5
  SNRK WILD-TYPE  22  89 166  92
D167V4, multiclass
    clus
vv   SNRK MUTATED SNRK WILD-TYPE
  T1            0             22
  T2            3             89
  T3            7            166
  T4            5             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
  SNRK MUTATED     6   4   1   4
  SNRK WILD-TYPE 112 100  76  73
D167V5, multiclass
    clus
vv   SNRK MUTATED SNRK WILD-TYPE
  N0            6            112
  N1            4            100
  N2            1             76
  N3            4             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"
D167V6, binary
                cls
clus               0   1
  SNRK MUTATED    15   0
  SNRK WILD-TYPE 331  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNRK MUTATED     15    0
  SNRK WILD-TYPE  331   29
   clus
vv  SNRK MUTATED SNRK WILD-TYPE
  0           15            331
  1            0             29
[1] 2 2
[1] FALSE
D167V7, binary
                cls
clus               0   1
  SNRK MUTATED     6  10
  SNRK WILD-TYPE 139 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNRK MUTATED      6   10
  SNRK WILD-TYPE  139  238
        clus
vv       SNRK MUTATED SNRK WILD-TYPE
  FEMALE            6            139
  MALE             10            238
[1] 2 2
[1] FALSE
D167V8, binary
                cls
clus               0   1
  SNRK MUTATED    13   2
  SNRK WILD-TYPE 279  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNRK MUTATED     13    2
  SNRK WILD-TYPE  279   57
     clus
vv    SNRK MUTATED SNRK WILD-TYPE
  NO            13            279
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SNRK MUTATED                                          0
  SNRK WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SNRK MUTATED                                       2
  SNRK WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SNRK MUTATED                                                        8
  SNRK WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SNRK MUTATED                                                   1
  SNRK WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SNRK MUTATED                                                                   5
  SNRK WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SNRK MUTATED                                                    0
  SNRK WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SNRK MUTATED                                                  0
  SNRK WILD-TYPE                                               61
D167V9, multiclass
                                                                   clus
vv                                                                  SNRK MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  SNRK WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SNRK MUTATED    12   0   0   3
  SNRK WILD-TYPE 299  14  15  21
D167V10, multiclass
    clus
vv   SNRK MUTATED SNRK WILD-TYPE
  R0           12            299
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SNRK MUTATED       3                         0
  SNRK WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SNRK MUTATED                                           0    12
  SNRK WILD-TYPE                                         1   231
D167V12, multiclass
                                           clus
vv                                          SNRK MUTATED SNRK WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               12            231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V13, binary
                cls
clus               0   1
  SNRK MUTATED     0  14
  SNRK WILD-TYPE   4 296
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNRK MUTATED      0   14
  SNRK WILD-TYPE    4  296
                        clus
vv                       SNRK MUTATED SNRK WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           14            296
[1] 2 2
[1] FALSE

Clustering(168) Variable = SNAPC1 MUTATION ANALYSIS
D168V1, survival
                  sevent
clus2                0   1
  SNAPC1 MUTATED     6   2
  SNAPC1 WILD-TYPE 224 137
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               8              361 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               2              137 
$`SNAPC1 MUTATED`
TCGA-B7-5816 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8487 TCGA-CG-5726 TCGA-D7-A4YV 
       26.70        29.59        31.10         1.12        28.96         5.92 
TCGA-HU-A4G9 TCGA-SW-A7EA 
       24.20        19.04 

$`SNAPC1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
            1.12             0.00 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
            31.1            122.3 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
           25.45            14.07 
[1] "1.1 - 31.1 (25.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D168V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SNAPC1 MUTATED         0        2        1        0         1         3
  SNAPC1 WILD-TYPE       2       13       39       30        36        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNAPC1 MUTATED           0          0          0          1        0
  SNAPC1 WILD-TYPE         3         70         53         31       38
D168V3, multiclass
            clus
vv           SNAPC1 MUTATED SNAPC1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                2               13
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SNAPC1 MUTATED     2   1   2   3
  SNAPC1 WILD-TYPE  20  91 171  94
D168V4, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  T1              2               20
  T2              1               91
  T3              2              171
  T4              3               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
  SNAPC1 MUTATED     6   1   1   0
  SNAPC1 WILD-TYPE 112 103  76  77
D168V5, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  N0              6              112
  N1              1              103
  N2              1               76
  N3              0               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"
D168V6, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     8   0
  SNAPC1 WILD-TYPE 338  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      8    0
  SNAPC1 WILD-TYPE  338   29
   clus
vv  SNAPC1 MUTATED SNAPC1 WILD-TYPE
  0              8              338
  1              0               29
[1] 2 2
[1] FALSE
D168V7, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     7   1
  SNAPC1 WILD-TYPE 138 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      7    1
  SNAPC1 WILD-TYPE  138  247
        clus
vv       SNAPC1 MUTATED SNAPC1 WILD-TYPE
  FEMALE              7              138
  MALE                1              247
[1] 2 2
[1] FALSE
D168V8, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     7   0
  SNAPC1 WILD-TYPE 285  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      7    0
  SNAPC1 WILD-TYPE  285   59
     clus
vv    SNAPC1 MUTATED SNAPC1 WILD-TYPE
  NO               7              285
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SNAPC1 MUTATED                                          0
  SNAPC1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SNAPC1 MUTATED                                       2
  SNAPC1 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SNAPC1 MUTATED                                                        3
  SNAPC1 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SNAPC1 MUTATED                                                   0
  SNAPC1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SNAPC1 MUTATED                                                                   1
  SNAPC1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SNAPC1 MUTATED                                                    0
  SNAPC1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SNAPC1 MUTATED                                                  2
  SNAPC1 WILD-TYPE                                               59
D168V9, multiclass
                                                                   clus
vv                                                                  SNAPC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  SNAPC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SNAPC1 MUTATED     8   0   0   0
  SNAPC1 WILD-TYPE 303  14  15  24
D168V10, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SNAPC1 MUTATED       1                         0
  SNAPC1 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SNAPC1 MUTATED                                           0     6
  SNAPC1 WILD-TYPE                                         1   237
D168V12, multiclass
                                           clus
vv                                          SNAPC1 MUTATED SNAPC1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V13, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     0   7
  SNAPC1 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      0    7
  SNAPC1 WILD-TYPE    4  303
                        clus
vv                       SNAPC1 MUTATED SNAPC1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(169) Variable = ALG10 MUTATION ANALYSIS
D169V1, survival
                 sevent
clus2               0   1
  ALG10 MUTATED     6   7
  ALG10 WILD-TYPE 224 132
  ALG10 MUTATED ALG10 WILD-TYPE 
             13             356 
  ALG10 MUTATED ALG10 WILD-TYPE 
              7             132 
$`ALG10 MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6455 TCGA-CD-A4MI 
        6.61         6.97        30.90        34.68        13.87        11.77 
TCGA-CG-5726 TCGA-D7-6818 TCGA-D7-A4YY TCGA-HU-8602 TCGA-HU-A4GU TCGA-HU-A4H3 
       28.96        12.36        13.78        22.32         6.58        29.00 
TCGA-VQ-AA6A 
       38.93 

$`ALG10 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        9.47         9.44         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-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-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-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
       17.19        10.26        15.22        15.98        12.79        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-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-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-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 

  ALG10 MUTATED ALG10 WILD-TYPE 
           6.58            0.00 
  ALG10 MUTATED ALG10 WILD-TYPE 
          38.93          122.30 
  ALG10 MUTATED ALG10 WILD-TYPE 
          13.87           14.35 
[1] "6.6 - 38.9 (13.9)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D169V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ALG10 MUTATED         0        1        0        0         1         4
  ALG10 WILD-TYPE       2       14       40       30        36        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ALG10 MUTATED           0          4          1          2        0
  ALG10 WILD-TYPE         3         66         52         30       38
D169V3, multiclass
            clus
vv           ALG10 MUTATED ALG10 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALG10 MUTATED     1   2   7   4
  ALG10 WILD-TYPE  21  90 166  93
D169V4, multiclass
    clus
vv   ALG10 MUTATED ALG10 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             7             166
  T4             4              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
  ALG10 MUTATED     4   5   0   4
  ALG10 WILD-TYPE 114  99  77  73
D169V5, multiclass
    clus
vv   ALG10 MUTATED ALG10 WILD-TYPE
  N0             4             114
  N1             5              99
  N2             0              77
  N3             4              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"
D169V6, binary
                 cls
clus                0   1
  ALG10 MUTATED    13   0
  ALG10 WILD-TYPE 333  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG10 MUTATED     13    0
  ALG10 WILD-TYPE  333   29
   clus
vv  ALG10 MUTATED ALG10 WILD-TYPE
  0            13             333
  1             0              29
[1] 2 2
[1] FALSE
D169V7, binary
                 cls
clus                0   1
  ALG10 MUTATED     5   9
  ALG10 WILD-TYPE 140 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG10 MUTATED      5    9
  ALG10 WILD-TYPE  140  239
        clus
vv       ALG10 MUTATED ALG10 WILD-TYPE
  FEMALE             5             140
  MALE               9             239
[1] 2 2
[1] FALSE
D169V8, binary
                 cls
clus                0   1
  ALG10 MUTATED     9   3
  ALG10 WILD-TYPE 283  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG10 MUTATED      9    3
  ALG10 WILD-TYPE  283   56
     clus
vv    ALG10 MUTATED ALG10 WILD-TYPE
  NO              9             283
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ALG10 MUTATED                                          0
  ALG10 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ALG10 MUTATED                                       4
  ALG10 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ALG10 MUTATED                                                        7
  ALG10 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ALG10 MUTATED                                                   0
  ALG10 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ALG10 MUTATED                                                                   3
  ALG10 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ALG10 MUTATED                                                    0
  ALG10 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ALG10 MUTATED                                                  0
  ALG10 WILD-TYPE                                               61
D169V9, multiclass
                                                                   clus
vv                                                                  ALG10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  ALG10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ALG10 MUTATED    10   0   0   3
  ALG10 WILD-TYPE 301  14  15  21
D169V10, multiclass
    clus
vv   ALG10 MUTATED ALG10 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ALG10 MUTATED       4                         0
  ALG10 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ALG10 MUTATED                                           0     9
  ALG10 WILD-TYPE                                         1   234
D169V12, multiclass
                                           clus
vv                                          ALG10 MUTATED ALG10 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V13, binary
                 cls
clus                0   1
  ALG10 MUTATED     0  12
  ALG10 WILD-TYPE   4 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG10 MUTATED      0   12
  ALG10 WILD-TYPE    4  298
                        clus
vv                       ALG10 MUTATED ALG10 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(170) Variable = HDLBP MUTATION ANALYSIS
D170V1, survival
                 sevent
clus2               0   1
  HDLBP MUTATED    20   8
  HDLBP WILD-TYPE 210 131
  HDLBP MUTATED HDLBP WILD-TYPE 
             28             341 
  HDLBP MUTATED HDLBP WILD-TYPE 
              8             131 
$`HDLBP MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6852 
       21.99        26.70        19.56         9.34         9.67        44.94 
TCGA-BR-7704 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-A4QL 
       35.24        29.59         0.26         4.31        25.05        16.14 
TCGA-CD-8530 TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-6518 TCGA-D7-A4YT 
       12.39        15.95         6.02        28.96        19.13        14.27 
TCGA-D7-A74A TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-8604 TCGA-HU-A4GN TCGA-HU-A4GT 
       19.96        11.08        30.51        22.82        29.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-RD-A7C1 TCGA-VQ-A8P2 
        6.58        23.84        16.67        38.14 

$`HDLBP WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
        9.86        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-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-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-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-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-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-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-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-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-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-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34         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-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-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-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 

  HDLBP MUTATED HDLBP WILD-TYPE 
           0.26            0.00 
  HDLBP MUTATED HDLBP WILD-TYPE 
          44.94          122.30 
  HDLBP MUTATED HDLBP WILD-TYPE 
         19.345          14.040 
[1] "0.3 - 44.9 (19.3)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.5"
D170V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HDLBP MUTATED         0        1        4        3         5         4
  HDLBP WILD-TYPE       2       14       36       27        32        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HDLBP MUTATED           0          6          1          3        2
  HDLBP WILD-TYPE         3         64         52         29       36
D170V3, multiclass
            clus
vv           HDLBP MUTATED HDLBP WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               4              36
  STAGE II               3              27
  STAGE IIA              5              32
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             6              64
  STAGE IIIB             1              52
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HDLBP MUTATED     1   9  10   9
  HDLBP WILD-TYPE  21  83 163  88
D170V4, multiclass
    clus
vv   HDLBP MUTATED HDLBP WILD-TYPE
  T1             1              21
  T2             9              83
  T3            10             163
  T4             9              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
  HDLBP MUTATED    14   8   2   6
  HDLBP WILD-TYPE 104  96  75  71
D170V5, multiclass
    clus
vv   HDLBP MUTATED HDLBP WILD-TYPE
  N0            14             104
  N1             8              96
  N2             2              75
  N3             6              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"
D170V6, binary
                 cls
clus                0   1
  HDLBP MUTATED    30   1
  HDLBP WILD-TYPE 316  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED     30    1
  HDLBP WILD-TYPE  316   28
   clus
vv  HDLBP MUTATED HDLBP WILD-TYPE
  0            30             316
  1             1              28
[1] 2 2
[1] FALSE
D170V7, binary
                 cls
clus                0   1
  HDLBP MUTATED    16  15
  HDLBP WILD-TYPE 129 233
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED     16   15
  HDLBP WILD-TYPE  129  233
        clus
vv       HDLBP MUTATED HDLBP WILD-TYPE
  FEMALE            16             129
  MALE              15             233
[1] 2 2
[1] FALSE
D170V8, binary
                 cls
clus                0   1
  HDLBP MUTATED    23   5
  HDLBP WILD-TYPE 269  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED     23    5
  HDLBP WILD-TYPE  269   54
     clus
vv    HDLBP MUTATED HDLBP WILD-TYPE
  NO             23             269
  YES             5              54
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HDLBP MUTATED                                          0
  HDLBP WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HDLBP MUTATED                                       6
  HDLBP WILD-TYPE                                    64
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HDLBP MUTATED                                                       12
  HDLBP WILD-TYPE                                                    146
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HDLBP MUTATED                                                   2
  HDLBP WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HDLBP MUTATED                                                                   5
  HDLBP WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HDLBP MUTATED                                                    0
  HDLBP WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HDLBP MUTATED                                                  6
  HDLBP WILD-TYPE                                               55
D170V9, multiclass
                                                                   clus
vv                                                                  HDLBP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              6
                                                                   clus
vv                                                                  HDLBP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HDLBP MUTATED    23   3   1   3
  HDLBP WILD-TYPE 288  11  14  21
D170V10, multiclass
    clus
vv   HDLBP MUTATED HDLBP WILD-TYPE
  R0            23             288
  R1             3              11
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HDLBP MUTATED       6                         1
  HDLBP WILD-TYPE    81                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HDLBP MUTATED                                           0    17
  HDLBP WILD-TYPE                                         1   226
D170V12, multiclass
                                           clus
vv                                          HDLBP MUTATED HDLBP WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V13, binary
                 cls
clus                0   1
  HDLBP MUTATED     0  23
  HDLBP WILD-TYPE   4 287
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED      0   23
  HDLBP WILD-TYPE    4  287
                        clus
vv                       HDLBP MUTATED HDLBP WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            23             287
[1] 2 2
[1] FALSE

Clustering(171) Variable = GRINA MUTATION ANALYSIS
D171V1, survival
                 sevent
clus2               0   1
  GRINA MUTATED     6   1
  GRINA WILD-TYPE 224 138
  GRINA MUTATED GRINA WILD-TYPE 
              7             362 
  GRINA MUTATED GRINA WILD-TYPE 
              1             138 
$`GRINA MUTATED`
TCGA-BR-8591 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5728 TCGA-HF-7132 TCGA-HU-A4GX 
       28.14         6.58         6.02        65.10        77.29        20.25 
TCGA-SW-A7EA 
       19.04 

$`GRINA WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  GRINA MUTATED GRINA WILD-TYPE 
           6.02            0.00 
  GRINA MUTATED GRINA WILD-TYPE 
          77.29          122.30 
  GRINA MUTATED GRINA WILD-TYPE 
          20.25           14.12 
[1] "6.0 - 77.3 (20.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.8"
D171V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GRINA MUTATED         1        0        3        1         1         0
  GRINA WILD-TYPE       1       15       37       29        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GRINA MUTATED           0          0          0          2        1
  GRINA WILD-TYPE         3         70         53         30       37
D171V3, multiclass
            clus
vv           GRINA MUTATED GRINA WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GRINA MUTATED     1   4   1   3
  GRINA WILD-TYPE  21  88 172  94
D171V4, multiclass
    clus
vv   GRINA MUTATED GRINA WILD-TYPE
  T1             1              21
  T2             4              88
  T3             1             172
  T4             3              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
  GRINA MUTATED     4   3   1   1
  GRINA WILD-TYPE 114 101  76  76
D171V5, multiclass
    clus
vv   GRINA MUTATED GRINA WILD-TYPE
  N0             4             114
  N1             3             101
  N2             1              76
  N3             1              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"
D171V6, binary
                 cls
clus                0   1
  GRINA MUTATED     8   0
  GRINA WILD-TYPE 338  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      8    0
  GRINA WILD-TYPE  338   29
   clus
vv  GRINA MUTATED GRINA WILD-TYPE
  0             8             338
  1             0              29
[1] 2 2
[1] FALSE
D171V7, binary
                 cls
clus                0   1
  GRINA MUTATED     3   6
  GRINA WILD-TYPE 142 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      3    6
  GRINA WILD-TYPE  142  242
        clus
vv       GRINA MUTATED GRINA WILD-TYPE
  FEMALE             3             142
  MALE               6             242
[1] 2 2
[1] FALSE
D171V8, binary
                 cls
clus                0   1
  GRINA MUTATED     6   1
  GRINA WILD-TYPE 286  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      6    1
  GRINA WILD-TYPE  286   58
     clus
vv    GRINA MUTATED GRINA WILD-TYPE
  NO              6             286
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GRINA MUTATED                                          0
  GRINA WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GRINA MUTATED                                       3
  GRINA WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GRINA MUTATED                                                        2
  GRINA WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GRINA MUTATED                                                   1
  GRINA WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GRINA MUTATED                                                                   3
  GRINA WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GRINA MUTATED                                                    0
  GRINA WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GRINA MUTATED                                                  0
  GRINA WILD-TYPE                                               61
D171V9, multiclass
                                                                   clus
vv                                                                  GRINA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  GRINA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GRINA MUTATED     8   0   0   0
  GRINA WILD-TYPE 303  14  15  24
D171V10, multiclass
    clus
vv   GRINA MUTATED GRINA WILD-TYPE
  R0             8             303
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GRINA MUTATED       2                         1
  GRINA WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GRINA MUTATED                                           0     2
  GRINA WILD-TYPE                                         1   241
D171V12, multiclass
                                           clus
vv                                          GRINA MUTATED GRINA WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V13, binary
                 cls
clus                0   1
  GRINA MUTATED     0   5
  GRINA WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      0    5
  GRINA WILD-TYPE    4  305
                        clus
vv                       GRINA MUTATED GRINA WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(172) Variable = RAB42 MUTATION ANALYSIS
D172V1, survival
                 sevent
clus2               0   1
  RAB42 MUTATED     3   2
  RAB42 WILD-TYPE 227 137
  RAB42 MUTATED RAB42 WILD-TYPE 
              5             364 
  RAB42 MUTATED RAB42 WILD-TYPE 
              2             137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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           14.22 
[1] "6.6 - 77.3 (19.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D172V2, 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       2       14       40       29        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAB42 MUTATED           1          1          1          0        0
  RAB42 WILD-TYPE         2         69         52         32       38
D172V3, multiclass
            clus
vv           RAB42 MUTATED RAB42 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              1               2
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAB42 MUTATED     1   2   2   0
  RAB42 WILD-TYPE  21  90 171  97
D172V4, multiclass
    clus
vv   RAB42 MUTATED RAB42 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             2             171
  T4             0              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
  RAB42 MUTATED     1   2   1   1
  RAB42 WILD-TYPE 117 102  76  76
D172V5, multiclass
    clus
vv   RAB42 MUTATED RAB42 WILD-TYPE
  N0             1             117
  N1             2             102
  N2             1              76
  N3             1              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"
D172V6, binary
                 cls
clus                0   1
  RAB42 MUTATED     5   0
  RAB42 WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      5    0
  RAB42 WILD-TYPE  341   29
   clus
vv  RAB42 MUTATED RAB42 WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D172V7, binary
                 cls
clus                0   1
  RAB42 MUTATED     3   2
  RAB42 WILD-TYPE 142 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      3    2
  RAB42 WILD-TYPE  142  246
        clus
vv       RAB42 MUTATED RAB42 WILD-TYPE
  FEMALE             3             142
  MALE               2             246
[1] 2 2
[1] FALSE
D172V8, binary
                 cls
clus                0   1
  RAB42 MUTATED     4   1
  RAB42 WILD-TYPE 288  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      4    1
  RAB42 WILD-TYPE  288   58
     clus
vv    RAB42 MUTATED RAB42 WILD-TYPE
  NO              4             288
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RAB42 MUTATED                                          0
  RAB42 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RAB42 MUTATED                                       0
  RAB42 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RAB42 MUTATED                                                        1
  RAB42 WILD-TYPE                                                    157
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RAB42 MUTATED                                                   1
  RAB42 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RAB42 MUTATED                                                                   0
  RAB42 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RAB42 MUTATED                                                    1
  RAB42 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RAB42 MUTATED                                                  2
  RAB42 WILD-TYPE                                               59
D172V9, multiclass
                                                                   clus
vv                                                                  RAB42 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  RAB42 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RAB42 MUTATED     4   0   0   1
  RAB42 WILD-TYPE 307  14  15  23
D172V10, multiclass
    clus
vv   RAB42 MUTATED RAB42 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RAB42 MUTATED       0                         0
  RAB42 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAB42 MUTATED                                           0     4
  RAB42 WILD-TYPE                                         1   239
D172V12, multiclass
                                           clus
vv                                          RAB42 MUTATED RAB42 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V13, binary
                 cls
clus                0   1
  RAB42 MUTATED     0   4
  RAB42 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      0    4
  RAB42 WILD-TYPE    4  306
                        clus
vv                       RAB42 MUTATED RAB42 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(173) Variable = SAMD9L MUTATION ANALYSIS
D173V1, survival
                  sevent
clus2                0   1
  SAMD9L MUTATED    17   3
  SAMD9L WILD-TYPE 213 136
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              20              349 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
               3              136 
$`SAMD9L MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8370 
       21.99        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-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-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
        9.86        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-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-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-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-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-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-A4GY 
       11.77        21.37        29.98         8.98         0.10         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-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-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-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 

  SAMD9L MUTATED SAMD9L WILD-TYPE 
            0.26             0.00 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
            65.1            122.3 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
          16.435           14.270 
[1] "0.3 - 65.1 (16.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.6"
D173V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SAMD9L MUTATED         0        0        5        1         3         5
  SAMD9L WILD-TYPE       2       15       35       29        34        47
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SAMD9L MUTATED           0          2          1          1        4
  SAMD9L WILD-TYPE         3         68         52         31       34
D173V3, multiclass
            clus
vv           SAMD9L MUTATED SAMD9L WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                5               35
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               5               47
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                4               34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SAMD9L MUTATED     0   7   6   9
  SAMD9L WILD-TYPE  22  85 167  88
D173V4, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  T1              0               22
  T2              7               85
  T3              6              167
  T4              9               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
  SAMD9L MUTATED    11   6   4   1
  SAMD9L WILD-TYPE 107  98  73  76
D173V5, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  N0             11              107
  N1              6               98
  N2              4               73
  N3              1               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"
D173V6, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    20   2
  SAMD9L WILD-TYPE 326  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     20    2
  SAMD9L WILD-TYPE  326   27
   clus
vv  SAMD9L MUTATED SAMD9L WILD-TYPE
  0             20              326
  1              2               27
[1] 2 2
[1] FALSE
D173V7, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    12  10
  SAMD9L WILD-TYPE 133 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     12   10
  SAMD9L WILD-TYPE  133  238
        clus
vv       SAMD9L MUTATED SAMD9L WILD-TYPE
  FEMALE             12              133
  MALE               10              238
[1] 2 2
[1] FALSE
D173V8, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    18   1
  SAMD9L WILD-TYPE 274  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     18    1
  SAMD9L WILD-TYPE  274   58
     clus
vv    SAMD9L MUTATED SAMD9L WILD-TYPE
  NO              18              274
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SAMD9L MUTATED                                          0
  SAMD9L WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SAMD9L MUTATED                                       6
  SAMD9L WILD-TYPE                                    64
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SAMD9L MUTATED                                                        7
  SAMD9L WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SAMD9L MUTATED                                                   0
  SAMD9L WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SAMD9L MUTATED                                                                   4
  SAMD9L WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SAMD9L MUTATED                                                    1
  SAMD9L WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SAMD9L MUTATED                                                  4
  SAMD9L WILD-TYPE                                               57
D173V9, multiclass
                                                                   clus
vv                                                                  SAMD9L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  SAMD9L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SAMD9L MUTATED    18   0   1   2
  SAMD9L WILD-TYPE 293  14  14  22
D173V10, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  R0             18              293
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SAMD9L MUTATED       8                         0
  SAMD9L WILD-TYPE    79                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SAMD9L MUTATED                                           0    10
  SAMD9L WILD-TYPE                                         1   233
D173V12, multiclass
                                           clus
vv                                          SAMD9L MUTATED SAMD9L WILD-TYPE
  ASIAN                                                  8               79
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V13, binary
                  cls
clus                 0   1
  SAMD9L MUTATED     0  17
  SAMD9L WILD-TYPE   4 293
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED      0   17
  SAMD9L WILD-TYPE    4  293
                        clus
vv                       SAMD9L MUTATED SAMD9L WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             17              293
[1] 2 2
[1] FALSE

Clustering(174) Variable = GLT6D1 MUTATION ANALYSIS
D174V1, survival
                  sevent
clus2                0   1
  GLT6D1 MUTATED     9   4
  GLT6D1 WILD-TYPE 221 135
  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
              13              356 
  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
               4              135 
$`GLT6D1 MUTATED`
TCGA-B7-A5TK TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8366 TCGA-BR-A44U TCGA-BR-A4J2 
        9.47        29.59         8.05         0.95        13.87        14.17 
TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8534 TCGA-CG-5725 TCGA-FP-8209 TCGA-FP-8211 
       12.59        12.33        12.07        15.02        59.54        13.58 
TCGA-HU-A4GP 
        8.98 

$`GLT6D1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        26.70        11.70        19.56        11.01 
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-8285 
       14.43        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-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-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-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-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-8529 
       12.10        12.39        12.76        12.53         7.17        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-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-D7-6526 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-8210 
        3.48        19.53        14.07        22.29        17.06         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-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-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 

  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
            0.95             0.00 
  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
           59.54           122.30 
  GLT6D1 MUTATED GLT6D1 WILD-TYPE 
           12.59            14.71 
[1] "0.9 - 59.5 (12.6)"  "0.0 - 122.3 (14.7)"
[1] "hr=" "1.1"
D174V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLT6D1 MUTATED         0        0        2        1         2         3
  GLT6D1 WILD-TYPE       2       15       38       29        35        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLT6D1 MUTATED           0          4          1          1        0
  GLT6D1 WILD-TYPE         3         66         52         31       38
D174V3, multiclass
            clus
vv           GLT6D1 MUTATED GLT6D1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GLT6D1 MUTATED     0   3   5   6
  GLT6D1 WILD-TYPE  22  89 168  91
D174V4, multiclass
    clus
vv   GLT6D1 MUTATED GLT6D1 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              5              168
  T4              6               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
  GLT6D1 MUTATED     8   3   0   2
  GLT6D1 WILD-TYPE 110 101  77  75
D174V5, multiclass
    clus
vv   GLT6D1 MUTATED GLT6D1 WILD-TYPE
  N0              8              110
  N1              3              101
  N2              0               77
  N3              2               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"
D174V6, binary
                  cls
clus                 0   1
  GLT6D1 MUTATED    13   0
  GLT6D1 WILD-TYPE 333  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT6D1 MUTATED     13    0
  GLT6D1 WILD-TYPE  333   29
   clus
vv  GLT6D1 MUTATED GLT6D1 WILD-TYPE
  0             13              333
  1              0               29
[1] 2 2
[1] FALSE
D174V7, binary
                  cls
clus                 0   1
  GLT6D1 MUTATED     7   7
  GLT6D1 WILD-TYPE 138 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT6D1 MUTATED      7    7
  GLT6D1 WILD-TYPE  138  241
        clus
vv       GLT6D1 MUTATED GLT6D1 WILD-TYPE
  FEMALE              7              138
  MALE                7              241
[1] 2 2
[1] FALSE
D174V8, binary
                  cls
clus                 0   1
  GLT6D1 MUTATED     9   4
  GLT6D1 WILD-TYPE 283  55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT6D1 MUTATED      9    4
  GLT6D1 WILD-TYPE  283   55
     clus
vv    GLT6D1 MUTATED GLT6D1 WILD-TYPE
  NO               9              283
  YES              4               55
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GLT6D1 MUTATED                                          0
  GLT6D1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GLT6D1 MUTATED                                       4
  GLT6D1 WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GLT6D1 MUTATED                                                        7
  GLT6D1 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GLT6D1 MUTATED                                                   1
  GLT6D1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GLT6D1 MUTATED                                                                   2
  GLT6D1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GLT6D1 MUTATED                                                    0
  GLT6D1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GLT6D1 MUTATED                                                  0
  GLT6D1 WILD-TYPE                                               61
D174V9, multiclass
                                                                   clus
vv                                                                  GLT6D1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  GLT6D1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GLT6D1 MUTATED    11   1   0   1
  GLT6D1 WILD-TYPE 300  13  15  23
D174V10, multiclass
    clus
vv   GLT6D1 MUTATED GLT6D1 WILD-TYPE
  R0             11              300
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GLT6D1 MUTATED       5                         0
  GLT6D1 WILD-TYPE    82                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GLT6D1 MUTATED                                           0     8
  GLT6D1 WILD-TYPE                                         1   235
D174V12, multiclass
                                           clus
vv                                          GLT6D1 MUTATED GLT6D1 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V13, binary
                  cls
clus                 0   1
  GLT6D1 MUTATED     0  13
  GLT6D1 WILD-TYPE   4 297
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT6D1 MUTATED      0   13
  GLT6D1 WILD-TYPE    4  297
                        clus
vv                       GLT6D1 MUTATED GLT6D1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             13              297
[1] 2 2
[1] FALSE

Clustering(175) Variable = SLC22A6 MUTATION ANALYSIS
D175V1, survival
                   sevent
clus2                 0   1
  SLC22A6 MUTATED     7   6
  SLC22A6 WILD-TYPE 223 133
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
               13               356 
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
                6               133 
$`SLC22A6 MUTATED`
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6457 TCGA-BR-8363 TCGA-CD-8536 TCGA-CD-A4MG 
        9.34        34.68        13.68         0.26        12.43         6.58 
TCGA-CG-4305 TCGA-CG-4465 TCGA-CG-5726 TCGA-D7-A6EY TCGA-HF-A5NB TCGA-HU-A4GH 
       15.95         9.01        28.96        11.44        30.51        11.77 
TCGA-SW-A7EA 
       19.04 

$`SLC22A6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-6458 
        9.57         6.61        15.95        13.87        17.29        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-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-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-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-F1-6874 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-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-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 

  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
             0.26              0.00 
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
            34.68            122.30 
  SLC22A6 MUTATED SLC22A6 WILD-TYPE 
            12.43             14.45 
[1] "0.3 - 34.7 (12.4)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.4"
D175V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC22A6 MUTATED         0        2        2        2         3         0
  SLC22A6 WILD-TYPE       2       13       38       28        34        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A6 MUTATED           0          1          1          1        1
  SLC22A6 WILD-TYPE         3         69         52         31       37
D175V3, multiclass
            clus
vv           SLC22A6 MUTATED SLC22A6 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                13
  STAGE IB                 2                38
  STAGE II                 2                28
  STAGE IIA                3                34
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC22A6 MUTATED     2   3   5   3
  SLC22A6 WILD-TYPE  20  89 168  94
D175V4, multiclass
    clus
vv   SLC22A6 MUTATED SLC22A6 WILD-TYPE
  T1               2                20
  T2               3                89
  T3               5               168
  T4               3                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
  SLC22A6 MUTATED     9   2   0   3
  SLC22A6 WILD-TYPE 109 102  77  74
D175V5, multiclass
    clus
vv   SLC22A6 MUTATED SLC22A6 WILD-TYPE
  N0               9               109
  N1               2               102
  N2               0                77
  N3               3                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"
D175V6, binary
                   cls
clus                  0   1
  SLC22A6 MUTATED    13   1
  SLC22A6 WILD-TYPE 333  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A6 MUTATED     13    1
  SLC22A6 WILD-TYPE  333   28
   clus
vv  SLC22A6 MUTATED SLC22A6 WILD-TYPE
  0              13               333
  1               1                28
[1] 2 2
[1] FALSE
D175V7, binary
                   cls
clus                  0   1
  SLC22A6 MUTATED     7   7
  SLC22A6 WILD-TYPE 138 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A6 MUTATED      7    7
  SLC22A6 WILD-TYPE  138  241
        clus
vv       SLC22A6 MUTATED SLC22A6 WILD-TYPE
  FEMALE               7               138
  MALE                 7               241
[1] 2 2
[1] FALSE
D175V8, binary
                   cls
clus                  0   1
  SLC22A6 MUTATED    10   1
  SLC22A6 WILD-TYPE 282  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A6 MUTATED     10    1
  SLC22A6 WILD-TYPE  282   58
     clus
vv    SLC22A6 MUTATED SLC22A6 WILD-TYPE
  NO               10               282
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC22A6 MUTATED                                          0
  SLC22A6 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC22A6 MUTATED                                       3
  SLC22A6 WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC22A6 MUTATED                                                        7
  SLC22A6 WILD-TYPE                                                    151
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC22A6 MUTATED                                                   1
  SLC22A6 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC22A6 MUTATED                                                                   1
  SLC22A6 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC22A6 MUTATED                                                    0
  SLC22A6 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC22A6 MUTATED                                                  2
  SLC22A6 WILD-TYPE                                               59
D175V9, multiclass
                                                                   clus
vv                                                                  SLC22A6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  SLC22A6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC22A6 MUTATED     9   1   1   2
  SLC22A6 WILD-TYPE 302  13  14  22
D175V10, multiclass
    clus
vv   SLC22A6 MUTATED SLC22A6 WILD-TYPE
  R0               9               302
  R1               1                13
  R2               1                14
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC22A6 MUTATED       3                         0
  SLC22A6 WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC22A6 MUTATED                                           0     7
  SLC22A6 WILD-TYPE                                         1   236
D175V12, multiclass
                                           clus
vv                                          SLC22A6 MUTATED SLC22A6 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V13, binary
                   cls
clus                  0   1
  SLC22A6 MUTATED     0  10
  SLC22A6 WILD-TYPE   4 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A6 MUTATED      0   10
  SLC22A6 WILD-TYPE    4  300
                        clus
vv                       SLC22A6 MUTATED SLC22A6 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              10               300
[1] 2 2
[1] FALSE

Clustering(176) Variable = SVIL MUTATION ANALYSIS
D176V1, survival
                sevent
clus2              0   1
  SVIL MUTATED    18   7
  SVIL WILD-TYPE 212 132
  SVIL MUTATED SVIL WILD-TYPE 
            25            344 
  SVIL MUTATED SVIL WILD-TYPE 
             7            132 
$`SVIL MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-6803 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8361 
       21.99        34.68        31.20        35.84        29.59        31.10 
TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-A4MI 
       31.27         1.12        31.96        20.42        16.14        11.77 
TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-A4YV 
        9.01         6.02       105.07        28.96        65.10         5.92 
TCGA-D7-A6ET TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GX 
       26.43        11.44        22.32        22.68        29.98        20.25 
TCGA-VQ-A8P2 
       38.14 

$`SVIL WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-A4PF TCGA-BR-A4QI 
        0.66        32.52        13.51        20.65         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-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-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        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-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EV 
       14.27        16.44        36.43        13.78        14.76        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-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-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 

  SVIL MUTATED SVIL WILD-TYPE 
          1.12           0.00 
  SVIL MUTATED SVIL WILD-TYPE 
        105.07         122.30 
  SVIL MUTATED SVIL WILD-TYPE 
         26.43          13.94 
[1] "1.1 - 105.1 (26.4)" "0.0 - 122.3 (13.9)"
[1] "hr=" "2"  
D176V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SVIL MUTATED         1        1        3        1         4         4
  SVIL WILD-TYPE       1       14       37       29        33        48
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SVIL MUTATED           0          3          3          4        5
  SVIL WILD-TYPE         3         67         50         28       33
D176V3, multiclass
            clus
vv           SVIL MUTATED SVIL WILD-TYPE
  STAGE I               1              1
  STAGE IA              1             14
  STAGE IB              3             37
  STAGE II              1             29
  STAGE IIA             4             33
  STAGE IIB             4             48
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            3             50
  STAGE IIIC            4             28
  STAGE IV              5             33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SVIL MUTATED     3   5   9  13
  SVIL WILD-TYPE  19  87 164  84
D176V4, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  T1            3             19
  T2            5             87
  T3            9            164
  T4           13             84
[1] 4 2
[1] TRUE
[1] "dimension of 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    10   9   4   6
  SVIL WILD-TYPE 108  95  73  71
D176V5, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  N0           10            108
  N1            9             95
  N2            4             73
  N3            6             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"
D176V6, binary
                cls
clus               0   1
  SVIL MUTATED    26   3
  SVIL WILD-TYPE 320  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     26    3
  SVIL WILD-TYPE  320   26
   clus
vv  SVIL MUTATED SVIL WILD-TYPE
  0           26            320
  1            3             26
[1] 2 2
[1] FALSE
D176V7, binary
                cls
clus               0   1
  SVIL MUTATED    19  11
  SVIL WILD-TYPE 126 237
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     19   11
  SVIL WILD-TYPE  126  237
        clus
vv       SVIL MUTATED SVIL WILD-TYPE
  FEMALE           19            126
  MALE             11            237
[1] 2 2
[1] FALSE
D176V8, binary
                cls
clus               0   1
  SVIL MUTATED    22   1
  SVIL WILD-TYPE 270  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     22    1
  SVIL WILD-TYPE  270   58
     clus
vv    SVIL MUTATED SVIL WILD-TYPE
  NO            22            270
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SVIL MUTATED                                          0
  SVIL WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SVIL MUTATED                                       6
  SVIL WILD-TYPE                                    64
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SVIL MUTATED                                                       14
  SVIL WILD-TYPE                                                    144
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SVIL MUTATED                                                   1
  SVIL WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SVIL MUTATED                                                                   4
  SVIL WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SVIL MUTATED                                                    0
  SVIL WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SVIL MUTATED                                                  5
  SVIL WILD-TYPE                                               56
D176V9, multiclass
                                                                   clus
vv                                                                  SVIL MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             5
                                                                   clus
vv                                                                  SVIL WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SVIL MUTATED    23   0   2   3
  SVIL WILD-TYPE 288  14  13  21
D176V10, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  R0           23            288
  R1            0             14
  R2            2             13
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SVIL MUTATED       6                         1
  SVIL WILD-TYPE    81                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SVIL MUTATED                                           0    16
  SVIL WILD-TYPE                                         1   227
D176V12, multiclass
                                           clus
vv                                          SVIL MUTATED SVIL WILD-TYPE
  ASIAN                                                6             81
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               16            227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V13, binary
                cls
clus               0   1
  SVIL MUTATED     0  22
  SVIL WILD-TYPE   4 288
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED      0   22
  SVIL WILD-TYPE    4  288
                        clus
vv                       SVIL MUTATED SVIL WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           22            288
[1] 2 2
[1] FALSE

Clustering(177) Variable = CCDC148 MUTATION ANALYSIS
D177V1, survival
                   sevent
clus2                 0   1
  CCDC148 MUTATED     6   2
  CCDC148 WILD-TYPE 224 137
  CCDC148 MUTATED CCDC148 WILD-TYPE 
                8               361 
  CCDC148 MUTATED CCDC148 WILD-TYPE 
                2               137 
$`CCDC148 MUTATED`
TCGA-BR-A4QL TCGA-CG-5726 TCGA-D7-6524 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GU 
       16.14        28.96        17.85        22.68        29.98         6.58 
TCGA-VQ-A8P2 TCGA-VQ-A91V 
       38.14        42.64 

$`CCDC148 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.54        18.61        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-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-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 

  CCDC148 MUTATED CCDC148 WILD-TYPE 
             6.58              0.00 
  CCDC148 MUTATED CCDC148 WILD-TYPE 
            42.64            122.30 
  CCDC148 MUTATED CCDC148 WILD-TYPE 
            25.82             14.07 
[1] "6.6 - 42.6 (25.8)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.1"
D177V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC148 MUTATED         0        1        0        1         1         2
  CCDC148 WILD-TYPE       2       14       40       29        36        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC148 MUTATED           0          2          1          0        0
  CCDC148 WILD-TYPE         3         68         52         32       38
D177V3, multiclass
            clus
vv           CCDC148 MUTATED CCDC148 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 0                40
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC148 MUTATED     1   2   4   1
  CCDC148 WILD-TYPE  21  90 169  96
D177V4, multiclass
    clus
vv   CCDC148 MUTATED CCDC148 WILD-TYPE
  T1               1                21
  T2               2                90
  T3               4               169
  T4               1                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
  CCDC148 MUTATED     1   5   1   1
  CCDC148 WILD-TYPE 117  99  76  76
D177V5, multiclass
    clus
vv   CCDC148 MUTATED CCDC148 WILD-TYPE
  N0               1               117
  N1               5                99
  N2               1                76
  N3               1                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"
D177V6, binary
                   cls
clus                  0   1
  CCDC148 MUTATED     8   0
  CCDC148 WILD-TYPE 338  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC148 MUTATED      8    0
  CCDC148 WILD-TYPE  338   29
   clus
vv  CCDC148 MUTATED CCDC148 WILD-TYPE
  0               8               338
  1               0                29
[1] 2 2
[1] FALSE
D177V7, binary
                   cls
clus                  0   1
  CCDC148 MUTATED     2   6
  CCDC148 WILD-TYPE 143 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC148 MUTATED      2    6
  CCDC148 WILD-TYPE  143  242
        clus
vv       CCDC148 MUTATED CCDC148 WILD-TYPE
  FEMALE               2               143
  MALE                 6               242
[1] 2 2
[1] FALSE
D177V8, binary
                   cls
clus                  0   1
  CCDC148 MUTATED     5   2
  CCDC148 WILD-TYPE 287  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC148 MUTATED      5    2
  CCDC148 WILD-TYPE  287   57
     clus
vv    CCDC148 MUTATED CCDC148 WILD-TYPE
  NO                5               287
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CCDC148 MUTATED                                          0
  CCDC148 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CCDC148 MUTATED                                       3
  CCDC148 WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC148 MUTATED                                                        1
  CCDC148 WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CCDC148 MUTATED                                                   1
  CCDC148 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC148 MUTATED                                                                   1
  CCDC148 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CCDC148 MUTATED                                                    0
  CCDC148 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CCDC148 MUTATED                                                  2
  CCDC148 WILD-TYPE                                               59
D177V9, multiclass
                                                                   clus
vv                                                                  CCDC148 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  CCDC148 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC148 MUTATED     6   1   0   0
  CCDC148 WILD-TYPE 305  13  15  24
D177V10, multiclass
    clus
vv   CCDC148 MUTATED CCDC148 WILD-TYPE
  R0               6               305
  R1               1                13
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CCDC148 MUTATED       3                         0
  CCDC148 WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC148 MUTATED                                           0     3
  CCDC148 WILD-TYPE                                         1   240
D177V12, multiclass
                                           clus
vv                                          CCDC148 MUTATED CCDC148 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V13, binary
                   cls
clus                  0   1
  CCDC148 MUTATED     0   5
  CCDC148 WILD-TYPE   4 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC148 MUTATED      0    5
  CCDC148 WILD-TYPE    4  305
                        clus
vv                       CCDC148 MUTATED CCDC148 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(178) Variable = MOBKL1A MUTATION ANALYSIS
D178V1, survival
                   sevent
clus2                 0   1
  MOBKL1A MUTATED     5   0
  MOBKL1A WILD-TYPE 225 139
  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
                5               364 
  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
                0               139 
$`MOBKL1A MUTATED`
TCGA-BR-6452 TCGA-CG-4305 TCGA-CG-5723 TCGA-FP-A4BE TCGA-HU-A4GT 
       34.68        15.95       105.07        11.08         6.51 

$`MOBKL1A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
             6.51              0.00 
  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
           105.07            122.30 
  MOBKL1A MUTATED MOBKL1A WILD-TYPE 
            15.95             14.22 
[1] "6.5 - 105.1 (15.9)" "0.0 - 122.3 (14.2)"
[1] "hr="     "9300000"
D178V2, 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       2       15       40       28        34        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MOBKL1A MUTATED           0          0          0          0        1
  MOBKL1A WILD-TYPE         3         70         53         32       37
D178V3, multiclass
            clus
vv           MOBKL1A MUTATED MOBKL1A WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 2                28
  STAGE IIA                3                34
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  MOBKL1A MUTATED     0   2   3   1
  MOBKL1A WILD-TYPE  22  90 170  96
D178V4, multiclass
    clus
vv   MOBKL1A MUTATED MOBKL1A WILD-TYPE
  T1               0                22
  T2               2                90
  T3               3               170
  T4               1                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
  MOBKL1A MUTATED     3   2   1   0
  MOBKL1A WILD-TYPE 115 102  76  77
D178V5, multiclass
    clus
vv   MOBKL1A MUTATED MOBKL1A WILD-TYPE
  N0               3               115
  N1               2               102
  N2               1                76
  N3               0                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"
D178V6, binary
                   cls
clus                  0   1
  MOBKL1A MUTATED     6   0
  MOBKL1A WILD-TYPE 340  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL1A MUTATED      6    0
  MOBKL1A WILD-TYPE  340   29
   clus
vv  MOBKL1A MUTATED MOBKL1A WILD-TYPE
  0               6               340
  1               0                29
[1] 2 2
[1] FALSE
D178V7, binary
                   cls
clus                  0   1
  MOBKL1A MUTATED     3   3
  MOBKL1A WILD-TYPE 142 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL1A MUTATED      3    3
  MOBKL1A WILD-TYPE  142  245
        clus
vv       MOBKL1A MUTATED MOBKL1A WILD-TYPE
  FEMALE               3               142
  MALE                 3               245
[1] 2 2
[1] FALSE
D178V8, binary
                   cls
clus                  0   1
  MOBKL1A MUTATED     4   1
  MOBKL1A WILD-TYPE 288  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL1A MUTATED      4    1
  MOBKL1A WILD-TYPE  288   58
     clus
vv    MOBKL1A MUTATED MOBKL1A WILD-TYPE
  NO                4               288
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MOBKL1A MUTATED                                          0
  MOBKL1A WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MOBKL1A MUTATED                                       0
  MOBKL1A WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MOBKL1A MUTATED                                                        5
  MOBKL1A WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MOBKL1A MUTATED                                                   0
  MOBKL1A WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MOBKL1A MUTATED                                                                   0
  MOBKL1A WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MOBKL1A MUTATED                                                    0
  MOBKL1A WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MOBKL1A MUTATED                                                  1
  MOBKL1A WILD-TYPE                                               60
D178V9, multiclass
                                                                   clus
vv                                                                  MOBKL1A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  MOBKL1A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  MOBKL1A MUTATED     5   0   0   1
  MOBKL1A WILD-TYPE 306  14  15  23
D178V10, multiclass
    clus
vv   MOBKL1A MUTATED MOBKL1A WILD-TYPE
  R0               5               306
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  MOBKL1A MUTATED       1                         1
  MOBKL1A WILD-TYPE    86                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MOBKL1A MUTATED                                           0     2
  MOBKL1A WILD-TYPE                                         1   241
D178V12, multiclass
                                           clus
vv                                          MOBKL1A MUTATED MOBKL1A WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V13, binary
                   cls
clus                  0   1
  MOBKL1A MUTATED     0   4
  MOBKL1A WILD-TYPE   4 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL1A MUTATED      0    4
  MOBKL1A WILD-TYPE    4  306
                        clus
vv                       MOBKL1A MUTATED MOBKL1A WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4               306
[1] 2 2
[1] FALSE

Clustering(179) Variable = SETDB2 MUTATION ANALYSIS
D179V1, survival
                  sevent
clus2                0   1
  SETDB2 MUTATED     7   3
  SETDB2 WILD-TYPE 223 136
  SETDB2 MUTATED SETDB2 WILD-TYPE 
              10              359 
  SETDB2 MUTATED SETDB2 WILD-TYPE 
               3              136 
$`SETDB2 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8368 
       26.70         6.97        30.90        34.68        31.10         4.31 
TCGA-BR-8591 TCGA-CG-4305 TCGA-CG-4443 TCGA-VQ-AA64 
       28.14        15.95        29.98        18.41 

$`SETDB2 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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 
            4.31             0.00 
  SETDB2 MUTATED SETDB2 WILD-TYPE 
           34.68           122.30 
  SETDB2 MUTATED SETDB2 WILD-TYPE 
           27.42            14.07 
[1] "4.3 - 34.7 (27.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D179V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SETDB2 MUTATED         0        1        2        1         1         1
  SETDB2 WILD-TYPE       2       14       38       29        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SETDB2 MUTATED           0          1          1          2        0
  SETDB2 WILD-TYPE         3         69         52         30       38
D179V3, multiclass
            clus
vv           SETDB2 MUTATED SETDB2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              2               30
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SETDB2 MUTATED     1   4   3   3
  SETDB2 WILD-TYPE  21  88 170  94
D179V4, multiclass
    clus
vv   SETDB2 MUTATED SETDB2 WILD-TYPE
  T1              1               21
  T2              4               88
  T3              3              170
  T4              3               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
  SETDB2 MUTATED     5   2   2   1
  SETDB2 WILD-TYPE 113 102  75  76
D179V5, multiclass
    clus
vv   SETDB2 MUTATED SETDB2 WILD-TYPE
  N0              5              113
  N1              2              102
  N2              2               75
  N3              1               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"
D179V6, binary
                  cls
clus                 0   1
  SETDB2 MUTATED    11   0
  SETDB2 WILD-TYPE 335  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB2 MUTATED     11    0
  SETDB2 WILD-TYPE  335   29
   clus
vv  SETDB2 MUTATED SETDB2 WILD-TYPE
  0             11              335
  1              0               29
[1] 2 2
[1] FALSE
D179V7, binary
                  cls
clus                 0   1
  SETDB2 MUTATED     6   6
  SETDB2 WILD-TYPE 139 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB2 MUTATED      6    6
  SETDB2 WILD-TYPE  139  242
        clus
vv       SETDB2 MUTATED SETDB2 WILD-TYPE
  FEMALE              6              139
  MALE                6              242
[1] 2 2
[1] FALSE
D179V8, binary
                  cls
clus                 0   1
  SETDB2 MUTATED     8   1
  SETDB2 WILD-TYPE 284  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB2 MUTATED      8    1
  SETDB2 WILD-TYPE  284   58
     clus
vv    SETDB2 MUTATED SETDB2 WILD-TYPE
  NO               8              284
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SETDB2 MUTATED                                          0
  SETDB2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SETDB2 MUTATED                                       1
  SETDB2 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SETDB2 MUTATED                                                        8
  SETDB2 WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SETDB2 MUTATED                                                   0
  SETDB2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SETDB2 MUTATED                                                                   3
  SETDB2 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SETDB2 MUTATED                                                    0
  SETDB2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SETDB2 MUTATED                                                  0
  SETDB2 WILD-TYPE                                               61
D179V9, multiclass
                                                                   clus
vv                                                                  SETDB2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  SETDB2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SETDB2 MUTATED     9   0   0   3
  SETDB2 WILD-TYPE 302  14  15  21
D179V10, multiclass
    clus
vv   SETDB2 MUTATED SETDB2 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SETDB2 MUTATED       0                         0
  SETDB2 WILD-TYPE    87                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SETDB2 MUTATED                                           0     9
  SETDB2 WILD-TYPE                                         1   234
D179V12, multiclass
                                           clus
vv                                          SETDB2 MUTATED SETDB2 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V13, binary
                  cls
clus                 0   1
  SETDB2 MUTATED     0   8
  SETDB2 WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETDB2 MUTATED      0    8
  SETDB2 WILD-TYPE    4  302
                        clus
vv                       SETDB2 MUTATED SETDB2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(180) Variable = ZNF43 MUTATION ANALYSIS
D180V1, survival
                 sevent
clus2               0   1
  ZNF43 MUTATED    19   3
  ZNF43 WILD-TYPE 211 136
  ZNF43 MUTATED ZNF43 WILD-TYPE 
             22             347 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
              3             136 
$`ZNF43 MUTATED`
TCGA-KB-A93G TCGA-BR-4183 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6458 TCGA-BR-6566 
       20.15         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-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-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         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-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
        6.61        13.87        17.29        13.68        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-7703 TCGA-BR-7704 
       40.21        30.90        31.20        21.90        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-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-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-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-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-D7-5579 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-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-A7NT 
       13.35        19.53         6.44         6.74        12.59        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 

  ZNF43 MUTATED ZNF43 WILD-TYPE 
           6.02            0.00 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
           65.1           122.3 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
          19.74           14.04 
[1] "6.0 - 65.1 (19.7)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "3.5"
D180V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF43 MUTATED         1        0        3        2         5         4
  ZNF43 WILD-TYPE       1       15       37       28        32        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF43 MUTATED           0          4          2          0        3
  ZNF43 WILD-TYPE         3         66         51         32       35
D180V3, multiclass
            clus
vv           ZNF43 MUTATED ZNF43 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               2              28
  STAGE IIA              5              32
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             2              51
  STAGE IIIC             0              32
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZNF43 MUTATED     1   6  10   7
  ZNF43 WILD-TYPE  21  86 163  90
D180V4, multiclass
    clus
vv   ZNF43 MUTATED ZNF43 WILD-TYPE
  T1             1              21
  T2             6              86
  T3            10             163
  T4             7              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
  ZNF43 MUTATED    10  10   4   1
  ZNF43 WILD-TYPE 108  94  73  76
D180V5, multiclass
    clus
vv   ZNF43 MUTATED ZNF43 WILD-TYPE
  N0            10             108
  N1            10              94
  N2             4              73
  N3             1              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"
D180V6, binary
                 cls
clus                0   1
  ZNF43 MUTATED    22   2
  ZNF43 WILD-TYPE 324  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED     22    2
  ZNF43 WILD-TYPE  324   27
   clus
vv  ZNF43 MUTATED ZNF43 WILD-TYPE
  0            22             324
  1             2              27
[1] 2 2
[1] FALSE
D180V7, binary
                 cls
clus                0   1
  ZNF43 MUTATED    12  13
  ZNF43 WILD-TYPE 133 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED     12   13
  ZNF43 WILD-TYPE  133  235
        clus
vv       ZNF43 MUTATED ZNF43 WILD-TYPE
  FEMALE            12             133
  MALE              13             235
[1] 2 2
[1] FALSE
D180V8, binary
                 cls
clus                0   1
  ZNF43 MUTATED    20   2
  ZNF43 WILD-TYPE 272  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED     20    2
  ZNF43 WILD-TYPE  272   57
     clus
vv    ZNF43 MUTATED ZNF43 WILD-TYPE
  NO             20             272
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF43 MUTATED                                          1
  ZNF43 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF43 MUTATED                                       2
  ZNF43 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF43 MUTATED                                                       15
  ZNF43 WILD-TYPE                                                    143
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF43 MUTATED                                                   2
  ZNF43 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF43 MUTATED                                                                   3
  ZNF43 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF43 MUTATED                                                    0
  ZNF43 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF43 MUTATED                                                  2
  ZNF43 WILD-TYPE                                               59
D180V9, multiclass
                                                                   clus
vv                                                                  ZNF43 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  ZNF43 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZNF43 MUTATED    21   0   0   3
  ZNF43 WILD-TYPE 290  14  15  21
D180V10, multiclass
    clus
vv   ZNF43 MUTATED ZNF43 WILD-TYPE
  R0            21             290
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZNF43 MUTATED       3                         2
  ZNF43 WILD-TYPE    84                         7
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF43 MUTATED                                           0    17
  ZNF43 WILD-TYPE                                         1   226
D180V12, multiclass
                                           clus
vv                                          ZNF43 MUTATED ZNF43 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             2               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V13, binary
                 cls
clus                0   1
  ZNF43 MUTATED     0  19
  ZNF43 WILD-TYPE   4 291
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED      0   19
  ZNF43 WILD-TYPE    4  291
                        clus
vv                       ZNF43 MUTATED ZNF43 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            19             291
[1] 2 2
[1] FALSE

Clustering(181) Variable = NOX5 MUTATION ANALYSIS
D181V1, survival
                sevent
clus2              0   1
  NOX5 MUTATED    10   6
  NOX5 WILD-TYPE 220 133
  NOX5 MUTATED NOX5 WILD-TYPE 
            16            353 
  NOX5 MUTATED NOX5 WILD-TYPE 
             6            133 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-D7-5579 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-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-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 

  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         14.070 
[1] "5.9 - 32.2 (16.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D181V2, 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       2       15       38       29        37        47
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOX5 MUTATED           0          2          1          3        2
  NOX5 WILD-TYPE         3         68         52         29       36
D181V3, multiclass
            clus
vv           NOX5 MUTATED NOX5 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             0             37
  STAGE IIB             5             47
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            3             29
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOX5 MUTATED     1   3   5   7
  NOX5 WILD-TYPE  21  89 168  90
D181V4, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  T1            1             21
  T2            3             89
  T3            5            168
  T4            7             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
  NOX5 MUTATED     3   6   5   2
  NOX5 WILD-TYPE 115  98  72  75
D181V5, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  N0            3            115
  N1            6             98
  N2            5             72
  N3            2             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"
D181V6, binary
                cls
clus               0   1
  NOX5 MUTATED    15   1
  NOX5 WILD-TYPE 331  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED     15    1
  NOX5 WILD-TYPE  331   28
   clus
vv  NOX5 MUTATED NOX5 WILD-TYPE
  0           15            331
  1            1             28
[1] 2 2
[1] FALSE
D181V7, binary
                cls
clus               0   1
  NOX5 MUTATED    10   7
  NOX5 WILD-TYPE 135 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED     10    7
  NOX5 WILD-TYPE  135  241
        clus
vv       NOX5 MUTATED NOX5 WILD-TYPE
  FEMALE           10            135
  MALE              7            241
[1] 2 2
[1] FALSE
D181V8, binary
                cls
clus               0   1
  NOX5 MUTATED    17   0
  NOX5 WILD-TYPE 275  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED     17    0
  NOX5 WILD-TYPE  275   59
     clus
vv    NOX5 MUTATED NOX5 WILD-TYPE
  NO            17            275
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NOX5 MUTATED                                          0
  NOX5 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NOX5 MUTATED                                       2
  NOX5 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NOX5 MUTATED                                                        9
  NOX5 WILD-TYPE                                                    149
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NOX5 MUTATED                                                   0
  NOX5 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NOX5 MUTATED                                                                   2
  NOX5 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NOX5 MUTATED                                                    0
  NOX5 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NOX5 MUTATED                                                  4
  NOX5 WILD-TYPE                                               57
D181V9, multiclass
                                                                   clus
vv                                                                  NOX5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  NOX5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NOX5 MUTATED    14   1   0   2
  NOX5 WILD-TYPE 297  13  15  22
D181V10, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  R0           14            297
  R1            1             13
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NOX5 MUTATED       4                         0
  NOX5 WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOX5 MUTATED                                           0    11
  NOX5 WILD-TYPE                                         1   232
D181V12, multiclass
                                           clus
vv                                          NOX5 MUTATED NOX5 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V13, binary
                cls
clus               0   1
  NOX5 MUTATED     0  15
  NOX5 WILD-TYPE   4 295
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      0   15
  NOX5 WILD-TYPE    4  295
                        clus
vv                       NOX5 MUTATED NOX5 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           15            295
[1] 2 2
[1] FALSE

Clustering(182) Variable = ANKRD34A MUTATION ANALYSIS
D182V1, survival
                    sevent
clus2                  0   1
  ANKRD34A MUTATED     5   4
  ANKRD34A WILD-TYPE 225 135
  ANKRD34A MUTATED ANKRD34A WILD-TYPE 
                 9                360 
  ANKRD34A MUTATED ANKRD34A WILD-TYPE 
                 4                135 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  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              14.12 
[1] "0.1 - 105.1 (22.7)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D182V2, 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       2       15       39       29        34        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD34A MUTATED           0          1          0          2        2
  ANKRD34A WILD-TYPE         3         69         53         30       36
D182V3, multiclass
            clus
vv           ANKRD34A MUTATED ANKRD34A WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  1                 29
  STAGE IIA                 3                 34
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                0                 53
  STAGE IIIC                2                 30
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ANKRD34A MUTATED     0   3   3   5
  ANKRD34A WILD-TYPE  22  89 170  92
D182V4, multiclass
    clus
vv   ANKRD34A MUTATED ANKRD34A WILD-TYPE
  T1                0                 22
  T2                3                 89
  T3                3                170
  T4                5                 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
  ANKRD34A MUTATED     3   5   2   1
  ANKRD34A WILD-TYPE 115  99  75  76
D182V5, multiclass
    clus
vv   ANKRD34A MUTATED ANKRD34A WILD-TYPE
  N0                3                115
  N1                5                 99
  N2                2                 75
  N3                1                 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"
D182V6, binary
                    cls
clus                   0   1
  ANKRD34A MUTATED     9   1
  ANKRD34A WILD-TYPE 337  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD34A MUTATED      9    1
  ANKRD34A WILD-TYPE  337   28
   clus
vv  ANKRD34A MUTATED ANKRD34A WILD-TYPE
  0                9                337
  1                1                 28
[1] 2 2
[1] FALSE
D182V7, binary
                    cls
clus                   0   1
  ANKRD34A MUTATED     6   5
  ANKRD34A WILD-TYPE 139 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD34A MUTATED      6    5
  ANKRD34A WILD-TYPE  139  243
        clus
vv       ANKRD34A MUTATED ANKRD34A WILD-TYPE
  FEMALE                6                139
  MALE                  5                243
[1] 2 2
[1] FALSE
D182V8, binary
                    cls
clus                   0   1
  ANKRD34A MUTATED     9   1
  ANKRD34A WILD-TYPE 283  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD34A MUTATED      9    1
  ANKRD34A WILD-TYPE  283   58
     clus
vv    ANKRD34A MUTATED ANKRD34A WILD-TYPE
  NO                 9                283
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ANKRD34A MUTATED                                          1
  ANKRD34A WILD-TYPE                                        7
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ANKRD34A MUTATED                                       2
  ANKRD34A WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANKRD34A MUTATED                                                        4
  ANKRD34A WILD-TYPE                                                    154
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ANKRD34A MUTATED                                                   1
  ANKRD34A WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANKRD34A MUTATED                                                                   1
  ANKRD34A WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ANKRD34A MUTATED                                                    0
  ANKRD34A WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ANKRD34A MUTATED                                                  2
  ANKRD34A WILD-TYPE                                               59
D182V9, multiclass
                                                                   clus
vv                                                                  ANKRD34A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  ANKRD34A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ANKRD34A MUTATED     7   0   1   1
  ANKRD34A WILD-TYPE 304  14  14  23
D182V10, multiclass
    clus
vv   ANKRD34A MUTATED ANKRD34A WILD-TYPE
  R0                7                304
  R1                0                 14
  R2                1                 14
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ANKRD34A MUTATED       4                         0
  ANKRD34A WILD-TYPE    83                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANKRD34A MUTATED                                           0     5
  ANKRD34A WILD-TYPE                                         1   238
D182V12, multiclass
                                           clus
vv                                          ANKRD34A MUTATED ANKRD34A WILD-TYPE
  ASIAN                                                    4                 83
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V13, binary
                    cls
clus                   0   1
  ANKRD34A MUTATED     0   8
  ANKRD34A WILD-TYPE   4 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD34A MUTATED      0    8
  ANKRD34A WILD-TYPE    4  302
                        clus
vv                       ANKRD34A MUTATED ANKRD34A WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                8                302
[1] 2 2
[1] FALSE

Clustering(183) Variable = PHACTR4 MUTATION ANALYSIS
D183V1, survival
                   sevent
clus2                 0   1
  PHACTR4 MUTATED     6   3
  PHACTR4 WILD-TYPE 224 136
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
                9               360 
  PHACTR4 MUTATED PHACTR4 WILD-TYPE 
                3               136 
$`PHACTR4 MUTATED`
TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8487 TCGA-CG-5733 TCGA-D7-6525 TCGA-FP-7829 
       34.68         6.18         1.12        21.07        13.35        19.53 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-VQ-A8P2 
       29.98         0.10        38.14 

$`PHACTR4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-6526 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-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-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-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-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 

  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             14.22 
[1] "0.1 - 38.1 (19.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D183V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHACTR4 MUTATED         0        0        0        0         4         1
  PHACTR4 WILD-TYPE       2       15       40       30        33        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHACTR4 MUTATED           0          3          0          1        0
  PHACTR4 WILD-TYPE         3         67         53         31       38
D183V3, multiclass
            clus
vv           PHACTR4 MUTATED PHACTR4 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                4                33
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               3                67
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PHACTR4 MUTATED     0   3   4   2
  PHACTR4 WILD-TYPE  22  89 169  95
D183V4, multiclass
    clus
vv   PHACTR4 MUTATED PHACTR4 WILD-TYPE
  T1               0                22
  T2               3                89
  T3               4               169
  T4               2                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
  PHACTR4 MUTATED     3   4   3   0
  PHACTR4 WILD-TYPE 115 100  74  77
D183V5, multiclass
    clus
vv   PHACTR4 MUTATED PHACTR4 WILD-TYPE
  N0               3               115
  N1               4               100
  N2               3                74
  N3               0                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"
D183V6, binary
                   cls
clus                  0   1
  PHACTR4 MUTATED    10   0
  PHACTR4 WILD-TYPE 336  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR4 MUTATED     10    0
  PHACTR4 WILD-TYPE  336   29
   clus
vv  PHACTR4 MUTATED PHACTR4 WILD-TYPE
  0              10               336
  1               0                29
[1] 2 2
[1] FALSE
D183V7, binary
                   cls
clus                  0   1
  PHACTR4 MUTATED     4   6
  PHACTR4 WILD-TYPE 141 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR4 MUTATED      4    6
  PHACTR4 WILD-TYPE  141  242
        clus
vv       PHACTR4 MUTATED PHACTR4 WILD-TYPE
  FEMALE               4               141
  MALE                 6               242
[1] 2 2
[1] FALSE
D183V8, binary
                   cls
clus                  0   1
  PHACTR4 MUTATED     7   2
  PHACTR4 WILD-TYPE 285  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR4 MUTATED      7    2
  PHACTR4 WILD-TYPE  285   57
     clus
vv    PHACTR4 MUTATED PHACTR4 WILD-TYPE
  NO                7               285
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PHACTR4 MUTATED                                          0
  PHACTR4 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PHACTR4 MUTATED                                       1
  PHACTR4 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PHACTR4 MUTATED                                                        3
  PHACTR4 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PHACTR4 MUTATED                                                   2
  PHACTR4 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PHACTR4 MUTATED                                                                   2
  PHACTR4 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PHACTR4 MUTATED                                                    0
  PHACTR4 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PHACTR4 MUTATED                                                  2
  PHACTR4 WILD-TYPE                                               59
D183V9, multiclass
                                                                   clus
vv                                                                  PHACTR4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  PHACTR4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PHACTR4 MUTATED     9   0   0   1
  PHACTR4 WILD-TYPE 302  14  15  23
D183V10, multiclass
    clus
vv   PHACTR4 MUTATED PHACTR4 WILD-TYPE
  R0               9               302
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PHACTR4 MUTATED       2                         0
  PHACTR4 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PHACTR4 MUTATED                                           0     7
  PHACTR4 WILD-TYPE                                         1   236
D183V12, multiclass
                                           clus
vv                                          PHACTR4 MUTATED PHACTR4 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V13, binary
                   cls
clus                  0   1
  PHACTR4 MUTATED     0   8
  PHACTR4 WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR4 MUTATED      0    8
  PHACTR4 WILD-TYPE    4  302
                        clus
vv                       PHACTR4 MUTATED PHACTR4 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(184) Variable = RAD50 MUTATION ANALYSIS
D184V1, survival
                 sevent
clus2               0   1
  RAD50 MUTATED     6   5
  RAD50 WILD-TYPE 224 134
  RAD50 MUTATED RAD50 WILD-TYPE 
             11             358 
  RAD50 MUTATED RAD50 WILD-TYPE 
              5             134 
$`RAD50 MUTATED`
TCGA-BR-4257 TCGA-BR-8367 TCGA-BR-8382 TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-4306 
        9.67        26.33        25.05        16.14        12.62         1.02 
TCGA-CG-5721 TCGA-F1-A448 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-VQ-A8P2 
        6.02        21.27        29.98         6.51        38.14 

$`RAD50 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95         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-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-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-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-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-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 

  RAD50 MUTATED RAD50 WILD-TYPE 
           1.02            0.00 
  RAD50 MUTATED RAD50 WILD-TYPE 
          38.14          122.30 
  RAD50 MUTATED RAD50 WILD-TYPE 
          16.14           14.22 
[1] "1.0 - 38.1 (16.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D184V2, 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       2       15       39       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAD50 MUTATED           0          1          3          1        2
  RAD50 WILD-TYPE         3         69         50         31       36
D184V3, multiclass
            clus
vv           RAD50 MUTATED RAD50 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             3              50
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAD50 MUTATED     1   2   5   3
  RAD50 WILD-TYPE  21  90 168  94
D184V4, multiclass
    clus
vv   RAD50 MUTATED RAD50 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             5             168
  T4             3              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
  RAD50 MUTATED     2   3   1   4
  RAD50 WILD-TYPE 116 101  76  73
D184V5, multiclass
    clus
vv   RAD50 MUTATED RAD50 WILD-TYPE
  N0             2             116
  N1             3             101
  N2             1              76
  N3             4              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"
D184V6, binary
                 cls
clus                0   1
  RAD50 MUTATED    11   1
  RAD50 WILD-TYPE 335  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD50 MUTATED     11    1
  RAD50 WILD-TYPE  335   28
   clus
vv  RAD50 MUTATED RAD50 WILD-TYPE
  0            11             335
  1             1              28
[1] 2 2
[1] FALSE
D184V7, binary
                 cls
clus                0   1
  RAD50 MUTATED     5   7
  RAD50 WILD-TYPE 140 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD50 MUTATED      5    7
  RAD50 WILD-TYPE  140  241
        clus
vv       RAD50 MUTATED RAD50 WILD-TYPE
  FEMALE             5             140
  MALE               7             241
[1] 2 2
[1] FALSE
D184V8, binary
                 cls
clus                0   1
  RAD50 MUTATED     8   2
  RAD50 WILD-TYPE 284  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD50 MUTATED      8    2
  RAD50 WILD-TYPE  284   57
     clus
vv    RAD50 MUTATED RAD50 WILD-TYPE
  NO              8             284
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RAD50 MUTATED                                          0
  RAD50 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RAD50 MUTATED                                       0
  RAD50 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RAD50 MUTATED                                                        7
  RAD50 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RAD50 MUTATED                                                   2
  RAD50 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RAD50 MUTATED                                                                   1
  RAD50 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RAD50 MUTATED                                                    0
  RAD50 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RAD50 MUTATED                                                  2
  RAD50 WILD-TYPE                                               59
D184V9, multiclass
                                                                   clus
vv                                                                  RAD50 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  RAD50 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RAD50 MUTATED     8   0   1   2
  RAD50 WILD-TYPE 303  14  14  22
D184V10, multiclass
    clus
vv   RAD50 MUTATED RAD50 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RAD50 MUTATED       3                         0
  RAD50 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAD50 MUTATED                                           0     7
  RAD50 WILD-TYPE                                         1   236
D184V12, multiclass
                                           clus
vv                                          RAD50 MUTATED RAD50 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V13, binary
                 cls
clus                0   1
  RAD50 MUTATED     1   8
  RAD50 WILD-TYPE   3 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD50 MUTATED      1    8
  RAD50 WILD-TYPE    3  302
                        clus
vv                       RAD50 MUTATED RAD50 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(185) Variable = JAK1 MUTATION ANALYSIS
D185V1, survival
                sevent
clus2              0   1
  JAK1 MUTATED    10   5
  JAK1 WILD-TYPE 220 134
  JAK1 MUTATED JAK1 WILD-TYPE 
            15            354 
  JAK1 MUTATED JAK1 WILD-TYPE 
             5            134 
$`JAK1 MUTATED`
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8059 
       21.99        16.24        30.90        34.68        35.84        14.43 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-5728 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HJ-7597 
       12.43         6.58        65.10        11.08        77.29        26.47 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-VQ-A8P2 
       22.32        22.68        38.14 

$`JAK1 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       47.05        22.98        79.07         0.23        20.15         9.86 
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-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-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-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-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-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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  JAK1 MUTATED JAK1 WILD-TYPE 
          6.58           0.00 
  JAK1 MUTATED JAK1 WILD-TYPE 
         77.29         122.30 
  JAK1 MUTATED JAK1 WILD-TYPE 
         22.68          14.04 
[1] "6.6 - 77.3 (22.7)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.7"
D185V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  JAK1 MUTATED         0        0        4        2         3         2
  JAK1 WILD-TYPE       2       15       36       28        34        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  JAK1 MUTATED           1          1          1          0        1
  JAK1 WILD-TYPE         2         69         52         32       37
D185V3, multiclass
            clus
vv           JAK1 MUTATED JAK1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              4             36
  STAGE II              2             28
  STAGE IIA             3             34
  STAGE IIB             2             50
  STAGE III             1              2
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  JAK1 MUTATED     0   6   5   5
  JAK1 WILD-TYPE  22  86 168  92
D185V4, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  T1            0             22
  T2            6             86
  T3            5            168
  T4            5             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
  JAK1 MUTATED     9   6   0   0
  JAK1 WILD-TYPE 109  98  77  77
D185V5, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  N0            9            109
  N1            6             98
  N2            0             77
  N3            0             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"
D185V6, binary
                cls
clus               0   1
  JAK1 MUTATED    14   1
  JAK1 WILD-TYPE 332  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     14    1
  JAK1 WILD-TYPE  332   28
   clus
vv  JAK1 MUTATED JAK1 WILD-TYPE
  0           14            332
  1            1             28
[1] 2 2
[1] FALSE
D185V7, binary
                cls
clus               0   1
  JAK1 MUTATED     9   8
  JAK1 WILD-TYPE 136 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED      9    8
  JAK1 WILD-TYPE  136  240
        clus
vv       JAK1 MUTATED JAK1 WILD-TYPE
  FEMALE            9            136
  MALE              8            240
[1] 2 2
[1] FALSE
D185V8, binary
                cls
clus               0   1
  JAK1 MUTATED    10   4
  JAK1 WILD-TYPE 282  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     10    4
  JAK1 WILD-TYPE  282   55
     clus
vv    JAK1 MUTATED JAK1 WILD-TYPE
  NO            10            282
  YES            4             55
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  JAK1 MUTATED                                          1
  JAK1 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  JAK1 MUTATED                                       3
  JAK1 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  JAK1 MUTATED                                                        6
  JAK1 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  JAK1 MUTATED                                                   2
  JAK1 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  JAK1 MUTATED                                                                   4
  JAK1 WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  JAK1 MUTATED                                                    0
  JAK1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  JAK1 MUTATED                                                  0
  JAK1 WILD-TYPE                                               61
D185V9, multiclass
                                                                   clus
vv                                                                  JAK1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  JAK1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  JAK1 MUTATED    12   0   1   2
  JAK1 WILD-TYPE 299  14  14  22
D185V10, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  R0           12            299
  R1            0             14
  R2            1             14
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  JAK1 MUTATED       4                         1
  JAK1 WILD-TYPE    83                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  JAK1 MUTATED                                           0     8
  JAK1 WILD-TYPE                                         1   235
D185V12, multiclass
                                           clus
vv                                          JAK1 MUTATED JAK1 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V13, binary
                cls
clus               0   1
  JAK1 MUTATED     0  12
  JAK1 WILD-TYPE   4 298
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED      0   12
  JAK1 WILD-TYPE    4  298
                        clus
vv                       JAK1 MUTATED JAK1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           12            298
[1] 2 2
[1] FALSE

Clustering(186) Variable = FAM155B MUTATION ANALYSIS
D186V1, survival
                   sevent
clus2                 0   1
  FAM155B MUTATED     7   5
  FAM155B WILD-TYPE 223 134
  FAM155B MUTATED FAM155B WILD-TYPE 
               12               357 
  FAM155B MUTATED FAM155B WILD-TYPE 
                5               134 
$`FAM155B MUTATED`
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 
       36.16        35.84        31.10        31.27         1.12        28.14 
TCGA-CD-8532 TCGA-CD-A4MG TCGA-HF-7132 TCGA-RD-A7C1 TCGA-VQ-A8DZ TCGA-VQ-A94T 
       11.64         6.58        77.29        16.67        13.02        11.24 

$`FAM155B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-A8E2 TCGA-VQ-A8E7 
        0.92        48.79         5.46        13.25        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-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 

  FAM155B MUTATED FAM155B WILD-TYPE 
             1.12              0.00 
  FAM155B MUTATED FAM155B WILD-TYPE 
            77.29            122.30 
  FAM155B MUTATED FAM155B WILD-TYPE 
           22.405            14.170 
[1] "1.1 - 77.3 (22.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D186V2, 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       2       14       38       28        35        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM155B MUTATED           0          0          1          3        2
  FAM155B WILD-TYPE         3         70         52         29       36
D186V3, multiclass
            clus
vv           FAM155B MUTATED FAM155B WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 2                38
  STAGE II                 2                28
  STAGE IIA                2                35
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               1                52
  STAGE IIIC               3                29
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM155B MUTATED     1   3   4   5
  FAM155B WILD-TYPE  21  89 169  92
D186V4, multiclass
    clus
vv   FAM155B MUTATED FAM155B WILD-TYPE
  T1               1                21
  T2               3                89
  T3               4               169
  T4               5                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
  FAM155B MUTATED     6   1   3   3
  FAM155B WILD-TYPE 112 103  74  74
D186V5, multiclass
    clus
vv   FAM155B MUTATED FAM155B WILD-TYPE
  N0               6               112
  N1               1               103
  N2               3                74
  N3               3                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"
D186V6, binary
                   cls
clus                  0   1
  FAM155B MUTATED    12   1
  FAM155B WILD-TYPE 334  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED     12    1
  FAM155B WILD-TYPE  334   28
   clus
vv  FAM155B MUTATED FAM155B WILD-TYPE
  0              12               334
  1               1                28
[1] 2 2
[1] FALSE
D186V7, binary
                   cls
clus                  0   1
  FAM155B MUTATED     4   9
  FAM155B WILD-TYPE 141 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      4    9
  FAM155B WILD-TYPE  141  239
        clus
vv       FAM155B MUTATED FAM155B WILD-TYPE
  FEMALE               4               141
  MALE                 9               239
[1] 2 2
[1] FALSE
D186V8, binary
                   cls
clus                  0   1
  FAM155B MUTATED    11   1
  FAM155B WILD-TYPE 281  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED     11    1
  FAM155B WILD-TYPE  281   58
     clus
vv    FAM155B MUTATED FAM155B WILD-TYPE
  NO               11               281
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM155B MUTATED                                          1
  FAM155B WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM155B MUTATED                                       3
  FAM155B WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM155B MUTATED                                                        7
  FAM155B WILD-TYPE                                                    151
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM155B MUTATED                                                   1
  FAM155B WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM155B MUTATED                                                                   0
  FAM155B WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM155B MUTATED                                                    1
  FAM155B WILD-TYPE                                                  4
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM155B MUTATED                                                  0
  FAM155B WILD-TYPE                                               61
D186V9, multiclass
                                                                   clus
vv                                                                  FAM155B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  FAM155B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM155B MUTATED    10   0   1   1
  FAM155B WILD-TYPE 301  14  14  23
D186V10, multiclass
    clus
vv   FAM155B MUTATED FAM155B WILD-TYPE
  R0              10               301
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM155B MUTATED       2                         1
  FAM155B WILD-TYPE    85                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM155B MUTATED                                           0     8
  FAM155B WILD-TYPE                                         1   235
D186V12, multiclass
                                           clus
vv                                          FAM155B MUTATED FAM155B WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V13, binary
                   cls
clus                  0   1
  FAM155B MUTATED     0  10
  FAM155B WILD-TYPE   4 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      0   10
  FAM155B WILD-TYPE    4  300
                        clus
vv                       FAM155B MUTATED FAM155B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              10               300
[1] 2 2
[1] FALSE

Clustering(187) Variable = DIDO1 MUTATION ANALYSIS
D187V1, survival
                 sevent
clus2               0   1
  DIDO1 MUTATED    22  12
  DIDO1 WILD-TYPE 208 127
  DIDO1 MUTATED DIDO1 WILD-TYPE 
             34             335 
  DIDO1 MUTATED DIDO1 WILD-TYPE 
             12             127 
$`DIDO1 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        26.70        11.70        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 
        9.44         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-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-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-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-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-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.65        20.42         1.15         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-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-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-A9TM TCGA-HF-7132 
       59.54         5.03        13.58         0.56         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-A4GU TCGA-HU-A4GY 
       11.77        21.37        29.98         8.98         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-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-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 

  DIDO1 MUTATED DIDO1 WILD-TYPE 
            0.1             0.0 
  DIDO1 MUTATED DIDO1 WILD-TYPE 
         105.07          122.30 
  DIDO1 MUTATED DIDO1 WILD-TYPE 
          15.52           14.17 
[1] "0.1 - 105.1 (15.5)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1"  
D187V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DIDO1 MUTATED         1        2        3        2         6         3
  DIDO1 WILD-TYPE       1       13       37       28        31        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DIDO1 MUTATED           0          6          4          5        3
  DIDO1 WILD-TYPE         3         64         49         27       35
D187V3, multiclass
            clus
vv           DIDO1 MUTATED DIDO1 WILD-TYPE
  STAGE I                1               1
  STAGE IA               2              13
  STAGE IB               3              37
  STAGE II               2              28
  STAGE IIA              6              31
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             6              64
  STAGE IIIB             4              49
  STAGE IIIC             5              27
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DIDO1 MUTATED     3   5  15  14
  DIDO1 WILD-TYPE  19  87 158  83
D187V4, multiclass
    clus
vv   DIDO1 MUTATED DIDO1 WILD-TYPE
  T1             3              19
  T2             5              87
  T3            15             158
  T4            14              83
[1] 4 2
[1] TRUE
[1] "dimension of 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    16   7   7   5
  DIDO1 WILD-TYPE 102  97  70  72
D187V5, multiclass
    clus
vv   DIDO1 MUTATED DIDO1 WILD-TYPE
  N0            16             102
  N1             7              97
  N2             7              70
  N3             5              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"
D187V6, binary
                 cls
clus                0   1
  DIDO1 MUTATED    34   1
  DIDO1 WILD-TYPE 312  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIDO1 MUTATED     34    1
  DIDO1 WILD-TYPE  312   28
   clus
vv  DIDO1 MUTATED DIDO1 WILD-TYPE
  0            34             312
  1             1              28
[1] 2 2
[1] FALSE
D187V7, binary
                 cls
clus                0   1
  DIDO1 MUTATED    18  20
  DIDO1 WILD-TYPE 127 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIDO1 MUTATED     18   20
  DIDO1 WILD-TYPE  127  228
        clus
vv       DIDO1 MUTATED DIDO1 WILD-TYPE
  FEMALE            18             127
  MALE              20             228
[1] 2 2
[1] FALSE
D187V8, binary
                 cls
clus                0   1
  DIDO1 MUTATED    30   2
  DIDO1 WILD-TYPE 262  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIDO1 MUTATED     30    2
  DIDO1 WILD-TYPE  262   57
     clus
vv    DIDO1 MUTATED DIDO1 WILD-TYPE
  NO             30             262
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DIDO1 MUTATED                                          1
  DIDO1 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DIDO1 MUTATED                                       5
  DIDO1 WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DIDO1 MUTATED                                                       19
  DIDO1 WILD-TYPE                                                    139
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DIDO1 MUTATED                                                   1
  DIDO1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DIDO1 MUTATED                                                                   5
  DIDO1 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DIDO1 MUTATED                                                    1
  DIDO1 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DIDO1 MUTATED                                                  6
  DIDO1 WILD-TYPE                                               55
D187V9, multiclass
                                                                   clus
vv                                                                  DIDO1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       19
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              6
                                                                   clus
vv                                                                  DIDO1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        139
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DIDO1 MUTATED    28   1   0   6
  DIDO1 WILD-TYPE 283  13  15  18
D187V10, multiclass
    clus
vv   DIDO1 MUTATED DIDO1 WILD-TYPE
  R0            28             283
  R1             1              13
  R2             0              15
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DIDO1 MUTATED      11                         2
  DIDO1 WILD-TYPE    76                         7
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DIDO1 MUTATED                                           0    23
  DIDO1 WILD-TYPE                                         1   220
D187V12, multiclass
                                           clus
vv                                          DIDO1 MUTATED DIDO1 WILD-TYPE
  ASIAN                                                11              76
  BLACK OR AFRICAN AMERICAN                             2               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                23             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V13, binary
                 cls
clus                0   1
  DIDO1 MUTATED     0  33
  DIDO1 WILD-TYPE   4 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIDO1 MUTATED      0   33
  DIDO1 WILD-TYPE    4  277
                        clus
vv                       DIDO1 MUTATED DIDO1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            33             277
[1] 2 2
[1] FALSE

Clustering(188) Variable = CASP8 MUTATION ANALYSIS
D188V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED     7   8
  CASP8 WILD-TYPE 223 131
  CASP8 MUTATED CASP8 WILD-TYPE 
             15             354 
  CASP8 MUTATED CASP8 WILD-TYPE 
              8             131 
$`CASP8 MUTATED`
TCGA-EQ-A4SO TCGA-BR-4256 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8059 
       16.24         9.34         6.61        34.68        44.94        14.43 
TCGA-BR-8285 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4306 TCGA-D7-8570 
        0.56         1.12         6.58        11.77         1.02        24.72 
TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-HU-A4G8 
        5.92        14.76        22.68 

$`CASP8 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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 
          44.94          122.30 
  CASP8 MUTATED CASP8 WILD-TYPE 
          11.77           14.37 
[1] "0.6 - 44.9 (11.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.9"
D188V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CASP8 MUTATED         0        0        0        0         4         3
  CASP8 WILD-TYPE       2       15       40       30        33        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASP8 MUTATED           2          1          2          1        1
  CASP8 WILD-TYPE         1         69         51         31       37
D188V3, multiclass
            clus
vv           CASP8 MUTATED CASP8 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              4              33
  STAGE IIB              3              49
  STAGE III              2               1
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASP8 MUTATED     1   2  10   3
  CASP8 WILD-TYPE  21  90 163  94
D188V4, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  T1             1              21
  T2             2              90
  T3            10             163
  T4             3              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
  CASP8 MUTATED     4   8   2   2
  CASP8 WILD-TYPE 114  96  75  75
D188V5, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0             4             114
  N1             8              96
  N2             2              75
  N3             2              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"
D188V6, binary
                 cls
clus                0   1
  CASP8 MUTATED    15   1
  CASP8 WILD-TYPE 331  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     15    1
  CASP8 WILD-TYPE  331   28
   clus
vv  CASP8 MUTATED CASP8 WILD-TYPE
  0            15             331
  1             1              28
[1] 2 2
[1] FALSE
D188V7, binary
                 cls
clus                0   1
  CASP8 MUTATED    11   7
  CASP8 WILD-TYPE 134 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     11    7
  CASP8 WILD-TYPE  134  241
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE            11             134
  MALE               7             241
[1] 2 2
[1] FALSE
D188V8, binary
                 cls
clus                0   1
  CASP8 MUTATED    12   2
  CASP8 WILD-TYPE 280  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     12    2
  CASP8 WILD-TYPE  280   57
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO             12             280
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CASP8 MUTATED                                          0
  CASP8 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CASP8 MUTATED                                       2
  CASP8 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CASP8 MUTATED                                                       10
  CASP8 WILD-TYPE                                                    148
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CASP8 MUTATED                                                   1
  CASP8 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CASP8 MUTATED                                                                   2
  CASP8 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CASP8 MUTATED                                                    0
  CASP8 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CASP8 MUTATED                                                  2
  CASP8 WILD-TYPE                                               59
D188V9, multiclass
                                                                   clus
vv                                                                  CASP8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  CASP8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CASP8 MUTATED     9   0   1   5
  CASP8 WILD-TYPE 302  14  14  19
D188V10, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  R0             9             302
  R1             0              14
  R2             1              14
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CASP8 MUTATED       3                         0
  CASP8 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CASP8 MUTATED                                           0    14
  CASP8 WILD-TYPE                                         1   229
D188V12, multiclass
                                           clus
vv                                          CASP8 MUTATED CASP8 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V13, binary
                 cls
clus                0   1
  CASP8 MUTATED     0  17
  CASP8 WILD-TYPE   4 293
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      0   17
  CASP8 WILD-TYPE    4  293
                        clus
vv                       CASP8 MUTATED CASP8 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            17             293
[1] 2 2
[1] FALSE

Clustering(189) Variable = NWD1 MUTATION ANALYSIS
D189V1, survival
                sevent
clus2              0   1
  NWD1 MUTATED    19  11
  NWD1 WILD-TYPE 211 128
  NWD1 MUTATED NWD1 WILD-TYPE 
            30            339 
  NWD1 MUTATED NWD1 WILD-TYPE 
            11            128 
$`NWD1 MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7717 
       11.70         6.97        34.68        44.94         9.21        18.15 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8367 TCGA-BR-8371 TCGA-BR-8382 
        0.69        29.59        32.25        26.33        11.80        25.05 
TCGA-BR-8487 TCGA-BR-8687 TCGA-BR-A4QI TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8529 
        1.12         8.22        21.44        12.76        12.33        12.30 
TCGA-CD-8534 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CG-5726 TCGA-FP-7829 TCGA-FP-8209 
       12.07        11.61         6.58        28.96        19.53        59.54 
TCGA-FP-8211 TCGA-FP-A4BE TCGA-HU-A4G6 TCGA-HU-A4GY TCGA-VQ-A8P2 TCGA-VQ-AA69 
       13.58        11.08        24.26         0.26        38.14        28.41 

$`NWD1 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-8368 
       31.10         0.26        22.19        17.52         0.95         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
       14.04         3.32        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-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-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        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-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       12.53         7.17        12.39        12.59        11.64        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-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-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-8210 TCGA-FP-8631 
        3.48        14.07        22.29        17.06         5.03         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-A4G8 
       22.82        21.07         0.76        24.30         5.59        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-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-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        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 

  NWD1 MUTATED NWD1 WILD-TYPE 
          0.26           0.00 
  NWD1 MUTATED NWD1 WILD-TYPE 
         59.54         122.30 
  NWD1 MUTATED NWD1 WILD-TYPE 
         13.17          14.43 
[1] "0.3 - 59.5 (13.2)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D189V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NWD1 MUTATED         1        2        2        3         6         5
  NWD1 WILD-TYPE       1       13       38       27        31        47
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NWD1 MUTATED           0          5          3          2        2
  NWD1 WILD-TYPE         3         65         50         30       36
D189V3, multiclass
            clus
vv           NWD1 MUTATED NWD1 WILD-TYPE
  STAGE I               1              1
  STAGE IA              2             13
  STAGE IB              2             38
  STAGE II              3             27
  STAGE IIA             6             31
  STAGE IIB             5             47
  STAGE III             0              3
  STAGE IIIA            5             65
  STAGE IIIB            3             50
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NWD1 MUTATED     4   2  16  10
  NWD1 WILD-TYPE  18  90 157  87
D189V4, multiclass
    clus
vv   NWD1 MUTATED NWD1 WILD-TYPE
  T1            4             18
  T2            2             90
  T3           16            157
  T4           10             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
  NWD1 MUTATED    17   9   2   3
  NWD1 WILD-TYPE 101  95  75  74
D189V5, multiclass
    clus
vv   NWD1 MUTATED NWD1 WILD-TYPE
  N0           17            101
  N1            9             95
  N2            2             75
  N3            3             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"
D189V6, binary
                cls
clus               0   1
  NWD1 MUTATED    28   1
  NWD1 WILD-TYPE 318  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  NWD1 MUTATED     28    1
  NWD1 WILD-TYPE  318   28
   clus
vv  NWD1 MUTATED NWD1 WILD-TYPE
  0           28            318
  1            1             28
[1] 2 2
[1] FALSE
D189V7, binary
                cls
clus               0   1
  NWD1 MUTATED    14  18
  NWD1 WILD-TYPE 131 230
[1] "tbl2"
                cls
clus             [,1] [,2]
  NWD1 MUTATED     14   18
  NWD1 WILD-TYPE  131  230
        clus
vv       NWD1 MUTATED NWD1 WILD-TYPE
  FEMALE           14            131
  MALE             18            230
[1] 2 2
[1] FALSE
D189V8, binary
                cls
clus               0   1
  NWD1 MUTATED    21   8
  NWD1 WILD-TYPE 271  51
[1] "tbl2"
                cls
clus             [,1] [,2]
  NWD1 MUTATED     21    8
  NWD1 WILD-TYPE  271   51
     clus
vv    NWD1 MUTATED NWD1 WILD-TYPE
  NO            21            271
  YES            8             51
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NWD1 MUTATED                                          0
  NWD1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NWD1 MUTATED                                       5
  NWD1 WILD-TYPE                                    65
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NWD1 MUTATED                                                       19
  NWD1 WILD-TYPE                                                    139
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NWD1 MUTATED                                                   3
  NWD1 WILD-TYPE                                                18
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NWD1 MUTATED                                                                   4
  NWD1 WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NWD1 MUTATED                                                    1
  NWD1 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NWD1 MUTATED                                                  0
  NWD1 WILD-TYPE                                               61
D189V9, multiclass
                                                                   clus
vv                                                                  NWD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      19
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  NWD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       139
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NWD1 MUTATED    26   2   0   2
  NWD1 WILD-TYPE 285  12  15  22
D189V10, multiclass
    clus
vv   NWD1 MUTATED NWD1 WILD-TYPE
  R0           26            285
  R1            2             12
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NWD1 MUTATED       8                         2
  NWD1 WILD-TYPE    79                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NWD1 MUTATED                                           0    21
  NWD1 WILD-TYPE                                         1   222
D189V12, multiclass
                                           clus
vv                                          NWD1 MUTATED NWD1 WILD-TYPE
  ASIAN                                                8             79
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               21            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V13, binary
                cls
clus               0   1
  NWD1 MUTATED     0  29
  NWD1 WILD-TYPE   4 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  NWD1 MUTATED      0   29
  NWD1 WILD-TYPE    4  281
                        clus
vv                       NWD1 MUTATED NWD1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           29            281
[1] 2 2
[1] FALSE

Clustering(190) Variable = RBM6 MUTATION ANALYSIS
D190V1, survival
                sevent
clus2              0   1
  RBM6 MUTATED    10   8
  RBM6 WILD-TYPE 220 131
  RBM6 MUTATED RBM6 WILD-TYPE 
            18            351 
  RBM6 MUTATED RBM6 WILD-TYPE 
             8            131 
$`RBM6 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8284 TCGA-BR-8295 
        6.97        30.90        34.68        44.94         8.05         2.20 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8371 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8680 
        0.95        26.33        11.80        25.05        28.14        31.96 
TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-5728 TCGA-HU-A4G8 TCGA-HU-A4H4 TCGA-VQ-A8P2 
        6.58        15.95        65.10        22.68        23.84        38.14 

$`RBM6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8373 
       17.52         4.31        14.04         3.32        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-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-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-D7-8572 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-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-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 

  RBM6 MUTATED RBM6 WILD-TYPE 
          0.95           0.00 
  RBM6 MUTATED RBM6 WILD-TYPE 
          65.1          122.3 
  RBM6 MUTATED RBM6 WILD-TYPE 
        24.445         14.070 
[1] "0.9 - 65.1 (24.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D190V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RBM6 MUTATED         1        0        2        1         4         3
  RBM6 WILD-TYPE       1       15       38       29        33        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RBM6 MUTATED           0          3          2          3        2
  RBM6 WILD-TYPE         3         67         51         29       36
D190V3, multiclass
            clus
vv           RBM6 MUTATED RBM6 WILD-TYPE
  STAGE I               1              1
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             4             33
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            2             51
  STAGE IIIC            3             29
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RBM6 MUTATED     2   5   8   8
  RBM6 WILD-TYPE  20  87 165  89
D190V4, multiclass
    clus
vv   RBM6 MUTATED RBM6 WILD-TYPE
  T1            2             20
  T2            5             87
  T3            8            165
  T4            8             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
  RBM6 MUTATED     8   5   3   5
  RBM6 WILD-TYPE 110  99  74  72
D190V5, multiclass
    clus
vv   RBM6 MUTATED RBM6 WILD-TYPE
  N0            8            110
  N1            5             99
  N2            3             74
  N3            5             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"
D190V6, binary
                cls
clus               0   1
  RBM6 MUTATED    20   1
  RBM6 WILD-TYPE 326  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM6 MUTATED     20    1
  RBM6 WILD-TYPE  326   28
   clus
vv  RBM6 MUTATED RBM6 WILD-TYPE
  0           20            326
  1            1             28
[1] 2 2
[1] FALSE
D190V7, binary
                cls
clus               0   1
  RBM6 MUTATED    13  10
  RBM6 WILD-TYPE 132 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM6 MUTATED     13   10
  RBM6 WILD-TYPE  132  238
        clus
vv       RBM6 MUTATED RBM6 WILD-TYPE
  FEMALE           13            132
  MALE             10            238
[1] 2 2
[1] FALSE
D190V8, binary
                cls
clus               0   1
  RBM6 MUTATED    17   1
  RBM6 WILD-TYPE 275  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM6 MUTATED     17    1
  RBM6 WILD-TYPE  275   58
     clus
vv    RBM6 MUTATED RBM6 WILD-TYPE
  NO            17            275
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RBM6 MUTATED                                          0
  RBM6 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RBM6 MUTATED                                       2
  RBM6 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RBM6 MUTATED                                                       15
  RBM6 WILD-TYPE                                                    143
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RBM6 MUTATED                                                   1
  RBM6 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RBM6 MUTATED                                                                   3
  RBM6 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RBM6 MUTATED                                                    0
  RBM6 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RBM6 MUTATED                                                  2
  RBM6 WILD-TYPE                                               59
D190V9, multiclass
                                                                   clus
vv                                                                  RBM6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  RBM6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RBM6 MUTATED    16   0   0   5
  RBM6 WILD-TYPE 295  14  15  19
D190V10, multiclass
    clus
vv   RBM6 MUTATED RBM6 WILD-TYPE
  R0           16            295
  R1            0             14
  R2            0             15
  RX            5             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RBM6 MUTATED       4                         1
  RBM6 WILD-TYPE    83                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RBM6 MUTATED                                           0    15
  RBM6 WILD-TYPE                                         1   228
D190V12, multiclass
                                           clus
vv                                          RBM6 MUTATED RBM6 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               15            228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V13, binary
                cls
clus               0   1
  RBM6 MUTATED     0  19
  RBM6 WILD-TYPE   4 291
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM6 MUTATED      0   19
  RBM6 WILD-TYPE    4  291
                        clus
vv                       RBM6 MUTATED RBM6 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           19            291
[1] 2 2
[1] FALSE

Clustering(191) Variable = PBRM1 MUTATION ANALYSIS
D191V1, survival
                 sevent
clus2               0   1
  PBRM1 MUTATED    15   7
  PBRM1 WILD-TYPE 215 132
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             22             347 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              7             132 
$`PBRM1 MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-6452 TCGA-BR-8284 TCGA-BR-8382 TCGA-BR-8589 
       26.70        19.56        34.68         8.05        25.05        27.12 
TCGA-CD-5801 TCGA-CD-5813 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4438 TCGA-CG-5721 
       13.18        12.39        12.43         6.58        54.08         6.02 
TCGA-CG-5728 TCGA-CG-5733 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GX 
       65.10        21.07        30.51        22.32        22.68        20.25 
TCGA-HU-A4H4 TCGA-IN-AB1X TCGA-VQ-A8DL TCGA-VQ-A8P2 
       23.84        13.51         0.92        38.14 

$`PBRM1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        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-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-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-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-5802 TCGA-CD-5803 TCGA-CD-5804 
       13.41        13.02        13.15        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-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-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-F1-6874 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-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-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       10.62        11.70        15.75         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-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 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
           0.92            0.00 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
           65.1           122.3 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
         21.695          14.070 
[1] "0.9 - 65.1 (21.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D191V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PBRM1 MUTATED         0        1        1        2         4         5
  PBRM1 WILD-TYPE       2       14       39       28        33        47
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PBRM1 MUTATED           0          3          1          5        3
  PBRM1 WILD-TYPE         3         67         52         27       35
D191V3, multiclass
            clus
vv           PBRM1 MUTATED PBRM1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              4              33
  STAGE IIB              5              47
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             5              27
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PBRM1 MUTATED     2   3   8  13
  PBRM1 WILD-TYPE  20  89 165  84
D191V4, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  T1             2              20
  T2             3              89
  T3             8             165
  T4            13              84
[1] 4 2
[1] TRUE
[1] "dimension of 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    11   5   5   4
  PBRM1 WILD-TYPE 107  99  72  73
D191V5, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  N0            11             107
  N1             5              99
  N2             5              72
  N3             4              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"
D191V6, binary
                 cls
clus                0   1
  PBRM1 MUTATED    26   0
  PBRM1 WILD-TYPE 320  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     26    0
  PBRM1 WILD-TYPE  320   29
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0            26             320
  1             0              29
[1] 2 2
[1] FALSE
D191V7, binary
                 cls
clus                0   1
  PBRM1 MUTATED    15  11
  PBRM1 WILD-TYPE 130 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     15   11
  PBRM1 WILD-TYPE  130  237
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  FEMALE            15             130
  MALE              11             237
[1] 2 2
[1] FALSE
D191V8, binary
                 cls
clus                0   1
  PBRM1 MUTATED    19   3
  PBRM1 WILD-TYPE 273  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     19    3
  PBRM1 WILD-TYPE  273   56
     clus
vv    PBRM1 MUTATED PBRM1 WILD-TYPE
  NO             19             273
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PBRM1 MUTATED                                          0
  PBRM1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PBRM1 MUTATED                                       6
  PBRM1 WILD-TYPE                                    64
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PBRM1 MUTATED                                                        9
  PBRM1 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PBRM1 MUTATED                                                   3
  PBRM1 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PBRM1 MUTATED                                                                   6
  PBRM1 WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PBRM1 MUTATED                                                    0
  PBRM1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PBRM1 MUTATED                                                  2
  PBRM1 WILD-TYPE                                               59
D191V9, multiclass
                                                                   clus
vv                                                                  PBRM1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  PBRM1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PBRM1 MUTATED    19   1   0   2
  PBRM1 WILD-TYPE 292  13  15  22
D191V10, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  R0            19             292
  R1             1              13
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PBRM1 MUTATED       9                         0
  PBRM1 WILD-TYPE    78                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PBRM1 MUTATED                                           0    12
  PBRM1 WILD-TYPE                                         1   231
D191V12, multiclass
                                           clus
vv                                          PBRM1 MUTATED PBRM1 WILD-TYPE
  ASIAN                                                 9              78
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V13, binary
                 cls
clus                0   1
  PBRM1 MUTATED     0  19
  PBRM1 WILD-TYPE   4 291
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      0   19
  PBRM1 WILD-TYPE    4  291
                        clus
vv                       PBRM1 MUTATED PBRM1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            19             291
[1] 2 2
[1] FALSE

Clustering(192) Variable = TOP2A MUTATION ANALYSIS
D192V1, survival
                 sevent
clus2               0   1
  TOP2A MUTATED     7   7
  TOP2A WILD-TYPE 223 132
  TOP2A MUTATED TOP2A WILD-TYPE 
             14             355 
  TOP2A MUTATED TOP2A WILD-TYPE 
              7             132 
$`TOP2A MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-5728 
        1.02         0.99         0.99       105.07        12.03        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-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        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-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-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 

  TOP2A MUTATED TOP2A WILD-TYPE 
           0.92            0.00 
  TOP2A MUTATED TOP2A WILD-TYPE 
          44.94          122.30 
  TOP2A MUTATED TOP2A WILD-TYPE 
          12.18           14.27 
[1] "0.9 - 44.9 (12.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D192V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TOP2A MUTATED         0        2        2        2         3         0
  TOP2A WILD-TYPE       2       13       38       28        34        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TOP2A MUTATED           0          2          0          0        2
  TOP2A WILD-TYPE         3         68         53         32       36
D192V3, multiclass
            clus
vv           TOP2A MUTATED TOP2A WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               2              38
  STAGE II               2              28
  STAGE IIA              3              34
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TOP2A MUTATED     2   4   6   1
  TOP2A WILD-TYPE  20  88 167  96
D192V4, multiclass
    clus
vv   TOP2A MUTATED TOP2A WILD-TYPE
  T1             2              20
  T2             4              88
  T3             6             167
  T4             1              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
  TOP2A MUTATED     7   5   2   0
  TOP2A WILD-TYPE 111  99  75  77
D192V5, multiclass
    clus
vv   TOP2A MUTATED TOP2A WILD-TYPE
  N0             7             111
  N1             5              99
  N2             2              75
  N3             0              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"
D192V6, binary
                 cls
clus                0   1
  TOP2A MUTATED    12   1
  TOP2A WILD-TYPE 334  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED     12    1
  TOP2A WILD-TYPE  334   28
   clus
vv  TOP2A MUTATED TOP2A WILD-TYPE
  0            12             334
  1             1              28
[1] 2 2
[1] FALSE
D192V7, binary
                 cls
clus                0   1
  TOP2A MUTATED     3  11
  TOP2A WILD-TYPE 142 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED      3   11
  TOP2A WILD-TYPE  142  237
        clus
vv       TOP2A MUTATED TOP2A WILD-TYPE
  FEMALE             3             142
  MALE              11             237
[1] 2 2
[1] FALSE
D192V8, binary
                 cls
clus                0   1
  TOP2A MUTATED    10   2
  TOP2A WILD-TYPE 282  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED     10    2
  TOP2A WILD-TYPE  282   57
     clus
vv    TOP2A MUTATED TOP2A WILD-TYPE
  NO             10             282
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TOP2A MUTATED                                          0
  TOP2A WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TOP2A MUTATED                                       2
  TOP2A WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TOP2A MUTATED                                                        6
  TOP2A WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TOP2A MUTATED                                                   0
  TOP2A WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TOP2A MUTATED                                                                   4
  TOP2A WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TOP2A MUTATED                                                    1
  TOP2A WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TOP2A MUTATED                                                  1
  TOP2A WILD-TYPE                                               60
D192V9, multiclass
                                                                   clus
vv                                                                  TOP2A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  TOP2A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TOP2A MUTATED    10   0   1   2
  TOP2A WILD-TYPE 301  14  14  22
D192V10, multiclass
    clus
vv   TOP2A MUTATED TOP2A WILD-TYPE
  R0            10             301
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TOP2A MUTATED       2                         0
  TOP2A WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TOP2A MUTATED                                           0     6
  TOP2A WILD-TYPE                                         1   237
D192V12, multiclass
                                           clus
vv                                          TOP2A MUTATED TOP2A WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V13, binary
                 cls
clus                0   1
  TOP2A MUTATED     0   6
  TOP2A WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED      0    6
  TOP2A WILD-TYPE    4  304
                        clus
vv                       TOP2A MUTATED TOP2A WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(193) Variable = KIF21A MUTATION ANALYSIS
D193V1, survival
                  sevent
clus2                0   1
  KIF21A MUTATED    11   5
  KIF21A WILD-TYPE 219 134
  KIF21A MUTATED KIF21A WILD-TYPE 
              16              353 
  KIF21A MUTATED KIF21A WILD-TYPE 
               5              134 
$`KIF21A MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  KIF21A MUTATED KIF21A WILD-TYPE 
             0.1              0.0 
  KIF21A MUTATED KIF21A WILD-TYPE 
           38.14           122.30 
  KIF21A MUTATED KIF21A WILD-TYPE 
           17.84            14.17 
[1] "0.1 - 38.1 (17.8)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D193V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIF21A MUTATED         0        0        1        1         2         4
  KIF21A WILD-TYPE       2       15       39       29        35        48
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF21A MUTATED           0          6          0          2        1
  KIF21A WILD-TYPE         3         64         53         30       37
D193V3, multiclass
            clus
vv           KIF21A MUTATED KIF21A WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               4               48
  STAGE III               0                3
  STAGE IIIA              6               64
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIF21A MUTATED     0   3   8   7
  KIF21A WILD-TYPE  22  89 165  90
D193V4, multiclass
    clus
vv   KIF21A MUTATED KIF21A WILD-TYPE
  T1              0               22
  T2              3               89
  T3              8              165
  T4              7               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
  KIF21A MUTATED     6   6   6   0
  KIF21A WILD-TYPE 112  98  71  77
D193V5, multiclass
    clus
vv   KIF21A MUTATED KIF21A WILD-TYPE
  N0              6              112
  N1              6               98
  N2              6               71
  N3              0               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"
D193V6, binary
                  cls
clus                 0   1
  KIF21A MUTATED    16   1
  KIF21A WILD-TYPE 330  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     16    1
  KIF21A WILD-TYPE  330   28
   clus
vv  KIF21A MUTATED KIF21A WILD-TYPE
  0             16              330
  1              1               28
[1] 2 2
[1] FALSE
D193V7, binary
                  cls
clus                 0   1
  KIF21A MUTATED     9   9
  KIF21A WILD-TYPE 136 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED      9    9
  KIF21A WILD-TYPE  136  239
        clus
vv       KIF21A MUTATED KIF21A WILD-TYPE
  FEMALE              9              136
  MALE                9              239
[1] 2 2
[1] FALSE
D193V8, binary
                  cls
clus                 0   1
  KIF21A MUTATED    15   2
  KIF21A WILD-TYPE 277  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     15    2
  KIF21A WILD-TYPE  277   57
     clus
vv    KIF21A MUTATED KIF21A WILD-TYPE
  NO              15              277
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIF21A MUTATED                                          0
  KIF21A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIF21A MUTATED                                       4
  KIF21A WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIF21A MUTATED                                                        7
  KIF21A WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIF21A MUTATED                                                   1
  KIF21A WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIF21A MUTATED                                                                   1
  KIF21A WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIF21A MUTATED                                                    0
  KIF21A WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIF21A MUTATED                                                  5
  KIF21A WILD-TYPE                                               56
D193V9, multiclass
                                                                   clus
vv                                                                  KIF21A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               5
                                                                   clus
vv                                                                  KIF21A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KIF21A MUTATED    13   0   0   2
  KIF21A WILD-TYPE 298  14  15  22
D193V10, multiclass
    clus
vv   KIF21A MUTATED KIF21A WILD-TYPE
  R0             13              298
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KIF21A MUTATED       9                         0
  KIF21A WILD-TYPE    78                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIF21A MUTATED                                           0     8
  KIF21A WILD-TYPE                                         1   235
D193V12, multiclass
                                           clus
vv                                          KIF21A MUTATED KIF21A WILD-TYPE
  ASIAN                                                  9               78
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V13, binary
                  cls
clus                 0   1
  KIF21A MUTATED     0  16
  KIF21A WILD-TYPE   4 294
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED      0   16
  KIF21A WILD-TYPE    4  294
                        clus
vv                       KIF21A MUTATED KIF21A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             16              294
[1] 2 2
[1] FALSE

Clustering(194) Variable = LTBP3 MUTATION ANALYSIS
D194V1, survival
                 sevent
clus2               0   1
  LTBP3 MUTATED     9   6
  LTBP3 WILD-TYPE 221 133
  LTBP3 MUTATED LTBP3 WILD-TYPE 
             15             354 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              6             133 
$`LTBP3 MUTATED`
TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4465 
       29.59         0.26         1.12        11.77        12.62         9.01 
TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A4YV TCGA-D7-A6EY TCGA-HF-7132 TCGA-HF-A5NB 
      105.07        28.96         5.92        11.44        77.29        30.51 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-R5-A7ZI 
       20.25        29.00        74.53 

$`LTBP3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
          20.25           14.22 
[1] "0.3 - 105.1 (20.2)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D194V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LTBP3 MUTATED         0        1        2        2         1         2
  LTBP3 WILD-TYPE       2       14       38       28        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LTBP3 MUTATED           0          2          1          3        2
  LTBP3 WILD-TYPE         3         68         52         29       36
D194V3, multiclass
            clus
vv           LTBP3 MUTATED LTBP3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               2              28
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LTBP3 MUTATED     1   4   4   7
  LTBP3 WILD-TYPE  21  88 169  90
D194V4, multiclass
    clus
vv   LTBP3 MUTATED LTBP3 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             4             169
  T4             7              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
  LTBP3 MUTATED     6   5   1   4
  LTBP3 WILD-TYPE 112  99  76  73
D194V5, multiclass
    clus
vv   LTBP3 MUTATED LTBP3 WILD-TYPE
  N0             6             112
  N1             5              99
  N2             1              76
  N3             4              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"
D194V6, binary
                 cls
clus                0   1
  LTBP3 MUTATED    15   2
  LTBP3 WILD-TYPE 331  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP3 MUTATED     15    2
  LTBP3 WILD-TYPE  331   27
   clus
vv  LTBP3 MUTATED LTBP3 WILD-TYPE
  0            15             331
  1             2              27
[1] 2 2
[1] FALSE
D194V7, binary
                 cls
clus                0   1
  LTBP3 MUTATED    12   5
  LTBP3 WILD-TYPE 133 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP3 MUTATED     12    5
  LTBP3 WILD-TYPE  133  243
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  FEMALE            12             133
  MALE               5             243
[1] 2 2
[1] FALSE
D194V8, binary
                 cls
clus                0   1
  LTBP3 MUTATED    10   2
  LTBP3 WILD-TYPE 282  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP3 MUTATED     10    2
  LTBP3 WILD-TYPE  282   57
     clus
vv    LTBP3 MUTATED LTBP3 WILD-TYPE
  NO             10             282
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LTBP3 MUTATED                                          0
  LTBP3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LTBP3 MUTATED                                       4
  LTBP3 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LTBP3 MUTATED                                                        8
  LTBP3 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LTBP3 MUTATED                                                   2
  LTBP3 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LTBP3 MUTATED                                                                   1
  LTBP3 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LTBP3 MUTATED                                                    0
  LTBP3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LTBP3 MUTATED                                                  2
  LTBP3 WILD-TYPE                                               59
D194V9, multiclass
                                                                   clus
vv                                                                  LTBP3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  LTBP3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LTBP3 MUTATED    11   1   1   2
  LTBP3 WILD-TYPE 300  13  14  22
D194V10, multiclass
    clus
vv   LTBP3 MUTATED LTBP3 WILD-TYPE
  R0            11             300
  R1             1              13
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LTBP3 MUTATED       4                         0
  LTBP3 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LTBP3 MUTATED                                           0     8
  LTBP3 WILD-TYPE                                         1   235
D194V12, multiclass
                                           clus
vv                                          LTBP3 MUTATED LTBP3 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V13, binary
                 cls
clus                0   1
  LTBP3 MUTATED     1  11
  LTBP3 WILD-TYPE   3 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP3 MUTATED      1   11
  LTBP3 WILD-TYPE    3  299
                        clus
vv                       LTBP3 MUTATED LTBP3 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(195) Variable = ZC3H4 MUTATION ANALYSIS
D195V1, survival
                 sevent
clus2               0   1
  ZC3H4 MUTATED    12   7
  ZC3H4 WILD-TYPE 218 132
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
             19             350 
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
              7             132 
$`ZC3H4 MUTATED`
TCGA-CG-4460 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-A4QL 
       21.99         9.34        34.68        32.25         4.31        16.14 
TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-6815 TCGA-D7-A6EY 
        6.58        15.95        28.96        65.10        15.98        11.44 
TCGA-F1-6874 TCGA-HU-8604 TCGA-HU-A4G8 TCGA-IN-8462 TCGA-IN-8663 TCGA-IP-7968 
       14.47        22.82        22.68        18.81         3.39         2.53 
TCGA-VQ-A8P2 
       38.14 

$`ZC3H4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-D7-6817 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-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-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-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-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 

  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
           2.53            0.00 
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
           65.1           122.3 
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
         16.140          14.055 
[1] "2.5 - 65.1 (16.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D195V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZC3H4 MUTATED         0        1        3        1         3         5
  ZC3H4 WILD-TYPE       2       14       37       29        34        47
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H4 MUTATED           0          2          3          0        1
  ZC3H4 WILD-TYPE         3         68         50         32       37
D195V3, multiclass
            clus
vv           ZC3H4 MUTATED ZC3H4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              5              47
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             3              50
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZC3H4 MUTATED     1   7   7   4
  ZC3H4 WILD-TYPE  21  85 166  93
D195V4, multiclass
    clus
vv   ZC3H4 MUTATED ZC3H4 WILD-TYPE
  T1             1              21
  T2             7              85
  T3             7             166
  T4             4              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
  ZC3H4 MUTATED     9   6   3   2
  ZC3H4 WILD-TYPE 109  98  74  75
D195V5, multiclass
    clus
vv   ZC3H4 MUTATED ZC3H4 WILD-TYPE
  N0             9             109
  N1             6              98
  N2             3              74
  N3             2              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"
D195V6, binary
                 cls
clus                0   1
  ZC3H4 MUTATED    18   1
  ZC3H4 WILD-TYPE 328  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H4 MUTATED     18    1
  ZC3H4 WILD-TYPE  328   28
   clus
vv  ZC3H4 MUTATED ZC3H4 WILD-TYPE
  0            18             328
  1             1              28
[1] 2 2
[1] FALSE
D195V7, binary
                 cls
clus                0   1
  ZC3H4 MUTATED    11   9
  ZC3H4 WILD-TYPE 134 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H4 MUTATED     11    9
  ZC3H4 WILD-TYPE  134  239
        clus
vv       ZC3H4 MUTATED ZC3H4 WILD-TYPE
  FEMALE            11             134
  MALE               9             239
[1] 2 2
[1] FALSE
D195V8, binary
                 cls
clus                0   1
  ZC3H4 MUTATED    15   1
  ZC3H4 WILD-TYPE 277  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H4 MUTATED     15    1
  ZC3H4 WILD-TYPE  277   58
     clus
vv    ZC3H4 MUTATED ZC3H4 WILD-TYPE
  NO             15             277
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZC3H4 MUTATED                                          0
  ZC3H4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZC3H4 MUTATED                                       2
  ZC3H4 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZC3H4 MUTATED                                                       10
  ZC3H4 WILD-TYPE                                                    148
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZC3H4 MUTATED                                                   1
  ZC3H4 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZC3H4 MUTATED                                                                   4
  ZC3H4 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZC3H4 MUTATED                                                    0
  ZC3H4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZC3H4 MUTATED                                                  3
  ZC3H4 WILD-TYPE                                               58
D195V9, multiclass
                                                                   clus
vv                                                                  ZC3H4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  ZC3H4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZC3H4 MUTATED    15   0   1   2
  ZC3H4 WILD-TYPE 296  14  14  22
D195V10, multiclass
    clus
vv   ZC3H4 MUTATED ZC3H4 WILD-TYPE
  R0            15             296
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZC3H4 MUTATED       3                         0
  ZC3H4 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZC3H4 MUTATED                                           0    13
  ZC3H4 WILD-TYPE                                         1   230
D195V12, multiclass
                                           clus
vv                                          ZC3H4 MUTATED ZC3H4 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V13, binary
                 cls
clus                0   1
  ZC3H4 MUTATED     0  15
  ZC3H4 WILD-TYPE   4 295
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H4 MUTATED      0   15
  ZC3H4 WILD-TYPE    4  295
                        clus
vv                       ZC3H4 MUTATED ZC3H4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            15             295
[1] 2 2
[1] FALSE

Clustering(196) Variable = TATDN1 MUTATION ANALYSIS
D196V1, survival
                  sevent
clus2                0   1
  TATDN1 MUTATED     4   2
  TATDN1 WILD-TYPE 226 137
  TATDN1 MUTATED TATDN1 WILD-TYPE 
               6              363 
  TATDN1 MUTATED TATDN1 WILD-TYPE 
               2              137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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           14.430 
[1] "6.0 - 29.6 (12.2)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1"  
D196V2, 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       2       14       39       30        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TATDN1 MUTATED           0          1          1          0        1
  TATDN1 WILD-TYPE         3         69         52         32       37
D196V3, multiclass
            clus
vv           TATDN1 MUTATED TATDN1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TATDN1 MUTATED     1   1   2   2
  TATDN1 WILD-TYPE  21  91 171  95
D196V4, multiclass
    clus
vv   TATDN1 MUTATED TATDN1 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              2              171
  T4              2               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
  TATDN1 MUTATED     3   2   0   1
  TATDN1 WILD-TYPE 115 102  77  76
D196V5, multiclass
    clus
vv   TATDN1 MUTATED TATDN1 WILD-TYPE
  N0              3              115
  N1              2              102
  N2              0               77
  N3              1               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"
D196V6, binary
                  cls
clus                 0   1
  TATDN1 MUTATED     6   0
  TATDN1 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN1 MUTATED      6    0
  TATDN1 WILD-TYPE  340   29
   clus
vv  TATDN1 MUTATED TATDN1 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D196V7, binary
                  cls
clus                 0   1
  TATDN1 MUTATED     3   3
  TATDN1 WILD-TYPE 142 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN1 MUTATED      3    3
  TATDN1 WILD-TYPE  142  245
        clus
vv       TATDN1 MUTATED TATDN1 WILD-TYPE
  FEMALE              3              142
  MALE                3              245
[1] 2 2
[1] FALSE
D196V8, binary
                  cls
clus                 0   1
  TATDN1 MUTATED     6   0
  TATDN1 WILD-TYPE 286  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN1 MUTATED      6    0
  TATDN1 WILD-TYPE  286   59
     clus
vv    TATDN1 MUTATED TATDN1 WILD-TYPE
  NO               6              286
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TATDN1 MUTATED                                          0
  TATDN1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TATDN1 MUTATED                                       0
  TATDN1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TATDN1 MUTATED                                                        3
  TATDN1 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TATDN1 MUTATED                                                   0
  TATDN1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TATDN1 MUTATED                                                                   1
  TATDN1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TATDN1 MUTATED                                                    0
  TATDN1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TATDN1 MUTATED                                                  2
  TATDN1 WILD-TYPE                                               59
D196V9, multiclass
                                                                   clus
vv                                                                  TATDN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  TATDN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TATDN1 MUTATED     4   0   0   0
  TATDN1 WILD-TYPE 307  14  15  24
D196V10, multiclass
    clus
vv   TATDN1 MUTATED TATDN1 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TATDN1 MUTATED       3                         0
  TATDN1 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TATDN1 MUTATED                                           0     2
  TATDN1 WILD-TYPE                                         1   241
D196V12, multiclass
                                           clus
vv                                          TATDN1 MUTATED TATDN1 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V13, binary
                  cls
clus                 0   1
  TATDN1 MUTATED     0   5
  TATDN1 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN1 MUTATED      0    5
  TATDN1 WILD-TYPE    4  305
                        clus
vv                       TATDN1 MUTATED TATDN1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(197) Variable = PPIP5K2 MUTATION ANALYSIS
D197V1, survival
                   sevent
clus2                 0   1
  PPIP5K2 MUTATED     7   4
  PPIP5K2 WILD-TYPE 223 135
  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE 
               11               358 
  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE 
                4               135 
$`PPIP5K2 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-8360 TCGA-BR-8363 TCGA-CD-5801 TCGA-CG-4305 
        6.97         6.61         6.18         0.26        13.18        15.95 
TCGA-CG-4466 TCGA-CG-5721 TCGA-D7-A6F0 TCGA-HU-A4GY TCGA-VQ-A8P2 
       18.97         6.02        22.29         0.26        38.14 

$`PPIP5K2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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 

  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             14.45 
[1] "0.3 - 38.1 (7.0)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.4"
D197V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPIP5K2 MUTATED         0        0        4        1         1         0
  PPIP5K2 WILD-TYPE       2       15       36       29        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPIP5K2 MUTATED           1          5          0          0        2
  PPIP5K2 WILD-TYPE         2         65         53         32       36
D197V3, multiclass
            clus
vv           PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 4                36
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                1                 2
  STAGE IIIA               5                65
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PPIP5K2 MUTATED     0   6   3   5
  PPIP5K2 WILD-TYPE  22  86 170  92
D197V4, multiclass
    clus
vv   PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  T1               0                22
  T2               6                86
  T3               3               170
  T4               5                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
  PPIP5K2 MUTATED     6   7   1   0
  PPIP5K2 WILD-TYPE 112  97  76  77
D197V5, multiclass
    clus
vv   PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  N0               6               112
  N1               7                97
  N2               1                76
  N3               0                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"
D197V6, binary
                   cls
clus                  0   1
  PPIP5K2 MUTATED    13   0
  PPIP5K2 WILD-TYPE 333  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIP5K2 MUTATED     13    0
  PPIP5K2 WILD-TYPE  333   29
   clus
vv  PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  0              13               333
  1               0                29
[1] 2 2
[1] FALSE
D197V7, binary
                   cls
clus                  0   1
  PPIP5K2 MUTATED     7   7
  PPIP5K2 WILD-TYPE 138 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIP5K2 MUTATED      7    7
  PPIP5K2 WILD-TYPE  138  241
        clus
vv       PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  FEMALE               7               138
  MALE                 7               241
[1] 2 2
[1] FALSE
D197V8, binary
                   cls
clus                  0   1
  PPIP5K2 MUTATED    10   1
  PPIP5K2 WILD-TYPE 282  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIP5K2 MUTATED     10    1
  PPIP5K2 WILD-TYPE  282   58
     clus
vv    PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  NO               10               282
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PPIP5K2 MUTATED                                          0
  PPIP5K2 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PPIP5K2 MUTATED                                       1
  PPIP5K2 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPIP5K2 MUTATED                                                        7
  PPIP5K2 WILD-TYPE                                                    151
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PPIP5K2 MUTATED                                                   1
  PPIP5K2 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPIP5K2 MUTATED                                                                   5
  PPIP5K2 WILD-TYPE                                                                63
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PPIP5K2 MUTATED                                                    0
  PPIP5K2 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PPIP5K2 MUTATED                                                  0
  PPIP5K2 WILD-TYPE                                               61
D197V9, multiclass
                                                                   clus
vv                                                                  PPIP5K2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  PPIP5K2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PPIP5K2 MUTATED    10   0   0   4
  PPIP5K2 WILD-TYPE 301  14  15  20
D197V10, multiclass
    clus
vv   PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  R0              10               301
  R1               0                14
  R2               0                15
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PPIP5K2 MUTATED       2                         0
  PPIP5K2 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPIP5K2 MUTATED                                           0     8
  PPIP5K2 WILD-TYPE                                         1   235
D197V12, multiclass
                                           clus
vv                                          PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V13, binary
                   cls
clus                  0   1
  PPIP5K2 MUTATED     0   9
  PPIP5K2 WILD-TYPE   4 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIP5K2 MUTATED      0    9
  PPIP5K2 WILD-TYPE    4  301
                        clus
vv                       PPIP5K2 MUTATED PPIP5K2 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               9               301
[1] 2 2
[1] FALSE

Clustering(198) Variable = C5ORF42 MUTATION ANALYSIS
D198V1, survival
                   sevent
clus2                 0   1
  C5ORF42 MUTATED    24   5
  C5ORF42 WILD-TYPE 206 134
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               29               340 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
                5               134 
$`C5ORF42 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6563 TCGA-BR-7707 TCGA-BR-8078 
        6.97        30.90        34.68        39.12        35.84        29.59 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 
       31.27        14.79        25.05         1.12        27.12        31.96 
TCGA-CD-8528 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4477 TCGA-D7-6525 TCGA-D7-A4Z0 
       12.33        12.43         6.58        30.97        13.35        14.76 
TCGA-F1-A448 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4GU 
       21.27        11.08        77.29        11.77         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-IN-A6RS TCGA-MX-A5UJ TCGA-VQ-A8P3 
       20.25        29.00        12.59        19.73        37.22 

$`C5ORF42 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-8381 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
       11.80         7.36         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-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-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-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-D7-6521 
       12.66        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-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-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-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        8.98         0.10         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-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-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-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 

  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
             1.12              0.00 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
            77.29            122.30 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
           20.250            14.055 
[1] "1.1 - 77.3 (20.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.8"
D198V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C5ORF42 MUTATED         1        2        3        2         5         4
  C5ORF42 WILD-TYPE       1       13       37       28        32        48
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C5ORF42 MUTATED           0          6          2          4        1
  C5ORF42 WILD-TYPE         3         64         51         28       37
D198V3, multiclass
            clus
vv           C5ORF42 MUTATED C5ORF42 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 2                13
  STAGE IB                 3                37
  STAGE II                 2                28
  STAGE IIA                5                32
  STAGE IIB                4                48
  STAGE III                0                 3
  STAGE IIIA               6                64
  STAGE IIIB               2                51
  STAGE IIIC               4                28
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C5ORF42 MUTATED     3   7  11  10
  C5ORF42 WILD-TYPE  19  85 162  87
D198V4, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  T1               3                19
  T2               7                85
  T3              11               162
  T4              10                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
  C5ORF42 MUTATED    13   8   5   4
  C5ORF42 WILD-TYPE 105  96  72  73
D198V5, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  N0              13               105
  N1               8                96
  N2               5                72
  N3               4                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"
D198V6, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    28   1
  C5ORF42 WILD-TYPE 318  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     28    1
  C5ORF42 WILD-TYPE  318   28
   clus
vv  C5ORF42 MUTATED C5ORF42 WILD-TYPE
  0              28               318
  1               1                28
[1] 2 2
[1] FALSE
D198V7, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    14  17
  C5ORF42 WILD-TYPE 131 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     14   17
  C5ORF42 WILD-TYPE  131  231
        clus
vv       C5ORF42 MUTATED C5ORF42 WILD-TYPE
  FEMALE              14               131
  MALE                17               231
[1] 2 2
[1] FALSE
D198V8, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    22   7
  C5ORF42 WILD-TYPE 270  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     22    7
  C5ORF42 WILD-TYPE  270   52
     clus
vv    C5ORF42 MUTATED C5ORF42 WILD-TYPE
  NO               22               270
  YES               7                52
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C5ORF42 MUTATED                                          0
  C5ORF42 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C5ORF42 MUTATED                                       5
  C5ORF42 WILD-TYPE                                    65
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C5ORF42 MUTATED                                                       15
  C5ORF42 WILD-TYPE                                                    143
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C5ORF42 MUTATED                                                   3
  C5ORF42 WILD-TYPE                                                18
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C5ORF42 MUTATED                                                                   3
  C5ORF42 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C5ORF42 MUTATED                                                    0
  C5ORF42 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C5ORF42 MUTATED                                                  5
  C5ORF42 WILD-TYPE                                               56
D198V9, multiclass
                                                                   clus
vv                                                                  C5ORF42 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                5
                                                                   clus
vv                                                                  C5ORF42 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C5ORF42 MUTATED    28   0   0   2
  C5ORF42 WILD-TYPE 283  14  15  22
D198V10, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  R0              28               283
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C5ORF42 MUTATED       9                         2
  C5ORF42 WILD-TYPE    78                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C5ORF42 MUTATED                                           0    17
  C5ORF42 WILD-TYPE                                         1   226
D198V12, multiclass
                                           clus
vv                                          C5ORF42 MUTATED C5ORF42 WILD-TYPE
  ASIAN                                                   9                78
  BLACK OR AFRICAN AMERICAN                               2                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  17               226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V13, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED     1  26
  C5ORF42 WILD-TYPE   3 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED      1   26
  C5ORF42 WILD-TYPE    3  284
                        clus
vv                       C5ORF42 MUTATED C5ORF42 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              26               284
[1] 2 2
[1] FALSE

Clustering(199) Variable = C13ORF33 MUTATION ANALYSIS
D199V1, survival
                    sevent
clus2                  0   1
  C13ORF33 MUTATED     5   2
  C13ORF33 WILD-TYPE 225 137
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 7                362 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
                 2                137 
$`C13ORF33 MUTATED`
TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-A4QL TCGA-HU-A4GQ 
       29.59        31.10        31.27        28.14        16.14         0.10 
TCGA-HU-A4H3 
       29.00 

$`C13ORF33 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
               0.1                0.0 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
             31.27             122.30 
  C13ORF33 MUTATED C13ORF33 WILD-TYPE 
             29.00              14.07 
[1] "0.1 - 31.3 (29.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D199V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C13ORF33 MUTATED         0        0        0        0         0         1
  C13ORF33 WILD-TYPE       2       15       40       30        37        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C13ORF33 MUTATED           0          0          1          5        0
  C13ORF33 WILD-TYPE         3         70         52         27       38
D199V3, multiclass
            clus
vv           C13ORF33 MUTATED C13ORF33 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 0                 37
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                1                 52
  STAGE IIIC                5                 27
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C13ORF33 MUTATED     0   0   1   6
  C13ORF33 WILD-TYPE  22  92 172  91
D199V4, multiclass
    clus
vv   C13ORF33 MUTATED C13ORF33 WILD-TYPE
  T1                0                 22
  T2                0                 92
  T3                1                172
  T4                6                 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
  C13ORF33 MUTATED     1   0   2   4
  C13ORF33 WILD-TYPE 117 104  75  73
D199V5, multiclass
    clus
vv   C13ORF33 MUTATED C13ORF33 WILD-TYPE
  N0                1                117
  N1                0                104
  N2                2                 75
  N3                4                 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"
D199V6, binary
                    cls
clus                   0   1
  C13ORF33 MUTATED     7   0
  C13ORF33 WILD-TYPE 339  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF33 MUTATED      7    0
  C13ORF33 WILD-TYPE  339   29
   clus
vv  C13ORF33 MUTATED C13ORF33 WILD-TYPE
  0                7                339
  1                0                 29
[1] 2 2
[1] FALSE
D199V7, binary
                    cls
clus                   0   1
  C13ORF33 MUTATED     4   3
  C13ORF33 WILD-TYPE 141 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF33 MUTATED      4    3
  C13ORF33 WILD-TYPE  141  245
        clus
vv       C13ORF33 MUTATED C13ORF33 WILD-TYPE
  FEMALE                4                141
  MALE                  3                245
[1] 2 2
[1] FALSE
D199V8, binary
                    cls
clus                   0   1
  C13ORF33 MUTATED     6   0
  C13ORF33 WILD-TYPE 286  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF33 MUTATED      6    0
  C13ORF33 WILD-TYPE  286   59
     clus
vv    C13ORF33 MUTATED C13ORF33 WILD-TYPE
  NO                 6                286
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C13ORF33 MUTATED                                          0
  C13ORF33 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C13ORF33 MUTATED                                       1
  C13ORF33 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C13ORF33 MUTATED                                                        5
  C13ORF33 WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C13ORF33 MUTATED                                                   0
  C13ORF33 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C13ORF33 MUTATED                                                                   0
  C13ORF33 WILD-TYPE                                                                68
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C13ORF33 MUTATED                                                    0
  C13ORF33 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C13ORF33 MUTATED                                                  1
  C13ORF33 WILD-TYPE                                               60
D199V9, multiclass
                                                                   clus
vv                                                                  C13ORF33 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  C13ORF33 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C13ORF33 MUTATED     7   0   0   0
  C13ORF33 WILD-TYPE 304  14  15  24
D199V10, multiclass
    clus
vv   C13ORF33 MUTATED C13ORF33 WILD-TYPE
  R0                7                304
  R1                0                 14
  R2                0                 15
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C13ORF33 MUTATED       2                         0
  C13ORF33 WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C13ORF33 MUTATED                                           0     5
  C13ORF33 WILD-TYPE                                         1   238
D199V12, multiclass
                                           clus
vv                                          C13ORF33 MUTATED C13ORF33 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V13, binary
                    cls
clus                   0   1
  C13ORF33 MUTATED     0   7
  C13ORF33 WILD-TYPE   4 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF33 MUTATED      0    7
  C13ORF33 WILD-TYPE    4  303
                        clus
vv                       C13ORF33 MUTATED C13ORF33 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                7                303
[1] 2 2
[1] FALSE

Clustering(200) Variable = COIL MUTATION ANALYSIS
D200V1, survival
                sevent
clus2              0   1
  COIL MUTATED     7   3
  COIL WILD-TYPE 223 136
  COIL MUTATED COIL WILD-TYPE 
            10            359 
  COIL MUTATED COIL WILD-TYPE 
             3            136 
$`COIL MUTATED`
TCGA-B7-5816 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-8536 
       26.70        29.59         0.26         1.12        31.96        12.43 
TCGA-CG-4469 TCGA-D7-A4YV TCGA-HU-A4GU TCGA-HU-A4GX 
        7.07         5.92         6.58        20.25 

$`COIL WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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 

  COIL MUTATED COIL WILD-TYPE 
          0.26           0.00 
  COIL MUTATED COIL WILD-TYPE 
         31.96         122.30 
  COIL MUTATED COIL WILD-TYPE 
          9.75          14.43 
[1] "0.3 - 32.0 (9.8)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1"  
D200V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  COIL MUTATED         0        0        1        1         1         4
  COIL WILD-TYPE       2       15       39       29        36        48
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COIL MUTATED           0          0          0          1        2
  COIL WILD-TYPE         3         70         53         31       36
D200V3, multiclass
            clus
vv           COIL MUTATED COIL WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             4             48
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  COIL MUTATED     0   1   5   4
  COIL WILD-TYPE  22  91 168  93
D200V4, multiclass
    clus
vv   COIL MUTATED COIL WILD-TYPE
  T1            0             22
  T2            1             91
  T3            5            168
  T4            4             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
  COIL MUTATED     5   2   2   1
  COIL WILD-TYPE 113 102  75  76
D200V5, multiclass
    clus
vv   COIL MUTATED COIL WILD-TYPE
  N0            5            113
  N1            2            102
  N2            2             75
  N3            1             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"
D200V6, binary
                cls
clus               0   1
  COIL MUTATED     9   1
  COIL WILD-TYPE 337  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  COIL MUTATED      9    1
  COIL WILD-TYPE  337   28
   clus
vv  COIL MUTATED COIL WILD-TYPE
  0            9            337
  1            1             28
[1] 2 2
[1] FALSE
D200V7, binary
                cls
clus               0   1
  COIL MUTATED     6   4
  COIL WILD-TYPE 139 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  COIL MUTATED      6    4
  COIL WILD-TYPE  139  244
        clus
vv       COIL MUTATED COIL WILD-TYPE
  FEMALE            6            139
  MALE              4            244
[1] 2 2
[1] FALSE
D200V8, binary
                cls
clus               0   1
  COIL MUTATED     9   0
  COIL WILD-TYPE 283  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  COIL MUTATED      9    0
  COIL WILD-TYPE  283   59
     clus
vv    COIL MUTATED COIL WILD-TYPE
  NO             9            283
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  COIL MUTATED                                          0
  COIL WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  COIL MUTATED                                       3
  COIL WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  COIL MUTATED                                                        4
  COIL WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  COIL MUTATED                                                   0
  COIL WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  COIL MUTATED                                                                   1
  COIL WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  COIL MUTATED                                                    0
  COIL WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  COIL MUTATED                                                  2
  COIL WILD-TYPE                                               59
D200V9, multiclass
                                                                   clus
vv                                                                  COIL MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  COIL WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  COIL MUTATED     9   1   0   0
  COIL WILD-TYPE 302  13  15  24
D200V10, multiclass
    clus
vv   COIL MUTATED COIL WILD-TYPE
  R0            9            302
  R1            1             13
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  COIL MUTATED       4                         0
  COIL WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  COIL MUTATED                                           0     5
  COIL WILD-TYPE                                         1   238
D200V12, multiclass
                                           clus
vv                                          COIL MUTATED COIL WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V13, binary
                cls
clus               0   1
  COIL MUTATED     0   9
  COIL WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  COIL MUTATED      0    9
  COIL WILD-TYPE    4  301
                        clus
vv                       COIL MUTATED COIL WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(201) Variable = TP53BP2 MUTATION ANALYSIS
D201V1, survival
                   sevent
clus2                 0   1
  TP53BP2 MUTATED    11   2
  TP53BP2 WILD-TYPE 219 137
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
               13               356 
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
                2               137 
$`TP53BP2 MUTATED`
TCGA-BR-6452 TCGA-BR-7715 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8680 TCGA-CG-4305 
       34.68        33.63         4.31        25.05        31.96        15.95 
TCGA-CG-5728 TCGA-D7-A4YX TCGA-D7-A6EY TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4GU 
       65.10        36.43        11.44        11.08        30.51         6.58 
TCGA-HU-A4GX 
       20.25 

$`TP53BP2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        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-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-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 

  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
             4.31              0.00 
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
             65.1             122.3 
  TP53BP2 MUTATED TP53BP2 WILD-TYPE 
            25.05             14.07 
[1] "4.3 - 65.1 (25.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.3"
D201V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TP53BP2 MUTATED         0        0        2        1         3         2
  TP53BP2 WILD-TYPE       2       15       38       29        34        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TP53BP2 MUTATED           0          1          1          3        1
  TP53BP2 WILD-TYPE         3         69         52         29       37
D201V3, multiclass
            clus
vv           TP53BP2 MUTATED TP53BP2 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 1                29
  STAGE IIA                3                34
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               3                29
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TP53BP2 MUTATED     0   3   6   5
  TP53BP2 WILD-TYPE  22  89 167  92
D201V4, multiclass
    clus
vv   TP53BP2 MUTATED TP53BP2 WILD-TYPE
  T1               0                22
  T2               3                89
  T3               6               167
  T4               5                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
  TP53BP2 MUTATED     6   3   2   3
  TP53BP2 WILD-TYPE 112 101  75  74
D201V5, multiclass
    clus
vv   TP53BP2 MUTATED TP53BP2 WILD-TYPE
  N0               6               112
  N1               3               101
  N2               2                75
  N3               3                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
  TP53BP2 MUTATED    13   1
  TP53BP2 WILD-TYPE 333  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP2 MUTATED     13    1
  TP53BP2 WILD-TYPE  333   28
   clus
vv  TP53BP2 MUTATED TP53BP2 WILD-TYPE
  0              13               333
  1               1                28
[1] 2 2
[1] FALSE
D201V7, binary
                   cls
clus                  0   1
  TP53BP2 MUTATED     8   6
  TP53BP2 WILD-TYPE 137 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP2 MUTATED      8    6
  TP53BP2 WILD-TYPE  137  242
        clus
vv       TP53BP2 MUTATED TP53BP2 WILD-TYPE
  FEMALE               8               137
  MALE                 6               242
[1] 2 2
[1] FALSE
D201V8, binary
                   cls
clus                  0   1
  TP53BP2 MUTATED    10   2
  TP53BP2 WILD-TYPE 282  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP2 MUTATED     10    2
  TP53BP2 WILD-TYPE  282   57
     clus
vv    TP53BP2 MUTATED TP53BP2 WILD-TYPE
  NO               10               282
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TP53BP2 MUTATED                                          0
  TP53BP2 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TP53BP2 MUTATED                                       2
  TP53BP2 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TP53BP2 MUTATED                                                        8
  TP53BP2 WILD-TYPE                                                    150
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TP53BP2 MUTATED                                                   1
  TP53BP2 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TP53BP2 MUTATED                                                                   1
  TP53BP2 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TP53BP2 MUTATED                                                    0
  TP53BP2 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TP53BP2 MUTATED                                                  2
  TP53BP2 WILD-TYPE                                               59
D201V9, multiclass
                                                                   clus
vv                                                                  TP53BP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  TP53BP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TP53BP2 MUTATED    12   1   0   1
  TP53BP2 WILD-TYPE 299  13  15  23
D201V10, multiclass
    clus
vv   TP53BP2 MUTATED TP53BP2 WILD-TYPE
  R0              12               299
  R1               1                13
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TP53BP2 MUTATED       3                         1
  TP53BP2 WILD-TYPE    84                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TP53BP2 MUTATED                                           0     7
  TP53BP2 WILD-TYPE                                         1   236
D201V12, multiclass
                                           clus
vv                                          TP53BP2 MUTATED TP53BP2 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V13, binary
                   cls
clus                  0   1
  TP53BP2 MUTATED     0  11
  TP53BP2 WILD-TYPE   4 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP2 MUTATED      0   11
  TP53BP2 WILD-TYPE    4  299
                        clus
vv                       TP53BP2 MUTATED TP53BP2 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              11               299
[1] 2 2
[1] FALSE

Clustering(202) Variable = TGFBR2 MUTATION ANALYSIS
D202V1, survival
                  sevent
clus2                0   1
  TGFBR2 MUTATED     9   6
  TGFBR2 WILD-TYPE 221 133
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              15              354 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               6              133 
$`TGFBR2 MUTATED`
TCGA-BR-4191 TCGA-BR-6452 TCGA-BR-6563 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-A453 
       18.35        34.68        39.12         1.12        12.79         6.08 
TCGA-CD-8531 TCGA-CG-4465 TCGA-CG-5726 TCGA-D7-6522 TCGA-D7-A4YT TCGA-HU-A4HD 
       12.59         9.01        28.96        18.61        14.27        33.40 
TCGA-MX-A5UJ TCGA-R5-A804 TCGA-RD-A7BW 
       19.73         4.60         5.13 

$`TGFBR2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        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-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-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-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-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-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.54        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-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-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        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-A805 TCGA-RD-A7BS 
       18.21         8.52        74.53         6.08         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-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 

  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
            1.12             0.00 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
           39.12           122.30 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
           14.27            14.30 
[1] "1.1 - 39.1 (14.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D202V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TGFBR2 MUTATED         0        1        2        0         2         2
  TGFBR2 WILD-TYPE       2       14       38       30        35        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TGFBR2 MUTATED           0          4          0          0        3
  TGFBR2 WILD-TYPE         3         66         53         32       35
D202V3, multiclass
            clus
vv           TGFBR2 MUTATED TGFBR2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TGFBR2 MUTATED     1   3   7   3
  TGFBR2 WILD-TYPE  21  89 166  94
D202V4, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              7              166
  T4              3               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
  TGFBR2 MUTATED     6   4   3   3
  TGFBR2 WILD-TYPE 112 100  74  74
D202V5, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  N0              6              112
  N1              4              100
  N2              3               74
  N3              3               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"
D202V6, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    13   3
  TGFBR2 WILD-TYPE 333  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     13    3
  TGFBR2 WILD-TYPE  333   26
   clus
vv  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  0             13              333
  1              3               26
[1] 2 2
[1] FALSE
D202V7, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     8   8
  TGFBR2 WILD-TYPE 137 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      8    8
  TGFBR2 WILD-TYPE  137  240
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  FEMALE              8              137
  MALE                8              240
[1] 2 2
[1] FALSE
D202V8, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    11   2
  TGFBR2 WILD-TYPE 281  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     11    2
  TGFBR2 WILD-TYPE  281   57
     clus
vv    TGFBR2 MUTATED TGFBR2 WILD-TYPE
  NO              11              281
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TGFBR2 MUTATED                                          1
  TGFBR2 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TGFBR2 MUTATED                                       5
  TGFBR2 WILD-TYPE                                    65
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TGFBR2 MUTATED                                                        6
  TGFBR2 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TGFBR2 MUTATED                                                   0
  TGFBR2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TGFBR2 MUTATED                                                                   1
  TGFBR2 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TGFBR2 MUTATED                                                    0
  TGFBR2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TGFBR2 MUTATED                                                  3
  TGFBR2 WILD-TYPE                                               58
D202V9, multiclass
                                                                   clus
vv                                                                  TGFBR2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  TGFBR2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TGFBR2 MUTATED    12   0   1   2
  TGFBR2 WILD-TYPE 299  14  14  22
D202V10, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  R0             12              299
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TGFBR2 MUTATED       3                         1
  TGFBR2 WILD-TYPE    84                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TGFBR2 MUTATED                                           0    10
  TGFBR2 WILD-TYPE                                         1   233
D202V12, multiclass
                                           clus
vv                                          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V13, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     0  14
  TGFBR2 WILD-TYPE   4 296
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      0   14
  TGFBR2 WILD-TYPE    4  296
                        clus
vv                       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             14              296
[1] 2 2
[1] FALSE

Clustering(203) Variable = FBXO21 MUTATION ANALYSIS
D203V1, survival
                  sevent
clus2                0   1
  FBXO21 MUTATED     6   7
  FBXO21 WILD-TYPE 224 132
  FBXO21 MUTATED FBXO21 WILD-TYPE 
              13              356 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
               7              132 
$`FBXO21 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 
       21.99         6.97        30.90         9.34         9.67        34.68 
TCGA-BR-8059 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8591 TCGA-D7-8579 TCGA-KB-A93J 
       14.43        31.10        31.27        28.14        20.91        36.95 
TCGA-VQ-A8PQ 
       15.65 

$`FBXO21 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-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-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-A91Q TCGA-VQ-A91U 
       37.22        22.19        17.85         1.87        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 

  FBXO21 MUTATED FBXO21 WILD-TYPE 
            6.97             0.00 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
           36.95           122.30 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
          21.990           14.055 
[1] "7.0 - 37.0 (22.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D203V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXO21 MUTATED         0        0        0        1         1         1
  FBXO21 WILD-TYPE       2       15       40       29        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO21 MUTATED           1          2          0          3        2
  FBXO21 WILD-TYPE         2         68         53         29       36
D203V3, multiclass
            clus
vv           FBXO21 MUTATED FBXO21 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               1                2
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              3               29
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO21 MUTATED     0   3   2   7
  FBXO21 WILD-TYPE  22  89 171  90
D203V4, multiclass
    clus
vv   FBXO21 MUTATED FBXO21 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              2              171
  T4              7               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
  FBXO21 MUTATED     2   7   2   2
  FBXO21 WILD-TYPE 116  97  75  75
D203V5, multiclass
    clus
vv   FBXO21 MUTATED FBXO21 WILD-TYPE
  N0              2              116
  N1              7               97
  N2              2               75
  N3              2               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"
D203V6, binary
                  cls
clus                 0   1
  FBXO21 MUTATED    12   2
  FBXO21 WILD-TYPE 334  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED     12    2
  FBXO21 WILD-TYPE  334   27
   clus
vv  FBXO21 MUTATED FBXO21 WILD-TYPE
  0             12              334
  1              2               27
[1] 2 2
[1] FALSE
D203V7, binary
                  cls
clus                 0   1
  FBXO21 MUTATED     9   6
  FBXO21 WILD-TYPE 136 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED      9    6
  FBXO21 WILD-TYPE  136  242
        clus
vv       FBXO21 MUTATED FBXO21 WILD-TYPE
  FEMALE              9              136
  MALE                6              242
[1] 2 2
[1] FALSE
D203V8, binary
                  cls
clus                 0   1
  FBXO21 MUTATED    11   2
  FBXO21 WILD-TYPE 281  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED     11    2
  FBXO21 WILD-TYPE  281   57
     clus
vv    FBXO21 MUTATED FBXO21 WILD-TYPE
  NO              11              281
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FBXO21 MUTATED                                          0
  FBXO21 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FBXO21 MUTATED                                       1
  FBXO21 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBXO21 MUTATED                                                       10
  FBXO21 WILD-TYPE                                                    148
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FBXO21 MUTATED                                                   0
  FBXO21 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBXO21 MUTATED                                                                   3
  FBXO21 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FBXO21 MUTATED                                                    0
  FBXO21 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FBXO21 MUTATED                                                  1
  FBXO21 WILD-TYPE                                               60
D203V9, multiclass
                                                                   clus
vv                                                                  FBXO21 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  FBXO21 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FBXO21 MUTATED     7   0   2   6
  FBXO21 WILD-TYPE 304  14  13  18
D203V10, multiclass
    clus
vv   FBXO21 MUTATED FBXO21 WILD-TYPE
  R0              7              304
  R1              0               14
  R2              2               13
  RX              6               18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FBXO21 MUTATED       0                         0
  FBXO21 WILD-TYPE    87                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXO21 MUTATED                                           0    14
  FBXO21 WILD-TYPE                                         1   229
D203V12, multiclass
                                           clus
vv                                          FBXO21 MUTATED FBXO21 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 14              229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V13, binary
                  cls
clus                 0   1
  FBXO21 MUTATED     0  12
  FBXO21 WILD-TYPE   4 298
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED      0   12
  FBXO21 WILD-TYPE    4  298
                        clus
vv                       FBXO21 MUTATED FBXO21 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             12              298
[1] 2 2
[1] FALSE

Clustering(204) Variable = CASP7 MUTATION ANALYSIS
D204V1, survival
                 sevent
clus2               0   1
  CASP7 MUTATED     2   2
  CASP7 WILD-TYPE 228 137
  CASP7 MUTATED CASP7 WILD-TYPE 
              4             365 
  CASP7 MUTATED CASP7 WILD-TYPE 
              2             137 
$`CASP7 MUTATED`
TCGA-BR-8361 TCGA-BR-8363 TCGA-CG-5726 TCGA-VQ-A8P2 
       31.10         0.26        28.96        38.14 

$`CASP7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  CASP7 MUTATED CASP7 WILD-TYPE 
           0.26            0.00 
  CASP7 MUTATED CASP7 WILD-TYPE 
          38.14          122.30 
  CASP7 MUTATED CASP7 WILD-TYPE 
          30.03           14.17 
[1] "0.3 - 38.1 (30.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1"  
D204V2, 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       2       14       39       30        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASP7 MUTATED           0          1          0          1        0
  CASP7 WILD-TYPE         3         69         53         31       38
D204V3, multiclass
            clus
vv           CASP7 MUTATED CASP7 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASP7 MUTATED     1   1   0   2
  CASP7 WILD-TYPE  21  91 173  95
D204V4, multiclass
    clus
vv   CASP7 MUTATED CASP7 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             0             173
  T4             2              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
  CASP7 MUTATED     2   1   1   0
  CASP7 WILD-TYPE 116 103  76  77
D204V5, multiclass
    clus
vv   CASP7 MUTATED CASP7 WILD-TYPE
  N0             2             116
  N1             1             103
  N2             1              76
  N3             0              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"
D204V6, binary
                 cls
clus                0   1
  CASP7 MUTATED     4   0
  CASP7 WILD-TYPE 342  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP7 MUTATED      4    0
  CASP7 WILD-TYPE  342   29
   clus
vv  CASP7 MUTATED CASP7 WILD-TYPE
  0             4             342
  1             0              29
[1] 2 2
[1] FALSE
D204V7, binary
                 cls
clus                0   1
  CASP7 MUTATED     2   2
  CASP7 WILD-TYPE 143 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP7 MUTATED      2    2
  CASP7 WILD-TYPE  143  246
        clus
vv       CASP7 MUTATED CASP7 WILD-TYPE
  FEMALE             2             143
  MALE               2             246
[1] 2 2
[1] FALSE
D204V8, binary
                 cls
clus                0   1
  CASP7 MUTATED     2   1
  CASP7 WILD-TYPE 290  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP7 MUTATED      2    1
  CASP7 WILD-TYPE  290   58
     clus
vv    CASP7 MUTATED CASP7 WILD-TYPE
  NO              2             290
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CASP7 MUTATED                                          0
  CASP7 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CASP7 MUTATED                                       0
  CASP7 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CASP7 MUTATED                                                        2
  CASP7 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CASP7 MUTATED                                                   1
  CASP7 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CASP7 MUTATED                                                                   1
  CASP7 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CASP7 MUTATED                                                    0
  CASP7 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CASP7 MUTATED                                                  0
  CASP7 WILD-TYPE                                               61
D204V9, multiclass
                                                                   clus
vv                                                                  CASP7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  CASP7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CASP7 MUTATED     4   0   0   0
  CASP7 WILD-TYPE 307  14  15  24
D204V10, multiclass
    clus
vv   CASP7 MUTATED CASP7 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CASP7 MUTATED       0                         0
  CASP7 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CASP7 MUTATED                                           0     3
  CASP7 WILD-TYPE                                         1   240
D204V12, multiclass
                                           clus
vv                                          CASP7 MUTATED CASP7 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V13, binary
                 cls
clus                0   1
  CASP7 MUTATED     0   2
  CASP7 WILD-TYPE   4 308
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP7 MUTATED      0    2
  CASP7 WILD-TYPE    4  308
                        clus
vv                       CASP7 MUTATED CASP7 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             2             308
[1] 2 2
[1] FALSE

Clustering(205) Variable = TMEM41B MUTATION ANALYSIS
D205V1, survival
                   sevent
clus2                 0   1
  TMEM41B MUTATED     1   3
  TMEM41B WILD-TYPE 229 136
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                4               365 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                3               136 
$`TMEM41B MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-A4QL TCGA-MX-A5UJ 
        6.97        30.90        16.14        19.73 

$`TMEM41B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  TMEM41B MUTATED TMEM41B WILD-TYPE 
             6.97              0.00 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
             30.9             122.3 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
           17.935            14.170 
[1] "7.0 - 30.9 (17.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.9"
D205V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM41B MUTATED         1        0        0        0         0         0
  TMEM41B WILD-TYPE       1       15       40       30        37        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM41B MUTATED           0          2          1          0        0
  TMEM41B WILD-TYPE         3         68         52         32       38
D205V3, multiclass
            clus
vv           TMEM41B MUTATED TMEM41B WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                0                37
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM41B MUTATED     1   1   3   0
  TMEM41B WILD-TYPE  21  91 170  97
D205V4, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  T1               1                21
  T2               1                91
  T3               3               170
  T4               0                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
  TMEM41B MUTATED     0   2   1   1
  TMEM41B WILD-TYPE 118 102  76  76
D205V5, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  N0               0               118
  N1               2               102
  N2               1                76
  N3               1                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"
D205V6, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     3   0
  TMEM41B WILD-TYPE 343  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      3    0
  TMEM41B WILD-TYPE  343   29
   clus
vv  TMEM41B MUTATED TMEM41B WILD-TYPE
  0               3               343
  1               0                29
[1] 2 2
[1] FALSE
D205V7, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     3   2
  TMEM41B WILD-TYPE 142 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      3    2
  TMEM41B WILD-TYPE  142  246
        clus
vv       TMEM41B MUTATED TMEM41B WILD-TYPE
  FEMALE               3               142
  MALE                 2               246
[1] 2 2
[1] FALSE
D205V8, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     5   0
  TMEM41B WILD-TYPE 287  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      5    0
  TMEM41B WILD-TYPE  287   59
     clus
vv    TMEM41B MUTATED TMEM41B WILD-TYPE
  NO                5               287
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TMEM41B MUTATED                                          0
  TMEM41B WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TMEM41B MUTATED                                       0
  TMEM41B WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM41B MUTATED                                                        4
  TMEM41B WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TMEM41B MUTATED                                                   0
  TMEM41B WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM41B MUTATED                                                                   0
  TMEM41B WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TMEM41B MUTATED                                                    0
  TMEM41B WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TMEM41B MUTATED                                                  1
  TMEM41B WILD-TYPE                                               60
D205V9, multiclass
                                                                   clus
vv                                                                  TMEM41B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  TMEM41B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM41B MUTATED     3   0   0   2
  TMEM41B WILD-TYPE 308  14  15  22
D205V10, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  R0               3               308
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM41B MUTATED       0                         1
  TMEM41B WILD-TYPE    87                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM41B MUTATED                                           0     4
  TMEM41B WILD-TYPE                                         1   239
D205V12, multiclass
                                           clus
vv                                          TMEM41B MUTATED TMEM41B WILD-TYPE
  ASIAN                                                   0                87
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V13, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     0   5
  TMEM41B WILD-TYPE   4 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      0    5
  TMEM41B WILD-TYPE    4  305
                        clus
vv                       TMEM41B MUTATED TMEM41B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(206) Variable = ORC3L MUTATION ANALYSIS
D206V1, survival
                 sevent
clus2               0   1
  ORC3L MUTATED     7   2
  ORC3L WILD-TYPE 223 137
  ORC3L MUTATED ORC3L WILD-TYPE 
              9             360 
  ORC3L MUTATED ORC3L WILD-TYPE 
              2             137 
$`ORC3L MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8058 TCGA-BR-8360 TCGA-BR-8591 
        6.97         9.34        34.68        37.25         6.18        28.14 
TCGA-HU-8238 TCGA-HU-A4GP TCGA-VQ-A8P2 
        1.51         8.98        38.14 

$`ORC3L WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         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 

  ORC3L MUTATED ORC3L WILD-TYPE 
           1.51            0.00 
  ORC3L MUTATED ORC3L WILD-TYPE 
          38.14          122.30 
  ORC3L MUTATED ORC3L WILD-TYPE 
           9.34           14.35 
[1] "1.5 - 38.1 (9.3)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "1.7"
D206V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ORC3L MUTATED         0        0        1        0         3         0
  ORC3L WILD-TYPE       2       15       39       30        34        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ORC3L MUTATED           0          2          1          1        0
  ORC3L WILD-TYPE         3         68         52         31       38
D206V3, multiclass
            clus
vv           ORC3L MUTATED ORC3L WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ORC3L MUTATED     0   2   5   3
  ORC3L WILD-TYPE  22  90 168  94
D206V4, multiclass
    clus
vv   ORC3L MUTATED ORC3L WILD-TYPE
  T1             0              22
  T2             2              90
  T3             5             168
  T4             3              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
  ORC3L MUTATED     3   5   2   1
  ORC3L WILD-TYPE 115  99  75  76
D206V5, multiclass
    clus
vv   ORC3L MUTATED ORC3L WILD-TYPE
  N0             3             115
  N1             5              99
  N2             2              75
  N3             1              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"
D206V6, binary
                 cls
clus                0   1
  ORC3L MUTATED    10   0
  ORC3L WILD-TYPE 336  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC3L MUTATED     10    0
  ORC3L WILD-TYPE  336   29
   clus
vv  ORC3L MUTATED ORC3L WILD-TYPE
  0            10             336
  1             0              29
[1] 2 2
[1] FALSE
D206V7, binary
                 cls
clus                0   1
  ORC3L MUTATED     5   7
  ORC3L WILD-TYPE 140 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC3L MUTATED      5    7
  ORC3L WILD-TYPE  140  241
        clus
vv       ORC3L MUTATED ORC3L WILD-TYPE
  FEMALE             5             140
  MALE               7             241
[1] 2 2
[1] FALSE
D206V8, binary
                 cls
clus                0   1
  ORC3L MUTATED     8   1
  ORC3L WILD-TYPE 284  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC3L MUTATED      8    1
  ORC3L WILD-TYPE  284   58
     clus
vv    ORC3L MUTATED ORC3L WILD-TYPE
  NO              8             284
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ORC3L MUTATED                                          0
  ORC3L WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ORC3L MUTATED                                       1
  ORC3L WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ORC3L MUTATED                                                        7
  ORC3L WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ORC3L MUTATED                                                   1
  ORC3L WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ORC3L MUTATED                                                                   2
  ORC3L WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ORC3L MUTATED                                                    0
  ORC3L WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ORC3L MUTATED                                                  1
  ORC3L WILD-TYPE                                               60
D206V9, multiclass
                                                                   clus
vv                                                                  ORC3L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  ORC3L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ORC3L MUTATED     8   0   0   4
  ORC3L WILD-TYPE 303  14  15  20
D206V10, multiclass
    clus
vv   ORC3L MUTATED ORC3L WILD-TYPE
  R0             8             303
  R1             0              14
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ORC3L MUTATED       2                         0
  ORC3L WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ORC3L MUTATED                                           0     9
  ORC3L WILD-TYPE                                         1   234
D206V12, multiclass
                                           clus
vv                                          ORC3L MUTATED ORC3L WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V13, binary
                 cls
clus                0   1
  ORC3L MUTATED     0  10
  ORC3L WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC3L MUTATED      0   10
  ORC3L WILD-TYPE    4  300
                        clus
vv                       ORC3L MUTATED ORC3L WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(207) Variable = CBWD6 MUTATION ANALYSIS
D207V1, survival
                 sevent
clus2               0   1
  CBWD6 MUTATED     5   1
  CBWD6 WILD-TYPE 225 138
  CBWD6 MUTATED CBWD6 WILD-TYPE 
              6             363 
  CBWD6 MUTATED CBWD6 WILD-TYPE 
              1             138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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          14.270 
[1] "6.5 - 32.0 (18.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.5"
D207V2, 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       2       15       39       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CBWD6 MUTATED           0          0          0          1        1
  CBWD6 WILD-TYPE         3         70         53         31       37
D207V3, multiclass
            clus
vv           CBWD6 MUTATED CBWD6 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CBWD6 MUTATED     1   0   4   2
  CBWD6 WILD-TYPE  21  92 169  95
D207V4, multiclass
    clus
vv   CBWD6 MUTATED CBWD6 WILD-TYPE
  T1             1              21
  T2             0              92
  T3             4             169
  T4             2              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
  CBWD6 MUTATED     2   2   1   1
  CBWD6 WILD-TYPE 116 102  76  76
D207V5, multiclass
    clus
vv   CBWD6 MUTATED CBWD6 WILD-TYPE
  N0             2             116
  N1             2             102
  N2             1              76
  N3             1              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"
D207V6, binary
                 cls
clus                0   1
  CBWD6 MUTATED     5   1
  CBWD6 WILD-TYPE 341  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD6 MUTATED      5    1
  CBWD6 WILD-TYPE  341   28
   clus
vv  CBWD6 MUTATED CBWD6 WILD-TYPE
  0             5             341
  1             1              28
[1] 2 2
[1] FALSE
D207V7, binary
                 cls
clus                0   1
  CBWD6 MUTATED     4   3
  CBWD6 WILD-TYPE 141 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD6 MUTATED      4    3
  CBWD6 WILD-TYPE  141  245
        clus
vv       CBWD6 MUTATED CBWD6 WILD-TYPE
  FEMALE             4             141
  MALE               3             245
[1] 2 2
[1] FALSE
D207V8, binary
                 cls
clus                0   1
  CBWD6 MUTATED     5   1
  CBWD6 WILD-TYPE 287  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD6 MUTATED      5    1
  CBWD6 WILD-TYPE  287   58
     clus
vv    CBWD6 MUTATED CBWD6 WILD-TYPE
  NO              5             287
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CBWD6 MUTATED                                          0
  CBWD6 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CBWD6 MUTATED                                       2
  CBWD6 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CBWD6 MUTATED                                                        1
  CBWD6 WILD-TYPE                                                    157
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CBWD6 MUTATED                                                   1
  CBWD6 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CBWD6 MUTATED                                                                   0
  CBWD6 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CBWD6 MUTATED                                                    0
  CBWD6 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CBWD6 MUTATED                                                  3
  CBWD6 WILD-TYPE                                               58
D207V9, multiclass
                                                                   clus
vv                                                                  CBWD6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  CBWD6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CBWD6 MUTATED     3   1   0   1
  CBWD6 WILD-TYPE 308  13  15  23
D207V10, multiclass
    clus
vv   CBWD6 MUTATED CBWD6 WILD-TYPE
  R0             3             308
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CBWD6 MUTATED       5                         0
  CBWD6 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CBWD6 MUTATED                                           0     1
  CBWD6 WILD-TYPE                                         1   242
D207V12, multiclass
                                           clus
vv                                          CBWD6 MUTATED CBWD6 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 1             242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V13, binary
                 cls
clus                0   1
  CBWD6 MUTATED     0   6
  CBWD6 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD6 MUTATED      0    6
  CBWD6 WILD-TYPE    4  304
                        clus
vv                       CBWD6 MUTATED CBWD6 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(208) Variable = PRKAB1 MUTATION ANALYSIS
D208V1, survival
                  sevent
clus2                0   1
  PRKAB1 MUTATED     4   5
  PRKAB1 WILD-TYPE 226 134
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
               9              360 
  PRKAB1 MUTATED PRKAB1 WILD-TYPE 
               5              134 
$`PRKAB1 MUTATED`
TCGA-BR-8289 TCGA-BR-8485 TCGA-BR-8591 TCGA-CG-5733 TCGA-HU-A4GQ TCGA-IN-AB1X 
        2.66         9.21        28.14        21.07         0.10        13.51 
TCGA-VQ-A8DV TCGA-VQ-A8P2 TCGA-VQ-A8PM 
       13.25        38.14         1.87 

$`PRKAB1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
        5.46        13.02        43.36        37.41        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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        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            14.45 
[1] "0.1 - 38.1 (13.2)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.9"
D208V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRKAB1 MUTATED         0        0        1        0         1         0
  PRKAB1 WILD-TYPE       2       15       39       30        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRKAB1 MUTATED           0          2          0          3        3
  PRKAB1 WILD-TYPE         3         68         53         29       35
D208V3, multiclass
            clus
vv           PRKAB1 MUTATED PRKAB1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              3               29
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PRKAB1 MUTATED     0   2   1   7
  PRKAB1 WILD-TYPE  22  90 172  90
D208V4, multiclass
    clus
vv   PRKAB1 MUTATED PRKAB1 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              1              172
  T4              7               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
  PRKAB1 MUTATED     2   1   3   4
  PRKAB1 WILD-TYPE 116 103  74  73
D208V5, multiclass
    clus
vv   PRKAB1 MUTATED PRKAB1 WILD-TYPE
  N0              2              116
  N1              1              103
  N2              3               74
  N3              4               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"
D208V6, binary
                  cls
clus                 0   1
  PRKAB1 MUTATED     9   1
  PRKAB1 WILD-TYPE 337  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAB1 MUTATED      9    1
  PRKAB1 WILD-TYPE  337   28
   clus
vv  PRKAB1 MUTATED PRKAB1 WILD-TYPE
  0              9              337
  1              1               28
[1] 2 2
[1] FALSE
D208V7, binary
                  cls
clus                 0   1
  PRKAB1 MUTATED     4   6
  PRKAB1 WILD-TYPE 141 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAB1 MUTATED      4    6
  PRKAB1 WILD-TYPE  141  242
        clus
vv       PRKAB1 MUTATED PRKAB1 WILD-TYPE
  FEMALE              4              141
  MALE                6              242
[1] 2 2
[1] FALSE
D208V8, binary
                  cls
clus                 0   1
  PRKAB1 MUTATED     8   1
  PRKAB1 WILD-TYPE 284  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAB1 MUTATED      8    1
  PRKAB1 WILD-TYPE  284   58
     clus
vv    PRKAB1 MUTATED PRKAB1 WILD-TYPE
  NO               8              284
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PRKAB1 MUTATED                                          1
  PRKAB1 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PRKAB1 MUTATED                                       0
  PRKAB1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRKAB1 MUTATED                                                        4
  PRKAB1 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PRKAB1 MUTATED                                                   1
  PRKAB1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRKAB1 MUTATED                                                                   3
  PRKAB1 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PRKAB1 MUTATED                                                    0
  PRKAB1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PRKAB1 MUTATED                                                  1
  PRKAB1 WILD-TYPE                                               60
D208V9, multiclass
                                                                   clus
vv                                                                  PRKAB1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  PRKAB1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PRKAB1 MUTATED     9   0   0   1
  PRKAB1 WILD-TYPE 302  14  15  23
D208V10, multiclass
    clus
vv   PRKAB1 MUTATED PRKAB1 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PRKAB1 MUTATED       1                         0
  PRKAB1 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRKAB1 MUTATED                                           0     8
  PRKAB1 WILD-TYPE                                         1   235
D208V12, multiclass
                                           clus
vv                                          PRKAB1 MUTATED PRKAB1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V13, binary
                  cls
clus                 0   1
  PRKAB1 MUTATED     0   6
  PRKAB1 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAB1 MUTATED      0    6
  PRKAB1 WILD-TYPE    4  304
                        clus
vv                       PRKAB1 MUTATED PRKAB1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(209) Variable = RABGAP1 MUTATION ANALYSIS
D209V1, survival
                   sevent
clus2                 0   1
  RABGAP1 MUTATED    15   5
  RABGAP1 WILD-TYPE 215 134
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
               20               349 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
                5               134 
$`RABGAP1 MUTATED`
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8361 
        9.67        34.68        35.84        29.59         6.18        31.10 
TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-4305 
        4.31         1.12        31.96        16.14        12.62        15.95 
TCGA-CG-5728 TCGA-CG-5733 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4GQ 
       65.10        21.07        21.27        11.08        26.47         0.10 
TCGA-HU-A4GT TCGA-VQ-A8P2 
        6.51        38.14 

$`RABGAP1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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-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 

  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
              0.1               0.0 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
             65.1             122.3 
  RABGAP1 MUTATED RABGAP1 WILD-TYPE 
           18.605            14.070 
[1] "0.1 - 65.1 (18.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D209V2, 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       2       15       34       29        32        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RABGAP1 MUTATED           0          2          2          2        1
  RABGAP1 WILD-TYPE         3         68         51         30       37
D209V3, multiclass
            clus
vv           RABGAP1 MUTATED RABGAP1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 6                34
  STAGE II                 1                29
  STAGE IIA                5                32
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               2                51
  STAGE IIIC               2                30
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RABGAP1 MUTATED     0   8   7   6
  RABGAP1 WILD-TYPE  22  84 166  91
D209V4, multiclass
    clus
vv   RABGAP1 MUTATED RABGAP1 WILD-TYPE
  T1               0                22
  T2               8                84
  T3               7               166
  T4               6                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
  RABGAP1 MUTATED    13   2   4   2
  RABGAP1 WILD-TYPE 105 102  73  75
D209V5, multiclass
    clus
vv   RABGAP1 MUTATED RABGAP1 WILD-TYPE
  N0              13               105
  N1               2               102
  N2               4                73
  N3               2                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"
D209V6, binary
                   cls
clus                  0   1
  RABGAP1 MUTATED    20   1
  RABGAP1 WILD-TYPE 326  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RABGAP1 MUTATED     20    1
  RABGAP1 WILD-TYPE  326   28
   clus
vv  RABGAP1 MUTATED RABGAP1 WILD-TYPE
  0              20               326
  1               1                28
[1] 2 2
[1] FALSE
D209V7, binary
                   cls
clus                  0   1
  RABGAP1 MUTATED    12  10
  RABGAP1 WILD-TYPE 133 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RABGAP1 MUTATED     12   10
  RABGAP1 WILD-TYPE  133  238
        clus
vv       RABGAP1 MUTATED RABGAP1 WILD-TYPE
  FEMALE              12               133
  MALE                10               238
[1] 2 2
[1] FALSE
D209V8, binary
                   cls
clus                  0   1
  RABGAP1 MUTATED    17   3
  RABGAP1 WILD-TYPE 275  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RABGAP1 MUTATED     17    3
  RABGAP1 WILD-TYPE  275   56
     clus
vv    RABGAP1 MUTATED RABGAP1 WILD-TYPE
  NO               17               275
  YES               3                56
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RABGAP1 MUTATED                                          1
  RABGAP1 WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RABGAP1 MUTATED                                       0
  RABGAP1 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RABGAP1 MUTATED                                                       11
  RABGAP1 WILD-TYPE                                                    147
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RABGAP1 MUTATED                                                   2
  RABGAP1 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RABGAP1 MUTATED                                                                   5
  RABGAP1 WILD-TYPE                                                                63
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RABGAP1 MUTATED                                                    0
  RABGAP1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RABGAP1 MUTATED                                                  3
  RABGAP1 WILD-TYPE                                               58
D209V9, multiclass
                                                                   clus
vv                                                                  RABGAP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  RABGAP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RABGAP1 MUTATED    20   0   0   1
  RABGAP1 WILD-TYPE 291  14  15  23
D209V10, multiclass
    clus
vv   RABGAP1 MUTATED RABGAP1 WILD-TYPE
  R0              20               291
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  RABGAP1 MUTATED       4                         1
  RABGAP1 WILD-TYPE    83                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RABGAP1 MUTATED                                           0    13
  RABGAP1 WILD-TYPE                                         1   230
D209V12, multiclass
                                           clus
vv                                          RABGAP1 MUTATED RABGAP1 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V13, binary
                   cls
clus                  0   1
  RABGAP1 MUTATED     1  16
  RABGAP1 WILD-TYPE   3 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RABGAP1 MUTATED      1   16
  RABGAP1 WILD-TYPE    3  294
                        clus
vv                       RABGAP1 MUTATED RABGAP1 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              16               294
[1] 2 2
[1] FALSE

Clustering(210) Variable = SRCIN1 MUTATION ANALYSIS
D210V1, survival
                  sevent
clus2                0   1
  SRCIN1 MUTATED     6   6
  SRCIN1 WILD-TYPE 224 133
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
              12              357 
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
               6              133 
$`SRCIN1 MUTATED`
TCGA-CG-4460 TCGA-BR-7707 TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-8529 TCGA-CD-A4MG 
       21.99        35.84         0.26         1.12        12.30         6.58 
TCGA-CG-4437 TCGA-CG-4469 TCGA-CG-5723 TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-VQ-A8DL 
        8.05         7.07       105.07        11.77         0.10         0.92 

$`SRCIN1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        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-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 

  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
             0.1              0.0 
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
          105.07           122.30 
  SRCIN1 MUTATED SRCIN1 WILD-TYPE 
            7.56            14.66 
[1] "0.1 - 105.1 (7.6)"  "0.0 - 122.3 (14.7)"
[1] "hr=" "1.9"
D210V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SRCIN1 MUTATED         1        1        3        2         3         0
  SRCIN1 WILD-TYPE       1       14       37       28        34        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SRCIN1 MUTATED           0          0          0          1        3
  SRCIN1 WILD-TYPE         3         70         53         31       35
D210V3, multiclass
            clus
vv           SRCIN1 MUTATED SRCIN1 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                3               37
  STAGE II                2               28
  STAGE IIA               3               34
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SRCIN1 MUTATED     2   5   4   3
  SRCIN1 WILD-TYPE  20  87 169  94
D210V4, multiclass
    clus
vv   SRCIN1 MUTATED SRCIN1 WILD-TYPE
  T1              2               20
  T2              5               87
  T3              4              169
  T4              3               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
  SRCIN1 MUTATED     8   4   1   1
  SRCIN1 WILD-TYPE 110 100  76  76
D210V5, multiclass
    clus
vv   SRCIN1 MUTATED SRCIN1 WILD-TYPE
  N0              8              110
  N1              4              100
  N2              1               76
  N3              1               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"
D210V6, binary
                  cls
clus                 0   1
  SRCIN1 MUTATED    11   2
  SRCIN1 WILD-TYPE 335  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRCIN1 MUTATED     11    2
  SRCIN1 WILD-TYPE  335   27
   clus
vv  SRCIN1 MUTATED SRCIN1 WILD-TYPE
  0             11              335
  1              2               27
[1] 2 2
[1] FALSE
D210V7, binary
                  cls
clus                 0   1
  SRCIN1 MUTATED     5   9
  SRCIN1 WILD-TYPE 140 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRCIN1 MUTATED      5    9
  SRCIN1 WILD-TYPE  140  239
        clus
vv       SRCIN1 MUTATED SRCIN1 WILD-TYPE
  FEMALE              5              140
  MALE                9              239
[1] 2 2
[1] FALSE
D210V8, binary
                  cls
clus                 0   1
  SRCIN1 MUTATED    11   1
  SRCIN1 WILD-TYPE 281  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRCIN1 MUTATED     11    1
  SRCIN1 WILD-TYPE  281   58
     clus
vv    SRCIN1 MUTATED SRCIN1 WILD-TYPE
  NO              11              281
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SRCIN1 MUTATED                                          0
  SRCIN1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SRCIN1 MUTATED                                       1
  SRCIN1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SRCIN1 MUTATED                                                        5
  SRCIN1 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SRCIN1 MUTATED                                                   1
  SRCIN1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SRCIN1 MUTATED                                                                   4
  SRCIN1 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SRCIN1 MUTATED                                                    0
  SRCIN1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SRCIN1 MUTATED                                                  3
  SRCIN1 WILD-TYPE                                               58
D210V9, multiclass
                                                                   clus
vv                                                                  SRCIN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  SRCIN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SRCIN1 MUTATED    11   1   1   0
  SRCIN1 WILD-TYPE 300  13  14  24
D210V10, multiclass
    clus
vv   SRCIN1 MUTATED SRCIN1 WILD-TYPE
  R0             11              300
  R1              1               13
  R2              1               14
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SRCIN1 MUTATED       4                         1
  SRCIN1 WILD-TYPE    83                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SRCIN1 MUTATED                                           0     4
  SRCIN1 WILD-TYPE                                         1   239
D210V12, multiclass
                                           clus
vv                                          SRCIN1 MUTATED SRCIN1 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V13, binary
                  cls
clus                 0   1
  SRCIN1 MUTATED     0   8
  SRCIN1 WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRCIN1 MUTATED      0    8
  SRCIN1 WILD-TYPE    4  302
                        clus
vv                       SRCIN1 MUTATED SRCIN1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(211) Variable = NIN MUTATION ANALYSIS
D211V1, survival
               sevent
clus2             0   1
  NIN MUTATED    17   5
  NIN WILD-TYPE 213 134
  NIN MUTATED NIN WILD-TYPE 
           22           347 
  NIN MUTATED NIN WILD-TYPE 
            5           134 
$`NIN MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7704 
       19.56         6.97        30.90         9.67        34.68        35.24 
TCGA-BR-7958 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-5804 
       29.56        31.10         4.31         1.12        31.96        12.10 
TCGA-CD-A4MJ TCGA-CG-4477 TCGA-D7-6524 TCGA-D7-A74A TCGA-F1-6875 TCGA-HU-A4G8 
       12.62        30.97        17.85        19.96        72.23        22.68 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-IN-A6RR TCGA-MX-A5UJ 
       29.98         6.51         6.74        19.73 

$`NIN WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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-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-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-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.54        18.61        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-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        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-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-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-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 

  NIN MUTATED NIN WILD-TYPE 
         1.12          0.00 
  NIN MUTATED NIN WILD-TYPE 
        72.23        122.30 
  NIN MUTATED NIN WILD-TYPE 
       19.845        14.070 
[1] "1.1 - 72.2 (19.8)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.1"
D211V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NIN MUTATED         0        1        3        2         4         2
  NIN WILD-TYPE       2       14       37       28        33        50
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NIN MUTATED           0          4          1          2        1
  NIN WILD-TYPE         3         66         52         30       37
D211V3, multiclass
            clus
vv           NIN MUTATED NIN WILD-TYPE
  STAGE I              0             2
  STAGE IA             1            14
  STAGE IB             3            37
  STAGE II             2            28
  STAGE IIA            4            33
  STAGE IIB            2            50
  STAGE III            0             3
  STAGE IIIA           4            66
  STAGE IIIB           1            52
  STAGE IIIC           2            30
  STAGE IV             1            37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NIN MUTATED     0   7  10   5
  NIN WILD-TYPE  22  85 163  92
D211V4, multiclass
    clus
vv   NIN MUTATED NIN WILD-TYPE
  T1           0            22
  T2           7            85
  T3          10           163
  T4           5            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
  NIN MUTATED    10   6   4   1
  NIN WILD-TYPE 108  98  73  76
D211V5, multiclass
    clus
vv   NIN MUTATED NIN WILD-TYPE
  N0          10           108
  N1           6            98
  N2           4            73
  N3           1            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"
D211V6, binary
               cls
clus              0   1
  NIN MUTATED    21   1
  NIN WILD-TYPE 325  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  NIN MUTATED     21    1
  NIN WILD-TYPE  325   28
   clus
vv  NIN MUTATED NIN WILD-TYPE
  0          21           325
  1           1            28
[1] 2 2
[1] FALSE
D211V7, binary
               cls
clus              0   1
  NIN MUTATED    12  11
  NIN WILD-TYPE 133 237
[1] "tbl2"
               cls
clus            [,1] [,2]
  NIN MUTATED     12   11
  NIN WILD-TYPE  133  237
        clus
vv       NIN MUTATED NIN WILD-TYPE
  FEMALE          12           133
  MALE            11           237
[1] 2 2
[1] FALSE
D211V8, binary
               cls
clus              0   1
  NIN MUTATED    22   1
  NIN WILD-TYPE 270  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  NIN MUTATED     22    1
  NIN WILD-TYPE  270   58
     clus
vv    NIN MUTATED NIN WILD-TYPE
  NO           22           270
  YES           1            58
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NIN MUTATED                                          0
  NIN WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NIN MUTATED                                       3
  NIN WILD-TYPE                                    67
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NIN MUTATED                                                       12
  NIN WILD-TYPE                                                    146
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NIN MUTATED                                                   0
  NIN WILD-TYPE                                                21
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NIN MUTATED                                                                   3
  NIN WILD-TYPE                                                                65
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NIN MUTATED                                                    0
  NIN WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NIN MUTATED                                                  5
  NIN WILD-TYPE                                               56
D211V9, multiclass
                                                                   clus
vv                                                                  NIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                     12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            5
                                                                   clus
vv                                                                  NIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  NIN MUTATED    16   1   0   3
  NIN WILD-TYPE 295  13  15  21
D211V10, multiclass
    clus
vv   NIN MUTATED NIN WILD-TYPE
  R0          16           295
  R1           1            13
  R2           0            15
  RX           3            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  NIN MUTATED       6                         1
  NIN WILD-TYPE    81                         8
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NIN MUTATED                                           0    15
  NIN WILD-TYPE                                         1   228
D211V12, multiclass
                                           clus
vv                                          NIN MUTATED NIN WILD-TYPE
  ASIAN                                               6            81
  BLACK OR AFRICAN AMERICAN                           1             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              15           228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V13, binary
               cls
clus              0   1
  NIN MUTATED     0  22
  NIN WILD-TYPE   4 288
[1] "tbl2"
               cls
clus            [,1] [,2]
  NIN MUTATED      0   22
  NIN WILD-TYPE    4  288
                        clus
vv                       NIN MUTATED NIN WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          22           288
[1] 2 2
[1] FALSE

Clustering(212) Variable = PET112L MUTATION ANALYSIS
D212V1, survival
                   sevent
clus2                 0   1
  PET112L MUTATED     3   5
  PET112L WILD-TYPE 227 134
  PET112L MUTATED PET112L WILD-TYPE 
                8               361 
  PET112L MUTATED PET112L WILD-TYPE 
                5               134 
$`PET112L MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-8382 TCGA-BR-8680 TCGA-CD-5801 TCGA-CG-5723 
       21.99         6.97        25.05        31.96        13.18       105.07 
TCGA-D7-A4YV TCGA-HU-A4GN 
        5.92        29.98 

$`PET112L WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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 

  PET112L MUTATED PET112L WILD-TYPE 
             5.92              0.00 
  PET112L MUTATED PET112L WILD-TYPE 
           105.07            122.30 
  PET112L MUTATED PET112L WILD-TYPE 
            23.52             14.17 
[1] "5.9 - 105.1 (23.5)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D212V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PET112L MUTATED         0        0        0        1         1         1
  PET112L WILD-TYPE       2       15       40       29        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PET112L MUTATED           0          2          0          1        2
  PET112L WILD-TYPE         3         68         53         31       36
D212V3, multiclass
            clus
vv           PET112L MUTATED PET112L WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PET112L MUTATED     0   2   3   3
  PET112L WILD-TYPE  22  90 170  94
D212V4, multiclass
    clus
vv   PET112L MUTATED PET112L WILD-TYPE
  T1               0                22
  T2               2                90
  T3               3               170
  T4               3                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
  PET112L MUTATED     0   6   1   1
  PET112L WILD-TYPE 118  98  76  76
D212V5, multiclass
    clus
vv   PET112L MUTATED PET112L WILD-TYPE
  N0               0               118
  N1               6                98
  N2               1                76
  N3               1                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"
D212V6, binary
                   cls
clus                  0   1
  PET112L MUTATED     5   2
  PET112L WILD-TYPE 341  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PET112L MUTATED      5    2
  PET112L WILD-TYPE  341   27
   clus
vv  PET112L MUTATED PET112L WILD-TYPE
  0               5               341
  1               2                27
[1] 2 2
[1] FALSE
D212V7, binary
                   cls
clus                  0   1
  PET112L MUTATED     3   5
  PET112L WILD-TYPE 142 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PET112L MUTATED      3    5
  PET112L WILD-TYPE  142  243
        clus
vv       PET112L MUTATED PET112L WILD-TYPE
  FEMALE               3               142
  MALE                 5               243
[1] 2 2
[1] FALSE
D212V8, binary
                   cls
clus                  0   1
  PET112L MUTATED     8   0
  PET112L WILD-TYPE 284  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PET112L MUTATED      8    0
  PET112L WILD-TYPE  284   59
     clus
vv    PET112L MUTATED PET112L WILD-TYPE
  NO                8               284
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PET112L MUTATED                                          0
  PET112L WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PET112L MUTATED                                       0
  PET112L WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PET112L MUTATED                                                        4
  PET112L WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PET112L MUTATED                                                   0
  PET112L WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PET112L MUTATED                                                                   1
  PET112L WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PET112L MUTATED                                                    0
  PET112L WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PET112L MUTATED                                                  3
  PET112L WILD-TYPE                                               58
D212V9, multiclass
                                                                   clus
vv                                                                  PET112L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  PET112L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PET112L MUTATED     6   0   1   1
  PET112L WILD-TYPE 305  14  14  23
D212V10, multiclass
    clus
vv   PET112L MUTATED PET112L WILD-TYPE
  R0               6               305
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PET112L MUTATED       3                         0
  PET112L WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PET112L MUTATED                                           0     3
  PET112L WILD-TYPE                                         1   240
D212V12, multiclass
                                           clus
vv                                          PET112L MUTATED PET112L WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V13, binary
                   cls
clus                  0   1
  PET112L MUTATED     0   6
  PET112L WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PET112L MUTATED      0    6
  PET112L WILD-TYPE    4  304
                        clus
vv                       PET112L MUTATED PET112L WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(213) Variable = ZKSCAN5 MUTATION ANALYSIS
D213V1, survival
                   sevent
clus2                 0   1
  ZKSCAN5 MUTATED     9   1
  ZKSCAN5 WILD-TYPE 221 138
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
               10               359 
  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE 
                1               138 
$`ZKSCAN5 MUTATED`
TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8078 TCGA-CD-8529 TCGA-CG-5721 
       26.70         9.67        34.68        29.59        12.30         6.02 
TCGA-F1-6874 TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-VQ-A8P2 
       14.47        20.25        14.07        38.14 

$`ZKSCAN5 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  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             14.17 
[1] "6.0 - 38.1 (17.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "4.5"
D213V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZKSCAN5 MUTATED         0        0        2        0         1         3
  ZKSCAN5 WILD-TYPE       2       15       38       30        36        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZKSCAN5 MUTATED           0          1          0          1        2
  ZKSCAN5 WILD-TYPE         3         69         53         31       36
D213V3, multiclass
            clus
vv           ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                3                49
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZKSCAN5 MUTATED     1   1   1   7
  ZKSCAN5 WILD-TYPE  21  91 172  90
D213V4, multiclass
    clus
vv   ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  T1               1                21
  T2               1                91
  T3               1               172
  T4               7                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
  ZKSCAN5 MUTATED     6   3   1   0
  ZKSCAN5 WILD-TYPE 112 101  76  77
D213V5, multiclass
    clus
vv   ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  N0               6               112
  N1               3               101
  N2               1                76
  N3               0                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"
D213V6, binary
                   cls
clus                  0   1
  ZKSCAN5 MUTATED    10   1
  ZKSCAN5 WILD-TYPE 336  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED     10    1
  ZKSCAN5 WILD-TYPE  336   28
   clus
vv  ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  0              10               336
  1               1                28
[1] 2 2
[1] FALSE
D213V7, binary
                   cls
clus                  0   1
  ZKSCAN5 MUTATED     5   6
  ZKSCAN5 WILD-TYPE 140 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED      5    6
  ZKSCAN5 WILD-TYPE  140  242
        clus
vv       ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  FEMALE               5               140
  MALE                 6               242
[1] 2 2
[1] FALSE
D213V8, binary
                   cls
clus                  0   1
  ZKSCAN5 MUTATED     9   2
  ZKSCAN5 WILD-TYPE 283  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED      9    2
  ZKSCAN5 WILD-TYPE  283   57
     clus
vv    ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  NO                9               283
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZKSCAN5 MUTATED                                          0
  ZKSCAN5 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZKSCAN5 MUTATED                                       2
  ZKSCAN5 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZKSCAN5 MUTATED                                                        3
  ZKSCAN5 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZKSCAN5 MUTATED                                                   2
  ZKSCAN5 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZKSCAN5 MUTATED                                                                   3
  ZKSCAN5 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZKSCAN5 MUTATED                                                    0
  ZKSCAN5 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZKSCAN5 MUTATED                                                  1
  ZKSCAN5 WILD-TYPE                                               60
D213V9, multiclass
                                                                   clus
vv                                                                  ZKSCAN5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  ZKSCAN5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZKSCAN5 MUTATED    10   0   0   1
  ZKSCAN5 WILD-TYPE 301  14  15  23
D213V10, multiclass
    clus
vv   ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  R0              10               301
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ZKSCAN5 MUTATED       3                         0
  ZKSCAN5 WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZKSCAN5 MUTATED                                           0     7
  ZKSCAN5 WILD-TYPE                                         1   236
D213V12, multiclass
                                           clus
vv                                          ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V13, binary
                   cls
clus                  0   1
  ZKSCAN5 MUTATED     0   9
  ZKSCAN5 WILD-TYPE   4 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN5 MUTATED      0    9
  ZKSCAN5 WILD-TYPE    4  301
                        clus
vv                       ZKSCAN5 MUTATED ZKSCAN5 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               9               301
[1] 2 2
[1] FALSE

Clustering(214) Variable = CTSC MUTATION ANALYSIS
D214V1, survival
                sevent
clus2              0   1
  CTSC MUTATED     5   4
  CTSC WILD-TYPE 225 135
  CTSC MUTATED CTSC WILD-TYPE 
             9            360 
  CTSC MUTATED CTSC WILD-TYPE 
             4            135 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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          14.07 
[1] "9.3 - 35.8 (22.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D214V2, 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       2       15       39       30        37        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTSC MUTATED           0          3          1          1        0
  CTSC WILD-TYPE         3         67         52         31       38
D214V3, multiclass
            clus
vv           CTSC MUTATED CTSC WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTSC MUTATED     0   2   4   3
  CTSC WILD-TYPE  22  90 169  94
D214V4, multiclass
    clus
vv   CTSC MUTATED CTSC WILD-TYPE
  T1            0             22
  T2            2             90
  T3            4            169
  T4            3             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
  CTSC MUTATED     3   4   1   2
  CTSC WILD-TYPE 115 100  76  75
D214V5, multiclass
    clus
vv   CTSC MUTATED CTSC WILD-TYPE
  N0            3            115
  N1            4            100
  N2            1             76
  N3            2             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"
D214V6, binary
                cls
clus               0   1
  CTSC MUTATED    11   0
  CTSC WILD-TYPE 335  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSC MUTATED     11    0
  CTSC WILD-TYPE  335   29
   clus
vv  CTSC MUTATED CTSC WILD-TYPE
  0           11            335
  1            0             29
[1] 2 2
[1] FALSE
D214V7, binary
                cls
clus               0   1
  CTSC MUTATED     8   3
  CTSC WILD-TYPE 137 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSC MUTATED      8    3
  CTSC WILD-TYPE  137  245
        clus
vv       CTSC MUTATED CTSC WILD-TYPE
  FEMALE            8            137
  MALE              3            245
[1] 2 2
[1] FALSE
D214V8, binary
                cls
clus               0   1
  CTSC MUTATED     9   0
  CTSC WILD-TYPE 283  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSC MUTATED      9    0
  CTSC WILD-TYPE  283   59
     clus
vv    CTSC MUTATED CTSC WILD-TYPE
  NO             9            283
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CTSC MUTATED                                          0
  CTSC WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CTSC MUTATED                                       1
  CTSC WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTSC MUTATED                                                        9
  CTSC WILD-TYPE                                                    149
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CTSC MUTATED                                                   0
  CTSC WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTSC MUTATED                                                                   0
  CTSC WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CTSC MUTATED                                                    0
  CTSC WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CTSC MUTATED                                                  1
  CTSC WILD-TYPE                                               60
D214V9, multiclass
                                                                   clus
vv                                                                  CTSC MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  CTSC WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CTSC MUTATED     5   0   0   4
  CTSC WILD-TYPE 306  14  15  20
D214V10, multiclass
    clus
vv   CTSC MUTATED CTSC WILD-TYPE
  R0            5            306
  R1            0             14
  R2            0             15
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CTSC MUTATED       2                         0
  CTSC WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTSC MUTATED                                           0     9
  CTSC WILD-TYPE                                         1   234
D214V12, multiclass
                                           clus
vv                                          CTSC MUTATED CTSC WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V13, binary
                cls
clus               0   1
  CTSC MUTATED     0  11
  CTSC WILD-TYPE   4 299
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSC MUTATED      0   11
  CTSC WILD-TYPE    4  299
                        clus
vv                       CTSC MUTATED CTSC WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           11            299
[1] 2 2
[1] FALSE

Clustering(215) Variable = AQP8 MUTATION ANALYSIS
D215V1, survival
                sevent
clus2              0   1
  AQP8 MUTATED     8   3
  AQP8 WILD-TYPE 222 136
  AQP8 MUTATED AQP8 WILD-TYPE 
            11            358 
  AQP8 MUTATED AQP8 WILD-TYPE 
             3            136 
$`AQP8 MUTATED`
TCGA-BR-4280 TCGA-BR-6457 TCGA-BR-8370 TCGA-BR-8382 TCGA-BR-8487 TCGA-CG-4437 
        6.61        13.68         3.32        25.05         1.12         8.05 
TCGA-HF-7132 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4GC TCGA-VQ-A92D 
       77.29        30.51        26.47         3.25        66.81 

$`AQP8 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        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-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-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-A94T TCGA-VQ-AA64 
       15.65        20.81         1.71        42.64        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 

  AQP8 MUTATED AQP8 WILD-TYPE 
          1.12           0.00 
  AQP8 MUTATED AQP8 WILD-TYPE 
         77.29         122.30 
  AQP8 MUTATED AQP8 WILD-TYPE 
         13.68          14.35 
[1] "1.1 - 77.3 (13.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D215V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AQP8 MUTATED         0        0        2        2         2         1
  AQP8 WILD-TYPE       2       15       38       28        35        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AQP8 MUTATED           1          1          2          2        0
  AQP8 WILD-TYPE         2         69         51         30       38
D215V3, multiclass
            clus
vv           AQP8 MUTATED AQP8 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              2             28
  STAGE IIA             2             35
  STAGE IIB             1             51
  STAGE III             1              2
  STAGE IIIA            1             69
  STAGE IIIB            2             51
  STAGE IIIC            2             30
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AQP8 MUTATED     0   5   3   5
  AQP8 WILD-TYPE  22  87 170  92
D215V4, multiclass
    clus
vv   AQP8 MUTATED AQP8 WILD-TYPE
  T1            0             22
  T2            5             87
  T3            3            170
  T4            5             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
  AQP8 MUTATED     6   3   1   3
  AQP8 WILD-TYPE 112 101  76  74
D215V5, multiclass
    clus
vv   AQP8 MUTATED AQP8 WILD-TYPE
  N0            6            112
  N1            3            101
  N2            1             76
  N3            3             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"
D215V6, binary
                cls
clus               0   1
  AQP8 MUTATED    12   0
  AQP8 WILD-TYPE 334  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP8 MUTATED     12    0
  AQP8 WILD-TYPE  334   29
   clus
vv  AQP8 MUTATED AQP8 WILD-TYPE
  0           12            334
  1            0             29
[1] 2 2
[1] FALSE
D215V7, binary
                cls
clus               0   1
  AQP8 MUTATED     6   7
  AQP8 WILD-TYPE 139 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP8 MUTATED      6    7
  AQP8 WILD-TYPE  139  241
        clus
vv       AQP8 MUTATED AQP8 WILD-TYPE
  FEMALE            6            139
  MALE              7            241
[1] 2 2
[1] FALSE
D215V8, binary
                cls
clus               0   1
  AQP8 MUTATED    10   2
  AQP8 WILD-TYPE 282  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP8 MUTATED     10    2
  AQP8 WILD-TYPE  282   57
     clus
vv    AQP8 MUTATED AQP8 WILD-TYPE
  NO            10            282
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AQP8 MUTATED                                          1
  AQP8 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AQP8 MUTATED                                       2
  AQP8 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AQP8 MUTATED                                                        5
  AQP8 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AQP8 MUTATED                                                   2
  AQP8 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AQP8 MUTATED                                                                   2
  AQP8 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AQP8 MUTATED                                                    0
  AQP8 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AQP8 MUTATED                                                  1
  AQP8 WILD-TYPE                                               60
D215V9, multiclass
                                                                   clus
vv                                                                  AQP8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  AQP8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AQP8 MUTATED    10   1   0   2
  AQP8 WILD-TYPE 301  13  15  22
D215V10, multiclass
    clus
vv   AQP8 MUTATED AQP8 WILD-TYPE
  R0           10            301
  R1            1             13
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  AQP8 MUTATED       1                         0
  AQP8 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AQP8 MUTATED                                           0     9
  AQP8 WILD-TYPE                                         1   234
D215V12, multiclass
                                           clus
vv                                          AQP8 MUTATED AQP8 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V13, binary
                cls
clus               0   1
  AQP8 MUTATED     0   9
  AQP8 WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP8 MUTATED      0    9
  AQP8 WILD-TYPE    4  301
                        clus
vv                       AQP8 MUTATED AQP8 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(216) Variable = KANK4 MUTATION ANALYSIS
D216V1, survival
                 sevent
clus2               0   1
  KANK4 MUTATED     7   7
  KANK4 WILD-TYPE 223 132
  KANK4 MUTATED KANK4 WILD-TYPE 
             14             355 
  KANK4 MUTATED KANK4 WILD-TYPE 
              7             132 
$`KANK4 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8687 
        6.61        34.68        35.84         1.12        28.14         8.22 
TCGA-BR-A4QL TCGA-CD-A48C TCGA-CG-5726 TCGA-D7-A6EY TCGA-HU-A4GX TCGA-IN-A7NU 
       16.14        11.61        28.96        11.44        20.25        11.70 
TCGA-SW-A7EA TCGA-VQ-A8PE 
       19.04        22.19 

$`KANK4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51        10.62        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-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 

  KANK4 MUTATED KANK4 WILD-TYPE 
           1.12            0.00 
  KANK4 MUTATED KANK4 WILD-TYPE 
          35.84          122.30 
  KANK4 MUTATED KANK4 WILD-TYPE 
          17.59           14.17 
[1] "1.1 - 35.8 (17.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D216V2, 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       2       14       38       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KANK4 MUTATED           1          0          4          3        0
  KANK4 WILD-TYPE         2         70         49         29       38
D216V3, multiclass
            clus
vv           KANK4 MUTATED KANK4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             0              70
  STAGE IIIB             4              49
  STAGE IIIC             3              29
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KANK4 MUTATED     1   3   7   3
  KANK4 WILD-TYPE  21  89 166  94
D216V4, multiclass
    clus
vv   KANK4 MUTATED KANK4 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             7             166
  T4             3              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
  KANK4 MUTATED     5   3   2   5
  KANK4 WILD-TYPE 113 101  75  72
D216V5, multiclass
    clus
vv   KANK4 MUTATED KANK4 WILD-TYPE
  N0             5             113
  N1             3             101
  N2             2              75
  N3             5              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"
D216V6, binary
                 cls
clus                0   1
  KANK4 MUTATED    15   0
  KANK4 WILD-TYPE 331  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK4 MUTATED     15    0
  KANK4 WILD-TYPE  331   29
   clus
vv  KANK4 MUTATED KANK4 WILD-TYPE
  0            15             331
  1             0              29
[1] 2 2
[1] FALSE
D216V7, binary
                 cls
clus                0   1
  KANK4 MUTATED    11   4
  KANK4 WILD-TYPE 134 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK4 MUTATED     11    4
  KANK4 WILD-TYPE  134  244
        clus
vv       KANK4 MUTATED KANK4 WILD-TYPE
  FEMALE            11             134
  MALE               4             244
[1] 2 2
[1] FALSE
D216V8, binary
                 cls
clus                0   1
  KANK4 MUTATED    13   0
  KANK4 WILD-TYPE 279  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK4 MUTATED     13    0
  KANK4 WILD-TYPE  279   59
     clus
vv    KANK4 MUTATED KANK4 WILD-TYPE
  NO             13             279
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KANK4 MUTATED                                          0
  KANK4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KANK4 MUTATED                                       2
  KANK4 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KANK4 MUTATED                                                       10
  KANK4 WILD-TYPE                                                    148
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KANK4 MUTATED                                                   0
  KANK4 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KANK4 MUTATED                                                                   1
  KANK4 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KANK4 MUTATED                                                    0
  KANK4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KANK4 MUTATED                                                  2
  KANK4 WILD-TYPE                                               59
D216V9, multiclass
                                                                   clus
vv                                                                  KANK4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  KANK4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KANK4 MUTATED    11   1   0   2
  KANK4 WILD-TYPE 300  13  15  22
D216V10, multiclass
    clus
vv   KANK4 MUTATED KANK4 WILD-TYPE
  R0            11             300
  R1             1              13
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KANK4 MUTATED       2                         0
  KANK4 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KANK4 MUTATED                                           0    12
  KANK4 WILD-TYPE                                         1   231
D216V12, multiclass
                                           clus
vv                                          KANK4 MUTATED KANK4 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V13, binary
                 cls
clus                0   1
  KANK4 MUTATED     0  13
  KANK4 WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KANK4 MUTATED      0   13
  KANK4 WILD-TYPE    4  297
                        clus
vv                       KANK4 MUTATED KANK4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(217) Variable = ACVR1B MUTATION ANALYSIS
D217V1, survival
                  sevent
clus2                0   1
  ACVR1B MUTATED     8   4
  ACVR1B WILD-TYPE 222 135
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              12              357 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
               4              135 
$`ACVR1B MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-8588 TCGA-BR-A4QL 
       19.56         6.97        32.78        36.16        12.79        16.14 
TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4477 TCGA-CG-5733 TCGA-HU-A4GF TCGA-IN-7806 
        6.58        15.95        30.97        21.07        25.81        36.36 

$`ACVR1B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        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-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-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-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-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        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-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 

  ACVR1B MUTATED ACVR1B WILD-TYPE 
            6.58             0.00 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
           36.36           122.30 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
          20.315           14.070 
[1] "6.6 - 36.4 (20.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D217V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACVR1B MUTATED         1        1        1        1         3         2
  ACVR1B WILD-TYPE       1       14       39       29        34        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACVR1B MUTATED           0          2          1          1        0
  ACVR1B WILD-TYPE         3         68         52         31       38
D217V3, multiclass
            clus
vv           ACVR1B MUTATED ACVR1B WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ACVR1B MUTATED     2   3   6   2
  ACVR1B WILD-TYPE  20  89 167  95
D217V4, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  T1              2               20
  T2              3               89
  T3              6              167
  T4              2               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
  ACVR1B MUTATED     6   4   1   2
  ACVR1B WILD-TYPE 112 100  76  75
D217V5, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  N0              6              112
  N1              4              100
  N2              1               76
  N3              2               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"
D217V6, binary
                  cls
clus                 0   1
  ACVR1B MUTATED    11   0
  ACVR1B WILD-TYPE 335  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     11    0
  ACVR1B WILD-TYPE  335   29
   clus
vv  ACVR1B MUTATED ACVR1B WILD-TYPE
  0             11              335
  1              0               29
[1] 2 2
[1] FALSE
D217V7, binary
                  cls
clus                 0   1
  ACVR1B MUTATED     5   8
  ACVR1B WILD-TYPE 140 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED      5    8
  ACVR1B WILD-TYPE  140  240
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  FEMALE              5              140
  MALE                8              240
[1] 2 2
[1] FALSE
D217V8, binary
                  cls
clus                 0   1
  ACVR1B MUTATED    12   1
  ACVR1B WILD-TYPE 280  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     12    1
  ACVR1B WILD-TYPE  280   58
     clus
vv    ACVR1B MUTATED ACVR1B WILD-TYPE
  NO              12              280
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ACVR1B MUTATED                                          0
  ACVR1B WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ACVR1B MUTATED                                       3
  ACVR1B WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ACVR1B MUTATED                                                        6
  ACVR1B WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ACVR1B MUTATED                                                   0
  ACVR1B WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ACVR1B MUTATED                                                                   2
  ACVR1B WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ACVR1B MUTATED                                                    1
  ACVR1B WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ACVR1B MUTATED                                                  1
  ACVR1B WILD-TYPE                                               60
D217V9, multiclass
                                                                   clus
vv                                                                  ACVR1B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ACVR1B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ACVR1B MUTATED    10   0   0   1
  ACVR1B WILD-TYPE 301  14  15  23
D217V10, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  R0             10              301
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ACVR1B MUTATED       2                         1
  ACVR1B WILD-TYPE    85                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ACVR1B MUTATED                                           0     7
  ACVR1B WILD-TYPE                                         1   236
D217V12, multiclass
                                           clus
vv                                          ACVR1B MUTATED ACVR1B WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V13, binary
                  cls
clus                 0   1
  ACVR1B MUTATED     0  10
  ACVR1B WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED      0   10
  ACVR1B WILD-TYPE    4  300
                        clus
vv                       ACVR1B MUTATED ACVR1B WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(218) Variable = STAT6 MUTATION ANALYSIS
D218V1, survival
                 sevent
clus2               0   1
  STAT6 MUTATED     1   4
  STAT6 WILD-TYPE 229 135
  STAT6 MUTATED STAT6 WILD-TYPE 
              5             364 
  STAT6 MUTATED STAT6 WILD-TYPE 
              4             135 
$`STAT6 MUTATED`
TCGA-BR-4184 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MI TCGA-D7-A6EY 
        6.97        16.14        12.43        11.77        11.44 

$`STAT6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  STAT6 MUTATED STAT6 WILD-TYPE 
           6.97            0.00 
  STAT6 MUTATED STAT6 WILD-TYPE 
          16.14          122.30 
  STAT6 MUTATED STAT6 WILD-TYPE 
          11.77           14.45 
[1] "7.0 - 16.1 (11.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "3.2"
D218V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STAT6 MUTATED         0        0        0        1         0         0
  STAT6 WILD-TYPE       2       15       40       29        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STAT6 MUTATED           0          2          2          0        0
  STAT6 WILD-TYPE         3         68         51         32       38
D218V3, multiclass
            clus
vv           STAT6 MUTATED STAT6 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STAT6 MUTATED     0   0   5   0
  STAT6 WILD-TYPE  22  92 168  97
D218V4, multiclass
    clus
vv   STAT6 MUTATED STAT6 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             5             168
  T4             0              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
  STAT6 MUTATED     1   3   0   2
  STAT6 WILD-TYPE 117 101  77  75
D218V5, multiclass
    clus
vv   STAT6 MUTATED STAT6 WILD-TYPE
  N0             1             117
  N1             3             101
  N2             0              77
  N3             2              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"
D218V6, binary
                 cls
clus                0   1
  STAT6 MUTATED     5   0
  STAT6 WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT6 MUTATED      5    0
  STAT6 WILD-TYPE  341   29
   clus
vv  STAT6 MUTATED STAT6 WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D218V7, binary
                 cls
clus                0   1
  STAT6 MUTATED     3   3
  STAT6 WILD-TYPE 142 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT6 MUTATED      3    3
  STAT6 WILD-TYPE  142  245
        clus
vv       STAT6 MUTATED STAT6 WILD-TYPE
  FEMALE             3             142
  MALE               3             245
[1] 2 2
[1] FALSE
D218V8, binary
                 cls
clus                0   1
  STAT6 MUTATED     5   0
  STAT6 WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT6 MUTATED      5    0
  STAT6 WILD-TYPE  287   59
     clus
vv    STAT6 MUTATED STAT6 WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  STAT6 MUTATED                                          0
  STAT6 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  STAT6 MUTATED                                       0
  STAT6 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  STAT6 MUTATED                                                        5
  STAT6 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  STAT6 MUTATED                                                   0
  STAT6 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  STAT6 MUTATED                                                                   0
  STAT6 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  STAT6 MUTATED                                                    0
  STAT6 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  STAT6 MUTATED                                                  1
  STAT6 WILD-TYPE                                               60
D218V9, multiclass
                                                                   clus
vv                                                                  STAT6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  STAT6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STAT6 MUTATED     3   0   0   2
  STAT6 WILD-TYPE 308  14  15  22
D218V10, multiclass
    clus
vv   STAT6 MUTATED STAT6 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  STAT6 MUTATED       2                         0
  STAT6 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  STAT6 MUTATED                                           0     4
  STAT6 WILD-TYPE                                         1   239
D218V12, multiclass
                                           clus
vv                                          STAT6 MUTATED STAT6 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V13, binary
                 cls
clus                0   1
  STAT6 MUTATED     0   6
  STAT6 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT6 MUTATED      0    6
  STAT6 WILD-TYPE    4  304
                        clus
vv                       STAT6 MUTATED STAT6 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(219) Variable = PUS7L MUTATION ANALYSIS
D219V1, survival
                 sevent
clus2               0   1
  PUS7L MUTATED     3   4
  PUS7L WILD-TYPE 227 135
  PUS7L MUTATED PUS7L WILD-TYPE 
              7             362 
  PUS7L MUTATED PUS7L WILD-TYPE 
              4             135 
$`PUS7L MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5733 TCGA-HU-A4GN 
       21.99         6.97         6.02        12.03        21.07        29.98 
TCGA-HU-A4H4 
       23.84 

$`PUS7L WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-5725 TCGA-CG-5726 
        1.02         0.99         0.99       105.07        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-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 

  PUS7L MUTATED PUS7L WILD-TYPE 
           6.02            0.00 
  PUS7L MUTATED PUS7L WILD-TYPE 
          29.98          122.30 
  PUS7L MUTATED PUS7L WILD-TYPE 
          21.07           14.22 
[1] "6.0 - 30.0 (21.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.5"
D219V2, 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       2       15       40       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PUS7L MUTATED           0          2          0          0        4
  PUS7L WILD-TYPE         3         68         53         32       34
D219V3, multiclass
            clus
vv           PUS7L MUTATED PUS7L WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PUS7L MUTATED     1   3   2   3
  PUS7L WILD-TYPE  21  89 171  94
D219V4, multiclass
    clus
vv   PUS7L MUTATED PUS7L WILD-TYPE
  T1             1              21
  T2             3              89
  T3             2             171
  T4             3              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
  PUS7L MUTATED     0   4   3   1
  PUS7L WILD-TYPE 118 100  74  76
D219V5, multiclass
    clus
vv   PUS7L MUTATED PUS7L WILD-TYPE
  N0             0             118
  N1             4             100
  N2             3              74
  N3             1              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"
D219V6, binary
                 cls
clus                0   1
  PUS7L MUTATED     6   2
  PUS7L WILD-TYPE 340  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PUS7L MUTATED      6    2
  PUS7L WILD-TYPE  340   27
   clus
vv  PUS7L MUTATED PUS7L WILD-TYPE
  0             6             340
  1             2              27
[1] 2 2
[1] FALSE
D219V7, binary
                 cls
clus                0   1
  PUS7L MUTATED     5   4
  PUS7L WILD-TYPE 140 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PUS7L MUTATED      5    4
  PUS7L WILD-TYPE  140  244
        clus
vv       PUS7L MUTATED PUS7L WILD-TYPE
  FEMALE             5             140
  MALE               4             244
[1] 2 2
[1] FALSE
D219V8, binary
                 cls
clus                0   1
  PUS7L MUTATED     7   0
  PUS7L WILD-TYPE 285  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PUS7L MUTATED      7    0
  PUS7L WILD-TYPE  285   59
     clus
vv    PUS7L MUTATED PUS7L WILD-TYPE
  NO              7             285
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PUS7L MUTATED                                          0
  PUS7L WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PUS7L MUTATED                                       1
  PUS7L WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PUS7L MUTATED                                                        3
  PUS7L WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PUS7L MUTATED                                                   0
  PUS7L WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PUS7L MUTATED                                                                   3
  PUS7L WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PUS7L MUTATED                                                    0
  PUS7L WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PUS7L MUTATED                                                  2
  PUS7L WILD-TYPE                                               59
D219V9, multiclass
                                                                   clus
vv                                                                  PUS7L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  PUS7L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PUS7L MUTATED     4   0   2   3
  PUS7L WILD-TYPE 307  14  13  21
D219V10, multiclass
    clus
vv   PUS7L MUTATED PUS7L WILD-TYPE
  R0             4             307
  R1             0              14
  R2             2              13
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PUS7L MUTATED       2                         0
  PUS7L WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PUS7L MUTATED                                           0     3
  PUS7L WILD-TYPE                                         1   240
D219V12, multiclass
                                           clus
vv                                          PUS7L MUTATED PUS7L WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V13, binary
                 cls
clus                0   1
  PUS7L MUTATED     0   5
  PUS7L WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PUS7L MUTATED      0    5
  PUS7L WILD-TYPE    4  305
                        clus
vv                       PUS7L MUTATED PUS7L WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(220) Variable = ARID2 MUTATION ANALYSIS
D220V1, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    17   8
  ARID2 WILD-TYPE 213 131
  ARID2 MUTATED ARID2 WILD-TYPE 
             25             344 
  ARID2 MUTATED ARID2 WILD-TYPE 
              8             131 
$`ARID2 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7704 
        6.97        34.68        13.87        30.90        44.94        35.24 
TCGA-BR-8078 TCGA-BR-8588 TCGA-BR-A4J6 TCGA-CD-A4MG TCGA-CG-5723 TCGA-CG-5733 
       29.59        12.79         0.66         6.58       105.07        21.07 
TCGA-D7-6525 TCGA-D7-A4YV TCGA-F1-A72C TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-8602 
       13.35         5.92        11.38        11.08        77.29        22.32 
TCGA-HU-A4GQ TCGA-HU-A4H8 TCGA-IN-A6RL TCGA-IN-A7NU TCGA-R5-A7ZI TCGA-VQ-A8P2 
        0.10        14.07        13.35        11.70        74.53        38.14 
TCGA-VQ-A8P3 
       37.22 

$`ARID2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-6803 TCGA-BR-7196 
       19.89        12.16         8.98        40.21        31.20        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-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-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       28.34        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-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-D7-6526 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-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       21.27         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-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-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-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-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-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 

  ARID2 MUTATED ARID2 WILD-TYPE 
            0.1             0.0 
  ARID2 MUTATED ARID2 WILD-TYPE 
         105.07          122.30 
  ARID2 MUTATED ARID2 WILD-TYPE 
          14.07           14.35 
[1] "0.1 - 105.1 (14.1)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D220V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID2 MUTATED         0        0        1        3         6         5
  ARID2 WILD-TYPE       2       15       39       27        31        47
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID2 MUTATED           0          7          1          1        2
  ARID2 WILD-TYPE         3         63         52         31       36
D220V3, multiclass
            clus
vv           ARID2 MUTATED ARID2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               3              27
  STAGE IIA              6              31
  STAGE IIB              5              47
  STAGE III              0               3
  STAGE IIIA             7              63
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARID2 MUTATED     2   5  13   8
  ARID2 WILD-TYPE  20  87 160  89
D220V4, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  T1             2              20
  T2             5              87
  T3            13             160
  T4             8              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
  ARID2 MUTATED    10  10   5   1
  ARID2 WILD-TYPE 108  94  72  76
D220V5, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  N0            10             108
  N1            10              94
  N2             5              72
  N3             1              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"
D220V6, binary
                 cls
clus                0   1
  ARID2 MUTATED    25   2
  ARID2 WILD-TYPE 321  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     25    2
  ARID2 WILD-TYPE  321   27
   clus
vv  ARID2 MUTATED ARID2 WILD-TYPE
  0            25             321
  1             2              27
[1] 2 2
[1] FALSE
D220V7, binary
                 cls
clus                0   1
  ARID2 MUTATED    14  15
  ARID2 WILD-TYPE 131 233
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     14   15
  ARID2 WILD-TYPE  131  233
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE            14             131
  MALE              15             233
[1] 2 2
[1] FALSE
D220V8, binary
                 cls
clus                0   1
  ARID2 MUTATED    21   4
  ARID2 WILD-TYPE 271  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     21    4
  ARID2 WILD-TYPE  271   55
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO             21             271
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARID2 MUTATED                                          0
  ARID2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARID2 MUTATED                                       5
  ARID2 WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARID2 MUTATED                                                       15
  ARID2 WILD-TYPE                                                    143
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARID2 MUTATED                                                   2
  ARID2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARID2 MUTATED                                                                   3
  ARID2 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARID2 MUTATED                                                    0
  ARID2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARID2 MUTATED                                                  4
  ARID2 WILD-TYPE                                               57
D220V9, multiclass
                                                                   clus
vv                                                                  ARID2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  ARID2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ARID2 MUTATED    23   0   1   4
  ARID2 WILD-TYPE 288  14  14  20
D220V10, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  R0            23             288
  R1             0              14
  R2             1              14
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ARID2 MUTATED       5                         1
  ARID2 WILD-TYPE    82                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID2 MUTATED                                           0    19
  ARID2 WILD-TYPE                                         1   224
D220V12, multiclass
                                           clus
vv                                          ARID2 MUTATED ARID2 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                19             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V13, binary
                 cls
clus                0   1
  ARID2 MUTATED     1  22
  ARID2 WILD-TYPE   3 288
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      1   22
  ARID2 WILD-TYPE    3  288
                        clus
vv                       ARID2 MUTATED ARID2 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            22             288
[1] 2 2
[1] FALSE

Clustering(221) Variable = ZMYM3 MUTATION ANALYSIS
D221V1, survival
                 sevent
clus2               0   1
  ZMYM3 MUTATED     9   6
  ZMYM3 WILD-TYPE 221 133
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
             15             354 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              6             133 
$`ZMYM3 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-6709 TCGA-BR-8368 TCGA-BR-8487 TCGA-CD-8531 
       21.99        26.70        12.16         4.31         1.12        12.59 
TCGA-CD-8536 TCGA-CG-4437 TCGA-CG-4465 TCGA-CG-5726 TCGA-D7-A6EY TCGA-FP-A4BE 
       12.43         8.05         9.01        28.96        11.44        11.08 
TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-VQ-A8P2 
       22.68         0.10        38.14 

$`ZMYM3 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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-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-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-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 

  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
            0.1             0.0 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
          38.14          122.30 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
         12.160          14.565 
[1] "0.1 - 38.1 (12.2)"  "0.0 - 122.3 (14.6)"
[1] "hr=" "1.3"
D221V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZMYM3 MUTATED         0        1        1        2         2         2
  ZMYM3 WILD-TYPE       2       14       39       28        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZMYM3 MUTATED           0          2          2          1        2
  ZMYM3 WILD-TYPE         3         68         51         31       36
D221V3, multiclass
            clus
vv           ZMYM3 MUTATED ZMYM3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZMYM3 MUTATED     1   2   7   5
  ZMYM3 WILD-TYPE  21  90 166  92
D221V4, multiclass
    clus
vv   ZMYM3 MUTATED ZMYM3 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             7             166
  T4             5              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
  ZMYM3 MUTATED     6   5   1   3
  ZMYM3 WILD-TYPE 112  99  76  74
D221V5, multiclass
    clus
vv   ZMYM3 MUTATED ZMYM3 WILD-TYPE
  N0             6             112
  N1             5              99
  N2             1              76
  N3             3              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"
D221V6, binary
                 cls
clus                0   1
  ZMYM3 MUTATED    13   2
  ZMYM3 WILD-TYPE 333  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED     13    2
  ZMYM3 WILD-TYPE  333   27
   clus
vv  ZMYM3 MUTATED ZMYM3 WILD-TYPE
  0            13             333
  1             2              27
[1] 2 2
[1] FALSE
D221V7, binary
                 cls
clus                0   1
  ZMYM3 MUTATED     9   6
  ZMYM3 WILD-TYPE 136 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED      9    6
  ZMYM3 WILD-TYPE  136  242
        clus
vv       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  FEMALE             9             136
  MALE               6             242
[1] 2 2
[1] FALSE
D221V8, binary
                 cls
clus                0   1
  ZMYM3 MUTATED    10   3
  ZMYM3 WILD-TYPE 282  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED     10    3
  ZMYM3 WILD-TYPE  282   56
     clus
vv    ZMYM3 MUTATED ZMYM3 WILD-TYPE
  NO             10             282
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZMYM3 MUTATED                                          0
  ZMYM3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZMYM3 MUTATED                                       4
  ZMYM3 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZMYM3 MUTATED                                                        5
  ZMYM3 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZMYM3 MUTATED                                                   1
  ZMYM3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZMYM3 MUTATED                                                                   3
  ZMYM3 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZMYM3 MUTATED                                                    0
  ZMYM3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZMYM3 MUTATED                                                  2
  ZMYM3 WILD-TYPE                                               59
D221V9, multiclass
                                                                   clus
vv                                                                  ZMYM3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  ZMYM3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZMYM3 MUTATED    11   1   2   0
  ZMYM3 WILD-TYPE 300  13  13  24
D221V10, multiclass
    clus
vv   ZMYM3 MUTATED ZMYM3 WILD-TYPE
  R0            11             300
  R1             1              13
  R2             2              13
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZMYM3 MUTATED       4                         1
  ZMYM3 WILD-TYPE    83                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZMYM3 MUTATED                                           0     6
  ZMYM3 WILD-TYPE                                         1   237
D221V12, multiclass
                                           clus
vv                                          ZMYM3 MUTATED ZMYM3 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V13, binary
                 cls
clus                0   1
  ZMYM3 MUTATED     0  10
  ZMYM3 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED      0   10
  ZMYM3 WILD-TYPE    4  300
                        clus
vv                       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(222) Variable = EOMES MUTATION ANALYSIS
D222V1, survival
                 sevent
clus2               0   1
  EOMES MUTATED     5   4
  EOMES WILD-TYPE 225 135
  EOMES MUTATED EOMES WILD-TYPE 
              9             360 
  EOMES MUTATED EOMES WILD-TYPE 
              4             135 
$`EOMES MUTATED`
TCGA-BR-4256 TCGA-BR-7704 TCGA-BR-8078 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MI 
        9.34        35.24        29.59        16.14        12.43        11.77 
TCGA-CG-4306 TCGA-D7-A6EV TCGA-VQ-A92D 
        1.02        11.24        66.81 

$`EOMES WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A6EX 
        5.92        36.43        13.78        14.76        26.43        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-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 

  EOMES MUTATED EOMES WILD-TYPE 
           1.02            0.00 
  EOMES MUTATED EOMES WILD-TYPE 
          66.81          122.30 
  EOMES MUTATED EOMES WILD-TYPE 
          12.43           14.35 
[1] "1.0 - 66.8 (12.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D222V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EOMES MUTATED         0        0        1        2         0         2
  EOMES WILD-TYPE       2       15       39       28        37        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EOMES MUTATED           0          1          1          0        1
  EOMES WILD-TYPE         3         69         52         32       37
D222V3, multiclass
            clus
vv           EOMES MUTATED EOMES WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              0              37
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EOMES MUTATED     0   2   5   1
  EOMES WILD-TYPE  22  90 168  96
D222V4, multiclass
    clus
vv   EOMES MUTATED EOMES WILD-TYPE
  T1             0              22
  T2             2              90
  T3             5             168
  T4             1              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
  EOMES MUTATED     4   2   2   1
  EOMES WILD-TYPE 114 102  75  76
D222V5, multiclass
    clus
vv   EOMES MUTATED EOMES WILD-TYPE
  N0             4             114
  N1             2             102
  N2             2              75
  N3             1              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"
D222V6, binary
                 cls
clus                0   1
  EOMES MUTATED     8   1
  EOMES WILD-TYPE 338  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      8    1
  EOMES WILD-TYPE  338   28
   clus
vv  EOMES MUTATED EOMES WILD-TYPE
  0             8             338
  1             1              28
[1] 2 2
[1] FALSE
D222V7, binary
                 cls
clus                0   1
  EOMES MUTATED     4   5
  EOMES WILD-TYPE 141 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      4    5
  EOMES WILD-TYPE  141  243
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  FEMALE             4             141
  MALE               5             243
[1] 2 2
[1] FALSE
D222V8, binary
                 cls
clus                0   1
  EOMES MUTATED     8   0
  EOMES WILD-TYPE 284  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      8    0
  EOMES WILD-TYPE  284   59
     clus
vv    EOMES MUTATED EOMES WILD-TYPE
  NO              8             284
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EOMES MUTATED                                          0
  EOMES WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EOMES MUTATED                                       0
  EOMES WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EOMES MUTATED                                                        7
  EOMES WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EOMES MUTATED                                                   0
  EOMES WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EOMES MUTATED                                                                   1
  EOMES WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EOMES MUTATED                                                    0
  EOMES WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EOMES MUTATED                                                  1
  EOMES WILD-TYPE                                               60
D222V9, multiclass
                                                                   clus
vv                                                                  EOMES MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  EOMES WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EOMES MUTATED     6   0   1   1
  EOMES WILD-TYPE 305  14  14  23
D222V10, multiclass
    clus
vv   EOMES MUTATED EOMES WILD-TYPE
  R0             6             305
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EOMES MUTATED       2                         0
  EOMES WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EOMES MUTATED                                           0     6
  EOMES WILD-TYPE                                         1   237
D222V12, multiclass
                                           clus
vv                                          EOMES MUTATED EOMES WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V13, binary
                 cls
clus                0   1
  EOMES MUTATED     0   7
  EOMES WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      0    7
  EOMES WILD-TYPE    4  303
                        clus
vv                       EOMES MUTATED EOMES WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(223) Variable = BPTF MUTATION ANALYSIS
D223V1, survival
                sevent
clus2              0   1
  BPTF MUTATED    15  10
  BPTF WILD-TYPE 215 129
  BPTF MUTATED BPTF WILD-TYPE 
            25            344 
  BPTF MUTATED BPTF WILD-TYPE 
            10            129 
$`BPTF MUTATED`
TCGA-CG-4460 TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7707 
       21.99         9.44         6.97         6.61        34.68        35.84 
TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8680 
       14.43        32.25         8.05        31.10         0.26        31.96 
TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MJ TCGA-CG-4305 TCGA-D7-6528 TCGA-D7-A4YV 
       16.14        12.43        12.62        15.95        15.22         5.92 
TCGA-F1-A448 TCGA-HU-8608 TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-RD-A7BT TCGA-VQ-A8P2 
       21.27        21.07         6.58        23.80         8.61        38.14 
TCGA-VQ-A8PK 
       17.85 

$`BPTF WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        26.70        11.70        19.56        11.01         9.47 
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-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-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8285 
       37.25        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-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-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-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-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-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-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-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        22.82         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-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-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-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 

  BPTF MUTATED BPTF WILD-TYPE 
          0.26           0.00 
  BPTF MUTATED BPTF WILD-TYPE 
         38.14         122.30 
  BPTF MUTATED BPTF WILD-TYPE 
         15.95          14.07 
[1] "0.3 - 38.1 (15.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D223V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BPTF MUTATED         1        0        5        2         1         5
  BPTF WILD-TYPE       1       15       35       28        36        47
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BPTF MUTATED           2          3          4          2        4
  BPTF WILD-TYPE         1         67         49         30       34
D223V3, multiclass
            clus
vv           BPTF MUTATED BPTF WILD-TYPE
  STAGE I               1              1
  STAGE IA              0             15
  STAGE IB              5             35
  STAGE II              2             28
  STAGE IIA             1             36
  STAGE IIB             5             47
  STAGE III             2              1
  STAGE IIIA            3             67
  STAGE IIIB            4             49
  STAGE IIIC            2             30
  STAGE IV              4             34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BPTF MUTATED     1   7   9  12
  BPTF WILD-TYPE  21  85 164  85
D223V4, multiclass
    clus
vv   BPTF MUTATED BPTF WILD-TYPE
  T1            1             21
  T2            7             85
  T3            9            164
  T4           12             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
  BPTF MUTATED    10  10   4   5
  BPTF WILD-TYPE 108  94  73  72
D223V5, multiclass
    clus
vv   BPTF MUTATED BPTF WILD-TYPE
  N0           10            108
  N1           10             94
  N2            4             73
  N3            5             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"
D223V6, binary
                cls
clus               0   1
  BPTF MUTATED    26   2
  BPTF WILD-TYPE 320  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  BPTF MUTATED     26    2
  BPTF WILD-TYPE  320   27
   clus
vv  BPTF MUTATED BPTF WILD-TYPE
  0           26            320
  1            2             27
[1] 2 2
[1] FALSE
D223V7, binary
                cls
clus               0   1
  BPTF MUTATED    14  16
  BPTF WILD-TYPE 131 232
[1] "tbl2"
                cls
clus             [,1] [,2]
  BPTF MUTATED     14   16
  BPTF WILD-TYPE  131  232
        clus
vv       BPTF MUTATED BPTF WILD-TYPE
  FEMALE           14            131
  MALE             16            232
[1] 2 2
[1] FALSE
D223V8, binary
                cls
clus               0   1
  BPTF MUTATED    24   3
  BPTF WILD-TYPE 268  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  BPTF MUTATED     24    3
  BPTF WILD-TYPE  268   56
     clus
vv    BPTF MUTATED BPTF WILD-TYPE
  NO            24            268
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BPTF MUTATED                                          0
  BPTF WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BPTF MUTATED                                       2
  BPTF WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BPTF MUTATED                                                       16
  BPTF WILD-TYPE                                                    142
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BPTF MUTATED                                                   2
  BPTF WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BPTF MUTATED                                                                   6
  BPTF WILD-TYPE                                                                62
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BPTF MUTATED                                                    1
  BPTF WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BPTF MUTATED                                                  3
  BPTF WILD-TYPE                                               58
D223V9, multiclass
                                                                   clus
vv                                                                  BPTF MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  BPTF WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BPTF MUTATED    21   0   2   5
  BPTF WILD-TYPE 290  14  13  19
D223V10, multiclass
    clus
vv   BPTF MUTATED BPTF WILD-TYPE
  R0           21            290
  R1            0             14
  R2            2             13
  RX            5             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BPTF MUTATED       6                         1
  BPTF WILD-TYPE    81                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BPTF MUTATED                                           1    20
  BPTF WILD-TYPE                                         0   223
D223V12, multiclass
                                           clus
vv                                          BPTF MUTATED BPTF WILD-TYPE
  ASIAN                                                6             81
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                               20            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V13, binary
                cls
clus               0   1
  BPTF MUTATED     1  25
  BPTF WILD-TYPE   3 285
[1] "tbl2"
                cls
clus             [,1] [,2]
  BPTF MUTATED      1   25
  BPTF WILD-TYPE    3  285
                        clus
vv                       BPTF MUTATED BPTF WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           25            285
[1] 2 2
[1] FALSE

Clustering(224) Variable = MTIF2 MUTATION ANALYSIS
D224V1, survival
                 sevent
clus2               0   1
  MTIF2 MUTATED    12   5
  MTIF2 WILD-TYPE 218 134
  MTIF2 MUTATED MTIF2 WILD-TYPE 
             17             352 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
              5             134 
$`MTIF2 MUTATED`
TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8589 
        6.97        44.94        36.16         0.26         1.12        27.12 
TCGA-BR-A4J4 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5728 
        0.53         6.58        11.77         1.02         6.02        65.10 
TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4H4 TCGA-KB-A6F7 
       77.29        30.51        22.68        23.84        63.62 

$`MTIF2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17        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-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-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-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-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-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 

  MTIF2 MUTATED MTIF2 WILD-TYPE 
           0.26            0.00 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
          77.29          122.30 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
          22.68           14.22 
[1] "0.3 - 77.3 (22.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.5"
D224V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTIF2 MUTATED         0        1        3        1         3         2
  MTIF2 WILD-TYPE       2       14       37       29        34        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MTIF2 MUTATED           0          3          2          1        2
  MTIF2 WILD-TYPE         3         67         51         31       36
D224V3, multiclass
            clus
vv           MTIF2 MUTATED MTIF2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MTIF2 MUTATED     2   4   7   5
  MTIF2 WILD-TYPE  20  88 166  92
D224V4, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  T1             2              20
  T2             4              88
  T3             7             166
  T4             5              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
  MTIF2 MUTATED     7   7   3   1
  MTIF2 WILD-TYPE 111  97  74  76
D224V5, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  N0             7             111
  N1             7              97
  N2             3              74
  N3             1              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"
D224V6, binary
                 cls
clus                0   1
  MTIF2 MUTATED    16   1
  MTIF2 WILD-TYPE 330  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED     16    1
  MTIF2 WILD-TYPE  330   28
   clus
vv  MTIF2 MUTATED MTIF2 WILD-TYPE
  0            16             330
  1             1              28
[1] 2 2
[1] FALSE
D224V7, binary
                 cls
clus                0   1
  MTIF2 MUTATED     9   9
  MTIF2 WILD-TYPE 136 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED      9    9
  MTIF2 WILD-TYPE  136  239
        clus
vv       MTIF2 MUTATED MTIF2 WILD-TYPE
  FEMALE             9             136
  MALE               9             239
[1] 2 2
[1] FALSE
D224V8, binary
                 cls
clus                0   1
  MTIF2 MUTATED    11   3
  MTIF2 WILD-TYPE 281  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED     11    3
  MTIF2 WILD-TYPE  281   56
     clus
vv    MTIF2 MUTATED MTIF2 WILD-TYPE
  NO             11             281
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MTIF2 MUTATED                                          0
  MTIF2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MTIF2 MUTATED                                       2
  MTIF2 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MTIF2 MUTATED                                                        9
  MTIF2 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MTIF2 MUTATED                                                   2
  MTIF2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MTIF2 MUTATED                                                                   3
  MTIF2 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MTIF2 MUTATED                                                    1
  MTIF2 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MTIF2 MUTATED                                                  1
  MTIF2 WILD-TYPE                                               60
D224V9, multiclass
                                                                   clus
vv                                                                  MTIF2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  MTIF2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MTIF2 MUTATED    11   1   1   2
  MTIF2 WILD-TYPE 300  13  14  22
D224V10, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  R0            11             300
  R1             1              13
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MTIF2 MUTATED       5                         0
  MTIF2 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MTIF2 MUTATED                                           0     7
  MTIF2 WILD-TYPE                                         1   236
D224V12, multiclass
                                           clus
vv                                          MTIF2 MUTATED MTIF2 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V13, binary
                 cls
clus                0   1
  MTIF2 MUTATED     0  12
  MTIF2 WILD-TYPE   4 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED      0   12
  MTIF2 WILD-TYPE    4  298
                        clus
vv                       MTIF2 MUTATED MTIF2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(225) Variable = ARHGAP18 MUTATION ANALYSIS
D225V1, survival
                    sevent
clus2                  0   1
  ARHGAP18 MUTATED     4   4
  ARHGAP18 WILD-TYPE 226 135
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                 8                361 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                 4                135 
$`ARHGAP18 MUTATED`
TCGA-BR-4257 TCGA-BR-7704 TCGA-BR-8363 TCGA-BR-A4QL TCGA-CD-A48C TCGA-D7-6815 
        9.67        35.24         0.26        16.14        11.61        15.98 
TCGA-HU-A4GN TCGA-VQ-A8P2 
       29.98        38.14 

$`ARHGAP18 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-D7-6817 
       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-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-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 

  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
              0.26               0.00 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
             38.14             122.30 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
             16.06              14.17 
[1] "0.3 - 38.1 (16.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D225V2, 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       2       15       39       29        36        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP18 MUTATED           0          1          1          0        0
  ARHGAP18 WILD-TYPE         3         69         52         32       38
D225V3, multiclass
            clus
vv           ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  1                 29
  STAGE IIA                 1                 36
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                1                 52
  STAGE IIIC                0                 32
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGAP18 MUTATED     1   3   3   1
  ARHGAP18 WILD-TYPE  21  89 170  96
D225V4, multiclass
    clus
vv   ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  T1                1                 21
  T2                3                 89
  T3                3                170
  T4                1                 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
  ARHGAP18 MUTATED     2   3   1   1
  ARHGAP18 WILD-TYPE 116 101  76  76
D225V5, multiclass
    clus
vv   ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  N0                2                116
  N1                3                101
  N2                1                 76
  N3                1                 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"
D225V6, binary
                    cls
clus                   0   1
  ARHGAP18 MUTATED     9   0
  ARHGAP18 WILD-TYPE 337  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      9    0
  ARHGAP18 WILD-TYPE  337   29
   clus
vv  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  0                9                337
  1                0                 29
[1] 2 2
[1] FALSE
D225V7, binary
                    cls
clus                   0   1
  ARHGAP18 MUTATED     7   2
  ARHGAP18 WILD-TYPE 138 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      7    2
  ARHGAP18 WILD-TYPE  138  246
        clus
vv       ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  FEMALE                7                138
  MALE                  2                246
[1] 2 2
[1] FALSE
D225V8, binary
                    cls
clus                   0   1
  ARHGAP18 MUTATED     7   1
  ARHGAP18 WILD-TYPE 285  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      7    1
  ARHGAP18 WILD-TYPE  285   58
     clus
vv    ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  NO                 7                285
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARHGAP18 MUTATED                                          0
  ARHGAP18 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARHGAP18 MUTATED                                       0
  ARHGAP18 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARHGAP18 MUTATED                                                        5
  ARHGAP18 WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARHGAP18 MUTATED                                                   1
  ARHGAP18 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARHGAP18 MUTATED                                                                   1
  ARHGAP18 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARHGAP18 MUTATED                                                    0
  ARHGAP18 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARHGAP18 MUTATED                                                  2
  ARHGAP18 WILD-TYPE                                               59
D225V9, multiclass
                                                                   clus
vv                                                                  ARHGAP18 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  ARHGAP18 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ARHGAP18 MUTATED     6   0   0   2
  ARHGAP18 WILD-TYPE 305  14  15  22
D225V10, multiclass
    clus
vv   ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  R0                6                305
  R1                0                 14
  R2                0                 15
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ARHGAP18 MUTATED       2                         0
  ARHGAP18 WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARHGAP18 MUTATED                                           0     7
  ARHGAP18 WILD-TYPE                                         1   236
D225V12, multiclass
                                           clus
vv                                          ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V13, binary
                    cls
clus                   0   1
  ARHGAP18 MUTATED     0   8
  ARHGAP18 WILD-TYPE   4 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      0    8
  ARHGAP18 WILD-TYPE    4  302
                        clus
vv                       ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                8                302
[1] 2 2
[1] FALSE

Clustering(226) Variable = EFNB3 MUTATION ANALYSIS
D226V1, survival
                 sevent
clus2               0   1
  EFNB3 MUTATED     7   5
  EFNB3 WILD-TYPE 223 134
  EFNB3 MUTATED EFNB3 WILD-TYPE 
             12             357 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
              5             134 
$`EFNB3 MUTATED`
TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8372 
       30.90        32.78        30.90        31.10         0.26        31.27 
TCGA-BR-A4CS TCGA-CG-4441 TCGA-D7-A6EY TCGA-HF-A5NB TCGA-HU-A4H4 TCGA-MX-A5UJ 
        1.48        14.01        11.44        30.51        23.84        19.73 

$`EFNB3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-D7-8572 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-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-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 

  EFNB3 MUTATED EFNB3 WILD-TYPE 
           0.26            0.00 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
          32.78          122.30 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
         27.175          14.070 
[1] "0.3 - 32.8 (27.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D226V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EFNB3 MUTATED         0        0        1        0         1         2
  EFNB3 WILD-TYPE       2       15       39       30        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFNB3 MUTATED           0          3          1          4        0
  EFNB3 WILD-TYPE         3         67         52         28       38
D226V3, multiclass
            clus
vv           EFNB3 MUTATED EFNB3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             4              28
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EFNB3 MUTATED     0   4   4   5
  EFNB3 WILD-TYPE  22  88 169  92
D226V4, multiclass
    clus
vv   EFNB3 MUTATED EFNB3 WILD-TYPE
  T1             0              22
  T2             4              88
  T3             4             169
  T4             5              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
  EFNB3 MUTATED     3   0   5   4
  EFNB3 WILD-TYPE 115 104  72  73
D226V5, multiclass
    clus
vv   EFNB3 MUTATED EFNB3 WILD-TYPE
  N0             3             115
  N1             0             104
  N2             5              72
  N3             4              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"
D226V6, binary
                 cls
clus                0   1
  EFNB3 MUTATED    13   0
  EFNB3 WILD-TYPE 333  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED     13    0
  EFNB3 WILD-TYPE  333   29
   clus
vv  EFNB3 MUTATED EFNB3 WILD-TYPE
  0            13             333
  1             0              29
[1] 2 2
[1] FALSE
D226V7, binary
                 cls
clus                0   1
  EFNB3 MUTATED     8   5
  EFNB3 WILD-TYPE 137 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED      8    5
  EFNB3 WILD-TYPE  137  243
        clus
vv       EFNB3 MUTATED EFNB3 WILD-TYPE
  FEMALE             8             137
  MALE               5             243
[1] 2 2
[1] FALSE
D226V8, binary
                 cls
clus                0   1
  EFNB3 MUTATED    11   1
  EFNB3 WILD-TYPE 281  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED     11    1
  EFNB3 WILD-TYPE  281   58
     clus
vv    EFNB3 MUTATED EFNB3 WILD-TYPE
  NO             11             281
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EFNB3 MUTATED                                          0
  EFNB3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EFNB3 MUTATED                                       0
  EFNB3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EFNB3 MUTATED                                                        7
  EFNB3 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EFNB3 MUTATED                                                   1
  EFNB3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EFNB3 MUTATED                                                                   2
  EFNB3 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EFNB3 MUTATED                                                    0
  EFNB3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EFNB3 MUTATED                                                  3
  EFNB3 WILD-TYPE                                               58
D226V9, multiclass
                                                                   clus
vv                                                                  EFNB3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  EFNB3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EFNB3 MUTATED    11   1   0   1
  EFNB3 WILD-TYPE 300  13  15  23
D226V10, multiclass
    clus
vv   EFNB3 MUTATED EFNB3 WILD-TYPE
  R0            11             300
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EFNB3 MUTATED       1                         0
  EFNB3 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EFNB3 MUTATED                                           0    10
  EFNB3 WILD-TYPE                                         1   233
D226V12, multiclass
                                           clus
vv                                          EFNB3 MUTATED EFNB3 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V13, binary
                 cls
clus                0   1
  EFNB3 MUTATED     0  11
  EFNB3 WILD-TYPE   4 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED      0   11
  EFNB3 WILD-TYPE    4  299
                        clus
vv                       EFNB3 MUTATED EFNB3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(227) Variable = NDST2 MUTATION ANALYSIS
D227V1, survival
                 sevent
clus2               0   1
  NDST2 MUTATED     9   1
  NDST2 WILD-TYPE 221 138
  NDST2 MUTATED NDST2 WILD-TYPE 
             10             359 
  NDST2 MUTATED NDST2 WILD-TYPE 
              1             138 
$`NDST2 MUTATED`
TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-8372 TCGA-CG-4305 TCGA-CG-4449 TCGA-CG-5721 
       26.70         9.67        31.27        15.95        19.07         6.02 
TCGA-F1-A448 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-VQ-A8P2 
       21.27        22.32        22.68        38.14 

$`NDST2 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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 
           6.02            0.00 
  NDST2 MUTATED NDST2 WILD-TYPE 
          38.14          122.30 
  NDST2 MUTATED NDST2 WILD-TYPE 
         21.795          14.070 
[1] "6.0 - 38.1 (21.8)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "4.9"
D227V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NDST2 MUTATED         0        0        1        2         0         3
  NDST2 WILD-TYPE       2       15       39       28        37        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NDST2 MUTATED           0          1          1          1        1
  NDST2 WILD-TYPE         3         69         52         31       37
D227V3, multiclass
            clus
vv           NDST2 MUTATED NDST2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              0              37
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NDST2 MUTATED     0   3   2   5
  NDST2 WILD-TYPE  22  89 171  92
D227V4, multiclass
    clus
vv   NDST2 MUTATED NDST2 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             2             171
  T4             5              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
  NDST2 MUTATED     3   5   0   2
  NDST2 WILD-TYPE 115  99  77  75
D227V5, multiclass
    clus
vv   NDST2 MUTATED NDST2 WILD-TYPE
  N0             3             115
  N1             5              99
  N2             0              77
  N3             2              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"
D227V6, binary
                 cls
clus                0   1
  NDST2 MUTATED    11   0
  NDST2 WILD-TYPE 335  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST2 MUTATED     11    0
  NDST2 WILD-TYPE  335   29
   clus
vv  NDST2 MUTATED NDST2 WILD-TYPE
  0            11             335
  1             0              29
[1] 2 2
[1] FALSE
D227V7, binary
                 cls
clus                0   1
  NDST2 MUTATED     4   7
  NDST2 WILD-TYPE 141 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST2 MUTATED      4    7
  NDST2 WILD-TYPE  141  241
        clus
vv       NDST2 MUTATED NDST2 WILD-TYPE
  FEMALE             4             141
  MALE               7             241
[1] 2 2
[1] FALSE
D227V8, binary
                 cls
clus                0   1
  NDST2 MUTATED     8   2
  NDST2 WILD-TYPE 284  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST2 MUTATED      8    2
  NDST2 WILD-TYPE  284   57
     clus
vv    NDST2 MUTATED NDST2 WILD-TYPE
  NO              8             284
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NDST2 MUTATED                                          0
  NDST2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NDST2 MUTATED                                       3
  NDST2 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NDST2 MUTATED                                                        3
  NDST2 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NDST2 MUTATED                                                   3
  NDST2 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NDST2 MUTATED                                                                   2
  NDST2 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NDST2 MUTATED                                                    0
  NDST2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NDST2 MUTATED                                                  0
  NDST2 WILD-TYPE                                               61
D227V9, multiclass
                                                                   clus
vv                                                                  NDST2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  NDST2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NDST2 MUTATED     9   0   0   1
  NDST2 WILD-TYPE 302  14  15  23
D227V10, multiclass
    clus
vv   NDST2 MUTATED NDST2 WILD-TYPE
  R0             9             302
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NDST2 MUTATED       2                         0
  NDST2 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NDST2 MUTATED                                           0     5
  NDST2 WILD-TYPE                                         1   238
D227V12, multiclass
                                           clus
vv                                          NDST2 MUTATED NDST2 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V13, binary
                 cls
clus                0   1
  NDST2 MUTATED     1   5
  NDST2 WILD-TYPE   3 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST2 MUTATED      1    5
  NDST2 WILD-TYPE    3  305
                        clus
vv                       NDST2 MUTATED NDST2 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(228) Variable = MICALCL MUTATION ANALYSIS
D228V1, survival
                   sevent
clus2                 0   1
  MICALCL MUTATED     9   5
  MICALCL WILD-TYPE 221 134
  MICALCL MUTATED MICALCL WILD-TYPE 
               14               355 
  MICALCL MUTATED MICALCL WILD-TYPE 
                5               134 
$`MICALCL MUTATED`
TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8360 
        9.67         6.61        34.68        32.25         2.66         6.18 
TCGA-BR-8680 TCGA-CD-5804 TCGA-CD-8533 TCGA-D7-8573 TCGA-D7-8574 TCGA-F1-6874 
       31.96        12.10        15.39        19.50        17.19        14.47 
TCGA-FP-8209 TCGA-VQ-A8DV 
       59.54        13.25 

$`MICALCL WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        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-8210 TCGA-FP-8211 TCGA-FP-8631 
       14.07        22.29        17.06         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-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 

  MICALCL MUTATED MICALCL WILD-TYPE 
             2.66              0.00 
  MICALCL MUTATED MICALCL WILD-TYPE 
            59.54            122.30 
  MICALCL MUTATED MICALCL WILD-TYPE 
            14.93             14.17 
[1] "2.7 - 59.5 (14.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D228V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MICALCL MUTATED         0        0        3        1         3         1
  MICALCL WILD-TYPE       2       15       37       29        34        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MICALCL MUTATED           1          1          0          0        2
  MICALCL WILD-TYPE         2         69         53         32       36
D228V3, multiclass
            clus
vv           MICALCL MUTATED MICALCL WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 3                37
  STAGE II                 1                29
  STAGE IIA                3                34
  STAGE IIB                1                51
  STAGE III                1                 2
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  MICALCL MUTATED     0   5   6   3
  MICALCL WILD-TYPE  22  87 167  94
D228V4, multiclass
    clus
vv   MICALCL MUTATED MICALCL WILD-TYPE
  T1               0                22
  T2               5                87
  T3               6               167
  T4               3                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
  MICALCL MUTATED     8   2   1   2
  MICALCL WILD-TYPE 110 102  76  75
D228V5, multiclass
    clus
vv   MICALCL MUTATED MICALCL WILD-TYPE
  N0               8               110
  N1               2               102
  N2               1                76
  N3               2                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"
D228V6, binary
                   cls
clus                  0   1
  MICALCL MUTATED    12   2
  MICALCL WILD-TYPE 334  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALCL MUTATED     12    2
  MICALCL WILD-TYPE  334   27
   clus
vv  MICALCL MUTATED MICALCL WILD-TYPE
  0              12               334
  1               2                27
[1] 2 2
[1] FALSE
D228V7, binary
                   cls
clus                  0   1
  MICALCL MUTATED     5  10
  MICALCL WILD-TYPE 140 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALCL MUTATED      5   10
  MICALCL WILD-TYPE  140  238
        clus
vv       MICALCL MUTATED MICALCL WILD-TYPE
  FEMALE               5               140
  MALE                10               238
[1] 2 2
[1] FALSE
D228V8, binary
                   cls
clus                  0   1
  MICALCL MUTATED    13   1
  MICALCL WILD-TYPE 279  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALCL MUTATED     13    1
  MICALCL WILD-TYPE  279   58
     clus
vv    MICALCL MUTATED MICALCL WILD-TYPE
  NO               13               279
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MICALCL MUTATED                                          0
  MICALCL WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MICALCL MUTATED                                       1
  MICALCL WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MICALCL MUTATED                                                        8
  MICALCL WILD-TYPE                                                    150
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MICALCL MUTATED                                                   0
  MICALCL WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MICALCL MUTATED                                                                   4
  MICALCL WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MICALCL MUTATED                                                    0
  MICALCL WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MICALCL MUTATED                                                  2
  MICALCL WILD-TYPE                                               59
D228V9, multiclass
                                                                   clus
vv                                                                  MICALCL MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  MICALCL WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  MICALCL MUTATED    12   0   0   3
  MICALCL WILD-TYPE 299  14  15  21
D228V10, multiclass
    clus
vv   MICALCL MUTATED MICALCL WILD-TYPE
  R0              12               299
  R1               0                14
  R2               0                15
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  MICALCL MUTATED       3                         0
  MICALCL WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MICALCL MUTATED                                           0    12
  MICALCL WILD-TYPE                                         1   231
D228V12, multiclass
                                           clus
vv                                          MICALCL MUTATED MICALCL WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V13, binary
                   cls
clus                  0   1
  MICALCL MUTATED     0  14
  MICALCL WILD-TYPE   4 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALCL MUTATED      0   14
  MICALCL WILD-TYPE    4  296
                        clus
vv                       MICALCL MUTATED MICALCL WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              14               296
[1] 2 2
[1] FALSE

Clustering(229) Variable = MMP3 MUTATION ANALYSIS
D229V1, survival
                sevent
clus2              0   1
  MMP3 MUTATED     9   2
  MMP3 WILD-TYPE 221 137
  MMP3 MUTATED MMP3 WILD-TYPE 
            11            358 
  MMP3 MUTATED MMP3 WILD-TYPE 
             2            137 
$`MMP3 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A4YY TCGA-D7-A6EY 
       34.68        29.59         6.02       105.07        13.78        11.44 
TCGA-HF-A5NB TCGA-HU-8602 TCGA-IN-A6RL TCGA-R5-A7ZI TCGA-VQ-A8P2 
       30.51        22.32        13.35        74.53        38.14 

$`MMP3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-A4Z0 
       20.91        14.27        16.44         5.92        36.43        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-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-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 

  MMP3 MUTATED MMP3 WILD-TYPE 
          6.02           0.00 
  MMP3 MUTATED MMP3 WILD-TYPE 
        105.07         122.30 
  MMP3 MUTATED MMP3 WILD-TYPE 
         29.59          14.12 
[1] "6.0 - 105.1 (29.6)" "0.0 - 122.3 (14.1)"
[1] "hr=" "3.4"
D229V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MMP3 MUTATED         0        0        0        1         1         2
  MMP3 WILD-TYPE       2       15       40       29        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MMP3 MUTATED           0          2          2          1        2
  MMP3 WILD-TYPE         3         68         51         31       36
D229V3, multiclass
            clus
vv           MMP3 MUTATED MMP3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            2             51
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MMP3 MUTATED     0   2   4   6
  MMP3 WILD-TYPE  22  90 169  91
D229V4, multiclass
    clus
vv   MMP3 MUTATED MMP3 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            4            169
  T4            6             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
  MMP3 MUTATED     3   5   0   3
  MMP3 WILD-TYPE 115  99  77  74
D229V5, multiclass
    clus
vv   MMP3 MUTATED MMP3 WILD-TYPE
  N0            3            115
  N1            5             99
  N2            0             77
  N3            3             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"
D229V6, binary
                cls
clus               0   1
  MMP3 MUTATED    10   1
  MMP3 WILD-TYPE 336  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP3 MUTATED     10    1
  MMP3 WILD-TYPE  336   28
   clus
vv  MMP3 MUTATED MMP3 WILD-TYPE
  0           10            336
  1            1             28
[1] 2 2
[1] FALSE
D229V7, binary
                cls
clus               0   1
  MMP3 MUTATED     7   5
  MMP3 WILD-TYPE 138 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP3 MUTATED      7    5
  MMP3 WILD-TYPE  138  243
        clus
vv       MMP3 MUTATED MMP3 WILD-TYPE
  FEMALE            7            138
  MALE              5            243
[1] 2 2
[1] FALSE
D229V8, binary
                cls
clus               0   1
  MMP3 MUTATED     8   3
  MMP3 WILD-TYPE 284  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP3 MUTATED      8    3
  MMP3 WILD-TYPE  284   56
     clus
vv    MMP3 MUTATED MMP3 WILD-TYPE
  NO             8            284
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MMP3 MUTATED                                          0
  MMP3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MMP3 MUTATED                                       2
  MMP3 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MMP3 MUTATED                                                        6
  MMP3 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MMP3 MUTATED                                                   2
  MMP3 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MMP3 MUTATED                                                                   1
  MMP3 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MMP3 MUTATED                                                    0
  MMP3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MMP3 MUTATED                                                  1
  MMP3 WILD-TYPE                                               60
D229V9, multiclass
                                                                   clus
vv                                                                  MMP3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  MMP3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MMP3 MUTATED    10   1   0   1
  MMP3 WILD-TYPE 301  13  15  23
D229V10, multiclass
    clus
vv   MMP3 MUTATED MMP3 WILD-TYPE
  R0           10            301
  R1            1             13
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MMP3 MUTATED       1                         0
  MMP3 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MMP3 MUTATED                                           0     8
  MMP3 WILD-TYPE                                         1   235
D229V12, multiclass
                                           clus
vv                                          MMP3 MUTATED MMP3 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V13, binary
                cls
clus               0   1
  MMP3 MUTATED     1   7
  MMP3 WILD-TYPE   3 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP3 MUTATED      1    7
  MMP3 WILD-TYPE    3  303
                        clus
vv                       MMP3 MUTATED MMP3 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(230) Variable = OPTN MUTATION ANALYSIS
D230V1, survival
                sevent
clus2              0   1
  OPTN MUTATED     5   3
  OPTN WILD-TYPE 225 136
  OPTN MUTATED OPTN WILD-TYPE 
             8            361 
  OPTN MUTATED OPTN WILD-TYPE 
             3            136 
$`OPTN MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8060 TCGA-BR-8487 TCGA-CD-8529 TCGA-CG-5723 
       30.90        34.68        11.44         1.12        12.30       105.07 
TCGA-CG-5726 TCGA-HU-A4GU 
       28.96         6.58 

$`OPTN WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-5721 
       30.97         6.97        36.00         1.02         0.99         6.02 
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-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 

  OPTN MUTATED OPTN WILD-TYPE 
          1.12           0.00 
  OPTN MUTATED OPTN WILD-TYPE 
        105.07         122.30 
  OPTN MUTATED OPTN WILD-TYPE 
         20.63          14.27 
[1] "1.1 - 105.1 (20.6)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D230V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OPTN MUTATED         1        1        1        1         2         3
  OPTN WILD-TYPE       1       14       39       29        35        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OPTN MUTATED           0          1          0          0        1
  OPTN WILD-TYPE         3         69         53         32       37
D230V3, multiclass
            clus
vv           OPTN MUTATED OPTN WILD-TYPE
  STAGE I               1              1
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OPTN MUTATED     2   4   3   3
  OPTN WILD-TYPE  20  88 170  94
D230V4, multiclass
    clus
vv   OPTN MUTATED OPTN WILD-TYPE
  T1            2             20
  T2            4             88
  T3            3            170
  T4            3             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
  OPTN MUTATED     7   3   1   0
  OPTN WILD-TYPE 111 101  76  77
D230V5, multiclass
    clus
vv   OPTN MUTATED OPTN WILD-TYPE
  N0            7            111
  N1            3            101
  N2            1             76
  N3            0             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"
D230V6, binary
                cls
clus               0   1
  OPTN MUTATED    10   1
  OPTN WILD-TYPE 336  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTN MUTATED     10    1
  OPTN WILD-TYPE  336   28
   clus
vv  OPTN MUTATED OPTN WILD-TYPE
  0           10            336
  1            1             28
[1] 2 2
[1] FALSE
D230V7, binary
                cls
clus               0   1
  OPTN MUTATED     5   7
  OPTN WILD-TYPE 140 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTN MUTATED      5    7
  OPTN WILD-TYPE  140  241
        clus
vv       OPTN MUTATED OPTN WILD-TYPE
  FEMALE            5            140
  MALE              7            241
[1] 2 2
[1] FALSE
D230V8, binary
                cls
clus               0   1
  OPTN MUTATED     8   1
  OPTN WILD-TYPE 284  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTN MUTATED      8    1
  OPTN WILD-TYPE  284   58
     clus
vv    OPTN MUTATED OPTN WILD-TYPE
  NO             8            284
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OPTN MUTATED                                          0
  OPTN WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OPTN MUTATED                                       1
  OPTN WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OPTN MUTATED                                                        7
  OPTN WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OPTN MUTATED                                                   1
  OPTN WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OPTN MUTATED                                                                   3
  OPTN WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OPTN MUTATED                                                    0
  OPTN WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OPTN MUTATED                                                  0
  OPTN WILD-TYPE                                               61
D230V9, multiclass
                                                                   clus
vv                                                                  OPTN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  OPTN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  OPTN MUTATED    10   0   0   2
  OPTN WILD-TYPE 301  14  15  22
D230V10, multiclass
    clus
vv   OPTN MUTATED OPTN WILD-TYPE
  R0           10            301
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  OPTN MUTATED       2                         1
  OPTN WILD-TYPE    85                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OPTN MUTATED                                           0     6
  OPTN WILD-TYPE                                         1   237
D230V12, multiclass
                                           clus
vv                                          OPTN MUTATED OPTN WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V13, binary
                cls
clus               0   1
  OPTN MUTATED     0   9
  OPTN WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTN MUTATED      0    9
  OPTN WILD-TYPE    4  301
                        clus
vv                       OPTN MUTATED OPTN WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(231) Variable = ZFHX3 MUTATION ANALYSIS
D231V1, survival
                 sevent
clus2               0   1
  ZFHX3 MUTATED    21  14
  ZFHX3 WILD-TYPE 209 125
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             35             334 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             14             125 
$`ZFHX3 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6452 
       21.99        26.70         6.97        30.90         9.67        34.68 
TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8382 
       32.78        35.84        14.43        29.59        31.10        25.05 
TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-8526 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        1.12        31.96        12.53        11.61         6.58        11.77 
TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 
        1.02         6.02       105.07        28.96        65.10        21.07 
TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-8099 TCGA-HF-7132 TCGA-HU-8249 TCGA-HU-8602 
        7.99        19.53        17.06        77.29        28.96        22.32 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-VQ-A8P2 
        0.10         6.51        20.25        23.84        38.14 

$`ZFHX3 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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-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-A4MH TCGA-CD-A4MJ 
        6.31        12.30        11.31        12.43        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-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
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-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-7916 TCGA-FP-7998 
       72.23        21.27        11.38         3.48        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-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-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
        5.92        24.39        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-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-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 

  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
            0.1             0.0 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
         105.07          122.30 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
         21.990          14.025 
[1] "0.1 - 105.1 (22.0)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.2"
D231V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZFHX3 MUTATED         0        1        2        2         6         7
  ZFHX3 WILD-TYPE       2       14       38       28        31        45
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFHX3 MUTATED           1          7          0          4        5
  ZFHX3 WILD-TYPE         2         63         53         28       33
D231V3, multiclass
            clus
vv           ZFHX3 MUTATED ZFHX3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               2              28
  STAGE IIA              6              31
  STAGE IIB              7              45
  STAGE III              1               2
  STAGE IIIA             7              63
  STAGE IIIB             0              53
  STAGE IIIC             4              28
  STAGE IV               5              33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZFHX3 MUTATED     2   7  14  14
  ZFHX3 WILD-TYPE  20  85 159  83
D231V4, multiclass
    clus
vv   ZFHX3 MUTATED ZFHX3 WILD-TYPE
  T1             2              20
  T2             7              85
  T3            14             159
  T4            14              83
[1] 4 2
[1] TRUE
[1] "dimension of 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    13  12   9   1
  ZFHX3 WILD-TYPE 105  92  68  76
D231V5, multiclass
    clus
vv   ZFHX3 MUTATED ZFHX3 WILD-TYPE
  N0            13             105
  N1            12              92
  N2             9              68
  N3             1              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"
D231V6, binary
                 cls
clus                0   1
  ZFHX3 MUTATED    32   3
  ZFHX3 WILD-TYPE 314  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED     32    3
  ZFHX3 WILD-TYPE  314   26
   clus
vv  ZFHX3 MUTATED ZFHX3 WILD-TYPE
  0            32             314
  1             3              26
[1] 2 2
[1] FALSE
D231V7, binary
                 cls
clus                0   1
  ZFHX3 MUTATED    23  15
  ZFHX3 WILD-TYPE 122 233
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED     23   15
  ZFHX3 WILD-TYPE  122  233
        clus
vv       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  FEMALE            23             122
  MALE              15             233
[1] 2 2
[1] FALSE
D231V8, binary
                 cls
clus                0   1
  ZFHX3 MUTATED    28   4
  ZFHX3 WILD-TYPE 264  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED     28    4
  ZFHX3 WILD-TYPE  264   55
     clus
vv    ZFHX3 MUTATED ZFHX3 WILD-TYPE
  NO             28             264
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZFHX3 MUTATED                                          0
  ZFHX3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZFHX3 MUTATED                                       4
  ZFHX3 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZFHX3 MUTATED                                                       18
  ZFHX3 WILD-TYPE                                                    140
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZFHX3 MUTATED                                                   3
  ZFHX3 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZFHX3 MUTATED                                                                   8
  ZFHX3 WILD-TYPE                                                                60
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZFHX3 MUTATED                                                    0
  ZFHX3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZFHX3 MUTATED                                                  5
  ZFHX3 WILD-TYPE                                               56
D231V9, multiclass
                                                                   clus
vv                                                                  ZFHX3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       18
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             8
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              5
                                                                   clus
vv                                                                  ZFHX3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        140
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              60
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZFHX3 MUTATED    26   0   2   6
  ZFHX3 WILD-TYPE 285  14  13  18
D231V10, multiclass
    clus
vv   ZFHX3 MUTATED ZFHX3 WILD-TYPE
  R0            26             285
  R1             0              14
  R2             2              13
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZFHX3 MUTATED      11                         0
  ZFHX3 WILD-TYPE    76                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZFHX3 MUTATED                                           0    19
  ZFHX3 WILD-TYPE                                         1   224
D231V12, multiclass
                                           clus
vv                                          ZFHX3 MUTATED ZFHX3 WILD-TYPE
  ASIAN                                                11              76
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                19             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V13, binary
                 cls
clus                0   1
  ZFHX3 MUTATED     0  29
  ZFHX3 WILD-TYPE   4 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED      0   29
  ZFHX3 WILD-TYPE    4  281
                        clus
vv                       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            29             281
[1] 2 2
[1] FALSE

Clustering(232) Variable = ACP1 MUTATION ANALYSIS
D232V1, survival
                sevent
clus2              0   1
  ACP1 MUTATED     5   2
  ACP1 WILD-TYPE 225 137
  ACP1 MUTATED ACP1 WILD-TYPE 
             7            362 
  ACP1 MUTATED ACP1 WILD-TYPE 
             2            137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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          14.22 
[1] "5.9 - 30.5 (19.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D232V2, 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       2       15       40       29        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACP1 MUTATED           0          3          0          1        0
  ACP1 WILD-TYPE         3         67         53         31       38
D232V3, multiclass
            clus
vv           ACP1 MUTATED ACP1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ACP1 MUTATED     0   1   5   2
  ACP1 WILD-TYPE  22  91 168  95
D232V4, multiclass
    clus
vv   ACP1 MUTATED ACP1 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            5            168
  T4            2             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
  ACP1 MUTATED     2   5   1   1
  ACP1 WILD-TYPE 116  99  76  76
D232V5, multiclass
    clus
vv   ACP1 MUTATED ACP1 WILD-TYPE
  N0            2            116
  N1            5             99
  N2            1             76
  N3            1             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"
D232V6, binary
                cls
clus               0   1
  ACP1 MUTATED     8   0
  ACP1 WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP1 MUTATED      8    0
  ACP1 WILD-TYPE  338   29
   clus
vv  ACP1 MUTATED ACP1 WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D232V7, binary
                cls
clus               0   1
  ACP1 MUTATED     6   3
  ACP1 WILD-TYPE 139 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP1 MUTATED      6    3
  ACP1 WILD-TYPE  139  245
        clus
vv       ACP1 MUTATED ACP1 WILD-TYPE
  FEMALE            6            139
  MALE              3            245
[1] 2 2
[1] FALSE
D232V8, binary
                cls
clus               0   1
  ACP1 MUTATED     6   1
  ACP1 WILD-TYPE 286  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP1 MUTATED      6    1
  ACP1 WILD-TYPE  286   58
     clus
vv    ACP1 MUTATED ACP1 WILD-TYPE
  NO             6            286
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ACP1 MUTATED                                          0
  ACP1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ACP1 MUTATED                                       1
  ACP1 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ACP1 MUTATED                                                        4
  ACP1 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ACP1 MUTATED                                                   1
  ACP1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ACP1 MUTATED                                                                   0
  ACP1 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ACP1 MUTATED                                                    0
  ACP1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ACP1 MUTATED                                                  3
  ACP1 WILD-TYPE                                               58
D232V9, multiclass
                                                                   clus
vv                                                                  ACP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  ACP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ACP1 MUTATED     4   1   0   3
  ACP1 WILD-TYPE 307  13  15  21
D232V10, multiclass
    clus
vv   ACP1 MUTATED ACP1 WILD-TYPE
  R0            4            307
  R1            1             13
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ACP1 MUTATED       3                         0
  ACP1 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ACP1 MUTATED                                           0     5
  ACP1 WILD-TYPE                                         1   238
D232V12, multiclass
                                           clus
vv                                          ACP1 MUTATED ACP1 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V13, binary
                cls
clus               0   1
  ACP1 MUTATED     0   8
  ACP1 WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP1 MUTATED      0    8
  ACP1 WILD-TYPE    4  302
                        clus
vv                       ACP1 MUTATED ACP1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(233) Variable = YY1 MUTATION ANALYSIS
D233V1, survival
               sevent
clus2             0   1
  YY1 MUTATED     6   0
  YY1 WILD-TYPE 224 139
  YY1 MUTATED YY1 WILD-TYPE 
            6           363 
  YY1 MUTATED YY1 WILD-TYPE 
            0           139 
$`YY1 MUTATED`
TCGA-BR-7715 TCGA-BR-8078 TCGA-BR-8591 TCGA-CD-8531 TCGA-SW-A7EA TCGA-VQ-A8P2 
       33.63        29.59        28.14        12.59        19.04        38.14 

$`YY1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  YY1 MUTATED YY1 WILD-TYPE 
        12.59          0.00 
  YY1 MUTATED YY1 WILD-TYPE 
        38.14        122.30 
  YY1 MUTATED YY1 WILD-TYPE 
       28.865        14.070 
[1] "12.6 - 38.1 (28.9)" "0.0 - 122.3 (14.1)"
[1] "hr="     "9300000"
D233V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  YY1 MUTATED         0        0        1        0         1         1
  YY1 WILD-TYPE       2       15       39       30        36        51
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  YY1 MUTATED           0          2          0          1        1
  YY1 WILD-TYPE         3         68         53         31       37
D233V3, multiclass
            clus
vv           YY1 MUTATED YY1 WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             1            39
  STAGE II             0            30
  STAGE IIA            1            36
  STAGE IIB            1            51
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           0            53
  STAGE IIIC           1            31
  STAGE IV             1            37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  YY1 MUTATED     1   1   2   4
  YY1 WILD-TYPE  21  91 171  93
D233V4, multiclass
    clus
vv   YY1 MUTATED YY1 WILD-TYPE
  T1           1            21
  T2           1            91
  T3           2           171
  T4           4            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
  YY1 MUTATED     3   2   1   1
  YY1 WILD-TYPE 115 102  76  76
D233V5, multiclass
    clus
vv   YY1 MUTATED YY1 WILD-TYPE
  N0           3           115
  N1           2           102
  N2           1            76
  N3           1            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"
D233V6, binary
               cls
clus              0   1
  YY1 MUTATED     8   0
  YY1 WILD-TYPE 338  29
[1] "tbl2"
               cls
clus            [,1] [,2]
  YY1 MUTATED      8    0
  YY1 WILD-TYPE  338   29
   clus
vv  YY1 MUTATED YY1 WILD-TYPE
  0           8           338
  1           0            29
[1] 2 2
[1] FALSE
D233V7, binary
               cls
clus              0   1
  YY1 MUTATED     5   3
  YY1 WILD-TYPE 140 245
[1] "tbl2"
               cls
clus            [,1] [,2]
  YY1 MUTATED      5    3
  YY1 WILD-TYPE  140  245
        clus
vv       YY1 MUTATED YY1 WILD-TYPE
  FEMALE           5           140
  MALE             3           245
[1] 2 2
[1] FALSE
D233V8, binary
               cls
clus              0   1
  YY1 MUTATED     4   2
  YY1 WILD-TYPE 288  57
[1] "tbl2"
               cls
clus            [,1] [,2]
  YY1 MUTATED      4    2
  YY1 WILD-TYPE  288   57
     clus
vv    YY1 MUTATED YY1 WILD-TYPE
  NO            4           288
  YES           2            57
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  YY1 MUTATED                                          0
  YY1 WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  YY1 MUTATED                                       2
  YY1 WILD-TYPE                                    68
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  YY1 MUTATED                                                        5
  YY1 WILD-TYPE                                                    153
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  YY1 MUTATED                                                   1
  YY1 WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  YY1 MUTATED                                                                   0
  YY1 WILD-TYPE                                                                68
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  YY1 MUTATED                                                    0
  YY1 WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  YY1 MUTATED                                                  0
  YY1 WILD-TYPE                                               61
D233V9, multiclass
                                                                   clus
vv                                                                  YY1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            0
                                                                   clus
vv                                                                  YY1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  YY1 MUTATED     6   0   0   2
  YY1 WILD-TYPE 305  14  15  22
D233V10, multiclass
    clus
vv   YY1 MUTATED YY1 WILD-TYPE
  R0           6           305
  R1           0            14
  R2           0            15
  RX           2            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  YY1 MUTATED       1                         0
  YY1 WILD-TYPE    86                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  YY1 MUTATED                                           0     7
  YY1 WILD-TYPE                                         1   236
D233V12, multiclass
                                           clus
vv                                          YY1 MUTATED YY1 WILD-TYPE
  ASIAN                                               1            86
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               7           236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V13, binary
               cls
clus              0   1
  YY1 MUTATED     0   7
  YY1 WILD-TYPE   4 303
[1] "tbl2"
               cls
clus            [,1] [,2]
  YY1 MUTATED      0    7
  YY1 WILD-TYPE    4  303
                        clus
vv                       YY1 MUTATED YY1 WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           7           303
[1] 2 2
[1] FALSE

Clustering(234) Variable = CUL2 MUTATION ANALYSIS
D234V1, survival
                sevent
clus2              0   1
  CUL2 MUTATED     6   2
  CUL2 WILD-TYPE 224 137
  CUL2 MUTATED CUL2 WILD-TYPE 
             8            361 
  CUL2 MUTATED CUL2 WILD-TYPE 
             2            137 
$`CUL2 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8081 TCGA-HU-8602 TCGA-HU-A4GQ 
        6.97        34.68        44.94        32.25        22.32         0.10 
TCGA-HU-A4GX TCGA-SW-A7EA 
       20.25        19.04 

$`CUL2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  CUL2 MUTATED CUL2 WILD-TYPE 
           0.1            0.0 
  CUL2 MUTATED CUL2 WILD-TYPE 
         44.94         122.30 
  CUL2 MUTATED CUL2 WILD-TYPE 
        21.285         14.070 
[1] "0.1 - 44.9 (21.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D234V2, 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       2       15       38       30        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CUL2 MUTATED           0          1          0          2        0
  CUL2 WILD-TYPE         3         69         53         30       38
D234V3, multiclass
            clus
vv           CUL2 MUTATED CUL2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CUL2 MUTATED     0   2   3   4
  CUL2 WILD-TYPE  22  90 170  93
D234V4, multiclass
    clus
vv   CUL2 MUTATED CUL2 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            3            170
  T4            4             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
  CUL2 MUTATED     6   1   2   0
  CUL2 WILD-TYPE 112 103  75  77
D234V5, multiclass
    clus
vv   CUL2 MUTATED CUL2 WILD-TYPE
  N0            6            112
  N1            1            103
  N2            2             75
  N3            0             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"
D234V6, binary
                cls
clus               0   1
  CUL2 MUTATED     8   0
  CUL2 WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED      8    0
  CUL2 WILD-TYPE  338   29
   clus
vv  CUL2 MUTATED CUL2 WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D234V7, binary
                cls
clus               0   1
  CUL2 MUTATED     7   2
  CUL2 WILD-TYPE 138 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED      7    2
  CUL2 WILD-TYPE  138  246
        clus
vv       CUL2 MUTATED CUL2 WILD-TYPE
  FEMALE            7            138
  MALE              2            246
[1] 2 2
[1] FALSE
D234V8, binary
                cls
clus               0   1
  CUL2 MUTATED     9   0
  CUL2 WILD-TYPE 283  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED      9    0
  CUL2 WILD-TYPE  283   59
     clus
vv    CUL2 MUTATED CUL2 WILD-TYPE
  NO             9            283
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CUL2 MUTATED                                          0
  CUL2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CUL2 MUTATED                                       3
  CUL2 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CUL2 MUTATED                                                        5
  CUL2 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CUL2 MUTATED                                                   0
  CUL2 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CUL2 MUTATED                                                                   0
  CUL2 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CUL2 MUTATED                                                    0
  CUL2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CUL2 MUTATED                                                  1
  CUL2 WILD-TYPE                                               60
D234V9, multiclass
                                                                   clus
vv                                                                  CUL2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  CUL2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CUL2 MUTATED     8   0   0   1
  CUL2 WILD-TYPE 303  14  15  23
D234V10, multiclass
    clus
vv   CUL2 MUTATED CUL2 WILD-TYPE
  R0            8            303
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CUL2 MUTATED       3                         0
  CUL2 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CUL2 MUTATED                                           0     6
  CUL2 WILD-TYPE                                         1   237
D234V12, multiclass
                                           clus
vv                                          CUL2 MUTATED CUL2 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V13, binary
                cls
clus               0   1
  CUL2 MUTATED     0   9
  CUL2 WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED      0    9
  CUL2 WILD-TYPE    4  301
                        clus
vv                       CUL2 MUTATED CUL2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(235) Variable = DAO MUTATION ANALYSIS
D235V1, survival
               sevent
clus2             0   1
  DAO MUTATED     8   3
  DAO WILD-TYPE 222 136
  DAO MUTATED DAO WILD-TYPE 
           11           358 
  DAO MUTATED DAO WILD-TYPE 
            3           136 
$`DAO MUTATED`
TCGA-CG-4460 TCGA-BR-6563 TCGA-BR-6706 TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-A4PE 
       21.99        39.12        18.05        25.05        31.96        20.42 
TCGA-CG-4466 TCGA-F1-A448 TCGA-HU-A4G9 TCGA-HU-A4GX TCGA-HU-A4H6 
       18.97        21.27        24.20        20.25        21.17 

$`DAO WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68        19.33        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-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-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-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-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-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-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-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-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 

  DAO MUTATED DAO WILD-TYPE 
        18.05          0.00 
  DAO MUTATED DAO WILD-TYPE 
        39.12        122.30 
  DAO MUTATED DAO WILD-TYPE 
       21.270        14.025 
[1] "18.1 - 39.1 (21.3)" "0.0 - 122.3 (14.0)"
[1] "hr=" "2"  
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       1       14       37       30        37        50
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DAO MUTATED           0          2          1          2        2
  DAO WILD-TYPE         3         68         52         30       36
D235V3, multiclass
            clus
vv           DAO MUTATED DAO WILD-TYPE
  STAGE I              1             1
  STAGE IA             1            14
  STAGE IB             3            37
  STAGE II             0            30
  STAGE IIA            0            37
  STAGE IIB            2            50
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           1            52
  STAGE IIIC           2            30
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  DAO MUTATED     2   3   4   5
  DAO WILD-TYPE  20  89 169  92
D235V4, multiclass
    clus
vv   DAO MUTATED DAO WILD-TYPE
  T1           2            20
  T2           3            89
  T3           4           169
  T4           5            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
  DAO MUTATED     5   4   3   2
  DAO WILD-TYPE 113 100  74  75
D235V5, multiclass
    clus
vv   DAO MUTATED DAO WILD-TYPE
  N0           5           113
  N1           4           100
  N2           3            74
  N3           2            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"
D235V6, binary
               cls
clus              0   1
  DAO MUTATED    11   2
  DAO WILD-TYPE 335  27
[1] "tbl2"
               cls
clus            [,1] [,2]
  DAO MUTATED     11    2
  DAO WILD-TYPE  335   27
   clus
vv  DAO MUTATED DAO WILD-TYPE
  0          11           335
  1           2            27
[1] 2 2
[1] FALSE
D235V7, binary
               cls
clus              0   1
  DAO MUTATED     7   7
  DAO WILD-TYPE 138 241
[1] "tbl2"
               cls
clus            [,1] [,2]
  DAO MUTATED      7    7
  DAO WILD-TYPE  138  241
        clus
vv       DAO MUTATED DAO WILD-TYPE
  FEMALE           7           138
  MALE             7           241
[1] 2 2
[1] FALSE
D235V8, binary
               cls
clus              0   1
  DAO MUTATED    12   1
  DAO WILD-TYPE 280  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  DAO MUTATED     12    1
  DAO WILD-TYPE  280   58
     clus
vv    DAO MUTATED DAO WILD-TYPE
  NO           12           280
  YES           1            58
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DAO MUTATED                                          0
  DAO WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DAO MUTATED                                       1
  DAO WILD-TYPE                                    69
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DAO MUTATED                                                        5
  DAO WILD-TYPE                                                    153
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DAO MUTATED                                                   1
  DAO WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DAO MUTATED                                                                   4
  DAO WILD-TYPE                                                                64
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DAO MUTATED                                                    0
  DAO WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DAO MUTATED                                                  3
  DAO WILD-TYPE                                               58
D235V9, multiclass
                                                                   clus
vv                                                                  DAO MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            3
                                                                   clus
vv                                                                  DAO WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  DAO MUTATED    13   0   1   0
  DAO WILD-TYPE 298  14  14  24
D235V10, multiclass
    clus
vv   DAO MUTATED DAO WILD-TYPE
  R0          13           298
  R1           0            14
  R2           1            14
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  DAO MUTATED       4                         1
  DAO WILD-TYPE    83                         8
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DAO MUTATED                                           0     6
  DAO WILD-TYPE                                         1   237
D235V12, multiclass
                                           clus
vv                                          DAO MUTATED DAO WILD-TYPE
  ASIAN                                               4            83
  BLACK OR AFRICAN AMERICAN                           1             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               6           237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V13, binary
               cls
clus              0   1
  DAO MUTATED     1  10
  DAO WILD-TYPE   3 300
[1] "tbl2"
               cls
clus            [,1] [,2]
  DAO MUTATED      1   10
  DAO WILD-TYPE    3  300
                        clus
vv                       DAO MUTATED DAO WILD-TYPE
  HISPANIC OR LATINO               1             3
  NOT HISPANIC OR LATINO          10           300
[1] 2 2
[1] FALSE

Clustering(236) Variable = TRUB1 MUTATION ANALYSIS
D236V1, survival
                 sevent
clus2               0   1
  TRUB1 MUTATED     8   2
  TRUB1 WILD-TYPE 222 137
  TRUB1 MUTATED TRUB1 WILD-TYPE 
             10             359 
  TRUB1 MUTATED TRUB1 WILD-TYPE 
              2             137 
$`TRUB1 MUTATED`
TCGA-BR-4256 TCGA-BR-6802 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 
        9.34        30.90        31.27         1.12        28.14        31.96 
TCGA-CD-8536 TCGA-CG-5721 TCGA-F1-6874 TCGA-IN-7808 
       12.43         6.02        14.47         3.45 

$`TRUB1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  TRUB1 MUTATED TRUB1 WILD-TYPE 
           1.12            0.00 
  TRUB1 MUTATED TRUB1 WILD-TYPE 
          31.96          122.30 
  TRUB1 MUTATED TRUB1 WILD-TYPE 
          13.45           14.27 
[1] "1.1 - 32.0 (13.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.8"
D236V2, 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       2       15       39       29        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRUB1 MUTATED           0          1          0          2        2
  TRUB1 WILD-TYPE         3         69         53         30       36
D236V3, multiclass
            clus
vv           TRUB1 MUTATED TRUB1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRUB1 MUTATED     0   1   5   4
  TRUB1 WILD-TYPE  22  91 168  93
D236V4, multiclass
    clus
vv   TRUB1 MUTATED TRUB1 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             5             168
  T4             4              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
  TRUB1 MUTATED     3   2   2   3
  TRUB1 WILD-TYPE 115 102  75  74
D236V5, multiclass
    clus
vv   TRUB1 MUTATED TRUB1 WILD-TYPE
  N0             3             115
  N1             2             102
  N2             2              75
  N3             3              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"
D236V6, binary
                 cls
clus                0   1
  TRUB1 MUTATED     8   2
  TRUB1 WILD-TYPE 338  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRUB1 MUTATED      8    2
  TRUB1 WILD-TYPE  338   27
   clus
vv  TRUB1 MUTATED TRUB1 WILD-TYPE
  0             8             338
  1             2              27
[1] 2 2
[1] FALSE
D236V7, binary
                 cls
clus                0   1
  TRUB1 MUTATED     1  10
  TRUB1 WILD-TYPE 144 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRUB1 MUTATED      1   10
  TRUB1 WILD-TYPE  144  238
        clus
vv       TRUB1 MUTATED TRUB1 WILD-TYPE
  FEMALE             1             144
  MALE              10             238
[1] 2 2
[1] FALSE
D236V8, binary
                 cls
clus                0   1
  TRUB1 MUTATED    10   0
  TRUB1 WILD-TYPE 282  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRUB1 MUTATED     10    0
  TRUB1 WILD-TYPE  282   59
     clus
vv    TRUB1 MUTATED TRUB1 WILD-TYPE
  NO             10             282
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TRUB1 MUTATED                                          0
  TRUB1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TRUB1 MUTATED                                       1
  TRUB1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRUB1 MUTATED                                                        7
  TRUB1 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TRUB1 MUTATED                                                   0
  TRUB1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRUB1 MUTATED                                                                   2
  TRUB1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TRUB1 MUTATED                                                    0
  TRUB1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TRUB1 MUTATED                                                  1
  TRUB1 WILD-TYPE                                               60
D236V9, multiclass
                                                                   clus
vv                                                                  TRUB1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  TRUB1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRUB1 MUTATED     8   0   0   2
  TRUB1 WILD-TYPE 303  14  15  22
D236V10, multiclass
    clus
vv   TRUB1 MUTATED TRUB1 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TRUB1 MUTATED       2                         0
  TRUB1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRUB1 MUTATED                                           0     8
  TRUB1 WILD-TYPE                                         1   235
D236V12, multiclass
                                           clus
vv                                          TRUB1 MUTATED TRUB1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V13, binary
                 cls
clus                0   1
  TRUB1 MUTATED     0  10
  TRUB1 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRUB1 MUTATED      0   10
  TRUB1 WILD-TYPE    4  300
                        clus
vv                       TRUB1 MUTATED TRUB1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(237) Variable = PKN2 MUTATION ANALYSIS
D237V1, survival
                sevent
clus2              0   1
  PKN2 MUTATED    11   4
  PKN2 WILD-TYPE 219 135
  PKN2 MUTATED PKN2 WILD-TYPE 
            15            354 
  PKN2 MUTATED PKN2 WILD-TYPE 
             4            135 
$`PKN2 MUTATED`
TCGA-BR-4280 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8680 
        6.61        11.44         9.60        32.25         4.31        31.96 
TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-5728 TCGA-D7-6524 TCGA-HU-A4G8 TCGA-HU-A4GU 
       16.14        15.95        65.10        17.85        22.68         6.58 
TCGA-HU-A4H8 TCGA-R5-A7ZI TCGA-SW-A7EA 
       14.07        74.53        19.04 

$`PKN2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8077 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       14.43         0.69        29.59         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-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-D7-6525 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-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-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-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 

  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          14.12 
[1] "4.3 - 74.5 (16.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D237V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PKN2 MUTATED         0        0        4        2         0         4
  PKN2 WILD-TYPE       2       15       36       28        37        48
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PKN2 MUTATED           1          0          1          1        2
  PKN2 WILD-TYPE         2         70         52         31       36
D237V3, multiclass
            clus
vv           PKN2 MUTATED PKN2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              4             36
  STAGE II              2             28
  STAGE IIA             0             37
  STAGE IIB             4             48
  STAGE III             1              2
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PKN2 MUTATED     1   7   3   4
  PKN2 WILD-TYPE  21  85 170  93
D237V4, multiclass
    clus
vv   PKN2 MUTATED PKN2 WILD-TYPE
  T1            1             21
  T2            7             85
  T3            3            170
  T4            4             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
  PKN2 MUTATED     4   7   2   2
  PKN2 WILD-TYPE 114  97  75  75
D237V5, multiclass
    clus
vv   PKN2 MUTATED PKN2 WILD-TYPE
  N0            4            114
  N1            7             97
  N2            2             75
  N3            2             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"
D237V6, binary
                cls
clus               0   1
  PKN2 MUTATED    14   2
  PKN2 WILD-TYPE 332  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN2 MUTATED     14    2
  PKN2 WILD-TYPE  332   27
   clus
vv  PKN2 MUTATED PKN2 WILD-TYPE
  0           14            332
  1            2             27
[1] 2 2
[1] FALSE
D237V7, binary
                cls
clus               0   1
  PKN2 MUTATED    11   5
  PKN2 WILD-TYPE 134 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN2 MUTATED     11    5
  PKN2 WILD-TYPE  134  243
        clus
vv       PKN2 MUTATED PKN2 WILD-TYPE
  FEMALE           11            134
  MALE              5            243
[1] 2 2
[1] FALSE
D237V8, binary
                cls
clus               0   1
  PKN2 MUTATED    14   0
  PKN2 WILD-TYPE 278  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN2 MUTATED     14    0
  PKN2 WILD-TYPE  278   59
     clus
vv    PKN2 MUTATED PKN2 WILD-TYPE
  NO            14            278
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PKN2 MUTATED                                          0
  PKN2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PKN2 MUTATED                                       5
  PKN2 WILD-TYPE                                    65
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PKN2 MUTATED                                                        7
  PKN2 WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PKN2 MUTATED                                                   1
  PKN2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PKN2 MUTATED                                                                   1
  PKN2 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PKN2 MUTATED                                                    0
  PKN2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PKN2 MUTATED                                                  2
  PKN2 WILD-TYPE                                               59
D237V9, multiclass
                                                                   clus
vv                                                                  PKN2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  PKN2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PKN2 MUTATED    12   1   0   2
  PKN2 WILD-TYPE 299  13  15  22
D237V10, multiclass
    clus
vv   PKN2 MUTATED PKN2 WILD-TYPE
  R0           12            299
  R1            1             13
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PKN2 MUTATED       4                         0
  PKN2 WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PKN2 MUTATED                                           0    10
  PKN2 WILD-TYPE                                         1   233
D237V12, multiclass
                                           clus
vv                                          PKN2 MUTATED PKN2 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V13, binary
                cls
clus               0   1
  PKN2 MUTATED     1  13
  PKN2 WILD-TYPE   3 297
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN2 MUTATED      1   13
  PKN2 WILD-TYPE    3  297
                        clus
vv                       PKN2 MUTATED PKN2 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           13            297
[1] 2 2
[1] FALSE

Clustering(238) Variable = KLHDC5 MUTATION ANALYSIS
D238V1, survival
                  sevent
clus2                0   1
  KLHDC5 MUTATED     5   3
  KLHDC5 WILD-TYPE 225 136
  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
               8              361 
  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
               3              136 
$`KLHDC5 MUTATED`
TCGA-BR-4201 TCGA-BR-7707 TCGA-BR-8078 TCGA-CD-A4MG TCGA-CG-5723 TCGA-CG-5728 
       30.90        35.84        29.59         6.58       105.07        65.10 
TCGA-HF-A5NB TCGA-IN-A6RL 
       30.51        13.35 

$`KLHDC5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
            6.58             0.00 
  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
          105.07           122.30 
  KLHDC5 MUTATED KLHDC5 WILD-TYPE 
          30.705           14.070 
[1] "6.6 - 105.1 (30.7)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D238V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLHDC5 MUTATED         1        0        2        1         1         1
  KLHDC5 WILD-TYPE       1       15       38       29        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLHDC5 MUTATED           0          1          0          1        0
  KLHDC5 WILD-TYPE         3         69         53         31       38
D238V3, multiclass
            clus
vv           KLHDC5 MUTATED KLHDC5 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KLHDC5 MUTATED     2   5   1   2
  KLHDC5 WILD-TYPE  20  87 172  95
D238V4, multiclass
    clus
vv   KLHDC5 MUTATED KLHDC5 WILD-TYPE
  T1              2               20
  T2              5               87
  T3              1              172
  T4              2               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
  KLHDC5 MUTATED     4   3   0   1
  KLHDC5 WILD-TYPE 114 101  77  76
D238V5, multiclass
    clus
vv   KLHDC5 MUTATED KLHDC5 WILD-TYPE
  N0              4              114
  N1              3              101
  N2              0               77
  N3              1               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"
D238V6, binary
                  cls
clus                 0   1
  KLHDC5 MUTATED     9   0
  KLHDC5 WILD-TYPE 337  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHDC5 MUTATED      9    0
  KLHDC5 WILD-TYPE  337   29
   clus
vv  KLHDC5 MUTATED KLHDC5 WILD-TYPE
  0              9              337
  1              0               29
[1] 2 2
[1] FALSE
D238V7, binary
                  cls
clus                 0   1
  KLHDC5 MUTATED     6   4
  KLHDC5 WILD-TYPE 139 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHDC5 MUTATED      6    4
  KLHDC5 WILD-TYPE  139  244
        clus
vv       KLHDC5 MUTATED KLHDC5 WILD-TYPE
  FEMALE              6              139
  MALE                4              244
[1] 2 2
[1] FALSE
D238V8, binary
                  cls
clus                 0   1
  KLHDC5 MUTATED     7   1
  KLHDC5 WILD-TYPE 285  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHDC5 MUTATED      7    1
  KLHDC5 WILD-TYPE  285   58
     clus
vv    KLHDC5 MUTATED KLHDC5 WILD-TYPE
  NO               7              285
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KLHDC5 MUTATED                                          0
  KLHDC5 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KLHDC5 MUTATED                                       1
  KLHDC5 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KLHDC5 MUTATED                                                        7
  KLHDC5 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KLHDC5 MUTATED                                                   1
  KLHDC5 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KLHDC5 MUTATED                                                                   1
  KLHDC5 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KLHDC5 MUTATED                                                    0
  KLHDC5 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KLHDC5 MUTATED                                                  0
  KLHDC5 WILD-TYPE                                               61
D238V9, multiclass
                                                                   clus
vv                                                                  KLHDC5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  KLHDC5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KLHDC5 MUTATED     6   1   0   2
  KLHDC5 WILD-TYPE 305  13  15  22
D238V10, multiclass
    clus
vv   KLHDC5 MUTATED KLHDC5 WILD-TYPE
  R0              6              305
  R1              1               13
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KLHDC5 MUTATED       1                         1
  KLHDC5 WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLHDC5 MUTATED                                           0     5
  KLHDC5 WILD-TYPE                                         1   238
D238V12, multiclass
                                           clus
vv                                          KLHDC5 MUTATED KLHDC5 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V13, binary
                  cls
clus                 0   1
  KLHDC5 MUTATED     0   7
  KLHDC5 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHDC5 MUTATED      0    7
  KLHDC5 WILD-TYPE    4  303
                        clus
vv                       KLHDC5 MUTATED KLHDC5 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(239) Variable = TFE3 MUTATION ANALYSIS
D239V1, survival
                sevent
clus2              0   1
  TFE3 MUTATED     5   3
  TFE3 WILD-TYPE 225 136
  TFE3 MUTATED TFE3 WILD-TYPE 
             8            361 
  TFE3 MUTATED TFE3 WILD-TYPE 
             3            136 
$`TFE3 MUTATED`
TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8487 TCGA-BR-A4CS TCGA-BR-A4QL TCGA-CD-A4MG 
       32.78        44.94         1.12         1.48        16.14         6.58 
TCGA-HU-A4G8 TCGA-HU-A4GU 
       22.68         6.58 

$`TFE3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  TFE3 MUTATED TFE3 WILD-TYPE 
          1.12           0.00 
  TFE3 MUTATED TFE3 WILD-TYPE 
         44.94         122.30 
  TFE3 MUTATED TFE3 WILD-TYPE 
         11.36          14.27 
[1] "1.1 - 44.9 (11.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D239V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TFE3 MUTATED         0        0        0        0         4         2
  TFE3 WILD-TYPE       2       15       40       30        33        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TFE3 MUTATED           0          0          1          1        0
  TFE3 WILD-TYPE         3         70         52         31       38
D239V3, multiclass
            clus
vv           TFE3 MUTATED TFE3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             4             33
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TFE3 MUTATED     1   0   7   1
  TFE3 WILD-TYPE  21  92 166  96
D239V4, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  T1            1             21
  T2            0             92
  T3            7            166
  T4            1             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
  TFE3 MUTATED     4   2   0   2
  TFE3 WILD-TYPE 114 102  77  75
D239V5, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  N0            4            114
  N1            2            102
  N2            0             77
  N3            2             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"
D239V6, binary
                cls
clus               0   1
  TFE3 MUTATED     9   0
  TFE3 WILD-TYPE 337  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      9    0
  TFE3 WILD-TYPE  337   29
   clus
vv  TFE3 MUTATED TFE3 WILD-TYPE
  0            9            337
  1            0             29
[1] 2 2
[1] FALSE
D239V7, binary
                cls
clus               0   1
  TFE3 MUTATED     6   3
  TFE3 WILD-TYPE 139 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      6    3
  TFE3 WILD-TYPE  139  245
        clus
vv       TFE3 MUTATED TFE3 WILD-TYPE
  FEMALE            6            139
  MALE              3            245
[1] 2 2
[1] FALSE
D239V8, binary
                cls
clus               0   1
  TFE3 MUTATED     8   0
  TFE3 WILD-TYPE 284  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      8    0
  TFE3 WILD-TYPE  284   59
     clus
vv    TFE3 MUTATED TFE3 WILD-TYPE
  NO             8            284
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TFE3 MUTATED                                          0
  TFE3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TFE3 MUTATED                                       3
  TFE3 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TFE3 MUTATED                                                        6
  TFE3 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TFE3 MUTATED                                                   0
  TFE3 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TFE3 MUTATED                                                                   0
  TFE3 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TFE3 MUTATED                                                    0
  TFE3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TFE3 MUTATED                                                  0
  TFE3 WILD-TYPE                                               61
D239V9, multiclass
                                                                   clus
vv                                                                  TFE3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  TFE3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TFE3 MUTATED     6   0   0   1
  TFE3 WILD-TYPE 305  14  15  23
D239V10, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  R0            6            305
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TFE3 MUTATED       3                         0
  TFE3 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TFE3 MUTATED                                           0     6
  TFE3 WILD-TYPE                                         1   237
D239V12, multiclass
                                           clus
vv                                          TFE3 MUTATED TFE3 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V13, binary
                cls
clus               0   1
  TFE3 MUTATED     0   9
  TFE3 WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      0    9
  TFE3 WILD-TYPE    4  301
                        clus
vv                       TFE3 MUTATED TFE3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(240) Variable = GCC2 MUTATION ANALYSIS
D240V1, survival
                sevent
clus2              0   1
  GCC2 MUTATED     6   6
  GCC2 WILD-TYPE 224 133
  GCC2 MUTATED GCC2 WILD-TYPE 
            12            357 
  GCC2 MUTATED GCC2 WILD-TYPE 
             6            133 
$`GCC2 MUTATED`
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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
       12.03        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-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-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 

  GCC2 MUTATED GCC2 WILD-TYPE 
          6.02           0.00 
  GCC2 MUTATED GCC2 WILD-TYPE 
         38.14         122.30 
  GCC2 MUTATED GCC2 WILD-TYPE 
        25.875         14.040 
[1] "6.0 - 38.1 (25.9)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1"  
D240V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GCC2 MUTATED         0        0        1        0         0         1
  GCC2 WILD-TYPE       2       15       39       30        37        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GCC2 MUTATED           0          3          1          2        2
  GCC2 WILD-TYPE         3         67         52         30       36
D240V3, multiclass
            clus
vv           GCC2 MUTATED GCC2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            1             52
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GCC2 MUTATED     0   3   2   7
  GCC2 WILD-TYPE  22  89 171  90
D240V4, multiclass
    clus
vv   GCC2 MUTATED GCC2 WILD-TYPE
  T1            0             22
  T2            3             89
  T3            2            171
  T4            7             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
  GCC2 MUTATED     2   4   3   2
  GCC2 WILD-TYPE 116 100  74  75
D240V5, multiclass
    clus
vv   GCC2 MUTATED GCC2 WILD-TYPE
  N0            2            116
  N1            4            100
  N2            3             74
  N3            2             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"
D240V6, binary
                cls
clus               0   1
  GCC2 MUTATED    12   1
  GCC2 WILD-TYPE 334  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED     12    1
  GCC2 WILD-TYPE  334   28
   clus
vv  GCC2 MUTATED GCC2 WILD-TYPE
  0           12            334
  1            1             28
[1] 2 2
[1] FALSE
D240V7, binary
                cls
clus               0   1
  GCC2 MUTATED     8   6
  GCC2 WILD-TYPE 137 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED      8    6
  GCC2 WILD-TYPE  137  242
        clus
vv       GCC2 MUTATED GCC2 WILD-TYPE
  FEMALE            8            137
  MALE              6            242
[1] 2 2
[1] FALSE
D240V8, binary
                cls
clus               0   1
  GCC2 MUTATED    10   1
  GCC2 WILD-TYPE 282  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED     10    1
  GCC2 WILD-TYPE  282   58
     clus
vv    GCC2 MUTATED GCC2 WILD-TYPE
  NO            10            282
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GCC2 MUTATED                                          0
  GCC2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GCC2 MUTATED                                       2
  GCC2 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GCC2 MUTATED                                                        7
  GCC2 WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GCC2 MUTATED                                                   1
  GCC2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GCC2 MUTATED                                                                   3
  GCC2 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GCC2 MUTATED                                                    0
  GCC2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GCC2 MUTATED                                                  1
  GCC2 WILD-TYPE                                               60
D240V9, multiclass
                                                                   clus
vv                                                                  GCC2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  GCC2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GCC2 MUTATED    10   0   0   4
  GCC2 WILD-TYPE 301  14  15  20
D240V10, multiclass
    clus
vv   GCC2 MUTATED GCC2 WILD-TYPE
  R0           10            301
  R1            0             14
  R2            0             15
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GCC2 MUTATED       2                         0
  GCC2 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GCC2 MUTATED                                           0     9
  GCC2 WILD-TYPE                                         1   234
D240V12, multiclass
                                           clus
vv                                          GCC2 MUTATED GCC2 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V13, binary
                cls
clus               0   1
  GCC2 MUTATED     0  10
  GCC2 WILD-TYPE   4 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCC2 MUTATED      0   10
  GCC2 WILD-TYPE    4  300
                        clus
vv                       GCC2 MUTATED GCC2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           10            300
[1] 2 2
[1] FALSE

Clustering(241) Variable = ARAF MUTATION ANALYSIS
D241V1, survival
                sevent
clus2              0   1
  ARAF MUTATED     7   2
  ARAF WILD-TYPE 223 137
  ARAF MUTATED ARAF WILD-TYPE 
             9            360 
  ARAF MUTATED ARAF WILD-TYPE 
             2            137 
$`ARAF MUTATED`
TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-A4YV 
       34.68         6.18         1.12         6.58         6.02         5.92 
TCGA-KB-A6F7 TCGA-MX-A5UJ TCGA-SW-A7EA 
       63.62        19.73        19.04 

$`ARAF WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        5.56        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 

  ARAF MUTATED ARAF WILD-TYPE 
          1.12           0.00 
  ARAF MUTATED ARAF WILD-TYPE 
         63.62         122.30 
  ARAF MUTATED ARAF WILD-TYPE 
          6.58          14.35 
[1] "1.1 - 63.6 (6.6)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D241V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARAF MUTATED         0        0        3        0         5         1
  ARAF WILD-TYPE       2       15       37       30        32        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARAF MUTATED           0          1          0          0        1
  ARAF WILD-TYPE         3         69         53         32       37
D241V3, multiclass
            clus
vv           ARAF MUTATED ARAF WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              3             37
  STAGE II              0             30
  STAGE IIA             5             32
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ARAF MUTATED     1   2   7   1
  ARAF WILD-TYPE  21  90 166  96
D241V4, multiclass
    clus
vv   ARAF MUTATED ARAF WILD-TYPE
  T1            1             21
  T2            2             90
  T3            7            166
  T4            1             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
  ARAF MUTATED     7   4   1   0
  ARAF WILD-TYPE 111 100  76  77
D241V5, multiclass
    clus
vv   ARAF MUTATED ARAF WILD-TYPE
  N0            7            111
  N1            4            100
  N2            1             76
  N3            0             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"
D241V6, binary
                cls
clus               0   1
  ARAF MUTATED    12   0
  ARAF WILD-TYPE 334  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED     12    0
  ARAF WILD-TYPE  334   29
   clus
vv  ARAF MUTATED ARAF WILD-TYPE
  0           12            334
  1            0             29
[1] 2 2
[1] FALSE
D241V7, binary
                cls
clus               0   1
  ARAF MUTATED     7   5
  ARAF WILD-TYPE 138 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED      7    5
  ARAF WILD-TYPE  138  243
        clus
vv       ARAF MUTATED ARAF WILD-TYPE
  FEMALE            7            138
  MALE              5            243
[1] 2 2
[1] FALSE
D241V8, binary
                cls
clus               0   1
  ARAF MUTATED     8   1
  ARAF WILD-TYPE 284  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED      8    1
  ARAF WILD-TYPE  284   58
     clus
vv    ARAF MUTATED ARAF WILD-TYPE
  NO             8            284
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARAF MUTATED                                          0
  ARAF WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARAF MUTATED                                       2
  ARAF WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARAF MUTATED                                                        4
  ARAF WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARAF MUTATED                                                   0
  ARAF WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARAF MUTATED                                                                   4
  ARAF WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARAF MUTATED                                                    0
  ARAF WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARAF MUTATED                                                  2
  ARAF WILD-TYPE                                               59
D241V9, multiclass
                                                                   clus
vv                                                                  ARAF MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  ARAF WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ARAF MUTATED    10   0   0   1
  ARAF WILD-TYPE 301  14  15  23
D241V10, multiclass
    clus
vv   ARAF MUTATED ARAF WILD-TYPE
  R0           10            301
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ARAF MUTATED       1                         0
  ARAF WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARAF MUTATED                                           0     8
  ARAF WILD-TYPE                                         1   235
D241V12, multiclass
                                           clus
vv                                          ARAF MUTATED ARAF WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V13, binary
                cls
clus               0   1
  ARAF MUTATED     0   9
  ARAF WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED      0    9
  ARAF WILD-TYPE    4  301
                        clus
vv                       ARAF MUTATED ARAF WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(242) Variable = CDKN2A MUTATION ANALYSIS
D242V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED     9   4
  CDKN2A WILD-TYPE 221 135
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              13              356 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               4              135 
$`CDKN2A MUTATED`
TCGA-MX-A663 TCGA-BR-8487 TCGA-CD-5799 TCGA-CD-A489 TCGA-FP-8099 TCGA-HU-A4G8 
        9.86         1.12        13.02        11.31        17.06        22.68 
TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-IN-A7NT TCGA-R5-A7O7 TCGA-VQ-A91V TCGA-VQ-AA64 
       20.25        14.07        10.62        45.67        42.64        18.41 
TCGA-VQ-AA6I 
       16.14 

$`CDKN2A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15        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-5800 
        1.15        21.44        16.14         5.13        13.41        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-8209 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        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-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-A7NU 
       19.53         6.44         6.74        12.59         6.51        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-A92D TCGA-VQ-A94T TCGA-VQ-AA68 
       15.65        20.81         1.71        66.81        11.24        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J 
       28.41        38.93        32.94        54.12        26.04        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            1.12             0.00 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           45.67           122.30 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           16.14            14.22 
[1] "1.1 - 45.7 (16.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D242V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDKN2A MUTATED         0        0        1        1         4         2
  CDKN2A WILD-TYPE       2       15       39       29        33        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDKN2A MUTATED           0          2          2          1        1
  CDKN2A WILD-TYPE         3         68         51         31       37
D242V3, multiclass
            clus
vv           CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               4               33
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              2               51
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CDKN2A MUTATED     1   1  11   1
  CDKN2A WILD-TYPE  21  91 162  96
D242V4, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  T1              1               21
  T2              1               91
  T3             11              162
  T4              1               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
  CDKN2A MUTATED     4   6   3   1
  CDKN2A WILD-TYPE 114  98  74  76
D242V5, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0              4              114
  N1              6               98
  N2              3               74
  N3              1               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"
D242V6, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    14   1
  CDKN2A WILD-TYPE 332  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     14    1
  CDKN2A WILD-TYPE  332   28
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             14              332
  1              1               28
[1] 2 2
[1] FALSE
D242V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     5  11
  CDKN2A WILD-TYPE 140 237
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      5   11
  CDKN2A WILD-TYPE  140  237
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              5              140
  MALE               11              237
[1] 2 2
[1] FALSE
D242V8, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    11   3
  CDKN2A WILD-TYPE 281  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     11    3
  CDKN2A WILD-TYPE  281   56
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              11              281
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CDKN2A MUTATED                                          0
  CDKN2A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CDKN2A MUTATED                                       3
  CDKN2A WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDKN2A MUTATED                                                        7
  CDKN2A WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CDKN2A MUTATED                                                   0
  CDKN2A WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDKN2A MUTATED                                                                   3
  CDKN2A WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CDKN2A MUTATED                                                    0
  CDKN2A WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CDKN2A MUTATED                                                  3
  CDKN2A WILD-TYPE                                               58
D242V9, multiclass
                                                                   clus
vv                                                                  CDKN2A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  CDKN2A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CDKN2A MUTATED     9   1   0   2
  CDKN2A WILD-TYPE 302  13  15  22
D242V10, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  R0              9              302
  R1              1               13
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CDKN2A MUTATED       5                         0
  CDKN2A WILD-TYPE    82                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDKN2A MUTATED                                           0     9
  CDKN2A WILD-TYPE                                         1   234
D242V12, multiclass
                                           clus
vv                                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V13, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     1  11
  CDKN2A WILD-TYPE   3 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      1   11
  CDKN2A WILD-TYPE    3  299
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(243) Variable = MDM2 MUTATION ANALYSIS
D243V1, survival
                sevent
clus2              0   1
  MDM2 MUTATED     3   4
  MDM2 WILD-TYPE 227 135
  MDM2 MUTATED MDM2 WILD-TYPE 
             7            362 
  MDM2 MUTATED MDM2 WILD-TYPE 
             4            135 
$`MDM2 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8365 TCGA-HJ-7597 TCGA-HU-A4GU 
       21.99         6.97        34.68        17.52        26.47         6.58 
TCGA-VQ-A8P2 
       38.14 

$`MDM2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-8366 TCGA-BR-8367 TCGA-BR-8368 
       31.10         0.26        22.19         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-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-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-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 

  MDM2 MUTATED MDM2 WILD-TYPE 
          6.58           0.00 
  MDM2 MUTATED MDM2 WILD-TYPE 
         38.14         122.30 
  MDM2 MUTATED MDM2 WILD-TYPE 
         21.99          14.12 
[1] "6.6 - 38.1 (22.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D243V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MDM2 MUTATED         0        0        1        0         2         1
  MDM2 WILD-TYPE       2       15       39       30        35        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MDM2 MUTATED           0          2          0          0        1
  MDM2 WILD-TYPE         3         68         53         32       37
D243V3, multiclass
            clus
vv           MDM2 MUTATED MDM2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MDM2 MUTATED     0   1   4   2
  MDM2 WILD-TYPE  22  91 169  95
D243V4, multiclass
    clus
vv   MDM2 MUTATED MDM2 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            4            169
  T4            2             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
  MDM2 MUTATED     3   4   0   0
  MDM2 WILD-TYPE 115 100  77  77
D243V5, multiclass
    clus
vv   MDM2 MUTATED MDM2 WILD-TYPE
  N0            3            115
  N1            4            100
  N2            0             77
  N3            0             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"
D243V6, binary
                cls
clus               0   1
  MDM2 MUTATED     4   1
  MDM2 WILD-TYPE 342  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      4    1
  MDM2 WILD-TYPE  342   28
   clus
vv  MDM2 MUTATED MDM2 WILD-TYPE
  0            4            342
  1            1             28
[1] 2 2
[1] FALSE
D243V7, binary
                cls
clus               0   1
  MDM2 MUTATED     4   3
  MDM2 WILD-TYPE 141 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      4    3
  MDM2 WILD-TYPE  141  245
        clus
vv       MDM2 MUTATED MDM2 WILD-TYPE
  FEMALE            4            141
  MALE              3            245
[1] 2 2
[1] FALSE
D243V8, binary
                cls
clus               0   1
  MDM2 MUTATED     6   1
  MDM2 WILD-TYPE 286  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      6    1
  MDM2 WILD-TYPE  286   58
     clus
vv    MDM2 MUTATED MDM2 WILD-TYPE
  NO             6            286
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MDM2 MUTATED                                          1
  MDM2 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MDM2 MUTATED                                       1
  MDM2 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MDM2 MUTATED                                                        3
  MDM2 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MDM2 MUTATED                                                   1
  MDM2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MDM2 MUTATED                                                                   1
  MDM2 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MDM2 MUTATED                                                    0
  MDM2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MDM2 MUTATED                                                  0
  MDM2 WILD-TYPE                                               61
D243V9, multiclass
                                                                   clus
vv                                                                  MDM2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  MDM2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MDM2 MUTATED     5   0   1   1
  MDM2 WILD-TYPE 306  14  14  23
D243V10, multiclass
    clus
vv   MDM2 MUTATED MDM2 WILD-TYPE
  R0            5            306
  R1            0             14
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MDM2 MUTATED       1                         0
  MDM2 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MDM2 MUTATED                                           0     5
  MDM2 WILD-TYPE                                         1   238
D243V12, multiclass
                                           clus
vv                                          MDM2 MUTATED MDM2 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V13, binary
                cls
clus               0   1
  MDM2 MUTATED     0   5
  MDM2 WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      0    5
  MDM2 WILD-TYPE    4  305
                        clus
vv                       MDM2 MUTATED MDM2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(244) Variable = C4ORF6 MUTATION ANALYSIS
D244V1, survival
                  sevent
clus2                0   1
  C4ORF6 MUTATED     8   1
  C4ORF6 WILD-TYPE 222 138
  C4ORF6 MUTATED C4ORF6 WILD-TYPE 
               9              360 
  C4ORF6 MUTATED C4ORF6 WILD-TYPE 
               1              138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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            14.22 
[1] "4.3 - 65.1 (19.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "4"  
D244V2, 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       1       15       37       30        36        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C4ORF6 MUTATED           0          3          0          0        2
  C4ORF6 WILD-TYPE         3         67         53         32       36
D244V3, multiclass
            clus
vv           C4ORF6 MUTATED C4ORF6 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  C4ORF6 MUTATED     1   3   3   5
  C4ORF6 WILD-TYPE  21  89 170  92
D244V4, multiclass
    clus
vv   C4ORF6 MUTATED C4ORF6 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              3              170
  T4              5               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
  C4ORF6 MUTATED     6   4   2   0
  C4ORF6 WILD-TYPE 112 100  75  77
D244V5, multiclass
    clus
vv   C4ORF6 MUTATED C4ORF6 WILD-TYPE
  N0              6              112
  N1              4              100
  N2              2               75
  N3              0               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"
D244V6, binary
                  cls
clus                 0   1
  C4ORF6 MUTATED     9   1
  C4ORF6 WILD-TYPE 337  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  C4ORF6 MUTATED      9    1
  C4ORF6 WILD-TYPE  337   28
   clus
vv  C4ORF6 MUTATED C4ORF6 WILD-TYPE
  0              9              337
  1              1               28
[1] 2 2
[1] FALSE
D244V7, binary
                  cls
clus                 0   1
  C4ORF6 MUTATED     4   8
  C4ORF6 WILD-TYPE 141 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  C4ORF6 MUTATED      4    8
  C4ORF6 WILD-TYPE  141  240
        clus
vv       C4ORF6 MUTATED C4ORF6 WILD-TYPE
  FEMALE              4              141
  MALE                8              240
[1] 2 2
[1] FALSE
D244V8, binary
                  cls
clus                 0   1
  C4ORF6 MUTATED     8   2
  C4ORF6 WILD-TYPE 284  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  C4ORF6 MUTATED      8    2
  C4ORF6 WILD-TYPE  284   57
     clus
vv    C4ORF6 MUTATED C4ORF6 WILD-TYPE
  NO               8              284
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C4ORF6 MUTATED                                          0
  C4ORF6 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C4ORF6 MUTATED                                       0
  C4ORF6 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C4ORF6 MUTATED                                                        5
  C4ORF6 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C4ORF6 MUTATED                                                   1
  C4ORF6 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C4ORF6 MUTATED                                                                   4
  C4ORF6 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C4ORF6 MUTATED                                                    0
  C4ORF6 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C4ORF6 MUTATED                                                  2
  C4ORF6 WILD-TYPE                                               59
D244V9, multiclass
                                                                   clus
vv                                                                  C4ORF6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  C4ORF6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  C4ORF6 MUTATED    11   0   0   1
  C4ORF6 WILD-TYPE 300  14  15  23
D244V10, multiclass
    clus
vv   C4ORF6 MUTATED C4ORF6 WILD-TYPE
  R0             11              300
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  C4ORF6 MUTATED       1                         2
  C4ORF6 WILD-TYPE    86                         7
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C4ORF6 MUTATED                                           0     6
  C4ORF6 WILD-TYPE                                         1   237
D244V12, multiclass
                                           clus
vv                                          C4ORF6 MUTATED C4ORF6 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              2                7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V13, binary
                  cls
clus                 0   1
  C4ORF6 MUTATED     0   8
  C4ORF6 WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  C4ORF6 MUTATED      0    8
  C4ORF6 WILD-TYPE    4  302
                        clus
vv                       C4ORF6 MUTATED C4ORF6 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(245) Variable = CASC3 MUTATION ANALYSIS
D245V1, survival
                 sevent
clus2               0   1
  CASC3 MUTATED     6   5
  CASC3 WILD-TYPE 224 134
  CASC3 MUTATED CASC3 WILD-TYPE 
             11             358 
  CASC3 MUTATED CASC3 WILD-TYPE 
              5             134 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A4YT TCGA-D7-A4YU 
       17.19        18.21        14.66        21.14        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-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-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-A94T TCGA-VQ-AA64 
       15.65        20.81         1.71        42.64        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 

  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           14.12 
[1] "8.0 - 77.3 (20.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D245V2, 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       2       15       39       29        37        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASC3 MUTATED           0          1          2          3        0
  CASC3 WILD-TYPE         3         69         51         29       38
D245V3, multiclass
            clus
vv           CASC3 MUTATED CASC3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             3              29
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASC3 MUTATED     0   3   5   3
  CASC3 WILD-TYPE  22  89 168  94
D245V4, multiclass
    clus
vv   CASC3 MUTATED CASC3 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             5             168
  T4             3              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
  CASC3 MUTATED     1   3   2   5
  CASC3 WILD-TYPE 117 101  75  72
D245V5, multiclass
    clus
vv   CASC3 MUTATED CASC3 WILD-TYPE
  N0             1             117
  N1             3             101
  N2             2              75
  N3             5              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"
D245V6, binary
                 cls
clus                0   1
  CASC3 MUTATED    10   0
  CASC3 WILD-TYPE 336  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC3 MUTATED     10    0
  CASC3 WILD-TYPE  336   29
   clus
vv  CASC3 MUTATED CASC3 WILD-TYPE
  0            10             336
  1             0              29
[1] 2 2
[1] FALSE
D245V7, binary
                 cls
clus                0   1
  CASC3 MUTATED     4   7
  CASC3 WILD-TYPE 141 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC3 MUTATED      4    7
  CASC3 WILD-TYPE  141  241
        clus
vv       CASC3 MUTATED CASC3 WILD-TYPE
  FEMALE             4             141
  MALE               7             241
[1] 2 2
[1] FALSE
D245V8, binary
                 cls
clus                0   1
  CASC3 MUTATED     8   3
  CASC3 WILD-TYPE 284  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC3 MUTATED      8    3
  CASC3 WILD-TYPE  284   56
     clus
vv    CASC3 MUTATED CASC3 WILD-TYPE
  NO              8             284
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CASC3 MUTATED                                          0
  CASC3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CASC3 MUTATED                                       1
  CASC3 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CASC3 MUTATED                                                        4
  CASC3 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CASC3 MUTATED                                                   1
  CASC3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CASC3 MUTATED                                                                   4
  CASC3 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CASC3 MUTATED                                                    0
  CASC3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CASC3 MUTATED                                                  1
  CASC3 WILD-TYPE                                               60
D245V9, multiclass
                                                                   clus
vv                                                                  CASC3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  CASC3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CASC3 MUTATED    10   0   0   0
  CASC3 WILD-TYPE 301  14  15  24
D245V10, multiclass
    clus
vv   CASC3 MUTATED CASC3 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CASC3 MUTATED       1                         0
  CASC3 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CASC3 MUTATED                                           0     9
  CASC3 WILD-TYPE                                         1   234
D245V12, multiclass
                                           clus
vv                                          CASC3 MUTATED CASC3 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V13, binary
                 cls
clus                0   1
  CASC3 MUTATED     0   9
  CASC3 WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC3 MUTATED      0    9
  CASC3 WILD-TYPE    4  301
                        clus
vv                       CASC3 MUTATED CASC3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(246) Variable = CCDC153 MUTATION ANALYSIS
D246V1, survival
                   sevent
clus2                 0   1
  CCDC153 MUTATED     5   2
  CCDC153 WILD-TYPE 225 137
  CCDC153 MUTATED CCDC153 WILD-TYPE 
                7               362 
  CCDC153 MUTATED CCDC153 WILD-TYPE 
                2               137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        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-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 

  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             14.35 
[1] "6.0 - 30.0 (11.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D246V2, 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       2       15       39       30        35        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC153 MUTATED           0          1          1          0        1
  CCDC153 WILD-TYPE         3         69         52         32       37
D246V3, multiclass
            clus
vv           CCDC153 MUTATED CCDC153 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC153 MUTATED     0   3   3   1
  CCDC153 WILD-TYPE  22  89 170  96
D246V4, multiclass
    clus
vv   CCDC153 MUTATED CCDC153 WILD-TYPE
  T1               0                22
  T2               3                89
  T3               3               170
  T4               1                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
  CCDC153 MUTATED     2   3   1   1
  CCDC153 WILD-TYPE 116 101  76  76
D246V5, multiclass
    clus
vv   CCDC153 MUTATED CCDC153 WILD-TYPE
  N0               2               116
  N1               3               101
  N2               1                76
  N3               1                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"
D246V6, binary
                   cls
clus                  0   1
  CCDC153 MUTATED     7   0
  CCDC153 WILD-TYPE 339  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC153 MUTATED      7    0
  CCDC153 WILD-TYPE  339   29
   clus
vv  CCDC153 MUTATED CCDC153 WILD-TYPE
  0               7               339
  1               0                29
[1] 2 2
[1] FALSE
D246V7, binary
                   cls
clus                  0   1
  CCDC153 MUTATED     2   5
  CCDC153 WILD-TYPE 143 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC153 MUTATED      2    5
  CCDC153 WILD-TYPE  143  243
        clus
vv       CCDC153 MUTATED CCDC153 WILD-TYPE
  FEMALE               2               143
  MALE                 5               243
[1] 2 2
[1] FALSE
D246V8, binary
                   cls
clus                  0   1
  CCDC153 MUTATED     7   0
  CCDC153 WILD-TYPE 285  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC153 MUTATED      7    0
  CCDC153 WILD-TYPE  285   59
     clus
vv    CCDC153 MUTATED CCDC153 WILD-TYPE
  NO                7               285
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CCDC153 MUTATED                                          0
  CCDC153 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CCDC153 MUTATED                                       0
  CCDC153 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC153 MUTATED                                                        1
  CCDC153 WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CCDC153 MUTATED                                                   0
  CCDC153 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC153 MUTATED                                                                   3
  CCDC153 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CCDC153 MUTATED                                                    0
  CCDC153 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CCDC153 MUTATED                                                  3
  CCDC153 WILD-TYPE                                               58
D246V9, multiclass
                                                                   clus
vv                                                                  CCDC153 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  CCDC153 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC153 MUTATED     6   0   0   0
  CCDC153 WILD-TYPE 305  14  15  24
D246V10, multiclass
    clus
vv   CCDC153 MUTATED CCDC153 WILD-TYPE
  R0               6               305
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CCDC153 MUTATED       2                         0
  CCDC153 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC153 MUTATED                                           0     4
  CCDC153 WILD-TYPE                                         1   239
D246V12, multiclass
                                           clus
vv                                          CCDC153 MUTATED CCDC153 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V13, binary
                   cls
clus                  0   1
  CCDC153 MUTATED     0   6
  CCDC153 WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC153 MUTATED      0    6
  CCDC153 WILD-TYPE    4  304
                        clus
vv                       CCDC153 MUTATED CCDC153 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(247) Variable = SF3B3 MUTATION ANALYSIS
D247V1, survival
                 sevent
clus2               0   1
  SF3B3 MUTATED    13   6
  SF3B3 WILD-TYPE 217 133
  SF3B3 MUTATED SF3B3 WILD-TYPE 
             19             350 
  SF3B3 MUTATED SF3B3 WILD-TYPE 
              6             133 
$`SF3B3 MUTATED`
TCGA-CG-4460 TCGA-BR-4255 TCGA-BR-6452 TCGA-BR-7716 TCGA-BR-8081 TCGA-BR-8284 
       21.99         4.08        34.68        39.78        32.25         8.05 
TCGA-BR-8295 TCGA-BR-8368 TCGA-BR-8680 TCGA-BR-A44U TCGA-CD-8525 TCGA-CD-8530 
        2.20         4.31        31.96        13.87        12.59        12.39 
TCGA-CD-8534 TCGA-CD-8536 TCGA-D7-8576 TCGA-FP-8211 TCGA-HU-A4GH TCGA-HU-A4GT 
       12.07        12.43        14.66        13.58        11.77         6.51 
TCGA-HU-A4GU 
        6.58 

$`SF3B3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         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-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-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       29.59         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-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-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-8526 
       13.35        11.21        12.10        12.39        12.76        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-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-D7-8578 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-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-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-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 

  SF3B3 MUTATED SF3B3 WILD-TYPE 
            2.2             0.0 
  SF3B3 MUTATED SF3B3 WILD-TYPE 
          39.78          122.30 
  SF3B3 MUTATED SF3B3 WILD-TYPE 
         12.430          14.775 
[1] "2.2 - 39.8 (12.4)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1"  
D247V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SF3B3 MUTATED         0        1        2        3         2         5
  SF3B3 WILD-TYPE       2       14       38       27        35        47
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SF3B3 MUTATED           0          2          2          1        2
  SF3B3 WILD-TYPE         3         68         51         31       36
D247V3, multiclass
            clus
vv           SF3B3 MUTATED SF3B3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               3              27
  STAGE IIA              2              35
  STAGE IIB              5              47
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SF3B3 MUTATED     1   2  12   5
  SF3B3 WILD-TYPE  21  90 161  92
D247V4, multiclass
    clus
vv   SF3B3 MUTATED SF3B3 WILD-TYPE
  T1             1              21
  T2             2              90
  T3            12             161
  T4             5              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
  SF3B3 MUTATED    10   6   1   3
  SF3B3 WILD-TYPE 108  98  76  74
D247V5, multiclass
    clus
vv   SF3B3 MUTATED SF3B3 WILD-TYPE
  N0            10             108
  N1             6              98
  N2             1              76
  N3             3              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"
D247V6, binary
                 cls
clus                0   1
  SF3B3 MUTATED    17   2
  SF3B3 WILD-TYPE 329  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B3 MUTATED     17    2
  SF3B3 WILD-TYPE  329   27
   clus
vv  SF3B3 MUTATED SF3B3 WILD-TYPE
  0            17             329
  1             2              27
[1] 2 2
[1] FALSE
D247V7, binary
                 cls
clus                0   1
  SF3B3 MUTATED    11   9
  SF3B3 WILD-TYPE 134 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B3 MUTATED     11    9
  SF3B3 WILD-TYPE  134  239
        clus
vv       SF3B3 MUTATED SF3B3 WILD-TYPE
  FEMALE            11             134
  MALE               9             239
[1] 2 2
[1] FALSE
D247V8, binary
                 cls
clus                0   1
  SF3B3 MUTATED    16   3
  SF3B3 WILD-TYPE 276  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B3 MUTATED     16    3
  SF3B3 WILD-TYPE  276   56
     clus
vv    SF3B3 MUTATED SF3B3 WILD-TYPE
  NO             16             276
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SF3B3 MUTATED                                          0
  SF3B3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SF3B3 MUTATED                                       3
  SF3B3 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SF3B3 MUTATED                                                        9
  SF3B3 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SF3B3 MUTATED                                                   1
  SF3B3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SF3B3 MUTATED                                                                   3
  SF3B3 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SF3B3 MUTATED                                                    0
  SF3B3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SF3B3 MUTATED                                                  4
  SF3B3 WILD-TYPE                                               57
D247V9, multiclass
                                                                   clus
vv                                                                  SF3B3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  SF3B3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SF3B3 MUTATED    17   1   1   1
  SF3B3 WILD-TYPE 294  13  14  23
D247V10, multiclass
    clus
vv   SF3B3 MUTATED SF3B3 WILD-TYPE
  R0            17             294
  R1             1              13
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SF3B3 MUTATED       8                         0
  SF3B3 WILD-TYPE    79                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SF3B3 MUTATED                                           0    10
  SF3B3 WILD-TYPE                                         1   233
D247V12, multiclass
                                           clus
vv                                          SF3B3 MUTATED SF3B3 WILD-TYPE
  ASIAN                                                 8              79
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V13, binary
                 cls
clus                0   1
  SF3B3 MUTATED     0  18
  SF3B3 WILD-TYPE   4 292
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B3 MUTATED      0   18
  SF3B3 WILD-TYPE    4  292
                        clus
vv                       SF3B3 MUTATED SF3B3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            18             292
[1] 2 2
[1] FALSE

Clustering(248) Variable = MLL3 MUTATION ANALYSIS
D248V1, survival
                sevent
clus2              0   1
  MLL3 MUTATED    32  15
  MLL3 WILD-TYPE 198 124
  MLL3 MUTATED MLL3 WILD-TYPE 
            47            322 
  MLL3 MUTATED MLL3 WILD-TYPE 
            15            124 
$`MLL3 MUTATED`
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 
       21.99        16.24         6.97         9.34         9.67        34.68 
TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8591 
       35.84        31.10         0.26        31.27        25.05        28.14 
TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8536 
        7.53        31.96        16.14        12.30        12.59        12.43 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        6.58        11.77        12.62        15.95         1.02         7.99 
TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5721 TCGA-D7-A4YT TCGA-D7-A4YU 
       19.07         9.01        30.97         6.02        14.27        16.44 
TCGA-FP-7916 TCGA-FP-A9TM TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GP TCGA-HU-A4GT 
       14.07         6.21        22.68        24.20         8.98         6.51 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NU TCGA-R5-A7O7 
       29.00        14.07        13.35        12.59        11.70        45.67 
TCGA-R5-A7ZI TCGA-R5-A805 TCGA-SW-A7EA TCGA-VQ-A8P2 TCGA-VQ-AA6K 
       74.53         9.24        19.04        38.14        12.43 

$`MLL3 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       47.05        22.98        79.07         0.23        20.15         9.86 
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 
        14.070         14.565 
[1] "0.3 - 74.5 (14.1)"  "0.0 - 122.3 (14.6)"
[1] "hr=" "1.2"
D248V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLL3 MUTATED         1        2        7        3         4         1
  MLL3 WILD-TYPE       1       13       33       27        33        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MLL3 MUTATED           0          6          6          7        9
  MLL3 WILD-TYPE         3         64         47         25       29
D248V3, multiclass
            clus
vv           MLL3 MUTATED MLL3 WILD-TYPE
  STAGE I               1              1
  STAGE IA              2             13
  STAGE IB              7             33
  STAGE II              3             27
  STAGE IIA             4             33
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            6             64
  STAGE IIIB            6             47
  STAGE IIIC            7             25
  STAGE IV              9             29
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MLL3 MUTATED     6  11  16  16
  MLL3 WILD-TYPE  16  81 157  81
D248V4, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  T1            6             16
  T2           11             81
  T3           16            157
  T4           16             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"
                vv
clus              N0  N1  N2  N3
  MLL3 MUTATED    13  18   5  12
  MLL3 WILD-TYPE 105  86  72  65
D248V5, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  N0           13            105
  N1           18             86
  N2            5             72
  N3           12             65
[1] 4 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
  MLL3 MUTATED    40   7
  MLL3 WILD-TYPE 306  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     40    7
  MLL3 WILD-TYPE  306   22
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0           40            306
  1            7             22
[1] 2 2
[1] FALSE
D248V7, binary
                cls
clus               0   1
  MLL3 MUTATED    21  31
  MLL3 WILD-TYPE 124 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     21   31
  MLL3 WILD-TYPE  124  217
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  FEMALE           21            124
  MALE             31            217
[1] 2 2
[1] FALSE
D248V8, binary
                cls
clus               0   1
  MLL3 MUTATED    37   7
  MLL3 WILD-TYPE 255  52
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     37    7
  MLL3 WILD-TYPE  255   52
     clus
vv    MLL3 MUTATED MLL3 WILD-TYPE
  NO            37            255
  YES            7             52
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MLL3 MUTATED                                          1
  MLL3 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MLL3 MUTATED                                       9
  MLL3 WILD-TYPE                                    61
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MLL3 MUTATED                                                       25
  MLL3 WILD-TYPE                                                    133
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MLL3 MUTATED                                                   3
  MLL3 WILD-TYPE                                                18
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MLL3 MUTATED                                                                   6
  MLL3 WILD-TYPE                                                                62
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MLL3 MUTATED                                                    0
  MLL3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MLL3 MUTATED                                                  7
  MLL3 WILD-TYPE                                               54
D248V9, multiclass
                                                                   clus
vv                                                                  MLL3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      25
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             7
                                                                   clus
vv                                                                  MLL3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         61
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       133
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MLL3 MUTATED    34   1   3   7
  MLL3 WILD-TYPE 277  13  12  17
D248V10, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  R0           34            277
  R1            1             13
  R2            3             12
  RX            7             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MLL3 MUTATED      14                         1
  MLL3 WILD-TYPE    73                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MLL3 MUTATED                                           0    29
  MLL3 WILD-TYPE                                         1   214
D248V12, multiclass
                                           clus
vv                                          MLL3 MUTATED MLL3 WILD-TYPE
  ASIAN                                               14             73
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               29            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V13, binary
                cls
clus               0   1
  MLL3 MUTATED     2  40
  MLL3 WILD-TYPE   2 270
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      2   40
  MLL3 WILD-TYPE    2  270
                        clus
vv                       MLL3 MUTATED MLL3 WILD-TYPE
  HISPANIC OR LATINO                2              2
  NOT HISPANIC OR LATINO           40            270
[1] 2 2
[1] FALSE

Clustering(249) Variable = CA2 MUTATION ANALYSIS
D249V1, survival
               sevent
clus2             0   1
  CA2 MUTATED     5   1
  CA2 WILD-TYPE 225 138
  CA2 MUTATED CA2 WILD-TYPE 
            6           363 
  CA2 MUTATED CA2 WILD-TYPE 
            1           138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8370 TCGA-BR-8371 TCGA-BR-8373 
       17.52         0.95        26.33         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-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-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-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 

  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        14.270 
[1] "4.3 - 31.3 (17.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.2"
D249V2, 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       1       15       39       30        36        51
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CA2 MUTATED           0          0          1          2        0
  CA2 WILD-TYPE         3         70         52         30       38
D249V3, multiclass
            clus
vv           CA2 MUTATED CA2 WILD-TYPE
  STAGE I              1             1
  STAGE IA             0            15
  STAGE IB             1            39
  STAGE II             0            30
  STAGE IIA            1            36
  STAGE IIB            1            51
  STAGE III            0             3
  STAGE IIIA           0            70
  STAGE IIIB           1            52
  STAGE IIIC           2            30
  STAGE IV             0            38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CA2 MUTATED     1   1   2   3
  CA2 WILD-TYPE  21  91 171  94
D249V4, multiclass
    clus
vv   CA2 MUTATED CA2 WILD-TYPE
  T1           1            21
  T2           1            91
  T3           2           171
  T4           3            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
  CA2 MUTATED     3   1   1   2
  CA2 WILD-TYPE 115 103  76  75
D249V5, multiclass
    clus
vv   CA2 MUTATED CA2 WILD-TYPE
  N0           3           115
  N1           1           103
  N2           1            76
  N3           2            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"
D249V6, binary
               cls
clus              0   1
  CA2 MUTATED     6   0
  CA2 WILD-TYPE 340  29
[1] "tbl2"
               cls
clus            [,1] [,2]
  CA2 MUTATED      6    0
  CA2 WILD-TYPE  340   29
   clus
vv  CA2 MUTATED CA2 WILD-TYPE
  0           6           340
  1           0            29
[1] 2 2
[1] FALSE
D249V7, binary
               cls
clus              0   1
  CA2 MUTATED     4   3
  CA2 WILD-TYPE 141 245
[1] "tbl2"
               cls
clus            [,1] [,2]
  CA2 MUTATED      4    3
  CA2 WILD-TYPE  141  245
        clus
vv       CA2 MUTATED CA2 WILD-TYPE
  FEMALE           4           141
  MALE             3           245
[1] 2 2
[1] FALSE
D249V8, binary
               cls
clus              0   1
  CA2 MUTATED     7   0
  CA2 WILD-TYPE 285  59
[1] "tbl2"
               cls
clus            [,1] [,2]
  CA2 MUTATED      7    0
  CA2 WILD-TYPE  285   59
     clus
vv    CA2 MUTATED CA2 WILD-TYPE
  NO            7           285
  YES           0            59
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CA2 MUTATED                                          0
  CA2 WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CA2 MUTATED                                       3
  CA2 WILD-TYPE                                    67
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CA2 MUTATED                                                        4
  CA2 WILD-TYPE                                                    154
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CA2 MUTATED                                                   0
  CA2 WILD-TYPE                                                21
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CA2 MUTATED                                                                   0
  CA2 WILD-TYPE                                                                68
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CA2 MUTATED                                                    0
  CA2 WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CA2 MUTATED                                                  0
  CA2 WILD-TYPE                                               61
D249V9, multiclass
                                                                   clus
vv                                                                  CA2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            0
                                                                   clus
vv                                                                  CA2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  CA2 MUTATED     6   0   0   0
  CA2 WILD-TYPE 305  14  15  24
D249V10, multiclass
    clus
vv   CA2 MUTATED CA2 WILD-TYPE
  R0           6           305
  R1           0            14
  R2           0            15
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CA2 MUTATED       3                         1
  CA2 WILD-TYPE    84                         8
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CA2 MUTATED                                           0     3
  CA2 WILD-TYPE                                         1   240
D249V12, multiclass
                                           clus
vv                                          CA2 MUTATED CA2 WILD-TYPE
  ASIAN                                               3            84
  BLACK OR AFRICAN AMERICAN                           1             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               3           240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V13, binary
               cls
clus              0   1
  CA2 MUTATED     0   7
  CA2 WILD-TYPE   4 303
[1] "tbl2"
               cls
clus            [,1] [,2]
  CA2 MUTATED      0    7
  CA2 WILD-TYPE    4  303
                        clus
vv                       CA2 MUTATED CA2 WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           7           303
[1] 2 2
[1] FALSE

Clustering(250) Variable = CNBD1 MUTATION ANALYSIS
D250V1, survival
                 sevent
clus2               0   1
  CNBD1 MUTATED     8   8
  CNBD1 WILD-TYPE 222 131
  CNBD1 MUTATED CNBD1 WILD-TYPE 
             16             353 
  CNBD1 MUTATED CNBD1 WILD-TYPE 
              8             131 
$`CNBD1 MUTATED`
TCGA-BR-4256 TCGA-BR-7901 TCGA-BR-A4QM TCGA-CD-A48C TCGA-D7-6519 TCGA-D7-6528 
        9.34         3.45         5.13        11.61        20.55        15.22 
TCGA-D7-A6EY TCGA-HU-8238 TCGA-HU-8602 TCGA-HU-A4GH TCGA-HU-A4HD TCGA-IN-8663 
       11.44         1.51        22.32        11.77        33.40         3.39 
TCGA-RD-A7C1 TCGA-VQ-A8DU TCGA-VQ-A8P2 TCGA-VQ-A8PK 
       16.67         5.46        38.14        17.85 

$`CNBD1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44        16.14        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-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-D7-6520 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-D7-6527 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-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-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       30.51        26.47         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-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-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
       14.07        15.68        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-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-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-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 

  CNBD1 MUTATED CNBD1 WILD-TYPE 
           1.51            0.00 
  CNBD1 MUTATED CNBD1 WILD-TYPE 
          38.14          122.30 
  CNBD1 MUTATED CNBD1 WILD-TYPE 
          11.69           14.43 
[1] "1.5 - 38.1 (11.7)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.7"
D250V2, 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       2       14       38       30        37        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNBD1 MUTATED           0          4          2          0        0
  CNBD1 WILD-TYPE         3         66         51         32       38
D250V3, multiclass
            clus
vv           CNBD1 MUTATED CNBD1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             2              51
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CNBD1 MUTATED     1   4   8   2
  CNBD1 WILD-TYPE  21  88 165  95
D250V4, multiclass
    clus
vv   CNBD1 MUTATED CNBD1 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             8             165
  T4             2              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
  CNBD1 MUTATED     4   5   5   2
  CNBD1 WILD-TYPE 114  99  72  75
D250V5, multiclass
    clus
vv   CNBD1 MUTATED CNBD1 WILD-TYPE
  N0             4             114
  N1             5              99
  N2             5              72
  N3             2              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"
D250V6, binary
                 cls
clus                0   1
  CNBD1 MUTATED    18   0
  CNBD1 WILD-TYPE 328  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNBD1 MUTATED     18    0
  CNBD1 WILD-TYPE  328   29
   clus
vv  CNBD1 MUTATED CNBD1 WILD-TYPE
  0            18             328
  1             0              29
[1] 2 2
[1] FALSE
D250V7, binary
                 cls
clus                0   1
  CNBD1 MUTATED     5  13
  CNBD1 WILD-TYPE 140 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNBD1 MUTATED      5   13
  CNBD1 WILD-TYPE  140  235
        clus
vv       CNBD1 MUTATED CNBD1 WILD-TYPE
  FEMALE             5             140
  MALE              13             235
[1] 2 2
[1] FALSE
D250V8, binary
                 cls
clus                0   1
  CNBD1 MUTATED    14   2
  CNBD1 WILD-TYPE 278  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNBD1 MUTATED     14    2
  CNBD1 WILD-TYPE  278   57
     clus
vv    CNBD1 MUTATED CNBD1 WILD-TYPE
  NO             14             278
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CNBD1 MUTATED                                          0
  CNBD1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CNBD1 MUTATED                                       3
  CNBD1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CNBD1 MUTATED                                                        7
  CNBD1 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CNBD1 MUTATED                                                   1
  CNBD1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CNBD1 MUTATED                                                                   1
  CNBD1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CNBD1 MUTATED                                                    0
  CNBD1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CNBD1 MUTATED                                                  6
  CNBD1 WILD-TYPE                                               55
D250V9, multiclass
                                                                   clus
vv                                                                  CNBD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              6
                                                                   clus
vv                                                                  CNBD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CNBD1 MUTATED    14   0   0   3
  CNBD1 WILD-TYPE 297  14  15  21
D250V10, multiclass
    clus
vv   CNBD1 MUTATED CNBD1 WILD-TYPE
  R0            14             297
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CNBD1 MUTATED       5                         0
  CNBD1 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CNBD1 MUTATED                                           0    13
  CNBD1 WILD-TYPE                                         1   230
D250V12, multiclass
                                           clus
vv                                          CNBD1 MUTATED CNBD1 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V13, binary
                 cls
clus                0   1
  CNBD1 MUTATED     0  15
  CNBD1 WILD-TYPE   4 295
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNBD1 MUTATED      0   15
  CNBD1 WILD-TYPE    4  295
                        clus
vv                       CNBD1 MUTATED CNBD1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            15             295
[1] 2 2
[1] FALSE

Clustering(251) Variable = DNAH7 MUTATION ANALYSIS
D251V1, survival
                 sevent
clus2               0   1
  DNAH7 MUTATED    33  14
  DNAH7 WILD-TYPE 197 125
  DNAH7 MUTATED DNAH7 WILD-TYPE 
             47             322 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
             14             125 
$`DNAH7 MUTATED`
TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-MX-A663 TCGA-BR-4184 TCGA-BR-4191 
       21.99        79.07        16.24         9.86         6.97        18.35 
TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 
       30.90         9.34        34.68        44.94        36.16        35.84 
TCGA-BR-7715 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8487 
       33.63         0.69        29.59        31.10         4.31         1.12 
TCGA-BR-8592 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J2 
        6.28        31.96         8.22        34.98        12.89        14.17 
TCGA-BR-A4QL TCGA-CD-5801 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4304 
       16.14        13.18        11.61         6.58        12.62        27.02 
TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 
       15.95         6.02       105.07        10.26        15.22        11.31 
TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-A4GF 
       14.76        11.24        15.65        77.29        26.47        25.81 
TCGA-HU-A4GH TCGA-HU-A4GT TCGA-IN-8462 TCGA-R5-A7ZI TCGA-VQ-A8P2 
       11.77         6.51        18.81        74.53        38.14 

$`DNAH7 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-FP-A8CX TCGA-KB-A93G TCGA-B7-5816 TCGA-B7-5818 
       47.05        22.98         0.23        20.15        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 
         105.07          122.30 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
          15.95           14.04 
[1] "0.7 - 105.1 (15.9)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.6"
D251V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DNAH7 MUTATED         0        3        8        5         8         9
  DNAH7 WILD-TYPE       2       12       32       25        29        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAH7 MUTATED           0          4          4          2        5
  DNAH7 WILD-TYPE         3         66         49         30       33
D251V3, multiclass
            clus
vv           DNAH7 MUTATED DNAH7 WILD-TYPE
  STAGE I                0               2
  STAGE IA               3              12
  STAGE IB               8              32
  STAGE II               5              25
  STAGE IIA              8              29
  STAGE IIB              9              43
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             4              49
  STAGE IIIC             2              30
  STAGE IV               5              33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DNAH7 MUTATED     3  17  13  16
  DNAH7 WILD-TYPE  19  75 160  81
D251V4, multiclass
    clus
vv   DNAH7 MUTATED DNAH7 WILD-TYPE
  T1             3              19
  T2            17              75
  T3            13             160
  T4            16              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"
                 vv
clus              N0 N1 N2 N3
  DNAH7 MUTATED   24 19  6  1
  DNAH7 WILD-TYPE 94 85 71 76
D251V5, multiclass
    clus
vv   DNAH7 MUTATED DNAH7 WILD-TYPE
  N0            24              94
  N1            19              85
  N2             6              71
  N3             1              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"
D251V6, binary
                 cls
clus                0   1
  DNAH7 MUTATED    46   3
  DNAH7 WILD-TYPE 300  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED     46    3
  DNAH7 WILD-TYPE  300   26
   clus
vv  DNAH7 MUTATED DNAH7 WILD-TYPE
  0            46             300
  1             3              26
[1] 2 2
[1] FALSE
D251V7, binary
                 cls
clus                0   1
  DNAH7 MUTATED    22  30
  DNAH7 WILD-TYPE 123 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED     22   30
  DNAH7 WILD-TYPE  123  218
        clus
vv       DNAH7 MUTATED DNAH7 WILD-TYPE
  FEMALE            22             123
  MALE              30             218
[1] 2 2
[1] FALSE
D251V8, binary
                 cls
clus                0   1
  DNAH7 MUTATED    41   6
  DNAH7 WILD-TYPE 251  53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED     41    6
  DNAH7 WILD-TYPE  251   53
     clus
vv    DNAH7 MUTATED DNAH7 WILD-TYPE
  NO             41             251
  YES             6              53
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DNAH7 MUTATED                                          1
  DNAH7 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DNAH7 MUTATED                                       4
  DNAH7 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DNAH7 MUTATED                                                       28
  DNAH7 WILD-TYPE                                                    130
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DNAH7 MUTATED                                                   3
  DNAH7 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DNAH7 MUTATED                                                                   6
  DNAH7 WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DNAH7 MUTATED                                                    2
  DNAH7 WILD-TYPE                                                  3
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DNAH7 MUTATED                                                  7
  DNAH7 WILD-TYPE                                               54
D251V9, multiclass
                                                                   clus
vv                                                                  DNAH7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       28
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              7
                                                                   clus
vv                                                                  DNAH7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        130
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DNAH7 MUTATED    41   1   1   6
  DNAH7 WILD-TYPE 270  13  14  18
D251V10, multiclass
    clus
vv   DNAH7 MUTATED DNAH7 WILD-TYPE
  R0            41             270
  R1             1              13
  R2             1              14
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DNAH7 MUTATED      11                         0
  DNAH7 WILD-TYPE    76                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DNAH7 MUTATED                                           0    33
  DNAH7 WILD-TYPE                                         1   210
D251V12, multiclass
                                           clus
vv                                          DNAH7 MUTATED DNAH7 WILD-TYPE
  ASIAN                                                11              76
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                33             210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V13, binary
                 cls
clus                0   1
  DNAH7 MUTATED     1  42
  DNAH7 WILD-TYPE   3 268
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      1   42
  DNAH7 WILD-TYPE    3  268
                        clus
vv                       DNAH7 MUTATED DNAH7 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            42             268
[1] 2 2
[1] FALSE

Clustering(252) Variable = ASB11 MUTATION ANALYSIS
D252V1, survival
                 sevent
clus2               0   1
  ASB11 MUTATED     7   3
  ASB11 WILD-TYPE 223 136
  ASB11 MUTATED ASB11 WILD-TYPE 
             10             359 
  ASB11 MUTATED ASB11 WILD-TYPE 
              3             136 
$`ASB11 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8372 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-5813 
       34.68        44.94        31.27        31.96        16.14        12.39 
TCGA-CG-4306 TCGA-CG-5721 TCGA-F1-6874 TCGA-HU-A4GT 
        1.02         6.02        14.47         6.51 

$`ASB11 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  ASB11 MUTATED ASB11 WILD-TYPE 
           1.02            0.00 
  ASB11 MUTATED ASB11 WILD-TYPE 
          44.94          122.30 
  ASB11 MUTATED ASB11 WILD-TYPE 
         15.305          14.170 
[1] "1.0 - 44.9 (15.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D252V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ASB11 MUTATED         0        0        1        1         3         0
  ASB11 WILD-TYPE       2       15       39       29        34        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ASB11 MUTATED           0          0          1          1        3
  ASB11 WILD-TYPE         3         70         52         31       35
D252V3, multiclass
            clus
vv           ASB11 MUTATED ASB11 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ASB11 MUTATED     0   1   6   3
  ASB11 WILD-TYPE  22  91 167  94
D252V4, multiclass
    clus
vv   ASB11 MUTATED ASB11 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             6             167
  T4             3              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
  ASB11 MUTATED     5   1   2   2
  ASB11 WILD-TYPE 113 103  75  75
D252V5, multiclass
    clus
vv   ASB11 MUTATED ASB11 WILD-TYPE
  N0             5             113
  N1             1             103
  N2             2              75
  N3             2              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"
D252V6, binary
                 cls
clus                0   1
  ASB11 MUTATED     8   2
  ASB11 WILD-TYPE 338  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      8    2
  ASB11 WILD-TYPE  338   27
   clus
vv  ASB11 MUTATED ASB11 WILD-TYPE
  0             8             338
  1             2              27
[1] 2 2
[1] FALSE
D252V7, binary
                 cls
clus                0   1
  ASB11 MUTATED     4   6
  ASB11 WILD-TYPE 141 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      4    6
  ASB11 WILD-TYPE  141  242
        clus
vv       ASB11 MUTATED ASB11 WILD-TYPE
  FEMALE             4             141
  MALE               6             242
[1] 2 2
[1] FALSE
D252V8, binary
                 cls
clus                0   1
  ASB11 MUTATED     9   0
  ASB11 WILD-TYPE 283  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      9    0
  ASB11 WILD-TYPE  283   59
     clus
vv    ASB11 MUTATED ASB11 WILD-TYPE
  NO              9             283
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ASB11 MUTATED                                          0
  ASB11 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ASB11 MUTATED                                       0
  ASB11 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ASB11 MUTATED                                                        5
  ASB11 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ASB11 MUTATED                                                   1
  ASB11 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ASB11 MUTATED                                                                   2
  ASB11 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ASB11 MUTATED                                                    0
  ASB11 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ASB11 MUTATED                                                  2
  ASB11 WILD-TYPE                                               59
D252V9, multiclass
                                                                   clus
vv                                                                  ASB11 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  ASB11 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ASB11 MUTATED     8   0   1   0
  ASB11 WILD-TYPE 303  14  14  24
D252V10, multiclass
    clus
vv   ASB11 MUTATED ASB11 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ASB11 MUTATED       3                         0
  ASB11 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ASB11 MUTATED                                           0     5
  ASB11 WILD-TYPE                                         1   238
D252V12, multiclass
                                           clus
vv                                          ASB11 MUTATED ASB11 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V13, binary
                 cls
clus                0   1
  ASB11 MUTATED     0   8
  ASB11 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      0    8
  ASB11 WILD-TYPE    4  302
                        clus
vv                       ASB11 MUTATED ASB11 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(253) Variable = CDC14A MUTATION ANALYSIS
D253V1, survival
                  sevent
clus2                0   1
  CDC14A MUTATED     8   4
  CDC14A WILD-TYPE 222 135
  CDC14A MUTATED CDC14A WILD-TYPE 
              12              357 
  CDC14A MUTATED CDC14A WILD-TYPE 
               4              135 
$`CDC14A MUTATED`
TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-4465 
       35.84        29.59         4.31         1.12        16.14         9.01 
TCGA-CG-4469 TCGA-CG-5721 TCGA-D7-5577 TCGA-HF-7132 TCGA-HU-A4GU TCGA-VQ-A8P2 
        7.07         6.02        25.71        77.29         6.58        38.14 

$`CDC14A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-4466 TCGA-CG-4477 TCGA-CG-5717 
       19.07        12.03         0.00        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-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-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-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 

  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           14.270 
[1] "1.1 - 77.3 (12.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
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       1       15       38       29        36        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC14A MUTATED           0          3          1          0        3
  CDC14A WILD-TYPE         3         67         52         32       35
D253V3, multiclass
            clus
vv           CDC14A MUTATED CDC14A WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CDC14A MUTATED     1   4   4   5
  CDC14A WILD-TYPE  21  88 169  92
D253V4, multiclass
    clus
vv   CDC14A MUTATED CDC14A WILD-TYPE
  T1              1               21
  T2              4               88
  T3              4              169
  T4              5               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
  CDC14A MUTATED     5   5   0   4
  CDC14A WILD-TYPE 113  99  77  73
D253V5, multiclass
    clus
vv   CDC14A MUTATED CDC14A WILD-TYPE
  N0              5              113
  N1              5               99
  N2              0               77
  N3              4               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"
D253V6, binary
                  cls
clus                 0   1
  CDC14A MUTATED    13   1
  CDC14A WILD-TYPE 333  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC14A MUTATED     13    1
  CDC14A WILD-TYPE  333   28
   clus
vv  CDC14A MUTATED CDC14A WILD-TYPE
  0             13              333
  1              1               28
[1] 2 2
[1] FALSE
D253V7, binary
                  cls
clus                 0   1
  CDC14A MUTATED     9   6
  CDC14A WILD-TYPE 136 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC14A MUTATED      9    6
  CDC14A WILD-TYPE  136  242
        clus
vv       CDC14A MUTATED CDC14A WILD-TYPE
  FEMALE              9              136
  MALE                6              242
[1] 2 2
[1] FALSE
D253V8, binary
                  cls
clus                 0   1
  CDC14A MUTATED     9   2
  CDC14A WILD-TYPE 283  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC14A MUTATED      9    2
  CDC14A WILD-TYPE  283   57
     clus
vv    CDC14A MUTATED CDC14A WILD-TYPE
  NO               9              283
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CDC14A MUTATED                                          0
  CDC14A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CDC14A MUTATED                                       2
  CDC14A WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDC14A MUTATED                                                        8
  CDC14A WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CDC14A MUTATED                                                   2
  CDC14A WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDC14A MUTATED                                                                   2
  CDC14A WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CDC14A MUTATED                                                    0
  CDC14A WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CDC14A MUTATED                                                  1
  CDC14A WILD-TYPE                                               60
D253V9, multiclass
                                                                   clus
vv                                                                  CDC14A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  CDC14A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CDC14A MUTATED    11   1   1   2
  CDC14A WILD-TYPE 300  13  14  22
D253V10, multiclass
    clus
vv   CDC14A MUTATED CDC14A WILD-TYPE
  R0             11              300
  R1              1               13
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CDC14A MUTATED       1                         1
  CDC14A WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDC14A MUTATED                                           0     9
  CDC14A WILD-TYPE                                         1   234
D253V12, multiclass
                                           clus
vv                                          CDC14A MUTATED CDC14A WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V13, binary
                  cls
clus                 0   1
  CDC14A MUTATED     0  10
  CDC14A WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC14A MUTATED      0   10
  CDC14A WILD-TYPE    4  300
                        clus
vv                       CDC14A MUTATED CDC14A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(254) Variable = NHLRC1 MUTATION ANALYSIS
D254V1, survival
                  sevent
clus2                0   1
  NHLRC1 MUTATED     4   6
  NHLRC1 WILD-TYPE 226 133
  NHLRC1 MUTATED NHLRC1 WILD-TYPE 
              10              359 
  NHLRC1 MUTATED NHLRC1 WILD-TYPE 
               6              133 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  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            14.17 
[1] "1.0 - 38.1 (23.8)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D254V2, 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       2       15       38       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NHLRC1 MUTATED           0          4          1          0        1
  NHLRC1 WILD-TYPE         3         66         52         32       37
D254V3, multiclass
            clus
vv           NHLRC1 MUTATED NHLRC1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NHLRC1 MUTATED     0   4   5   2
  NHLRC1 WILD-TYPE  22  88 168  95
D254V4, multiclass
    clus
vv   NHLRC1 MUTATED NHLRC1 WILD-TYPE
  T1              0               22
  T2              4               88
  T3              5              168
  T4              2               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
  NHLRC1 MUTATED     4   4   2   1
  NHLRC1 WILD-TYPE 114 100  75  76
D254V5, multiclass
    clus
vv   NHLRC1 MUTATED NHLRC1 WILD-TYPE
  N0              4              114
  N1              4              100
  N2              2               75
  N3              1               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"
D254V6, binary
                  cls
clus                 0   1
  NHLRC1 MUTATED    10   1
  NHLRC1 WILD-TYPE 336  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC1 MUTATED     10    1
  NHLRC1 WILD-TYPE  336   28
   clus
vv  NHLRC1 MUTATED NHLRC1 WILD-TYPE
  0             10              336
  1              1               28
[1] 2 2
[1] FALSE
D254V7, binary
                  cls
clus                 0   1
  NHLRC1 MUTATED     5   7
  NHLRC1 WILD-TYPE 140 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC1 MUTATED      5    7
  NHLRC1 WILD-TYPE  140  241
        clus
vv       NHLRC1 MUTATED NHLRC1 WILD-TYPE
  FEMALE              5              140
  MALE                7              241
[1] 2 2
[1] FALSE
D254V8, binary
                  cls
clus                 0   1
  NHLRC1 MUTATED     7   3
  NHLRC1 WILD-TYPE 285  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC1 MUTATED      7    3
  NHLRC1 WILD-TYPE  285   56
     clus
vv    NHLRC1 MUTATED NHLRC1 WILD-TYPE
  NO               7              285
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NHLRC1 MUTATED                                          1
  NHLRC1 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NHLRC1 MUTATED                                       0
  NHLRC1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NHLRC1 MUTATED                                                        8
  NHLRC1 WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NHLRC1 MUTATED                                                   1
  NHLRC1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NHLRC1 MUTATED                                                                   2
  NHLRC1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NHLRC1 MUTATED                                                    0
  NHLRC1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NHLRC1 MUTATED                                                  0
  NHLRC1 WILD-TYPE                                               61
D254V9, multiclass
                                                                   clus
vv                                                                  NHLRC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  NHLRC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NHLRC1 MUTATED     7   1   1   2
  NHLRC1 WILD-TYPE 304  13  14  22
D254V10, multiclass
    clus
vv   NHLRC1 MUTATED NHLRC1 WILD-TYPE
  R0              7              304
  R1              1               13
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NHLRC1 MUTATED       1                         0
  NHLRC1 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NHLRC1 MUTATED                                           0     7
  NHLRC1 WILD-TYPE                                         1   236
D254V12, multiclass
                                           clus
vv                                          NHLRC1 MUTATED NHLRC1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V13, binary
                  cls
clus                 0   1
  NHLRC1 MUTATED     0   7
  NHLRC1 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC1 MUTATED      0    7
  NHLRC1 WILD-TYPE    4  303
                        clus
vv                       NHLRC1 MUTATED NHLRC1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(255) Variable = ZC3H18 MUTATION ANALYSIS
D255V1, survival
                  sevent
clus2                0   1
  ZC3H18 MUTATED    11   7
  ZC3H18 WILD-TYPE 219 132
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
              18              351 
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
               7              132 
$`ZC3H18 MUTATED`
TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6566 TCGA-BR-8363 TCGA-BR-8591 TCGA-CD-A4MG 
       30.90         9.67        32.78         0.26        28.14         6.58 
TCGA-CD-A4MH TCGA-CG-4465 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6815 TCGA-FP-A4BE 
       12.20         9.01        65.10        21.07        15.98        11.08 
TCGA-HU-8243 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GX TCGA-MX-A5UJ TCGA-R5-A7ZI 
        5.92        24.20        29.98        20.25        19.73        74.53 

$`ZC3H18 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
           19.99            14.07 
[1] "0.3 - 74.5 (20.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D255V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZC3H18 MUTATED         0        1        2        0         5         1
  ZC3H18 WILD-TYPE       2       14       38       30        32        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H18 MUTATED           0          2          0          3        2
  ZC3H18 WILD-TYPE         3         68         53         29       36
D255V3, multiclass
            clus
vv           ZC3H18 MUTATED ZC3H18 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               5               32
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              3               29
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZC3H18 MUTATED     1   6   6   5
  ZC3H18 WILD-TYPE  21  86 167  92
D255V4, multiclass
    clus
vv   ZC3H18 MUTATED ZC3H18 WILD-TYPE
  T1              1               21
  T2              6               86
  T3              6              167
  T4              5               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
  ZC3H18 MUTATED     7   2   4   3
  ZC3H18 WILD-TYPE 111 102  73  74
D255V5, multiclass
    clus
vv   ZC3H18 MUTATED ZC3H18 WILD-TYPE
  N0              7              111
  N1              2              102
  N2              4               73
  N3              3               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"
D255V6, binary
                  cls
clus                 0   1
  ZC3H18 MUTATED    17   2
  ZC3H18 WILD-TYPE 329  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H18 MUTATED     17    2
  ZC3H18 WILD-TYPE  329   27
   clus
vv  ZC3H18 MUTATED ZC3H18 WILD-TYPE
  0             17              329
  1              2               27
[1] 2 2
[1] FALSE
D255V7, binary
                  cls
clus                 0   1
  ZC3H18 MUTATED    15   5
  ZC3H18 WILD-TYPE 130 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H18 MUTATED     15    5
  ZC3H18 WILD-TYPE  130  243
        clus
vv       ZC3H18 MUTATED ZC3H18 WILD-TYPE
  FEMALE             15              130
  MALE                5              243
[1] 2 2
[1] FALSE
D255V8, binary
                  cls
clus                 0   1
  ZC3H18 MUTATED    14   2
  ZC3H18 WILD-TYPE 278  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H18 MUTATED     14    2
  ZC3H18 WILD-TYPE  278   57
     clus
vv    ZC3H18 MUTATED ZC3H18 WILD-TYPE
  NO              14              278
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZC3H18 MUTATED                                          0
  ZC3H18 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZC3H18 MUTATED                                       4
  ZC3H18 WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZC3H18 MUTATED                                                        9
  ZC3H18 WILD-TYPE                                                    149
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZC3H18 MUTATED                                                   0
  ZC3H18 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZC3H18 MUTATED                                                                   2
  ZC3H18 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZC3H18 MUTATED                                                    0
  ZC3H18 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZC3H18 MUTATED                                                  5
  ZC3H18 WILD-TYPE                                               56
D255V9, multiclass
                                                                   clus
vv                                                                  ZC3H18 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               5
                                                                   clus
vv                                                                  ZC3H18 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZC3H18 MUTATED    13   0   1   4
  ZC3H18 WILD-TYPE 298  14  14  20
D255V10, multiclass
    clus
vv   ZC3H18 MUTATED ZC3H18 WILD-TYPE
  R0             13              298
  R1              0               14
  R2              1               14
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZC3H18 MUTATED       6                         1
  ZC3H18 WILD-TYPE    81                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZC3H18 MUTATED                                           0    10
  ZC3H18 WILD-TYPE                                         1   233
D255V12, multiclass
                                           clus
vv                                          ZC3H18 MUTATED ZC3H18 WILD-TYPE
  ASIAN                                                  6               81
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V13, binary
                  cls
clus                 0   1
  ZC3H18 MUTATED     1  16
  ZC3H18 WILD-TYPE   3 294
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H18 MUTATED      1   16
  ZC3H18 WILD-TYPE    3  294
                        clus
vv                       ZC3H18 MUTATED ZC3H18 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             16              294
[1] 2 2
[1] FALSE

Clustering(256) Variable = RGS9BP MUTATION ANALYSIS
D256V1, survival
                  sevent
clus2                0   1
  RGS9BP MUTATED     4   3
  RGS9BP WILD-TYPE 226 136
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               7              362 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
               3              136 
$`RGS9BP MUTATED`
TCGA-BR-8059 TCGA-BR-8368 TCGA-BR-8487 TCGA-D7-A6EY TCGA-HU-A4G8 TCGA-HU-A4GQ 
       14.43         4.31         1.12        11.44        22.68         0.10 
TCGA-HU-A4HD 
       33.40 

$`RGS9BP WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  RGS9BP MUTATED RGS9BP WILD-TYPE 
             0.1              0.0 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
            33.4            122.3 
  RGS9BP MUTATED RGS9BP WILD-TYPE 
           11.44            14.37 
[1] "0.1 - 33.4 (11.4)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.6"
D256V2, 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       2       15       39       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RGS9BP MUTATED           1          1          1          1        0
  RGS9BP WILD-TYPE         2         69         52         31       38
D256V3, multiclass
            clus
vv           RGS9BP MUTATED RGS9BP WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               1                2
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RGS9BP MUTATED     0   1   4   2
  RGS9BP WILD-TYPE  22  91 169  95
D256V4, multiclass
    clus
vv   RGS9BP MUTATED RGS9BP WILD-TYPE
  T1              0               22
  T2              1               91
  T3              4              169
  T4              2               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
  RGS9BP MUTATED     2   2   2   1
  RGS9BP WILD-TYPE 116 102  75  76
D256V5, multiclass
    clus
vv   RGS9BP MUTATED RGS9BP WILD-TYPE
  N0              2              116
  N1              2              102
  N2              2               75
  N3              1               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"
D256V6, binary
                  cls
clus                 0   1
  RGS9BP MUTATED     8   0
  RGS9BP WILD-TYPE 338  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      8    0
  RGS9BP WILD-TYPE  338   29
   clus
vv  RGS9BP MUTATED RGS9BP WILD-TYPE
  0              8              338
  1              0               29
[1] 2 2
[1] FALSE
D256V7, binary
                  cls
clus                 0   1
  RGS9BP MUTATED     5   3
  RGS9BP WILD-TYPE 140 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      5    3
  RGS9BP WILD-TYPE  140  245
        clus
vv       RGS9BP MUTATED RGS9BP WILD-TYPE
  FEMALE              5              140
  MALE                3              245
[1] 2 2
[1] FALSE
D256V8, binary
                  cls
clus                 0   1
  RGS9BP MUTATED     7   0
  RGS9BP WILD-TYPE 285  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      7    0
  RGS9BP WILD-TYPE  285   59
     clus
vv    RGS9BP MUTATED RGS9BP WILD-TYPE
  NO               7              285
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RGS9BP MUTATED                                          0
  RGS9BP WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RGS9BP MUTATED                                       1
  RGS9BP WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RGS9BP MUTATED                                                        3
  RGS9BP WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RGS9BP MUTATED                                                   0
  RGS9BP WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RGS9BP MUTATED                                                                   1
  RGS9BP WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RGS9BP MUTATED                                                    0
  RGS9BP WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RGS9BP MUTATED                                                  3
  RGS9BP WILD-TYPE                                               58
D256V9, multiclass
                                                                   clus
vv                                                                  RGS9BP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  RGS9BP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RGS9BP MUTATED     6   0   0   1
  RGS9BP WILD-TYPE 305  14  15  23
D256V10, multiclass
    clus
vv   RGS9BP MUTATED RGS9BP WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RGS9BP MUTATED       3                         0
  RGS9BP WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RGS9BP MUTATED                                           0     5
  RGS9BP WILD-TYPE                                         1   238
D256V12, multiclass
                                           clus
vv                                          RGS9BP MUTATED RGS9BP WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V13, binary
                  cls
clus                 0   1
  RGS9BP MUTATED     0   8
  RGS9BP WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RGS9BP MUTATED      0    8
  RGS9BP WILD-TYPE    4  302
                        clus
vv                       RGS9BP MUTATED RGS9BP WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(257) Variable = GLYR1 MUTATION ANALYSIS
D257V1, survival
                 sevent
clus2               0   1
  GLYR1 MUTATED    10   3
  GLYR1 WILD-TYPE 220 136
  GLYR1 MUTATED GLYR1 WILD-TYPE 
             13             356 
  GLYR1 MUTATED GLYR1 WILD-TYPE 
              3             136 
$`GLYR1 MUTATED`
TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A487 
        6.97        35.84        28.14        16.14        12.43        12.30 
TCGA-CG-4437 TCGA-D7-A4YV TCGA-F1-6874 TCGA-HF-7133 TCGA-HF-A5NB TCGA-R5-A7ZI 
        8.05         5.92        14.47        63.06        30.51        74.53 
TCGA-VQ-A8P2 
       38.14 

$`GLYR1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-7134 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        6.21        77.29        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-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 

  GLYR1 MUTATED GLYR1 WILD-TYPE 
           5.92            0.00 
  GLYR1 MUTATED GLYR1 WILD-TYPE 
          74.53          122.30 
  GLYR1 MUTATED GLYR1 WILD-TYPE 
          16.14           14.12 
[1] "5.9 - 74.5 (16.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.2"
D257V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLYR1 MUTATED         0        0        2        2         0         2
  GLYR1 WILD-TYPE       2       15       38       28        37        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLYR1 MUTATED           0          3          1          2        2
  GLYR1 WILD-TYPE         3         67         52         30       36
D257V3, multiclass
            clus
vv           GLYR1 MUTATED GLYR1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               2              28
  STAGE IIA              0              37
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GLYR1 MUTATED     0   4   5   5
  GLYR1 WILD-TYPE  22  88 168  92
D257V4, multiclass
    clus
vv   GLYR1 MUTATED GLYR1 WILD-TYPE
  T1             0              22
  T2             4              88
  T3             5             168
  T4             5              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
  GLYR1 MUTATED     4   6   0   4
  GLYR1 WILD-TYPE 114  98  77  73
D257V5, multiclass
    clus
vv   GLYR1 MUTATED GLYR1 WILD-TYPE
  N0             4             114
  N1             6              98
  N2             0              77
  N3             4              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"
D257V6, binary
                 cls
clus                0   1
  GLYR1 MUTATED    13   1
  GLYR1 WILD-TYPE 333  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLYR1 MUTATED     13    1
  GLYR1 WILD-TYPE  333   28
   clus
vv  GLYR1 MUTATED GLYR1 WILD-TYPE
  0            13             333
  1             1              28
[1] 2 2
[1] FALSE
D257V7, binary
                 cls
clus                0   1
  GLYR1 MUTATED     8   7
  GLYR1 WILD-TYPE 137 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLYR1 MUTATED      8    7
  GLYR1 WILD-TYPE  137  241
        clus
vv       GLYR1 MUTATED GLYR1 WILD-TYPE
  FEMALE             8             137
  MALE               7             241
[1] 2 2
[1] FALSE
D257V8, binary
                 cls
clus                0   1
  GLYR1 MUTATED    10   3
  GLYR1 WILD-TYPE 282  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLYR1 MUTATED     10    3
  GLYR1 WILD-TYPE  282   56
     clus
vv    GLYR1 MUTATED GLYR1 WILD-TYPE
  NO             10             282
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GLYR1 MUTATED                                          0
  GLYR1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GLYR1 MUTATED                                       2
  GLYR1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GLYR1 MUTATED                                                        7
  GLYR1 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GLYR1 MUTATED                                                   3
  GLYR1 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GLYR1 MUTATED                                                                   2
  GLYR1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GLYR1 MUTATED                                                    0
  GLYR1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GLYR1 MUTATED                                                  1
  GLYR1 WILD-TYPE                                               60
D257V9, multiclass
                                                                   clus
vv                                                                  GLYR1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  GLYR1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GLYR1 MUTATED    10   2   0   3
  GLYR1 WILD-TYPE 301  12  15  21
D257V10, multiclass
    clus
vv   GLYR1 MUTATED GLYR1 WILD-TYPE
  R0            10             301
  R1             2              12
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GLYR1 MUTATED       2                         0
  GLYR1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GLYR1 MUTATED                                           0    10
  GLYR1 WILD-TYPE                                         1   233
D257V12, multiclass
                                           clus
vv                                          GLYR1 MUTATED GLYR1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V13, binary
                 cls
clus                0   1
  GLYR1 MUTATED     1  10
  GLYR1 WILD-TYPE   3 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLYR1 MUTATED      1   10
  GLYR1 WILD-TYPE    3  300
                        clus
vv                       GLYR1 MUTATED GLYR1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(258) Variable = FILIP1L MUTATION ANALYSIS
D258V1, survival
                   sevent
clus2                 0   1
  FILIP1L MUTATED    12   6
  FILIP1L WILD-TYPE 218 133
  FILIP1L MUTATED FILIP1L WILD-TYPE 
               18               351 
  FILIP1L MUTATED FILIP1L WILD-TYPE 
                6               133 
$`FILIP1L MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       21.99        34.68        29.59         6.18        31.10         0.26 
TCGA-BR-8372 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4J1 TCGA-CG-4305 TCGA-D7-6525 
       31.27        28.14        31.96         0.72        15.95        13.35 
TCGA-D7-6820 TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-MX-A5UJ TCGA-SW-A7EA TCGA-VQ-AA6K 
       11.31         0.10        20.25        19.73        19.04        12.43 

$`FILIP1L WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-8364 
       29.42         2.66        19.96         2.20         7.40        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-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-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-D7-6526 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-D7-6822 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-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-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-ZA-A8F6 
       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            14.070 
[1] "0.1 - 34.7 (19.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D258V2, 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       2       15       37       29        35        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FILIP1L MUTATED           0          4          0          6        2
  FILIP1L WILD-TYPE         3         66         53         26       36
D258V3, multiclass
            clus
vv           FILIP1L MUTATED FILIP1L WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 3                37
  STAGE II                 1                29
  STAGE IIA                2                35
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               4                66
  STAGE IIIB               0                53
  STAGE IIIC               6                26
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FILIP1L MUTATED     1   6   3  11
  FILIP1L WILD-TYPE  21  86 170  86
D258V4, multiclass
    clus
vv   FILIP1L MUTATED FILIP1L WILD-TYPE
  T1               1                21
  T2               6                86
  T3               3               170
  T4              11                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
  FILIP1L MUTATED     7   4   6   3
  FILIP1L WILD-TYPE 111 100  71  74
D258V5, multiclass
    clus
vv   FILIP1L MUTATED FILIP1L WILD-TYPE
  N0               7               111
  N1               4               100
  N2               6                71
  N3               3                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"
D258V6, binary
                   cls
clus                  0   1
  FILIP1L MUTATED    19   2
  FILIP1L WILD-TYPE 327  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FILIP1L MUTATED     19    2
  FILIP1L WILD-TYPE  327   27
   clus
vv  FILIP1L MUTATED FILIP1L WILD-TYPE
  0              19               327
  1               2                27
[1] 2 2
[1] FALSE
D258V7, binary
                   cls
clus                  0   1
  FILIP1L MUTATED    10  11
  FILIP1L WILD-TYPE 135 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FILIP1L MUTATED     10   11
  FILIP1L WILD-TYPE  135  237
        clus
vv       FILIP1L MUTATED FILIP1L WILD-TYPE
  FEMALE              10               135
  MALE                11               237
[1] 2 2
[1] FALSE
D258V8, binary
                   cls
clus                  0   1
  FILIP1L MUTATED    16   1
  FILIP1L WILD-TYPE 276  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FILIP1L MUTATED     16    1
  FILIP1L WILD-TYPE  276   58
     clus
vv    FILIP1L MUTATED FILIP1L WILD-TYPE
  NO               16               276
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FILIP1L MUTATED                                          1
  FILIP1L WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FILIP1L MUTATED                                       3
  FILIP1L WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FILIP1L MUTATED                                                       10
  FILIP1L WILD-TYPE                                                    148
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FILIP1L MUTATED                                                   0
  FILIP1L WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FILIP1L MUTATED                                                                   3
  FILIP1L WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FILIP1L MUTATED                                                    0
  FILIP1L WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FILIP1L MUTATED                                                  4
  FILIP1L WILD-TYPE                                               57
D258V9, multiclass
                                                                   clus
vv                                                                  FILIP1L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                4
                                                                   clus
vv                                                                  FILIP1L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FILIP1L MUTATED    17   1   1   2
  FILIP1L WILD-TYPE 294  13  14  22
D258V10, multiclass
    clus
vv   FILIP1L MUTATED FILIP1L WILD-TYPE
  R0              17               294
  R1               1                13
  R2               1                14
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FILIP1L MUTATED       4                         0
  FILIP1L WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FILIP1L MUTATED                                           0    14
  FILIP1L WILD-TYPE                                         1   229
D258V12, multiclass
                                           clus
vv                                          FILIP1L MUTATED FILIP1L WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  14               229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V13, binary
                   cls
clus                  0   1
  FILIP1L MUTATED     0  17
  FILIP1L WILD-TYPE   4 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FILIP1L MUTATED      0   17
  FILIP1L WILD-TYPE    4  293
                        clus
vv                       FILIP1L MUTATED FILIP1L WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              17               293
[1] 2 2
[1] FALSE

Clustering(259) Variable = USP26 MUTATION ANALYSIS
D259V1, survival
                 sevent
clus2               0   1
  USP26 MUTATED    15   6
  USP26 WILD-TYPE 215 133
  USP26 MUTATED USP26 WILD-TYPE 
             21             348 
  USP26 MUTATED USP26 WILD-TYPE 
              6             133 
$`USP26 MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-6852 
        6.97         9.34         9.67        34.68        18.05        44.94 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4J5 TCGA-CD-A4MI 
       35.84        33.63        28.14        31.96        28.34        11.77 
TCGA-CG-5728 TCGA-D7-6520 TCGA-EQ-8122 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GN 
       65.10        18.84         7.99        30.51        22.68        29.98 
TCGA-MX-A5UJ TCGA-SW-A7EA TCGA-VQ-A8P2 
       19.73        19.04        38.14 

$`USP26 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-4267 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         4.08         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-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-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-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-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-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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        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-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-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-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-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-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 

  USP26 MUTATED USP26 WILD-TYPE 
           6.97            0.00 
  USP26 MUTATED USP26 WILD-TYPE 
           65.1           122.3 
  USP26 MUTATED USP26 WILD-TYPE 
         28.140          14.025 
[1] "7.0 - 65.1 (28.1)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.9"
D259V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP26 MUTATED         0        0        3        0         4         2
  USP26 WILD-TYPE       2       15       37       30        33        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  USP26 MUTATED           0          7          0          2        1
  USP26 WILD-TYPE         3         63         53         30       37
D259V3, multiclass
            clus
vv           USP26 MUTATED USP26 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               0              30
  STAGE IIA              4              33
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             7              63
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP26 MUTATED     0   5   9   5
  USP26 WILD-TYPE  22  87 164  92
D259V4, multiclass
    clus
vv   USP26 MUTATED USP26 WILD-TYPE
  T1             0              22
  T2             5              87
  T3             9             164
  T4             5              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
  USP26 MUTATED     6   9   3   2
  USP26 WILD-TYPE 112  95  74  75
D259V5, multiclass
    clus
vv   USP26 MUTATED USP26 WILD-TYPE
  N0             6             112
  N1             9              95
  N2             3              74
  N3             2              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"
D259V6, binary
                 cls
clus                0   1
  USP26 MUTATED    19   1
  USP26 WILD-TYPE 327  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     19    1
  USP26 WILD-TYPE  327   28
   clus
vv  USP26 MUTATED USP26 WILD-TYPE
  0            19             327
  1             1              28
[1] 2 2
[1] FALSE
D259V7, binary
                 cls
clus                0   1
  USP26 MUTATED    11  11
  USP26 WILD-TYPE 134 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     11   11
  USP26 WILD-TYPE  134  237
        clus
vv       USP26 MUTATED USP26 WILD-TYPE
  FEMALE            11             134
  MALE              11             237
[1] 2 2
[1] FALSE
D259V8, binary
                 cls
clus                0   1
  USP26 MUTATED    17   3
  USP26 WILD-TYPE 275  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     17    3
  USP26 WILD-TYPE  275   56
     clus
vv    USP26 MUTATED USP26 WILD-TYPE
  NO             17             275
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  USP26 MUTATED                                          0
  USP26 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  USP26 MUTATED                                       2
  USP26 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  USP26 MUTATED                                                       11
  USP26 WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  USP26 MUTATED                                                   3
  USP26 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  USP26 MUTATED                                                                   2
  USP26 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  USP26 MUTATED                                                    0
  USP26 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  USP26 MUTATED                                                  4
  USP26 WILD-TYPE                                               57
D259V9, multiclass
                                                                   clus
vv                                                                  USP26 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  USP26 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP26 MUTATED    14   1   0   4
  USP26 WILD-TYPE 297  13  15  20
D259V10, multiclass
    clus
vv   USP26 MUTATED USP26 WILD-TYPE
  R0            14             297
  R1             1              13
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  USP26 MUTATED       5                         0
  USP26 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP26 MUTATED                                           0    15
  USP26 WILD-TYPE                                         1   228
D259V12, multiclass
                                           clus
vv                                          USP26 MUTATED USP26 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V13, binary
                 cls
clus                0   1
  USP26 MUTATED     0  19
  USP26 WILD-TYPE   4 291
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED      0   19
  USP26 WILD-TYPE    4  291
                        clus
vv                       USP26 MUTATED USP26 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            19             291
[1] 2 2
[1] FALSE

Clustering(260) Variable = VPS13B MUTATION ANALYSIS
D260V1, survival
                  sevent
clus2                0   1
  VPS13B MUTATED    28  17
  VPS13B WILD-TYPE 202 122
  VPS13B MUTATED VPS13B WILD-TYPE 
              45              324 
  VPS13B MUTATED VPS13B WILD-TYPE 
              17              122 
$`VPS13B MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 
       21.99        26.70         6.97        30.90         9.34        34.68 
TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8289 TCGA-BR-8360 
       44.94        35.84        14.43        29.59         2.66         6.18 
TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-8529 
        0.26        25.05         1.12        28.14        31.96        12.30 
TCGA-CD-8533 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
       15.39        15.95         1.02         6.02       105.07        28.96 
TCGA-D7-6525 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-F1-A448 TCGA-HF-7134 TCGA-HJ-7597 
       13.35        11.31        11.44        21.27        52.21        26.47 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       22.68        24.20         0.10         6.51         6.58        20.25 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-KB-A93J TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-RD-A7C1 
        2.10        29.00        36.95        19.73        74.53        16.67 
TCGA-VQ-A8DV TCGA-VQ-A8P2 TCGA-VQ-A8PM 
       13.25        38.14         1.87 

$`VPS13B WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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-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-8534 
        7.17        12.33        12.39        12.59        11.64        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-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99         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-D7-6526 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-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-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       77.29        63.06        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-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-A4GY TCGA-HU-A4H2 TCGA-HU-A4H4 
       21.37        29.98         8.98         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-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-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-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-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PE 
        5.46        13.02        43.36        37.41        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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        27.55        12.43        17.26 

  VPS13B MUTATED VPS13B WILD-TYPE 
             0.1              0.0 
  VPS13B MUTATED VPS13B WILD-TYPE 
          105.07           122.30 
  VPS13B MUTATED VPS13B WILD-TYPE 
           19.73            14.04 
[1] "0.1 - 105.1 (19.7)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.1"
D260V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VPS13B MUTATED         0        4        6        4         5         4
  VPS13B WILD-TYPE       2       11       34       26        32        48
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPS13B MUTATED           1          6          2          6        8
  VPS13B WILD-TYPE         2         64         51         26       30
D260V3, multiclass
            clus
vv           VPS13B MUTATED VPS13B WILD-TYPE
  STAGE I                 0                2
  STAGE IA                4               11
  STAGE IB                6               34
  STAGE II                4               26
  STAGE IIA               5               32
  STAGE IIB               4               48
  STAGE III               1                2
  STAGE IIIA              6               64
  STAGE IIIB              2               51
  STAGE IIIC              6               26
  STAGE IV                8               30
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  VPS13B MUTATED     4  11  14  18
  VPS13B WILD-TYPE  18  81 159  79
D260V4, multiclass
    clus
vv   VPS13B MUTATED VPS13B WILD-TYPE
  T1              4               18
  T2             11               81
  T3             14              159
  T4             18               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"
                  vv
clus               N0 N1 N2 N3
  VPS13B MUTATED   20 13  7  8
  VPS13B WILD-TYPE 98 91 70 69
D260V5, multiclass
    clus
vv   VPS13B MUTATED VPS13B WILD-TYPE
  N0             20               98
  N1             13               91
  N2              7               70
  N3              8               69
[1] 4 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
  VPS13B MUTATED    41   6
  VPS13B WILD-TYPE 305  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     41    6
  VPS13B WILD-TYPE  305   23
   clus
vv  VPS13B MUTATED VPS13B WILD-TYPE
  0             41              305
  1              6               23
[1] 2 2
[1] FALSE
D260V7, binary
                  cls
clus                 0   1
  VPS13B MUTATED    22  27
  VPS13B WILD-TYPE 123 221
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     22   27
  VPS13B WILD-TYPE  123  221
        clus
vv       VPS13B MUTATED VPS13B WILD-TYPE
  FEMALE             22              123
  MALE               27              221
[1] 2 2
[1] FALSE
D260V8, binary
                  cls
clus                 0   1
  VPS13B MUTATED    38   5
  VPS13B WILD-TYPE 254  54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     38    5
  VPS13B WILD-TYPE  254   54
     clus
vv    VPS13B MUTATED VPS13B WILD-TYPE
  NO              38              254
  YES              5               54
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  VPS13B MUTATED                                          2
  VPS13B WILD-TYPE                                        6
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  VPS13B MUTATED                                      10
  VPS13B WILD-TYPE                                    60
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  VPS13B MUTATED                                                       18
  VPS13B WILD-TYPE                                                    140
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  VPS13B MUTATED                                                   3
  VPS13B WILD-TYPE                                                18
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  VPS13B MUTATED                                                                   9
  VPS13B WILD-TYPE                                                                59
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  VPS13B MUTATED                                                    0
  VPS13B WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  VPS13B MUTATED                                                  7
  VPS13B WILD-TYPE                                               54
D260V9, multiclass
                                                                   clus
vv                                                                  VPS13B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         10
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        18
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              9
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               7
                                                                   clus
vv                                                                  VPS13B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         140
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               59
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  VPS13B MUTATED    41   0   2   5
  VPS13B WILD-TYPE 270  14  13  19
D260V10, multiclass
    clus
vv   VPS13B MUTATED VPS13B WILD-TYPE
  R0             41              270
  R1              0               14
  R2              2               13
  RX              5               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  VPS13B MUTATED      12                         0
  VPS13B WILD-TYPE    75                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  VPS13B MUTATED                                           0    29
  VPS13B WILD-TYPE                                         1   214
D260V12, multiclass
                                           clus
vv                                          VPS13B MUTATED VPS13B WILD-TYPE
  ASIAN                                                 12               75
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 29              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V13, binary
                  cls
clus                 0   1
  VPS13B MUTATED     2  35
  VPS13B WILD-TYPE   2 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED      2   35
  VPS13B WILD-TYPE    2  275
                        clus
vv                       VPS13B MUTATED VPS13B WILD-TYPE
  HISPANIC OR LATINO                  2                2
  NOT HISPANIC OR LATINO             35              275
[1] 2 2
[1] FALSE

Clustering(261) Variable = RCOR3 MUTATION ANALYSIS
D261V1, survival
                 sevent
clus2               0   1
  RCOR3 MUTATED     7   6
  RCOR3 WILD-TYPE 223 133
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             13             356 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
              6             133 
$`RCOR3 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL 
        6.97        34.68         0.26        28.14        31.96        16.14 
TCGA-CG-5726 TCGA-CG-5728 TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4GQ TCGA-VQ-A8P2 
       28.96        65.10        11.08        22.32         0.10        38.14 
TCGA-VQ-AA64 
       18.41 

$`RCOR3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  RCOR3 MUTATED RCOR3 WILD-TYPE 
            0.1             0.0 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
           65.1           122.3 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
          22.32           14.07 
[1] "0.1 - 65.1 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D261V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RCOR3 MUTATED         0        1        2        0         2         1
  RCOR3 WILD-TYPE       2       14       38       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RCOR3 MUTATED           0          2          2          2        1
  RCOR3 WILD-TYPE         3         68         51         30       37
D261V3, multiclass
            clus
vv           RCOR3 MUTATED RCOR3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RCOR3 MUTATED     1   2   5   5
  RCOR3 WILD-TYPE  21  90 168  92
D261V4, multiclass
    clus
vv   RCOR3 MUTATED RCOR3 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             5             168
  T4             5              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
  RCOR3 MUTATED     6   3   3   2
  RCOR3 WILD-TYPE 112 101  74  75
D261V5, multiclass
    clus
vv   RCOR3 MUTATED RCOR3 WILD-TYPE
  N0             6             112
  N1             3             101
  N2             3              74
  N3             2              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"
D261V6, binary
                 cls
clus                0   1
  RCOR3 MUTATED    12   1
  RCOR3 WILD-TYPE 334  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED     12    1
  RCOR3 WILD-TYPE  334   28
   clus
vv  RCOR3 MUTATED RCOR3 WILD-TYPE
  0            12             334
  1             1              28
[1] 2 2
[1] FALSE
D261V7, binary
                 cls
clus                0   1
  RCOR3 MUTATED     6   8
  RCOR3 WILD-TYPE 139 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED      6    8
  RCOR3 WILD-TYPE  139  240
        clus
vv       RCOR3 MUTATED RCOR3 WILD-TYPE
  FEMALE             6             139
  MALE               8             240
[1] 2 2
[1] FALSE
D261V8, binary
                 cls
clus                0   1
  RCOR3 MUTATED     8   3
  RCOR3 WILD-TYPE 284  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED      8    3
  RCOR3 WILD-TYPE  284   56
     clus
vv    RCOR3 MUTATED RCOR3 WILD-TYPE
  NO              8             284
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RCOR3 MUTATED                                          0
  RCOR3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RCOR3 MUTATED                                       1
  RCOR3 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RCOR3 MUTATED                                                        7
  RCOR3 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RCOR3 MUTATED                                                   1
  RCOR3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RCOR3 MUTATED                                                                   3
  RCOR3 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RCOR3 MUTATED                                                    0
  RCOR3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RCOR3 MUTATED                                                  2
  RCOR3 WILD-TYPE                                               59
D261V9, multiclass
                                                                   clus
vv                                                                  RCOR3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  RCOR3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RCOR3 MUTATED    12   0   0   2
  RCOR3 WILD-TYPE 299  14  15  22
D261V10, multiclass
    clus
vv   RCOR3 MUTATED RCOR3 WILD-TYPE
  R0            12             299
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RCOR3 MUTATED       3                         1
  RCOR3 WILD-TYPE    84                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RCOR3 MUTATED                                           0     8
  RCOR3 WILD-TYPE                                         1   235
D261V12, multiclass
                                           clus
vv                                          RCOR3 MUTATED RCOR3 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V13, binary
                 cls
clus                0   1
  RCOR3 MUTATED     0  10
  RCOR3 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED      0   10
  RCOR3 WILD-TYPE    4  300
                        clus
vv                       RCOR3 MUTATED RCOR3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(262) Variable = CASD1 MUTATION ANALYSIS
D262V1, survival
                 sevent
clus2               0   1
  CASD1 MUTATED     8   3
  CASD1 WILD-TYPE 222 136
  CASD1 MUTATED CASD1 WILD-TYPE 
             11             358 
  CASD1 MUTATED CASD1 WILD-TYPE 
              3             136 
$`CASD1 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4438 TCGA-CG-5733 
       30.90        34.68         6.58        15.95        54.08        21.07 
TCGA-F1-A448 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4H3 
       21.27        30.51        22.32        22.68        29.00 

$`CASD1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  CASD1 MUTATED CASD1 WILD-TYPE 
           6.58            0.00 
  CASD1 MUTATED CASD1 WILD-TYPE 
          54.08          122.30 
  CASD1 MUTATED CASD1 WILD-TYPE 
          22.68           14.04 
[1] "6.6 - 54.1 (22.7)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "2"  
D262V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CASD1 MUTATED         1        0        0        1         2         2
  CASD1 WILD-TYPE       1       15       40       29        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASD1 MUTATED           0          1          1          2        1
  CASD1 WILD-TYPE         3         69         52         30       37
D262V3, multiclass
            clus
vv           CASD1 MUTATED CASD1 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASD1 MUTATED     1   3   4   4
  CASD1 WILD-TYPE  21  89 169  93
D262V4, multiclass
    clus
vv   CASD1 MUTATED CASD1 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             4             169
  T4             4              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
  CASD1 MUTATED     3   3   2   3
  CASD1 WILD-TYPE 115 101  75  74
D262V5, multiclass
    clus
vv   CASD1 MUTATED CASD1 WILD-TYPE
  N0             3             115
  N1             3             101
  N2             2              75
  N3             3              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"
D262V6, binary
                 cls
clus                0   1
  CASD1 MUTATED    11   0
  CASD1 WILD-TYPE 335  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASD1 MUTATED     11    0
  CASD1 WILD-TYPE  335   29
   clus
vv  CASD1 MUTATED CASD1 WILD-TYPE
  0            11             335
  1             0              29
[1] 2 2
[1] FALSE
D262V7, binary
                 cls
clus                0   1
  CASD1 MUTATED     7   5
  CASD1 WILD-TYPE 138 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASD1 MUTATED      7    5
  CASD1 WILD-TYPE  138  243
        clus
vv       CASD1 MUTATED CASD1 WILD-TYPE
  FEMALE             7             138
  MALE               5             243
[1] 2 2
[1] FALSE
D262V8, binary
                 cls
clus                0   1
  CASD1 MUTATED     8   2
  CASD1 WILD-TYPE 284  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASD1 MUTATED      8    2
  CASD1 WILD-TYPE  284   57
     clus
vv    CASD1 MUTATED CASD1 WILD-TYPE
  NO              8             284
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CASD1 MUTATED                                          0
  CASD1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CASD1 MUTATED                                       4
  CASD1 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CASD1 MUTATED                                                        4
  CASD1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CASD1 MUTATED                                                   2
  CASD1 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CASD1 MUTATED                                                                   2
  CASD1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CASD1 MUTATED                                                    0
  CASD1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CASD1 MUTATED                                                  0
  CASD1 WILD-TYPE                                               61
D262V9, multiclass
                                                                   clus
vv                                                                  CASD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  CASD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CASD1 MUTATED     8   1   0   1
  CASD1 WILD-TYPE 303  13  15  23
D262V10, multiclass
    clus
vv   CASD1 MUTATED CASD1 WILD-TYPE
  R0             8             303
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CASD1 MUTATED       4                         1
  CASD1 WILD-TYPE    83                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CASD1 MUTATED                                           0     3
  CASD1 WILD-TYPE                                         1   240
D262V12, multiclass
                                           clus
vv                                          CASD1 MUTATED CASD1 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V13, binary
                 cls
clus                0   1
  CASD1 MUTATED     1   7
  CASD1 WILD-TYPE   3 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASD1 MUTATED      1    7
  CASD1 WILD-TYPE    3  303
                        clus
vv                       CASD1 MUTATED CASD1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(263) Variable = CDC25C MUTATION ANALYSIS
D263V1, survival
                  sevent
clus2                0   1
  CDC25C MUTATED     6   4
  CDC25C WILD-TYPE 224 135
  CDC25C MUTATED CDC25C WILD-TYPE 
              10              359 
  CDC25C MUTATED CDC25C WILD-TYPE 
               4              135 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8682 TCGA-BR-8683 
        6.28         7.53        26.73        24.79        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-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-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         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-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-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 

  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           14.170 
[1] "0.1 - 34.7 (21.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D263V2, 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       2       15       38       30        35        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC25C MUTATED           0          1          1          2        1
  CDC25C WILD-TYPE         3         69         52         30       37
D263V3, multiclass
            clus
vv           CDC25C MUTATED CDC25C WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CDC25C MUTATED     1   2   3   5
  CDC25C WILD-TYPE  21  90 170  92
D263V4, multiclass
    clus
vv   CDC25C MUTATED CDC25C WILD-TYPE
  T1              1               21
  T2              2               90
  T3              3              170
  T4              5               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
  CDC25C MUTATED     4   3   3   1
  CDC25C WILD-TYPE 114 101  74  76
D263V5, multiclass
    clus
vv   CDC25C MUTATED CDC25C WILD-TYPE
  N0              4              114
  N1              3              101
  N2              3               74
  N3              1               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"
D263V6, binary
                  cls
clus                 0   1
  CDC25C MUTATED     8   1
  CDC25C WILD-TYPE 338  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25C MUTATED      8    1
  CDC25C WILD-TYPE  338   28
   clus
vv  CDC25C MUTATED CDC25C WILD-TYPE
  0              8              338
  1              1               28
[1] 2 2
[1] FALSE
D263V7, binary
                  cls
clus                 0   1
  CDC25C MUTATED     4   7
  CDC25C WILD-TYPE 141 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25C MUTATED      4    7
  CDC25C WILD-TYPE  141  241
        clus
vv       CDC25C MUTATED CDC25C WILD-TYPE
  FEMALE              4              141
  MALE                7              241
[1] 2 2
[1] FALSE
D263V8, binary
                  cls
clus                 0   1
  CDC25C MUTATED    11   0
  CDC25C WILD-TYPE 281  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25C MUTATED     11    0
  CDC25C WILD-TYPE  281   59
     clus
vv    CDC25C MUTATED CDC25C WILD-TYPE
  NO              11              281
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CDC25C MUTATED                                          1
  CDC25C WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CDC25C MUTATED                                       0
  CDC25C WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDC25C MUTATED                                                        4
  CDC25C WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CDC25C MUTATED                                                   0
  CDC25C WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDC25C MUTATED                                                                   1
  CDC25C WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CDC25C MUTATED                                                    0
  CDC25C WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CDC25C MUTATED                                                  5
  CDC25C WILD-TYPE                                               56
D263V9, multiclass
                                                                   clus
vv                                                                  CDC25C MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               5
                                                                   clus
vv                                                                  CDC25C WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CDC25C MUTATED     9   1   0   1
  CDC25C WILD-TYPE 302  13  15  23
D263V10, multiclass
    clus
vv   CDC25C MUTATED CDC25C WILD-TYPE
  R0              9              302
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CDC25C MUTATED       4                         0
  CDC25C WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDC25C MUTATED                                           0     7
  CDC25C WILD-TYPE                                         1   236
D263V12, multiclass
                                           clus
vv                                          CDC25C MUTATED CDC25C WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V13, binary
                  cls
clus                 0   1
  CDC25C MUTATED     0  11
  CDC25C WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25C MUTATED      0   11
  CDC25C WILD-TYPE    4  299
                        clus
vv                       CDC25C MUTATED CDC25C WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(264) Variable = BCL9L MUTATION ANALYSIS
D264V1, survival
                 sevent
clus2               0   1
  BCL9L MUTATED    17   7
  BCL9L WILD-TYPE 213 132
  BCL9L MUTATED BCL9L WILD-TYPE 
             24             345 
  BCL9L MUTATED BCL9L WILD-TYPE 
              7             132 
$`BCL9L MUTATED`
TCGA-BR-4280 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8382 TCGA-BR-8591 
        6.61        29.59         6.18        31.10        25.05        28.14 
TCGA-BR-8680 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4455 TCGA-CG-5721 TCGA-CG-5726 
       31.96        11.77        12.62        12.03         6.02        28.96 
TCGA-CG-5730 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-A4YY TCGA-F1-6874 TCGA-F1-A448 
        4.01        12.36        24.72        13.78        14.47        21.27 
TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-MX-A5UJ TCGA-VQ-AA6K 
       22.32         0.10         6.51         6.58        19.73        12.43 

$`BCL9L WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
          13.20           14.43 
[1] "0.1 - 32.0 (13.2)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D264V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCL9L MUTATED         0        1        3        1         2         3
  BCL9L WILD-TYPE       2       14       37       29        35        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCL9L MUTATED           1          4          3          5        3
  BCL9L WILD-TYPE         2         66         50         27       35
D264V3, multiclass
            clus
vv           BCL9L MUTATED BCL9L WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              3              49
  STAGE III              1               2
  STAGE IIIA             4              66
  STAGE IIIB             3              50
  STAGE IIIC             5              27
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BCL9L MUTATED     1   7   8  10
  BCL9L WILD-TYPE  21  85 165  87
D264V4, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  T1             1              21
  T2             7              85
  T3             8             165
  T4            10              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
  BCL9L MUTATED     9   6   4   7
  BCL9L WILD-TYPE 109  98  73  70
D264V5, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  N0             9             109
  N1             6              98
  N2             4              73
  N3             7              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"
D264V6, binary
                 cls
clus                0   1
  BCL9L MUTATED    24   2
  BCL9L WILD-TYPE 322  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED     24    2
  BCL9L WILD-TYPE  322   27
   clus
vv  BCL9L MUTATED BCL9L WILD-TYPE
  0            24             322
  1             2              27
[1] 2 2
[1] FALSE
D264V7, binary
                 cls
clus                0   1
  BCL9L MUTATED     9  17
  BCL9L WILD-TYPE 136 231
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      9   17
  BCL9L WILD-TYPE  136  231
        clus
vv       BCL9L MUTATED BCL9L WILD-TYPE
  FEMALE             9             136
  MALE              17             231
[1] 2 2
[1] FALSE
D264V8, binary
                 cls
clus                0   1
  BCL9L MUTATED    18   4
  BCL9L WILD-TYPE 274  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED     18    4
  BCL9L WILD-TYPE  274   55
     clus
vv    BCL9L MUTATED BCL9L WILD-TYPE
  NO             18             274
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BCL9L MUTATED                                          1
  BCL9L WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BCL9L MUTATED                                       3
  BCL9L WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BCL9L MUTATED                                                        9
  BCL9L WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BCL9L MUTATED                                                   2
  BCL9L WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BCL9L MUTATED                                                                   6
  BCL9L WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BCL9L MUTATED                                                    0
  BCL9L WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BCL9L MUTATED                                                  5
  BCL9L WILD-TYPE                                               56
D264V9, multiclass
                                                                   clus
vv                                                                  BCL9L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              5
                                                                   clus
vv                                                                  BCL9L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BCL9L MUTATED    20   1   1   2
  BCL9L WILD-TYPE 291  13  14  22
D264V10, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  R0            20             291
  R1             1              13
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BCL9L MUTATED       7                         0
  BCL9L WILD-TYPE    80                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BCL9L MUTATED                                           0    14
  BCL9L WILD-TYPE                                         1   229
D264V12, multiclass
                                           clus
vv                                          BCL9L MUTATED BCL9L WILD-TYPE
  ASIAN                                                 7              80
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V13, binary
                 cls
clus                0   1
  BCL9L MUTATED     1  19
  BCL9L WILD-TYPE   3 291
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      1   19
  BCL9L WILD-TYPE    3  291
                        clus
vv                       BCL9L MUTATED BCL9L WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            19             291
[1] 2 2
[1] FALSE

Clustering(265) Variable = TNFSF10 MUTATION ANALYSIS
D265V1, survival
                   sevent
clus2                 0   1
  TNFSF10 MUTATED     3   5
  TNFSF10 WILD-TYPE 227 134
  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
                8               361 
  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
                5               134 
$`TNFSF10 MUTATED`
TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6802 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4300 
        6.97         9.67        30.90        16.14         6.58        20.02 
TCGA-HU-8249 TCGA-VQ-A8P2 
       28.96        38.14 

$`TNFSF10 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
             6.58              0.00 
  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
            38.14            122.30 
  TNFSF10 MUTATED TNFSF10 WILD-TYPE 
            18.08             14.17 
[1] "6.6 - 38.1 (18.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.5"
D265V2, 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       2       15       40       30        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFSF10 MUTATED           0          4          2          0        0
  TNFSF10 WILD-TYPE         3         66         51         32       38
D265V3, multiclass
            clus
vv           TNFSF10 MUTATED TNFSF10 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               4                66
  STAGE IIIB               2                51
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TNFSF10 MUTATED     0   0   6   1
  TNFSF10 WILD-TYPE  22  92 167  96
D265V4, multiclass
    clus
vv   TNFSF10 MUTATED TNFSF10 WILD-TYPE
  T1               0                22
  T2               0                92
  T3               6               167
  T4               1                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
  TNFSF10 MUTATED     1   2   3   1
  TNFSF10 WILD-TYPE 117 102  74  76
D265V5, multiclass
    clus
vv   TNFSF10 MUTATED TNFSF10 WILD-TYPE
  N0               1               117
  N1               2               102
  N2               3                74
  N3               1                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"
D265V6, binary
                   cls
clus                  0   1
  TNFSF10 MUTATED     7   0
  TNFSF10 WILD-TYPE 339  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF10 MUTATED      7    0
  TNFSF10 WILD-TYPE  339   29
   clus
vv  TNFSF10 MUTATED TNFSF10 WILD-TYPE
  0               7               339
  1               0                29
[1] 2 2
[1] FALSE
D265V7, binary
                   cls
clus                  0   1
  TNFSF10 MUTATED     2   6
  TNFSF10 WILD-TYPE 143 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF10 MUTATED      2    6
  TNFSF10 WILD-TYPE  143  242
        clus
vv       TNFSF10 MUTATED TNFSF10 WILD-TYPE
  FEMALE               2               143
  MALE                 6               242
[1] 2 2
[1] FALSE
D265V8, binary
                   cls
clus                  0   1
  TNFSF10 MUTATED     6   1
  TNFSF10 WILD-TYPE 286  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF10 MUTATED      6    1
  TNFSF10 WILD-TYPE  286   58
     clus
vv    TNFSF10 MUTATED TNFSF10 WILD-TYPE
  NO                6               286
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TNFSF10 MUTATED                                          0
  TNFSF10 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TNFSF10 MUTATED                                       1
  TNFSF10 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNFSF10 MUTATED                                                        5
  TNFSF10 WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TNFSF10 MUTATED                                                   1
  TNFSF10 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNFSF10 MUTATED                                                                   0
  TNFSF10 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TNFSF10 MUTATED                                                    0
  TNFSF10 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TNFSF10 MUTATED                                                  1
  TNFSF10 WILD-TYPE                                               60
D265V9, multiclass
                                                                   clus
vv                                                                  TNFSF10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  TNFSF10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TNFSF10 MUTATED     5   0   0   2
  TNFSF10 WILD-TYPE 306  14  15  22
D265V10, multiclass
    clus
vv   TNFSF10 MUTATED TNFSF10 WILD-TYPE
  R0               5               306
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TNFSF10 MUTATED       2                         0
  TNFSF10 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNFSF10 MUTATED                                           0     5
  TNFSF10 WILD-TYPE                                         1   238
D265V12, multiclass
                                           clus
vv                                          TNFSF10 MUTATED TNFSF10 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V13, binary
                   cls
clus                  0   1
  TNFSF10 MUTATED     0   6
  TNFSF10 WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF10 MUTATED      0    6
  TNFSF10 WILD-TYPE    4  304
                        clus
vv                       TNFSF10 MUTATED TNFSF10 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(266) Variable = PIK3R3 MUTATION ANALYSIS
D266V1, survival
                  sevent
clus2                0   1
  PIK3R3 MUTATED     4   3
  PIK3R3 WILD-TYPE 226 136
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
               7              362 
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
               3              136 
$`PIK3R3 MUTATED`
TCGA-BR-4256 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-5801 TCGA-CG-4477 TCGA-HJ-7597 
        9.34        28.14        31.96        13.18        30.97        26.47 
TCGA-HU-A4G8 
       22.68 

$`PIK3R3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
            9.34             0.00 
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
           31.96           122.30 
  PIK3R3 MUTATED PIK3R3 WILD-TYPE 
           26.47            14.12 
[1] "9.3 - 32.0 (26.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D266V2, 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       2       15       37       30        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3R3 MUTATED           0          1          0          1        1
  PIK3R3 WILD-TYPE         3         69         53         31       37
D266V3, multiclass
            clus
vv           PIK3R3 MUTATED PIK3R3 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3R3 MUTATED     0   3   2   2
  PIK3R3 WILD-TYPE  22  89 171  95
D266V4, multiclass
    clus
vv   PIK3R3 MUTATED PIK3R3 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              2              171
  T4              2               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
  PIK3R3 MUTATED     3   3   1   1
  PIK3R3 WILD-TYPE 115 101  76  76
D266V5, multiclass
    clus
vv   PIK3R3 MUTATED PIK3R3 WILD-TYPE
  N0              3              115
  N1              3              101
  N2              1               76
  N3              1               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"
D266V6, binary
                  cls
clus                 0   1
  PIK3R3 MUTATED     6   1
  PIK3R3 WILD-TYPE 340  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R3 MUTATED      6    1
  PIK3R3 WILD-TYPE  340   28
   clus
vv  PIK3R3 MUTATED PIK3R3 WILD-TYPE
  0              6              340
  1              1               28
[1] 2 2
[1] FALSE
D266V7, binary
                  cls
clus                 0   1
  PIK3R3 MUTATED     4   4
  PIK3R3 WILD-TYPE 141 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R3 MUTATED      4    4
  PIK3R3 WILD-TYPE  141  244
        clus
vv       PIK3R3 MUTATED PIK3R3 WILD-TYPE
  FEMALE              4              141
  MALE                4              244
[1] 2 2
[1] FALSE
D266V8, binary
                  cls
clus                 0   1
  PIK3R3 MUTATED     7   1
  PIK3R3 WILD-TYPE 285  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R3 MUTATED      7    1
  PIK3R3 WILD-TYPE  285   58
     clus
vv    PIK3R3 MUTATED PIK3R3 WILD-TYPE
  NO               7              285
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PIK3R3 MUTATED                                          1
  PIK3R3 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PIK3R3 MUTATED                                       1
  PIK3R3 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIK3R3 MUTATED                                                        4
  PIK3R3 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PIK3R3 MUTATED                                                   0
  PIK3R3 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIK3R3 MUTATED                                                                   1
  PIK3R3 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PIK3R3 MUTATED                                                    0
  PIK3R3 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PIK3R3 MUTATED                                                  1
  PIK3R3 WILD-TYPE                                               60
D266V9, multiclass
                                                                   clus
vv                                                                  PIK3R3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  PIK3R3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PIK3R3 MUTATED     6   0   0   1
  PIK3R3 WILD-TYPE 305  14  15  23
D266V10, multiclass
    clus
vv   PIK3R3 MUTATED PIK3R3 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PIK3R3 MUTATED       3                         0
  PIK3R3 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIK3R3 MUTATED                                           0     4
  PIK3R3 WILD-TYPE                                         1   239
D266V12, multiclass
                                           clus
vv                                          PIK3R3 MUTATED PIK3R3 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V13, binary
                  cls
clus                 0   1
  PIK3R3 MUTATED     0   7
  PIK3R3 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R3 MUTATED      0    7
  PIK3R3 WILD-TYPE    4  303
                        clus
vv                       PIK3R3 MUTATED PIK3R3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(267) Variable = ZNF124 MUTATION ANALYSIS
D267V1, survival
                  sevent
clus2                0   1
  ZNF124 MUTATED     5   3
  ZNF124 WILD-TYPE 225 136
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               8              361 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               3              136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  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            14.17 
[1] "6.0 - 35.8 (17.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D267V2, 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       2       14       38       30        37        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF124 MUTATED           1          2          0          2        1
  ZNF124 WILD-TYPE         2         68         53         30       37
D267V3, multiclass
            clus
vv           ZNF124 MUTATED ZNF124 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               0               52
  STAGE III               1                2
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF124 MUTATED     1   2   1   5
  ZNF124 WILD-TYPE  21  90 172  92
D267V4, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  T1              1               21
  T2              2               90
  T3              1              172
  T4              5               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
  ZNF124 MUTATED     4   4   1   1
  ZNF124 WILD-TYPE 114 100  76  76
D267V5, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  N0              4              114
  N1              4              100
  N2              1               76
  N3              1               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"
D267V6, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     9   0
  ZNF124 WILD-TYPE 337  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      9    0
  ZNF124 WILD-TYPE  337   29
   clus
vv  ZNF124 MUTATED ZNF124 WILD-TYPE
  0              9              337
  1              0               29
[1] 2 2
[1] FALSE
D267V7, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     4   6
  ZNF124 WILD-TYPE 141 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      4    6
  ZNF124 WILD-TYPE  141  242
        clus
vv       ZNF124 MUTATED ZNF124 WILD-TYPE
  FEMALE              4              141
  MALE                6              242
[1] 2 2
[1] FALSE
D267V8, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     6   1
  ZNF124 WILD-TYPE 286  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      6    1
  ZNF124 WILD-TYPE  286   58
     clus
vv    ZNF124 MUTATED ZNF124 WILD-TYPE
  NO               6              286
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF124 MUTATED                                          0
  ZNF124 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF124 MUTATED                                       1
  ZNF124 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF124 MUTATED                                                        5
  ZNF124 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF124 MUTATED                                                   0
  ZNF124 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF124 MUTATED                                                                   4
  ZNF124 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF124 MUTATED                                                    0
  ZNF124 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF124 MUTATED                                                  0
  ZNF124 WILD-TYPE                                               61
D267V9, multiclass
                                                                   clus
vv                                                                  ZNF124 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  ZNF124 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF124 MUTATED     8   0   0   2
  ZNF124 WILD-TYPE 303  14  15  22
D267V10, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF124 MUTATED       2                         0
  ZNF124 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF124 MUTATED                                           0     5
  ZNF124 WILD-TYPE                                         1   238
D267V12, multiclass
                                           clus
vv                                          ZNF124 MUTATED ZNF124 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V13, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     0   7
  ZNF124 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      0    7
  ZNF124 WILD-TYPE    4  303
                        clus
vv                       ZNF124 MUTATED ZNF124 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(268) Variable = KNTC1 MUTATION ANALYSIS
D268V1, survival
                 sevent
clus2               0   1
  KNTC1 MUTATED    11   7
  KNTC1 WILD-TYPE 219 132
  KNTC1 MUTATED KNTC1 WILD-TYPE 
             18             351 
  KNTC1 MUTATED KNTC1 WILD-TYPE 
              7             132 
$`KNTC1 MUTATED`
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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-4253 
        9.44         6.61         6.97         4.64         7.43         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-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-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-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-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-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-A4BE 
       22.29        17.06        59.54         5.03        13.58        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-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-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 

  KNTC1 MUTATED KNTC1 WILD-TYPE 
           0.56            0.00 
  KNTC1 MUTATED KNTC1 WILD-TYPE 
         105.07          122.30 
  KNTC1 MUTATED KNTC1 WILD-TYPE 
          16.39           14.17 
[1] "0.6 - 105.1 (16.4)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D268V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KNTC1 MUTATED         0        0        3        1         2         2
  KNTC1 WILD-TYPE       2       15       37       29        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KNTC1 MUTATED           1          1          0          2        2
  KNTC1 WILD-TYPE         2         69         53         30       36
D268V3, multiclass
            clus
vv           KNTC1 MUTATED KNTC1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              1               2
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KNTC1 MUTATED     1   5   3   7
  KNTC1 WILD-TYPE  21  87 170  90
D268V4, multiclass
    clus
vv   KNTC1 MUTATED KNTC1 WILD-TYPE
  T1             1              21
  T2             5              87
  T3             3             170
  T4             7              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
  KNTC1 MUTATED     7   7   3   1
  KNTC1 WILD-TYPE 111  97  74  76
D268V5, multiclass
    clus
vv   KNTC1 MUTATED KNTC1 WILD-TYPE
  N0             7             111
  N1             7              97
  N2             3              74
  N3             1              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"
D268V6, binary
                 cls
clus                0   1
  KNTC1 MUTATED    18   1
  KNTC1 WILD-TYPE 328  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNTC1 MUTATED     18    1
  KNTC1 WILD-TYPE  328   28
   clus
vv  KNTC1 MUTATED KNTC1 WILD-TYPE
  0            18             328
  1             1              28
[1] 2 2
[1] FALSE
D268V7, binary
                 cls
clus                0   1
  KNTC1 MUTATED     7  13
  KNTC1 WILD-TYPE 138 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNTC1 MUTATED      7   13
  KNTC1 WILD-TYPE  138  235
        clus
vv       KNTC1 MUTATED KNTC1 WILD-TYPE
  FEMALE             7             138
  MALE              13             235
[1] 2 2
[1] FALSE
D268V8, binary
                 cls
clus                0   1
  KNTC1 MUTATED    15   1
  KNTC1 WILD-TYPE 277  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNTC1 MUTATED     15    1
  KNTC1 WILD-TYPE  277   58
     clus
vv    KNTC1 MUTATED KNTC1 WILD-TYPE
  NO             15             277
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KNTC1 MUTATED                                          0
  KNTC1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KNTC1 MUTATED                                       4
  KNTC1 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KNTC1 MUTATED                                                        9
  KNTC1 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KNTC1 MUTATED                                                   0
  KNTC1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KNTC1 MUTATED                                                                   6
  KNTC1 WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KNTC1 MUTATED                                                    0
  KNTC1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KNTC1 MUTATED                                                  1
  KNTC1 WILD-TYPE                                               60
D268V9, multiclass
                                                                   clus
vv                                                                  KNTC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  KNTC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KNTC1 MUTATED    13   0   0   5
  KNTC1 WILD-TYPE 298  14  15  19
D268V10, multiclass
    clus
vv   KNTC1 MUTATED KNTC1 WILD-TYPE
  R0            13             298
  R1             0              14
  R2             0              15
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KNTC1 MUTATED       5                         0
  KNTC1 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KNTC1 MUTATED                                           0    11
  KNTC1 WILD-TYPE                                         1   232
D268V12, multiclass
                                           clus
vv                                          KNTC1 MUTATED KNTC1 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V13, binary
                 cls
clus                0   1
  KNTC1 MUTATED     0  15
  KNTC1 WILD-TYPE   4 295
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNTC1 MUTATED      0   15
  KNTC1 WILD-TYPE    4  295
                        clus
vv                       KNTC1 MUTATED KNTC1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            15             295
[1] 2 2
[1] FALSE

Clustering(269) Variable = GAS6 MUTATION ANALYSIS
D269V1, survival
                sevent
clus2              0   1
  GAS6 MUTATED     8   7
  GAS6 WILD-TYPE 222 132
  GAS6 MUTATED GAS6 WILD-TYPE 
            15            354 
  GAS6 MUTATED GAS6 WILD-TYPE 
             7            132 
$`GAS6 MUTATED`
TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8591 TCGA-BR-A4CQ TCGA-BR-A4QL 
        6.97         9.67        34.68        28.14        34.98        16.14 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 TCGA-D7-A4YV 
        6.58         1.02         6.02        28.96        65.10         5.92 
TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-VQ-A8P2 
       22.68        20.25        38.14 

$`GAS6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  GAS6 MUTATED GAS6 WILD-TYPE 
          1.02           0.00 
  GAS6 MUTATED GAS6 WILD-TYPE 
          65.1          122.3 
  GAS6 MUTATED GAS6 WILD-TYPE 
         20.25          14.12 
[1] "1.0 - 65.1 (20.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D269V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GAS6 MUTATED         0        1        1        0         2         2
  GAS6 WILD-TYPE       2       14       39       30        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GAS6 MUTATED           0          3          1          2        3
  GAS6 WILD-TYPE         3         67         52         30       35
D269V3, multiclass
            clus
vv           GAS6 MUTATED GAS6 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            1             52
  STAGE IIIC            2             30
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GAS6 MUTATED     1   1   7   6
  GAS6 WILD-TYPE  21  91 166  91
D269V4, multiclass
    clus
vv   GAS6 MUTATED GAS6 WILD-TYPE
  T1            1             21
  T2            1             91
  T3            7            166
  T4            6             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
  GAS6 MUTATED     4   6   3   2
  GAS6 WILD-TYPE 114  98  74  75
D269V5, multiclass
    clus
vv   GAS6 MUTATED GAS6 WILD-TYPE
  N0            4            114
  N1            6             98
  N2            3             74
  N3            2             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"
D269V6, binary
                cls
clus               0   1
  GAS6 MUTATED    14   1
  GAS6 WILD-TYPE 332  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED     14    1
  GAS6 WILD-TYPE  332   28
   clus
vv  GAS6 MUTATED GAS6 WILD-TYPE
  0           14            332
  1            1             28
[1] 2 2
[1] FALSE
D269V7, binary
                cls
clus               0   1
  GAS6 MUTATED     8   8
  GAS6 WILD-TYPE 137 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      8    8
  GAS6 WILD-TYPE  137  240
        clus
vv       GAS6 MUTATED GAS6 WILD-TYPE
  FEMALE            8            137
  MALE              8            240
[1] 2 2
[1] FALSE
D269V8, binary
                cls
clus               0   1
  GAS6 MUTATED    11   1
  GAS6 WILD-TYPE 281  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED     11    1
  GAS6 WILD-TYPE  281   58
     clus
vv    GAS6 MUTATED GAS6 WILD-TYPE
  NO            11            281
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GAS6 MUTATED                                          0
  GAS6 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GAS6 MUTATED                                       3
  GAS6 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GAS6 MUTATED                                                        8
  GAS6 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GAS6 MUTATED                                                   1
  GAS6 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GAS6 MUTATED                                                                   3
  GAS6 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GAS6 MUTATED                                                    0
  GAS6 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GAS6 MUTATED                                                  1
  GAS6 WILD-TYPE                                               60
D269V9, multiclass
                                                                   clus
vv                                                                  GAS6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  GAS6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GAS6 MUTATED    10   0   1   3
  GAS6 WILD-TYPE 301  14  14  21
D269V10, multiclass
    clus
vv   GAS6 MUTATED GAS6 WILD-TYPE
  R0           10            301
  R1            0             14
  R2            1             14
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GAS6 MUTATED       3                         0
  GAS6 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GAS6 MUTATED                                           0     9
  GAS6 WILD-TYPE                                         1   234
D269V12, multiclass
                                           clus
vv                                          GAS6 MUTATED GAS6 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V13, binary
                cls
clus               0   1
  GAS6 MUTATED     0  11
  GAS6 WILD-TYPE   4 299
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS6 MUTATED      0   11
  GAS6 WILD-TYPE    4  299
                        clus
vv                       GAS6 MUTATED GAS6 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           11            299
[1] 2 2
[1] FALSE

Clustering(270) Variable = HCFC1R1 MUTATION ANALYSIS
D270V1, survival
                   sevent
clus2                 0   1
  HCFC1R1 MUTATED     5   1
  HCFC1R1 WILD-TYPE 225 138
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                6               363 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                1               138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         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 

  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            14.070 
[1] "1.1 - 30.9 (29.8)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.3"
D270V2, 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       2       15       40       30        35        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HCFC1R1 MUTATED           0          0          0          1        0
  HCFC1R1 WILD-TYPE         3         70         53         31       38
D270V3, multiclass
            clus
vv           HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  HCFC1R1 MUTATED     0   2   2   2
  HCFC1R1 WILD-TYPE  22  90 171  95
D270V4, multiclass
    clus
vv   HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  T1               0                22
  T2               2                90
  T3               2               171
  T4               2                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
  HCFC1R1 MUTATED     2   2   0   1
  HCFC1R1 WILD-TYPE 116 102  77  76
D270V5, multiclass
    clus
vv   HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  N0               2               116
  N1               2               102
  N2               0                77
  N3               1                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"
D270V6, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     6   0
  HCFC1R1 WILD-TYPE 340  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      6    0
  HCFC1R1 WILD-TYPE  340   29
   clus
vv  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  0               6               340
  1               0                29
[1] 2 2
[1] FALSE
D270V7, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     4   2
  HCFC1R1 WILD-TYPE 141 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      4    2
  HCFC1R1 WILD-TYPE  141  246
        clus
vv       HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  FEMALE               4               141
  MALE                 2               246
[1] 2 2
[1] FALSE
D270V8, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     5   1
  HCFC1R1 WILD-TYPE 287  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      5    1
  HCFC1R1 WILD-TYPE  287   58
     clus
vv    HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  NO                5               287
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HCFC1R1 MUTATED                                          0
  HCFC1R1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HCFC1R1 MUTATED                                       1
  HCFC1R1 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HCFC1R1 MUTATED                                                        3
  HCFC1R1 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HCFC1R1 MUTATED                                                   1
  HCFC1R1 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HCFC1R1 MUTATED                                                                   0
  HCFC1R1 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HCFC1R1 MUTATED                                                    0
  HCFC1R1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HCFC1R1 MUTATED                                                  1
  HCFC1R1 WILD-TYPE                                               60
D270V9, multiclass
                                                                   clus
vv                                                                  HCFC1R1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  HCFC1R1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  HCFC1R1 MUTATED     4   1   0   1
  HCFC1R1 WILD-TYPE 307  13  15  23
D270V10, multiclass
    clus
vv   HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  R0               4               307
  R1               1                13
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  HCFC1R1 MUTATED       2                         0
  HCFC1R1 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HCFC1R1 MUTATED                                           0     3
  HCFC1R1 WILD-TYPE                                         1   240
D270V12, multiclass
                                           clus
vv                                          HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V13, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     0   5
  HCFC1R1 WILD-TYPE   4 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      0    5
  HCFC1R1 WILD-TYPE    4  305
                        clus
vv                       HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(271) Variable = NCAPD3 MUTATION ANALYSIS
D271V1, survival
                  sevent
clus2                0   1
  NCAPD3 MUTATED    10   6
  NCAPD3 WILD-TYPE 220 133
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              16              353 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
               6              133 
$`NCAPD3 MUTATED`
TCGA-B7-A5TI TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8680 
       19.56        34.68        31.10        27.12        26.73        31.96 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5726 TCGA-D7-6524 TCGA-FP-7735 
       16.14         6.58         9.01        28.96        17.85         3.48 
TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4H8 TCGA-R5-A7ZI 
       11.08        26.47        14.07        74.53 

$`NCAPD3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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 
            3.48             0.00 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
           74.53           122.30 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
          23.015           14.040 
[1] "3.5 - 74.5 (23.0)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.3"
D271V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NCAPD3 MUTATED         0        1        3        1         3         1
  NCAPD3 WILD-TYPE       2       14       37       29        34        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NCAPD3 MUTATED           0          0          3          2        3
  NCAPD3 WILD-TYPE         3         70         50         30       35
D271V3, multiclass
            clus
vv           NCAPD3 MUTATED NCAPD3 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                3               37
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              3               50
  STAGE IIIC              2               30
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NCAPD3 MUTATED     3   3   5   7
  NCAPD3 WILD-TYPE  19  89 168  90
D271V4, multiclass
    clus
vv   NCAPD3 MUTATED NCAPD3 WILD-TYPE
  T1              3               19
  T2              3               89
  T3              5              168
  T4              7               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
  NCAPD3 MUTATED     7   4   2   4
  NCAPD3 WILD-TYPE 111 100  75  73
D271V5, multiclass
    clus
vv   NCAPD3 MUTATED NCAPD3 WILD-TYPE
  N0              7              111
  N1              4              100
  N2              2               75
  N3              4               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"
D271V6, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    14   3
  NCAPD3 WILD-TYPE 332  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     14    3
  NCAPD3 WILD-TYPE  332   26
   clus
vv  NCAPD3 MUTATED NCAPD3 WILD-TYPE
  0             14              332
  1              3               26
[1] 2 2
[1] FALSE
D271V7, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED     9  10
  NCAPD3 WILD-TYPE 136 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED      9   10
  NCAPD3 WILD-TYPE  136  238
        clus
vv       NCAPD3 MUTATED NCAPD3 WILD-TYPE
  FEMALE              9              136
  MALE               10              238
[1] 2 2
[1] FALSE
D271V8, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    14   1
  NCAPD3 WILD-TYPE 278  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     14    1
  NCAPD3 WILD-TYPE  278   58
     clus
vv    NCAPD3 MUTATED NCAPD3 WILD-TYPE
  NO              14              278
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NCAPD3 MUTATED                                          1
  NCAPD3 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NCAPD3 MUTATED                                       5
  NCAPD3 WILD-TYPE                                    65
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NCAPD3 MUTATED                                                        9
  NCAPD3 WILD-TYPE                                                    149
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NCAPD3 MUTATED                                                   0
  NCAPD3 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NCAPD3 MUTATED                                                                   2
  NCAPD3 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NCAPD3 MUTATED                                                    0
  NCAPD3 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NCAPD3 MUTATED                                                  2
  NCAPD3 WILD-TYPE                                               59
D271V9, multiclass
                                                                   clus
vv                                                                  NCAPD3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  NCAPD3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NCAPD3 MUTATED    13   1   1   2
  NCAPD3 WILD-TYPE 298  13  14  22
D271V10, multiclass
    clus
vv   NCAPD3 MUTATED NCAPD3 WILD-TYPE
  R0             13              298
  R1              1               13
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NCAPD3 MUTATED       3                         2
  NCAPD3 WILD-TYPE    84                         7
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NCAPD3 MUTATED                                           0    12
  NCAPD3 WILD-TYPE                                         1   231
D271V12, multiclass
                                           clus
vv                                          NCAPD3 MUTATED NCAPD3 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              2                7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V13, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED     1  16
  NCAPD3 WILD-TYPE   3 294
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED      1   16
  NCAPD3 WILD-TYPE    3  294
                        clus
vv                       NCAPD3 MUTATED NCAPD3 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             16              294
[1] 2 2
[1] FALSE

Clustering(272) Variable = TAF1L MUTATION ANALYSIS
D272V1, survival
                 sevent
clus2               0   1
  TAF1L MUTATED    19  10
  TAF1L WILD-TYPE 211 129
  TAF1L MUTATED TAF1L WILD-TYPE 
             29             340 
  TAF1L MUTATED TAF1L WILD-TYPE 
             10             129 
$`TAF1L MUTATED`
TCGA-B7-5818 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6705 TCGA-BR-6802 TCGA-BR-7707 
       11.70        30.90        34.68        25.61        30.90        35.84 
TCGA-BR-8284 TCGA-BR-8297 TCGA-BR-8485 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL 
        8.05         7.40         9.21        28.14        31.96        16.14 
TCGA-CG-4305 TCGA-CG-4477 TCGA-D7-6521 TCGA-D7-A4YX TCGA-F1-A448 TCGA-FP-A9TM 
       15.95        30.97        18.54        36.43        21.27         6.21 
TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4H8 TCGA-IN-A6RL TCGA-RD-A8N1 TCGA-RD-A8N5 
       11.77         0.10        14.07        13.35       115.69        57.44 
TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A91U TCGA-VQ-A94T 
       13.02        37.41        38.14         1.71        11.24 

$`TAF1L WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-6706 TCGA-BR-6707 
       39.12        26.10         9.17        32.78        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-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-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-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-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-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-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-D7-6522 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-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-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-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-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-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-A8N2 TCGA-RD-A8N4 
       16.67       122.30        37.91        40.64       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-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK 
        5.46        13.25        43.36        37.22        22.19        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-AA64 
        1.87        15.65        20.81        42.64        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 

  TAF1L MUTATED TAF1L WILD-TYPE 
            0.1             0.0 
  TAF1L MUTATED TAF1L WILD-TYPE 
         115.69          122.30 
  TAF1L MUTATED TAF1L WILD-TYPE 
         18.540          14.055 
[1] "0.1 - 115.7 (18.5)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D272V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAF1L MUTATED         1        1        4        1         1         1
  TAF1L WILD-TYPE       1       14       36       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAF1L MUTATED           0          5          5          5        3
  TAF1L WILD-TYPE         3         65         48         27       35
D272V3, multiclass
            clus
vv           TAF1L MUTATED TAF1L WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               4              36
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             5              65
  STAGE IIIB             5              48
  STAGE IIIC             5              27
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TAF1L MUTATED     4   8  11   8
  TAF1L WILD-TYPE  18  84 162  89
D272V4, multiclass
    clus
vv   TAF1L MUTATED TAF1L WILD-TYPE
  T1             4              18
  T2             8              84
  T3            11             162
  T4             8              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
  TAF1L MUTATED     5  10   6   8
  TAF1L WILD-TYPE 113  94  71  69
D272V5, multiclass
    clus
vv   TAF1L MUTATED TAF1L WILD-TYPE
  N0             5             113
  N1            10              94
  N2             6              71
  N3             8              69
[1] 4 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
  TAF1L MUTATED    27   3
  TAF1L WILD-TYPE 319  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED     27    3
  TAF1L WILD-TYPE  319   26
   clus
vv  TAF1L MUTATED TAF1L WILD-TYPE
  0            27             319
  1             3              26
[1] 2 2
[1] FALSE
D272V7, binary
                 cls
clus                0   1
  TAF1L MUTATED     8  23
  TAF1L WILD-TYPE 137 225
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED      8   23
  TAF1L WILD-TYPE  137  225
        clus
vv       TAF1L MUTATED TAF1L WILD-TYPE
  FEMALE             8             137
  MALE              23             225
[1] 2 2
[1] FALSE
D272V8, binary
                 cls
clus                0   1
  TAF1L MUTATED    24   6
  TAF1L WILD-TYPE 268  53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED     24    6
  TAF1L WILD-TYPE  268   53
     clus
vv    TAF1L MUTATED TAF1L WILD-TYPE
  NO             24             268
  YES             6              53
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TAF1L MUTATED                                          1
  TAF1L WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TAF1L MUTATED                                       5
  TAF1L WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TAF1L MUTATED                                                       13
  TAF1L WILD-TYPE                                                    145
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TAF1L MUTATED                                                   3
  TAF1L WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TAF1L MUTATED                                                                   3
  TAF1L WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TAF1L MUTATED                                                    0
  TAF1L WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TAF1L MUTATED                                                  6
  TAF1L WILD-TYPE                                               55
D272V9, multiclass
                                                                   clus
vv                                                                  TAF1L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              6
                                                                   clus
vv                                                                  TAF1L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TAF1L MUTATED    27   1   1   2
  TAF1L WILD-TYPE 284  13  14  22
D272V10, multiclass
    clus
vv   TAF1L MUTATED TAF1L WILD-TYPE
  R0            27             284
  R1             1              13
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TAF1L MUTATED       5                         2
  TAF1L WILD-TYPE    82                         7
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAF1L MUTATED                                           0    21
  TAF1L WILD-TYPE                                         1   222
D272V12, multiclass
                                           clus
vv                                          TAF1L MUTATED TAF1L WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             2               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                21             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V13, binary
                 cls
clus                0   1
  TAF1L MUTATED     1  23
  TAF1L WILD-TYPE   3 287
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED      1   23
  TAF1L WILD-TYPE    3  287
                        clus
vv                       TAF1L MUTATED TAF1L WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            23             287
[1] 2 2
[1] FALSE

Clustering(273) Variable = LRRN2 MUTATION ANALYSIS
D273V1, survival
                 sevent
clus2               0   1
  LRRN2 MUTATED    21  12
  LRRN2 WILD-TYPE 209 127
  LRRN2 MUTATED LRRN2 WILD-TYPE 
             33             336 
  LRRN2 MUTATED LRRN2 WILD-TYPE 
             12             127 
$`LRRN2 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8284 
       21.99        34.68        44.94        14.43        29.59         8.05 
TCGA-BR-8360 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8382 TCGA-BR-8487 
        6.18        26.33         4.31        11.80        25.05         1.12 
TCGA-BR-8677 TCGA-BR-8683 TCGA-BR-A4J2 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
       26.73         9.86        14.17        12.59        12.53        12.33 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 
       12.30        12.39        12.59        11.64        12.07        12.43 
TCGA-CD-A48A TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-FP-8211 TCGA-HU-8243 
       12.43        19.50        17.19        14.66        13.58         5.92 
TCGA-HU-A4GP TCGA-RD-A7BW TCGA-VQ-A91U 
        8.98         5.13         1.71 

$`LRRN2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
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-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-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
        0.95        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-8678 
       27.12         9.34        28.14         6.28         7.53        24.79 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58        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-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98         0.72         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-8527 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        7.17        15.39        12.82         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-D7-8575 TCGA-D7-8578 
       11.31        12.33        24.72        16.80        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-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-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-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-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-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-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 

  LRRN2 MUTATED LRRN2 WILD-TYPE 
           1.12            0.00 
  LRRN2 MUTATED LRRN2 WILD-TYPE 
          44.94          122.30 
  LRRN2 MUTATED LRRN2 WILD-TYPE 
          12.43           15.27 
[1] "1.1 - 44.9 (12.4)"  "0.0 - 122.3 (15.3)"
[1] "hr=" "1.2"
D273V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRRN2 MUTATED         0        0        2        4         7         4
  LRRN2 WILD-TYPE       2       15       38       26        30        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRN2 MUTATED           1          6          5          3        2
  LRRN2 WILD-TYPE         2         64         48         29       36
D273V3, multiclass
            clus
vv           LRRN2 MUTATED LRRN2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               4              26
  STAGE IIA              7              30
  STAGE IIB              4              48
  STAGE III              1               2
  STAGE IIIA             6              64
  STAGE IIIB             5              48
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LRRN2 MUTATED     0   4  19  11
  LRRN2 WILD-TYPE  22  88 154  86
D273V4, multiclass
    clus
vv   LRRN2 MUTATED LRRN2 WILD-TYPE
  T1             0              22
  T2             4              88
  T3            19             154
  T4            11              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
  LRRN2 MUTATED    17   8   1   8
  LRRN2 WILD-TYPE 101  96  76  69
D273V5, multiclass
    clus
vv   LRRN2 MUTATED LRRN2 WILD-TYPE
  N0            17             101
  N1             8              96
  N2             1              76
  N3             8              69
[1] 4 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
  LRRN2 MUTATED    31   2
  LRRN2 WILD-TYPE 315  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN2 MUTATED     31    2
  LRRN2 WILD-TYPE  315   27
   clus
vv  LRRN2 MUTATED LRRN2 WILD-TYPE
  0            31             315
  1             2              27
[1] 2 2
[1] FALSE
D273V7, binary
                 cls
clus                0   1
  LRRN2 MUTATED    16  18
  LRRN2 WILD-TYPE 129 230
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN2 MUTATED     16   18
  LRRN2 WILD-TYPE  129  230
        clus
vv       LRRN2 MUTATED LRRN2 WILD-TYPE
  FEMALE            16             129
  MALE              18             230
[1] 2 2
[1] FALSE
D273V8, binary
                 cls
clus                0   1
  LRRN2 MUTATED    26   8
  LRRN2 WILD-TYPE 266  51
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN2 MUTATED     26    8
  LRRN2 WILD-TYPE  266   51
     clus
vv    LRRN2 MUTATED LRRN2 WILD-TYPE
  NO             26             266
  YES             8              51
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LRRN2 MUTATED                                          0
  LRRN2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LRRN2 MUTATED                                       6
  LRRN2 WILD-TYPE                                    64
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LRRN2 MUTATED                                                       15
  LRRN2 WILD-TYPE                                                    143
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LRRN2 MUTATED                                                   2
  LRRN2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LRRN2 MUTATED                                                                   7
  LRRN2 WILD-TYPE                                                                61
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LRRN2 MUTATED                                                    0
  LRRN2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LRRN2 MUTATED                                                  4
  LRRN2 WILD-TYPE                                               57
D273V9, multiclass
                                                                   clus
vv                                                                  LRRN2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             7
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  LRRN2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              61
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LRRN2 MUTATED    31   1   1   0
  LRRN2 WILD-TYPE 280  13  14  24
D273V10, multiclass
    clus
vv   LRRN2 MUTATED LRRN2 WILD-TYPE
  R0            31             280
  R1             1              13
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LRRN2 MUTATED      15                         0
  LRRN2 WILD-TYPE    72                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LRRN2 MUTATED                                           0    18
  LRRN2 WILD-TYPE                                         1   225
D273V12, multiclass
                                           clus
vv                                          LRRN2 MUTATED LRRN2 WILD-TYPE
  ASIAN                                                15              72
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                18             225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V13, binary
                 cls
clus                0   1
  LRRN2 MUTATED     0  32
  LRRN2 WILD-TYPE   4 278
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN2 MUTATED      0   32
  LRRN2 WILD-TYPE    4  278
                        clus
vv                       LRRN2 MUTATED LRRN2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            32             278
[1] 2 2
[1] FALSE

Clustering(274) Variable = C17ORF57 MUTATION ANALYSIS
D274V1, survival
                    sevent
clus2                  0   1
  C17ORF57 MUTATED     8   1
  C17ORF57 WILD-TYPE 222 138
  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
                 9                360 
  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
                 1                138 
$`C17ORF57 MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 
       19.56         6.97        31.10         1.12        31.96         6.02 
TCGA-HF-A5NB TCGA-HU-A4GT TCGA-VQ-A8P2 
       30.51         6.51        38.14 

$`C17ORF57 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
              1.12               0.00 
  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
             38.14             122.30 
  C17ORF57 MUTATED C17ORF57 WILD-TYPE 
             19.56              14.22 
[1] "1.1 - 38.1 (19.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3.6"
D274V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C17ORF57 MUTATED         0        1        0        0         2         0
  C17ORF57 WILD-TYPE       2       14       40       30        35        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C17ORF57 MUTATED           0          2          0          3        2
  C17ORF57 WILD-TYPE         3         68         53         29       36
D274V3, multiclass
            clus
vv           C17ORF57 MUTATED C17ORF57 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 2                 35
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                0                 53
  STAGE IIIC                3                 29
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C17ORF57 MUTATED     1   0   3   6
  C17ORF57 WILD-TYPE  21  92 170  91
D274V4, multiclass
    clus
vv   C17ORF57 MUTATED C17ORF57 WILD-TYPE
  T1                1                 21
  T2                0                 92
  T3                3                170
  T4                6                 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
  C17ORF57 MUTATED     3   4   2   2
  C17ORF57 WILD-TYPE 115 100  75  75
D274V5, multiclass
    clus
vv   C17ORF57 MUTATED C17ORF57 WILD-TYPE
  N0                3                115
  N1                4                100
  N2                2                 75
  N3                2                 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"
D274V6, binary
                    cls
clus                   0   1
  C17ORF57 MUTATED    10   1
  C17ORF57 WILD-TYPE 336  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF57 MUTATED     10    1
  C17ORF57 WILD-TYPE  336   28
   clus
vv  C17ORF57 MUTATED C17ORF57 WILD-TYPE
  0               10                336
  1                1                 28
[1] 2 2
[1] FALSE
D274V7, binary
                    cls
clus                   0   1
  C17ORF57 MUTATED     6   6
  C17ORF57 WILD-TYPE 139 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF57 MUTATED      6    6
  C17ORF57 WILD-TYPE  139  242
        clus
vv       C17ORF57 MUTATED C17ORF57 WILD-TYPE
  FEMALE                6                139
  MALE                  6                242
[1] 2 2
[1] FALSE
D274V8, binary
                    cls
clus                   0   1
  C17ORF57 MUTATED     7   3
  C17ORF57 WILD-TYPE 285  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF57 MUTATED      7    3
  C17ORF57 WILD-TYPE  285   56
     clus
vv    C17ORF57 MUTATED C17ORF57 WILD-TYPE
  NO                 7                285
  YES                3                 56
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C17ORF57 MUTATED                                          0
  C17ORF57 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C17ORF57 MUTATED                                       1
  C17ORF57 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C17ORF57 MUTATED                                                        6
  C17ORF57 WILD-TYPE                                                    152
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C17ORF57 MUTATED                                                   2
  C17ORF57 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C17ORF57 MUTATED                                                                   1
  C17ORF57 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C17ORF57 MUTATED                                                    0
  C17ORF57 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C17ORF57 MUTATED                                                  2
  C17ORF57 WILD-TYPE                                               59
D274V9, multiclass
                                                                   clus
vv                                                                  C17ORF57 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  C17ORF57 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C17ORF57 MUTATED     7   1   0   3
  C17ORF57 WILD-TYPE 304  13  15  21
D274V10, multiclass
    clus
vv   C17ORF57 MUTATED C17ORF57 WILD-TYPE
  R0                7                304
  R1                1                 13
  R2                0                 15
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C17ORF57 MUTATED       3                         0
  C17ORF57 WILD-TYPE    84                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C17ORF57 MUTATED                                           0     7
  C17ORF57 WILD-TYPE                                         1   236
D274V12, multiclass
                                           clus
vv                                          C17ORF57 MUTATED C17ORF57 WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V13, binary
                    cls
clus                   0   1
  C17ORF57 MUTATED     0   9
  C17ORF57 WILD-TYPE   4 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF57 MUTATED      0    9
  C17ORF57 WILD-TYPE    4  301
                        clus
vv                       C17ORF57 MUTATED C17ORF57 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                9                301
[1] 2 2
[1] FALSE

Clustering(275) Variable = BEND3 MUTATION ANALYSIS
D275V1, survival
                 sevent
clus2               0   1
  BEND3 MUTATED     6   4
  BEND3 WILD-TYPE 224 135
  BEND3 MUTATED BEND3 WILD-TYPE 
             10             359 
  BEND3 MUTATED BEND3 WILD-TYPE 
              4             135 
$`BEND3 MUTATED`
TCGA-BR-4257 TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5723 
        9.67         0.26         1.12        12.43        11.77       105.07 
TCGA-CG-5733 TCGA-D7-6528 TCGA-HU-A4H8 TCGA-MX-A5UJ 
       21.07        15.22        14.07        19.73 

$`BEND3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-D7-6815 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-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 

  BEND3 MUTATED BEND3 WILD-TYPE 
           0.26            0.00 
  BEND3 MUTATED BEND3 WILD-TYPE 
         105.07          122.30 
  BEND3 MUTATED BEND3 WILD-TYPE 
          13.25           14.43 
[1] "0.3 - 105.1 (13.2)" "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D275V2, 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       2       15       36       28        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BEND3 MUTATED           0          3          0          0        0
  BEND3 WILD-TYPE         3         67         53         32       38
D275V3, multiclass
            clus
vv           BEND3 MUTATED BEND3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               4              36
  STAGE II               2              28
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BEND3 MUTATED     1   5   4   0
  BEND3 WILD-TYPE  21  87 169  97
D275V4, multiclass
    clus
vv   BEND3 MUTATED BEND3 WILD-TYPE
  T1             1              21
  T2             5              87
  T3             4             169
  T4             0              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
  BEND3 MUTATED     5   3   2   0
  BEND3 WILD-TYPE 113 101  75  77
D275V5, multiclass
    clus
vv   BEND3 MUTATED BEND3 WILD-TYPE
  N0             5             113
  N1             3             101
  N2             2              75
  N3             0              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"
D275V6, binary
                 cls
clus                0   1
  BEND3 MUTATED    12   0
  BEND3 WILD-TYPE 334  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND3 MUTATED     12    0
  BEND3 WILD-TYPE  334   29
   clus
vv  BEND3 MUTATED BEND3 WILD-TYPE
  0            12             334
  1             0              29
[1] 2 2
[1] FALSE
D275V7, binary
                 cls
clus                0   1
  BEND3 MUTATED     7   5
  BEND3 WILD-TYPE 138 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND3 MUTATED      7    5
  BEND3 WILD-TYPE  138  243
        clus
vv       BEND3 MUTATED BEND3 WILD-TYPE
  FEMALE             7             138
  MALE               5             243
[1] 2 2
[1] FALSE
D275V8, binary
                 cls
clus                0   1
  BEND3 MUTATED    10   0
  BEND3 WILD-TYPE 282  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND3 MUTATED     10    0
  BEND3 WILD-TYPE  282   59
     clus
vv    BEND3 MUTATED BEND3 WILD-TYPE
  NO             10             282
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BEND3 MUTATED                                          0
  BEND3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BEND3 MUTATED                                       0
  BEND3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BEND3 MUTATED                                                        7
  BEND3 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BEND3 MUTATED                                                   0
  BEND3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BEND3 MUTATED                                                                   2
  BEND3 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BEND3 MUTATED                                                    0
  BEND3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BEND3 MUTATED                                                  3
  BEND3 WILD-TYPE                                               58
D275V9, multiclass
                                                                   clus
vv                                                                  BEND3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  BEND3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BEND3 MUTATED     9   0   0   2
  BEND3 WILD-TYPE 302  14  15  22
D275V10, multiclass
    clus
vv   BEND3 MUTATED BEND3 WILD-TYPE
  R0             9             302
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BEND3 MUTATED       3                         0
  BEND3 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BEND3 MUTATED                                           0     6
  BEND3 WILD-TYPE                                         1   237
D275V12, multiclass
                                           clus
vv                                          BEND3 MUTATED BEND3 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V13, binary
                 cls
clus                0   1
  BEND3 MUTATED     0   9
  BEND3 WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND3 MUTATED      0    9
  BEND3 WILD-TYPE    4  301
                        clus
vv                       BEND3 MUTATED BEND3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(276) Variable = FAM98C MUTATION ANALYSIS
D276V1, survival
                  sevent
clus2                0   1
  FAM98C MUTATED     6   0
  FAM98C WILD-TYPE 224 139
  FAM98C MUTATED FAM98C WILD-TYPE 
               6              363 
  FAM98C MUTATED FAM98C WILD-TYPE 
               0              139 
$`FAM98C MUTATED`
TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8591 TCGA-BR-8680 TCGA-CG-4305 TCGA-HU-A4GT 
       44.94        29.59        28.14        31.96        15.95         6.51 

$`FAM98C WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-6822 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 

  FAM98C MUTATED FAM98C WILD-TYPE 
            6.51             0.00 
  FAM98C MUTATED FAM98C WILD-TYPE 
           44.94           122.30 
  FAM98C MUTATED FAM98C WILD-TYPE 
          28.865           14.070 
[1] "6.5 - 44.9 (28.9)"  "0.0 - 122.3 (14.1)"
[1] "hr="     "9300000"
D276V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM98C MUTATED         0        0        1        1         2         1
  FAM98C WILD-TYPE       2       15       39       29        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM98C MUTATED           0          0          0          1        2
  FAM98C WILD-TYPE         3         70         53         31       36
D276V3, multiclass
            clus
vv           FAM98C MUTATED FAM98C WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM98C MUTATED     0   2   2   4
  FAM98C WILD-TYPE  22  90 171  93
D276V4, multiclass
    clus
vv   FAM98C MUTATED FAM98C WILD-TYPE
  T1              0               22
  T2              2               90
  T3              2              171
  T4              4               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
  FAM98C MUTATED     4   1   2   1
  FAM98C WILD-TYPE 114 103  75  76
D276V5, multiclass
    clus
vv   FAM98C MUTATED FAM98C WILD-TYPE
  N0              4              114
  N1              1              103
  N2              2               75
  N3              1               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"
D276V6, binary
                  cls
clus                 0   1
  FAM98C MUTATED     7   1
  FAM98C WILD-TYPE 339  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98C MUTATED      7    1
  FAM98C WILD-TYPE  339   28
   clus
vv  FAM98C MUTATED FAM98C WILD-TYPE
  0              7              339
  1              1               28
[1] 2 2
[1] FALSE
D276V7, binary
                  cls
clus                 0   1
  FAM98C MUTATED     4   4
  FAM98C WILD-TYPE 141 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98C MUTATED      4    4
  FAM98C WILD-TYPE  141  244
        clus
vv       FAM98C MUTATED FAM98C WILD-TYPE
  FEMALE              4              141
  MALE                4              244
[1] 2 2
[1] FALSE
D276V8, binary
                  cls
clus                 0   1
  FAM98C MUTATED     6   0
  FAM98C WILD-TYPE 286  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98C MUTATED      6    0
  FAM98C WILD-TYPE  286   59
     clus
vv    FAM98C MUTATED FAM98C WILD-TYPE
  NO               6              286
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM98C MUTATED                                          0
  FAM98C WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM98C MUTATED                                       0
  FAM98C WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM98C MUTATED                                                        5
  FAM98C WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM98C MUTATED                                                   0
  FAM98C WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM98C MUTATED                                                                   1
  FAM98C WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM98C MUTATED                                                    0
  FAM98C WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM98C MUTATED                                                  2
  FAM98C WILD-TYPE                                               59
D276V9, multiclass
                                                                   clus
vv                                                                  FAM98C MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  FAM98C WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAM98C MUTATED     7   0   0   1
  FAM98C WILD-TYPE 304  14  15  23
D276V10, multiclass
    clus
vv   FAM98C MUTATED FAM98C WILD-TYPE
  R0              7              304
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAM98C MUTATED       2                         0
  FAM98C WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM98C MUTATED                                           0     4
  FAM98C WILD-TYPE                                         1   239
D276V12, multiclass
                                           clus
vv                                          FAM98C MUTATED FAM98C WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V13, binary
                  cls
clus                 0   1
  FAM98C MUTATED     0   6
  FAM98C WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98C MUTATED      0    6
  FAM98C WILD-TYPE    4  304
                        clus
vv                       FAM98C MUTATED FAM98C WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(277) Variable = KIAA0100 MUTATION ANALYSIS
D277V1, survival
                    sevent
clus2                  0   1
  KIAA0100 MUTATED    12   7
  KIAA0100 WILD-TYPE 218 132
  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
                19                350 
  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
                 7                132 
$`KIAA0100 MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8361 TCGA-BR-8382 TCGA-CD-A4MG TCGA-CG-4306 
       34.68        36.16        31.10        25.05         6.58         1.02 
TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A4YT TCGA-D7-A6EY 
        9.01        30.97       105.07        28.96        14.27        11.44 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-IN-A6RS TCGA-MX-A5UJ 
       22.68        24.20        11.77         0.10        12.59        19.73 
TCGA-RD-A8N9 
       35.61 

$`KIAA0100 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        1.02         0.99         6.02         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-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-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-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-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-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-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-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 

  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
               0.1                0.0 
  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
            105.07             122.30 
  KIAA0100 MUTATED KIAA0100 WILD-TYPE 
             22.68              14.07 
[1] "0.1 - 105.1 (22.7)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D277V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0100 MUTATED         0        5        2        2         2         2
  KIAA0100 WILD-TYPE       2       10       38       28        35        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0100 MUTATED           0          3          1          3        3
  KIAA0100 WILD-TYPE         3         67         52         29       35
D277V3, multiclass
            clus
vv           KIAA0100 MUTATED KIAA0100 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  5                 10
  STAGE IB                  2                 38
  STAGE II                  2                 28
  STAGE IIA                 2                 35
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                3                 67
  STAGE IIIB                1                 52
  STAGE IIIC                3                 29
  STAGE IV                  3                 35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0100 MUTATED     6   5   6   7
  KIAA0100 WILD-TYPE  16  87 167  90
D277V4, multiclass
    clus
vv   KIAA0100 MUTATED KIAA0100 WILD-TYPE
  T1                6                 16
  T2                5                 87
  T3                6                167
  T4                7                 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
  KIAA0100 MUTATED    11   4   5   4
  KIAA0100 WILD-TYPE 107 100  72  73
D277V5, multiclass
    clus
vv   KIAA0100 MUTATED KIAA0100 WILD-TYPE
  N0               11                107
  N1                4                100
  N2                5                 72
  N3                4                 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"
D277V6, binary
                    cls
clus                   0   1
  KIAA0100 MUTATED    24   2
  KIAA0100 WILD-TYPE 322  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0100 MUTATED     24    2
  KIAA0100 WILD-TYPE  322   27
   clus
vv  KIAA0100 MUTATED KIAA0100 WILD-TYPE
  0               24                322
  1                2                 27
[1] 2 2
[1] FALSE
D277V7, binary
                    cls
clus                   0   1
  KIAA0100 MUTATED    15  11
  KIAA0100 WILD-TYPE 130 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0100 MUTATED     15   11
  KIAA0100 WILD-TYPE  130  237
        clus
vv       KIAA0100 MUTATED KIAA0100 WILD-TYPE
  FEMALE               15                130
  MALE                 11                237
[1] 2 2
[1] FALSE
D277V8, binary
                    cls
clus                   0   1
  KIAA0100 MUTATED    15   2
  KIAA0100 WILD-TYPE 277  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0100 MUTATED     15    2
  KIAA0100 WILD-TYPE  277   57
     clus
vv    KIAA0100 MUTATED KIAA0100 WILD-TYPE
  NO                15                277
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA0100 MUTATED                                          0
  KIAA0100 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA0100 MUTATED                                       4
  KIAA0100 WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0100 MUTATED                                                       11
  KIAA0100 WILD-TYPE                                                    147
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA0100 MUTATED                                                   0
  KIAA0100 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0100 MUTATED                                                                   4
  KIAA0100 WILD-TYPE                                                                64
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA0100 MUTATED                                                    1
  KIAA0100 WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA0100 MUTATED                                                  6
  KIAA0100 WILD-TYPE                                               55
D277V9, multiclass
                                                                   clus
vv                                                                  KIAA0100 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 6
                                                                   clus
vv                                                                  KIAA0100 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0100 MUTATED    17   0   2   5
  KIAA0100 WILD-TYPE 294  14  13  19
D277V10, multiclass
    clus
vv   KIAA0100 MUTATED KIAA0100 WILD-TYPE
  R0               17                294
  R1                0                 14
  R2                2                 13
  RX                5                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0100 MUTATED       6                         0
  KIAA0100 WILD-TYPE    81                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0100 MUTATED                                           0    14
  KIAA0100 WILD-TYPE                                         1   229
D277V12, multiclass
                                           clus
vv                                          KIAA0100 MUTATED KIAA0100 WILD-TYPE
  ASIAN                                                    6                 81
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V13, binary
                    cls
clus                   0   1
  KIAA0100 MUTATED     0  20
  KIAA0100 WILD-TYPE   4 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0100 MUTATED      0   20
  KIAA0100 WILD-TYPE    4  290
                        clus
vv                       KIAA0100 MUTATED KIAA0100 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               20                290
[1] 2 2
[1] FALSE

Clustering(278) Variable = MYLK3 MUTATION ANALYSIS
D278V1, survival
                 sevent
clus2               0   1
  MYLK3 MUTATED     6   3
  MYLK3 WILD-TYPE 224 136
  MYLK3 MUTATED MYLK3 WILD-TYPE 
              9             360 
  MYLK3 MUTATED MYLK3 WILD-TYPE 
              3             136 
$`MYLK3 MUTATED`
TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8371 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8680 
        8.05         2.20        11.80        12.79        27.12        31.96 
TCGA-CD-8529 TCGA-CD-8534 TCGA-VQ-A8P2 
       12.30        12.07        38.14 

$`MYLK3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 
       32.25         0.56        29.42         2.66        19.96         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-8372 TCGA-BR-8373 
       26.33         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-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       20.22         1.12         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-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
       12.33        12.39        12.59        11.64        15.39        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-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 

  MYLK3 MUTATED MYLK3 WILD-TYPE 
            2.2             0.0 
  MYLK3 MUTATED MYLK3 WILD-TYPE 
          38.14          122.30 
  MYLK3 MUTATED MYLK3 WILD-TYPE 
          12.30           14.45 
[1] "2.2 - 38.1 (12.3)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D278V2, 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       2       15       40       29        37        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MYLK3 MUTATED           0          1          2          1        2
  MYLK3 WILD-TYPE         3         69         51         31       36
D278V3, multiclass
            clus
vv           MYLK3 MUTATED MYLK3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYLK3 MUTATED     0   0   2   7
  MYLK3 WILD-TYPE  22  92 171  90
D278V4, multiclass
    clus
vv   MYLK3 MUTATED MYLK3 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             2             171
  T4             7              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
  MYLK3 MUTATED     4   2   1   2
  MYLK3 WILD-TYPE 114 102  76  75
D278V5, multiclass
    clus
vv   MYLK3 MUTATED MYLK3 WILD-TYPE
  N0             4             114
  N1             2             102
  N2             1              76
  N3             2              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"
D278V6, binary
                 cls
clus                0   1
  MYLK3 MUTATED     7   2
  MYLK3 WILD-TYPE 339  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK3 MUTATED      7    2
  MYLK3 WILD-TYPE  339   27
   clus
vv  MYLK3 MUTATED MYLK3 WILD-TYPE
  0             7             339
  1             2              27
[1] 2 2
[1] FALSE
D278V7, binary
                 cls
clus                0   1
  MYLK3 MUTATED     3   6
  MYLK3 WILD-TYPE 142 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK3 MUTATED      3    6
  MYLK3 WILD-TYPE  142  242
        clus
vv       MYLK3 MUTATED MYLK3 WILD-TYPE
  FEMALE             3             142
  MALE               6             242
[1] 2 2
[1] FALSE
D278V8, binary
                 cls
clus                0   1
  MYLK3 MUTATED     7   2
  MYLK3 WILD-TYPE 285  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK3 MUTATED      7    2
  MYLK3 WILD-TYPE  285   57
     clus
vv    MYLK3 MUTATED MYLK3 WILD-TYPE
  NO              7             285
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MYLK3 MUTATED                                          0
  MYLK3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MYLK3 MUTATED                                       1
  MYLK3 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MYLK3 MUTATED                                                        4
  MYLK3 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MYLK3 MUTATED                                                   2
  MYLK3 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MYLK3 MUTATED                                                                   1
  MYLK3 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MYLK3 MUTATED                                                    0
  MYLK3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MYLK3 MUTATED                                                  1
  MYLK3 WILD-TYPE                                               60
D278V9, multiclass
                                                                   clus
vv                                                                  MYLK3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  MYLK3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYLK3 MUTATED     9   0   0   0
  MYLK3 WILD-TYPE 302  14  15  24
D278V10, multiclass
    clus
vv   MYLK3 MUTATED MYLK3 WILD-TYPE
  R0             9             302
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MYLK3 MUTATED       3                         0
  MYLK3 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MYLK3 MUTATED                                           0     6
  MYLK3 WILD-TYPE                                         1   237
D278V12, multiclass
                                           clus
vv                                          MYLK3 MUTATED MYLK3 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V13, binary
                 cls
clus                0   1
  MYLK3 MUTATED     0   8
  MYLK3 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK3 MUTATED      0    8
  MYLK3 WILD-TYPE    4  302
                        clus
vv                       MYLK3 MUTATED MYLK3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(279) Variable = PLOD3 MUTATION ANALYSIS
D279V1, survival
                 sevent
clus2               0   1
  PLOD3 MUTATED    11   3
  PLOD3 WILD-TYPE 219 136
  PLOD3 MUTATED PLOD3 WILD-TYPE 
             14             355 
  PLOD3 MUTATED PLOD3 WILD-TYPE 
              3             136 
$`PLOD3 MUTATED`
TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8487 TCGA-CD-A4MI 
       34.68         9.17         4.31        31.27         1.12        11.77 
TCGA-CG-4465 TCGA-CG-5723 TCGA-D7-A4Z0 TCGA-HU-A4GN TCGA-HU-A4GX TCGA-HU-A4H3 
        9.01       105.07        14.76        29.98        20.25        29.00 
TCGA-HU-A4H5 TCGA-VQ-A8P2 
       23.80        38.14 

$`PLOD3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        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-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 

  PLOD3 MUTATED PLOD3 WILD-TYPE 
           1.12            0.00 
  PLOD3 MUTATED PLOD3 WILD-TYPE 
         105.07          122.30 
  PLOD3 MUTATED PLOD3 WILD-TYPE 
         22.025          14.070 
[1] "1.1 - 105.1 (22.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.3"
D279V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLOD3 MUTATED         0        0        2        1         3         2
  PLOD3 WILD-TYPE       2       15       38       29        34        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLOD3 MUTATED           0          2          0          3        2
  PLOD3 WILD-TYPE         3         68         53         29       36
D279V3, multiclass
            clus
vv           PLOD3 MUTATED PLOD3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PLOD3 MUTATED     0   5   4   7
  PLOD3 WILD-TYPE  22  87 169  90
D279V4, multiclass
    clus
vv   PLOD3 MUTATED PLOD3 WILD-TYPE
  T1             0              22
  T2             5              87
  T3             4             169
  T4             7              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
  PLOD3 MUTATED     5   4   3   3
  PLOD3 WILD-TYPE 113 100  74  74
D279V5, multiclass
    clus
vv   PLOD3 MUTATED PLOD3 WILD-TYPE
  N0             5             113
  N1             4             100
  N2             3              74
  N3             3              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"
D279V6, binary
                 cls
clus                0   1
  PLOD3 MUTATED    14   1
  PLOD3 WILD-TYPE 332  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLOD3 MUTATED     14    1
  PLOD3 WILD-TYPE  332   28
   clus
vv  PLOD3 MUTATED PLOD3 WILD-TYPE
  0            14             332
  1             1              28
[1] 2 2
[1] FALSE
D279V7, binary
                 cls
clus                0   1
  PLOD3 MUTATED     8   8
  PLOD3 WILD-TYPE 137 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLOD3 MUTATED      8    8
  PLOD3 WILD-TYPE  137  240
        clus
vv       PLOD3 MUTATED PLOD3 WILD-TYPE
  FEMALE             8             137
  MALE               8             240
[1] 2 2
[1] FALSE
D279V8, binary
                 cls
clus                0   1
  PLOD3 MUTATED    10   2
  PLOD3 WILD-TYPE 282  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLOD3 MUTATED     10    2
  PLOD3 WILD-TYPE  282   57
     clus
vv    PLOD3 MUTATED PLOD3 WILD-TYPE
  NO             10             282
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PLOD3 MUTATED                                          0
  PLOD3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PLOD3 MUTATED                                       3
  PLOD3 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLOD3 MUTATED                                                        9
  PLOD3 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PLOD3 MUTATED                                                   2
  PLOD3 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLOD3 MUTATED                                                                   0
  PLOD3 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PLOD3 MUTATED                                                    1
  PLOD3 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PLOD3 MUTATED                                                  1
  PLOD3 WILD-TYPE                                               60
D279V9, multiclass
                                                                   clus
vv                                                                  PLOD3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  PLOD3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PLOD3 MUTATED    12   0   1   2
  PLOD3 WILD-TYPE 299  14  14  22
D279V10, multiclass
    clus
vv   PLOD3 MUTATED PLOD3 WILD-TYPE
  R0            12             299
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PLOD3 MUTATED       5                         0
  PLOD3 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLOD3 MUTATED                                           0     9
  PLOD3 WILD-TYPE                                         1   234
D279V12, multiclass
                                           clus
vv                                          PLOD3 MUTATED PLOD3 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V13, binary
                 cls
clus                0   1
  PLOD3 MUTATED     0  13
  PLOD3 WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLOD3 MUTATED      0   13
  PLOD3 WILD-TYPE    4  297
                        clus
vv                       PLOD3 MUTATED PLOD3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(280) Variable = RAD51AP2 MUTATION ANALYSIS
D280V1, survival
                    sevent
clus2                  0   1
  RAD51AP2 MUTATED    11   4
  RAD51AP2 WILD-TYPE 219 135
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                15                354 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                 4                135 
$`RAD51AP2 MUTATED`
TCGA-BR-4201 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8361 
       30.90        36.16        35.84        29.59         2.20        31.10 
TCGA-BR-8487 TCGA-CG-4306 TCGA-CG-5721 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8602 
        1.12         1.02         6.02        30.51        26.47        22.32 
TCGA-HU-A4GT TCGA-HU-A4HD TCGA-VQ-A8P2 
        6.51        33.40        38.14 

$`RAD51AP2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
        2.66        19.96         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-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-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-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-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-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 

  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
              1.02               0.00 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
             38.14             122.30 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
             29.59              14.07 
[1] "1.0 - 38.1 (29.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D280V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAD51AP2 MUTATED         0        1        2        0         2         3
  RAD51AP2 WILD-TYPE       2       14       38       30        35        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAD51AP2 MUTATED           0          2          0          2        2
  RAD51AP2 WILD-TYPE         3         68         53         30       36
D280V3, multiclass
            clus
vv           RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  2                 38
  STAGE II                  0                 30
  STAGE IIA                 2                 35
  STAGE IIB                 3                 49
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                0                 53
  STAGE IIIC                2                 30
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  RAD51AP2 MUTATED     1   3   4   7
  RAD51AP2 WILD-TYPE  21  89 169  90
D280V4, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  T1                1                 21
  T2                3                 89
  T3                4                169
  T4                7                 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
  RAD51AP2 MUTATED     8   2   3   1
  RAD51AP2 WILD-TYPE 110 102  74  76
D280V5, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  N0                8                110
  N1                2                102
  N2                3                 74
  N3                1                 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"
D280V6, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    14   1
  RAD51AP2 WILD-TYPE 332  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     14    1
  RAD51AP2 WILD-TYPE  332   28
   clus
vv  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  0               14                332
  1                1                 28
[1] 2 2
[1] FALSE
D280V7, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    11   5
  RAD51AP2 WILD-TYPE 134 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     11    5
  RAD51AP2 WILD-TYPE  134  243
        clus
vv       RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  FEMALE               11                134
  MALE                  5                243
[1] 2 2
[1] FALSE
D280V8, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    12   2
  RAD51AP2 WILD-TYPE 280  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     12    2
  RAD51AP2 WILD-TYPE  280   57
     clus
vv    RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  NO                12                280
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RAD51AP2 MUTATED                                          1
  RAD51AP2 WILD-TYPE                                        7
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RAD51AP2 MUTATED                                       1
  RAD51AP2 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RAD51AP2 MUTATED                                                        8
  RAD51AP2 WILD-TYPE                                                    150
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RAD51AP2 MUTATED                                                   2
  RAD51AP2 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RAD51AP2 MUTATED                                                                   1
  RAD51AP2 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RAD51AP2 MUTATED                                                    1
  RAD51AP2 WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RAD51AP2 MUTATED                                                  2
  RAD51AP2 WILD-TYPE                                               59
D280V9, multiclass
                                                                   clus
vv                                                                  RAD51AP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  RAD51AP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  RAD51AP2 MUTATED    12   1   1   2
  RAD51AP2 WILD-TYPE 299  13  14  22
D280V10, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  R0               12                299
  R1                1                 13
  R2                1                 14
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  RAD51AP2 MUTATED       3                         0
  RAD51AP2 WILD-TYPE    84                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAD51AP2 MUTATED                                           0    10
  RAD51AP2 WILD-TYPE                                         1   233
D280V12, multiclass
                                           clus
vv                                          RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   10                233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V13, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED     0  12
  RAD51AP2 WILD-TYPE   4 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED      0   12
  RAD51AP2 WILD-TYPE    4  298
                        clus
vv                       RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               12                298
[1] 2 2
[1] FALSE

Clustering(281) Variable = U2AF2 MUTATION ANALYSIS
D281V1, survival
                 sevent
clus2               0   1
  U2AF2 MUTATED     8   5
  U2AF2 WILD-TYPE 222 134
  U2AF2 MUTATED U2AF2 WILD-TYPE 
             13             356 
  U2AF2 MUTATED U2AF2 WILD-TYPE 
              5             134 
$`U2AF2 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CD-A4MI 
       21.99        34.68         4.31         1.12         6.58        11.77 
TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-KB-A93J TCGA-R5-A7ZI 
        5.92        11.08         0.10         6.51        36.95        74.53 
TCGA-VQ-A8P2 
       38.14 

$`U2AF2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-D7-8578 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-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-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         8.98         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-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 

  U2AF2 MUTATED U2AF2 WILD-TYPE 
            0.1             0.0 
  U2AF2 MUTATED U2AF2 WILD-TYPE 
          74.53          122.30 
  U2AF2 MUTATED U2AF2 WILD-TYPE 
          11.08           14.45 
[1] "0.1 - 74.5 (11.1)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D281V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  U2AF2 MUTATED         0        0        1        1         5         1
  U2AF2 WILD-TYPE       2       15       39       29        32        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  U2AF2 MUTATED           0          2          0          1        2
  U2AF2 WILD-TYPE         3         68         53         31       36
D281V3, multiclass
            clus
vv           U2AF2 MUTATED U2AF2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              5              32
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  U2AF2 MUTATED     0   2   7   4
  U2AF2 WILD-TYPE  22  90 166  93
D281V4, multiclass
    clus
vv   U2AF2 MUTATED U2AF2 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             7             166
  T4             4              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
  U2AF2 MUTATED     6   6   1   0
  U2AF2 WILD-TYPE 112  98  76  77
D281V5, multiclass
    clus
vv   U2AF2 MUTATED U2AF2 WILD-TYPE
  N0             6             112
  N1             6              98
  N2             1              76
  N3             0              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"
D281V6, binary
                 cls
clus                0   1
  U2AF2 MUTATED    12   2
  U2AF2 WILD-TYPE 334  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF2 MUTATED     12    2
  U2AF2 WILD-TYPE  334   27
   clus
vv  U2AF2 MUTATED U2AF2 WILD-TYPE
  0            12             334
  1             2              27
[1] 2 2
[1] FALSE
D281V7, binary
                 cls
clus                0   1
  U2AF2 MUTATED     8   6
  U2AF2 WILD-TYPE 137 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF2 MUTATED      8    6
  U2AF2 WILD-TYPE  137  242
        clus
vv       U2AF2 MUTATED U2AF2 WILD-TYPE
  FEMALE             8             137
  MALE               6             242
[1] 2 2
[1] FALSE
D281V8, binary
                 cls
clus                0   1
  U2AF2 MUTATED    10   3
  U2AF2 WILD-TYPE 282  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF2 MUTATED     10    3
  U2AF2 WILD-TYPE  282   56
     clus
vv    U2AF2 MUTATED U2AF2 WILD-TYPE
  NO             10             282
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  U2AF2 MUTATED                                          0
  U2AF2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  U2AF2 MUTATED                                       3
  U2AF2 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  U2AF2 MUTATED                                                        6
  U2AF2 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  U2AF2 MUTATED                                                   1
  U2AF2 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  U2AF2 MUTATED                                                                   1
  U2AF2 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  U2AF2 MUTATED                                                    0
  U2AF2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  U2AF2 MUTATED                                                  3
  U2AF2 WILD-TYPE                                               58
D281V9, multiclass
                                                                   clus
vv                                                                  U2AF2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  U2AF2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  U2AF2 MUTATED    10   0   1   1
  U2AF2 WILD-TYPE 301  14  14  23
D281V10, multiclass
    clus
vv   U2AF2 MUTATED U2AF2 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  U2AF2 MUTATED       4                         1
  U2AF2 WILD-TYPE    83                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  U2AF2 MUTATED                                           0     8
  U2AF2 WILD-TYPE                                         1   235
D281V12, multiclass
                                           clus
vv                                          U2AF2 MUTATED U2AF2 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V13, binary
                 cls
clus                0   1
  U2AF2 MUTATED     1  10
  U2AF2 WILD-TYPE   3 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF2 MUTATED      1   10
  U2AF2 WILD-TYPE    3  300
                        clus
vv                       U2AF2 MUTATED U2AF2 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(282) Variable = MFN1 MUTATION ANALYSIS
D282V1, survival
                sevent
clus2              0   1
  MFN1 MUTATED     6   3
  MFN1 WILD-TYPE 224 136
  MFN1 MUTATED MFN1 WILD-TYPE 
             9            360 
  MFN1 MUTATED MFN1 WILD-TYPE 
             3            136 
$`MFN1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-CG-4305 TCGA-CG-5726 TCGA-HF-7132 
       26.70         6.97        34.68        15.95        28.96        77.29 
TCGA-HU-A4H4 TCGA-R5-A7ZI TCGA-VQ-A8DV 
       23.84        74.53        13.25 

$`MFN1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  MFN1 MUTATED MFN1 WILD-TYPE 
          6.97           0.00 
  MFN1 MUTATED MFN1 WILD-TYPE 
         77.29         122.30 
  MFN1 MUTATED MFN1 WILD-TYPE 
         26.70          14.07 
[1] "7.0 - 77.3 (26.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D282V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MFN1 MUTATED         0        1        1        2         1         2
  MFN1 WILD-TYPE       2       14       39       28        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MFN1 MUTATED           0          1          0          0        1
  MFN1 WILD-TYPE         3         69         53         32       37
D282V3, multiclass
            clus
vv           MFN1 MUTATED MFN1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              2             28
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MFN1 MUTATED     1   4   2   2
  MFN1 WILD-TYPE  21  88 171  95
D282V4, multiclass
    clus
vv   MFN1 MUTATED MFN1 WILD-TYPE
  T1            1             21
  T2            4             88
  T3            2            171
  T4            2             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
  MFN1 MUTATED     4   4   1   0
  MFN1 WILD-TYPE 114 100  76  77
D282V5, multiclass
    clus
vv   MFN1 MUTATED MFN1 WILD-TYPE
  N0            4            114
  N1            4            100
  N2            1             76
  N3            0             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"
D282V6, binary
                cls
clus               0   1
  MFN1 MUTATED     7   1
  MFN1 WILD-TYPE 339  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED      7    1
  MFN1 WILD-TYPE  339   28
   clus
vv  MFN1 MUTATED MFN1 WILD-TYPE
  0            7            339
  1            1             28
[1] 2 2
[1] FALSE
D282V7, binary
                cls
clus               0   1
  MFN1 MUTATED     4   5
  MFN1 WILD-TYPE 141 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED      4    5
  MFN1 WILD-TYPE  141  243
        clus
vv       MFN1 MUTATED MFN1 WILD-TYPE
  FEMALE            4            141
  MALE              5            243
[1] 2 2
[1] FALSE
D282V8, binary
                cls
clus               0   1
  MFN1 MUTATED     7   1
  MFN1 WILD-TYPE 285  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED      7    1
  MFN1 WILD-TYPE  285   58
     clus
vv    MFN1 MUTATED MFN1 WILD-TYPE
  NO             7            285
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MFN1 MUTATED                                          0
  MFN1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MFN1 MUTATED                                       2
  MFN1 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MFN1 MUTATED                                                        3
  MFN1 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MFN1 MUTATED                                                   1
  MFN1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MFN1 MUTATED                                                                   2
  MFN1 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MFN1 MUTATED                                                    0
  MFN1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MFN1 MUTATED                                                  1
  MFN1 WILD-TYPE                                               60
D282V9, multiclass
                                                                   clus
vv                                                                  MFN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  MFN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MFN1 MUTATED     8   0   0   1
  MFN1 WILD-TYPE 303  14  15  23
D282V10, multiclass
    clus
vv   MFN1 MUTATED MFN1 WILD-TYPE
  R0            8            303
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MFN1 MUTATED       1                         0
  MFN1 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MFN1 MUTATED                                           0     5
  MFN1 WILD-TYPE                                         1   238
D282V12, multiclass
                                           clus
vv                                          MFN1 MUTATED MFN1 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V13, binary
                cls
clus               0   1
  MFN1 MUTATED     1   4
  MFN1 WILD-TYPE   3 306
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED      1    4
  MFN1 WILD-TYPE    3  306
                        clus
vv                       MFN1 MUTATED MFN1 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            4            306
[1] 2 2
[1] FALSE

Clustering(283) Variable = ATP6V1C2 MUTATION ANALYSIS
D283V1, survival
                    sevent
clus2                  0   1
  ATP6V1C2 MUTATED     8   5
  ATP6V1C2 WILD-TYPE 222 134
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                13                356 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
                 5                134 
$`ATP6V1C2 MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-6453 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8487 
       19.56         6.97        15.95         6.18         0.26         1.12 
TCGA-CD-A4MG TCGA-CG-5723 TCGA-HU-A4G3 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-IN-8663 
        6.58       105.07         5.59        29.98         0.10         3.39 
TCGA-VQ-A8P2 
       38.14 

$`ATP6V1C2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-A4G6 TCGA-HU-A4G8 
       22.82        21.07         0.76        24.30        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-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-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 

  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
               0.1                0.0 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
            105.07             122.30 
  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE 
              6.58              14.45 
[1] "0.1 - 105.1 (6.6)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.3"
D283V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP6V1C2 MUTATED         1        0        1        1         5         2
  ATP6V1C2 WILD-TYPE       1       15       39       29        32        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1C2 MUTATED           0          2          0          2        0
  ATP6V1C2 WILD-TYPE         3         68         53         30       38
D283V3, multiclass
            clus
vv           ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  1                 29
  STAGE IIA                 5                 32
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                0                 53
  STAGE IIIC                2                 30
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ATP6V1C2 MUTATED     1   6   4   3
  ATP6V1C2 WILD-TYPE  21  86 169  94
D283V4, multiclass
    clus
vv   ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  T1                1                 21
  T2                6                 86
  T3                4                169
  T4                3                 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
  ATP6V1C2 MUTATED     4   7   3   1
  ATP6V1C2 WILD-TYPE 114  97  74  76
D283V5, multiclass
    clus
vv   ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  N0                4                114
  N1                7                 97
  N2                3                 74
  N3                1                 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"
D283V6, binary
                    cls
clus                   0   1
  ATP6V1C2 MUTATED    13   0
  ATP6V1C2 WILD-TYPE 333  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1C2 MUTATED     13    0
  ATP6V1C2 WILD-TYPE  333   29
   clus
vv  ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  0               13                333
  1                0                 29
[1] 2 2
[1] FALSE
D283V7, binary
                    cls
clus                   0   1
  ATP6V1C2 MUTATED     3  12
  ATP6V1C2 WILD-TYPE 142 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1C2 MUTATED      3   12
  ATP6V1C2 WILD-TYPE  142  236
        clus
vv       ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  FEMALE                3                142
  MALE                 12                236
[1] 2 2
[1] FALSE
D283V8, binary
                    cls
clus                   0   1
  ATP6V1C2 MUTATED    13   1
  ATP6V1C2 WILD-TYPE 279  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1C2 MUTATED     13    1
  ATP6V1C2 WILD-TYPE  279   58
     clus
vv    ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  NO                13                279
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ATP6V1C2 MUTATED                                          0
  ATP6V1C2 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ATP6V1C2 MUTATED                                       2
  ATP6V1C2 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATP6V1C2 MUTATED                                                        8
  ATP6V1C2 WILD-TYPE                                                    150
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ATP6V1C2 MUTATED                                                   1
  ATP6V1C2 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATP6V1C2 MUTATED                                                                   1
  ATP6V1C2 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ATP6V1C2 MUTATED                                                    0
  ATP6V1C2 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ATP6V1C2 MUTATED                                                  3
  ATP6V1C2 WILD-TYPE                                               58
D283V9, multiclass
                                                                   clus
vv                                                                  ATP6V1C2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 3
                                                                   clus
vv                                                                  ATP6V1C2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ATP6V1C2 MUTATED    11   0   0   2
  ATP6V1C2 WILD-TYPE 300  14  15  22
D283V10, multiclass
    clus
vv   ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  R0               11                300
  R1                0                 14
  R2                0                 15
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ATP6V1C2 MUTATED       4                         1
  ATP6V1C2 WILD-TYPE    83                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATP6V1C2 MUTATED                                           0     9
  ATP6V1C2 WILD-TYPE                                         1   234
D283V12, multiclass
                                           clus
vv                                          ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  ASIAN                                                    4                 83
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    9                234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V13, binary
                    cls
clus                   0   1
  ATP6V1C2 MUTATED     0  13
  ATP6V1C2 WILD-TYPE   4 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1C2 MUTATED      0   13
  ATP6V1C2 WILD-TYPE    4  297
                        clus
vv                       ATP6V1C2 MUTATED ATP6V1C2 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               13                297
[1] 2 2
[1] FALSE

Clustering(284) Variable = NFE2L1 MUTATION ANALYSIS
D284V1, survival
                  sevent
clus2                0   1
  NFE2L1 MUTATED     5   4
  NFE2L1 WILD-TYPE 225 135
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
               9              360 
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
               4              135 
$`NFE2L1 MUTATED`
TCGA-EQ-A4SO TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-8487 TCGA-CD-8529 TCGA-CD-A4MI 
       16.24        18.35        30.90         1.12        12.30        11.77 
TCGA-D7-A6EY TCGA-F1-6874 TCGA-HU-A4GN 
       11.44        14.47        29.98 

$`NFE2L1 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-4253 
        9.44         6.61         6.97         4.64         7.43         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-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-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-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 

  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
            1.12             0.00 
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
            30.9            122.3 
  NFE2L1 MUTATED NFE2L1 WILD-TYPE 
           14.47            14.22 
[1] "1.1 - 30.9 (14.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D284V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NFE2L1 MUTATED         0        0        1        0         2         0
  NFE2L1 WILD-TYPE       2       15       39       30        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFE2L1 MUTATED           0          1          2          0        1
  NFE2L1 WILD-TYPE         3         69         51         32       37
D284V3, multiclass
            clus
vv           NFE2L1 MUTATED NFE2L1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              2               51
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NFE2L1 MUTATED     1   3   3   2
  NFE2L1 WILD-TYPE  21  89 170  95
D284V4, multiclass
    clus
vv   NFE2L1 MUTATED NFE2L1 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              3              170
  T4              2               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
  NFE2L1 MUTATED     3   5   0   1
  NFE2L1 WILD-TYPE 115  99  77  76
D284V5, multiclass
    clus
vv   NFE2L1 MUTATED NFE2L1 WILD-TYPE
  N0              3              115
  N1              5               99
  N2              0               77
  N3              1               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"
D284V6, binary
                  cls
clus                 0   1
  NFE2L1 MUTATED     9   1
  NFE2L1 WILD-TYPE 337  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L1 MUTATED      9    1
  NFE2L1 WILD-TYPE  337   28
   clus
vv  NFE2L1 MUTATED NFE2L1 WILD-TYPE
  0              9              337
  1              1               28
[1] 2 2
[1] FALSE
D284V7, binary
                  cls
clus                 0   1
  NFE2L1 MUTATED     5   6
  NFE2L1 WILD-TYPE 140 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L1 MUTATED      5    6
  NFE2L1 WILD-TYPE  140  242
        clus
vv       NFE2L1 MUTATED NFE2L1 WILD-TYPE
  FEMALE              5              140
  MALE                6              242
[1] 2 2
[1] FALSE
D284V8, binary
                  cls
clus                 0   1
  NFE2L1 MUTATED     7   2
  NFE2L1 WILD-TYPE 285  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L1 MUTATED      7    2
  NFE2L1 WILD-TYPE  285   57
     clus
vv    NFE2L1 MUTATED NFE2L1 WILD-TYPE
  NO               7              285
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NFE2L1 MUTATED                                          0
  NFE2L1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NFE2L1 MUTATED                                       0
  NFE2L1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NFE2L1 MUTATED                                                        6
  NFE2L1 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NFE2L1 MUTATED                                                   1
  NFE2L1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NFE2L1 MUTATED                                                                   1
  NFE2L1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NFE2L1 MUTATED                                                    0
  NFE2L1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NFE2L1 MUTATED                                                  2
  NFE2L1 WILD-TYPE                                               59
D284V9, multiclass
                                                                   clus
vv                                                                  NFE2L1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  NFE2L1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NFE2L1 MUTATED     6   0   0   4
  NFE2L1 WILD-TYPE 305  14  15  20
D284V10, multiclass
    clus
vv   NFE2L1 MUTATED NFE2L1 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NFE2L1 MUTATED       3                         0
  NFE2L1 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NFE2L1 MUTATED                                           0     8
  NFE2L1 WILD-TYPE                                         1   235
D284V12, multiclass
                                           clus
vv                                          NFE2L1 MUTATED NFE2L1 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V13, binary
                  cls
clus                 0   1
  NFE2L1 MUTATED     0  11
  NFE2L1 WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L1 MUTATED      0   11
  NFE2L1 WILD-TYPE    4  299
                        clus
vv                       NFE2L1 MUTATED NFE2L1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(285) Variable = ERF MUTATION ANALYSIS
D285V1, survival
               sevent
clus2             0   1
  ERF MUTATED     9   5
  ERF WILD-TYPE 221 134
  ERF MUTATED ERF WILD-TYPE 
           14           355 
  ERF MUTATED ERF WILD-TYPE 
            5           134 
$`ERF MUTATED`
TCGA-BR-6452 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-8361 TCGA-BR-8382 TCGA-CD-5813 
       34.68         9.21        39.78        31.10        25.05        12.39 
TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-A6EY TCGA-HF-A5NB 
       12.62         1.02         6.02        65.10        11.44        30.51 
TCGA-HJ-7597 TCGA-SW-A7EA 
       26.47        19.04 

$`ERF WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-7703 TCGA-BR-7704 
       30.90        31.20        44.94        21.90        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-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-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-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-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-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-F1-6874 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-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-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 

  ERF MUTATED ERF WILD-TYPE 
         1.02          0.00 
  ERF MUTATED ERF WILD-TYPE 
         65.1         122.3 
  ERF MUTATED ERF WILD-TYPE 
       22.045        14.170 
[1] "1.0 - 65.1 (22.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D285V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERF MUTATED         0        0        4        2         1         1
  ERF WILD-TYPE       2       15       36       28        36        51
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERF MUTATED           0          0          1          3        2
  ERF WILD-TYPE         3         70         52         29       36
D285V3, multiclass
            clus
vv           ERF MUTATED ERF WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             4            36
  STAGE II             2            28
  STAGE IIA            1            36
  STAGE IIB            1            51
  STAGE III            0             3
  STAGE IIIA           0            70
  STAGE IIIB           1            52
  STAGE IIIC           3            29
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ERF MUTATED     1   4   6   4
  ERF WILD-TYPE  21  88 167  93
D285V4, multiclass
    clus
vv   ERF MUTATED ERF WILD-TYPE
  T1           1            21
  T2           4            88
  T3           6           167
  T4           4            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
  ERF MUTATED     7   2   2   3
  ERF WILD-TYPE 111 102  75  74
D285V5, multiclass
    clus
vv   ERF MUTATED ERF WILD-TYPE
  N0           7           111
  N1           2           102
  N2           2            75
  N3           3            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"
D285V6, binary
               cls
clus              0   1
  ERF MUTATED    14   1
  ERF WILD-TYPE 332  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED     14    1
  ERF WILD-TYPE  332   28
   clus
vv  ERF MUTATED ERF WILD-TYPE
  0          14           332
  1           1            28
[1] 2 2
[1] FALSE
D285V7, binary
               cls
clus              0   1
  ERF MUTATED    11   5
  ERF WILD-TYPE 134 243
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED     11    5
  ERF WILD-TYPE  134  243
        clus
vv       ERF MUTATED ERF WILD-TYPE
  FEMALE          11           134
  MALE             5           243
[1] 2 2
[1] FALSE
D285V8, binary
               cls
clus              0   1
  ERF MUTATED    11   1
  ERF WILD-TYPE 281  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED     11    1
  ERF WILD-TYPE  281   58
     clus
vv    ERF MUTATED ERF WILD-TYPE
  NO           11           281
  YES           1            58
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ERF MUTATED                                          1
  ERF WILD-TYPE                                        7
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ERF MUTATED                                       1
  ERF WILD-TYPE                                    69
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ERF MUTATED                                                        9
  ERF WILD-TYPE                                                    149
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ERF MUTATED                                                   2
  ERF WILD-TYPE                                                19
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ERF MUTATED                                                                   2
  ERF WILD-TYPE                                                                66
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ERF MUTATED                                                    0
  ERF WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ERF MUTATED                                                  1
  ERF WILD-TYPE                                               60
D285V9, multiclass
                                                                   clus
vv                                                                  ERF MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            1
                                                                   clus
vv                                                                  ERF WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  ERF MUTATED    10   1   1   2
  ERF WILD-TYPE 301  13  14  22
D285V10, multiclass
    clus
vv   ERF MUTATED ERF WILD-TYPE
  R0          10           301
  R1           1            13
  R2           1            14
  RX           2            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  ERF MUTATED       2                         0
  ERF WILD-TYPE    85                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ERF MUTATED                                           0    10
  ERF WILD-TYPE                                         1   233
D285V12, multiclass
                                           clus
vv                                          ERF MUTATED ERF WILD-TYPE
  ASIAN                                               2            85
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              10           233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V13, binary
               cls
clus              0   1
  ERF MUTATED     0  12
  ERF WILD-TYPE   4 298
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED      0   12
  ERF WILD-TYPE    4  298
                        clus
vv                       ERF MUTATED ERF WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          12           298
[1] 2 2
[1] FALSE

Clustering(286) Variable = TAS2R10 MUTATION ANALYSIS
D286V1, survival
                   sevent
clus2                 0   1
  TAS2R10 MUTATED     2   1
  TAS2R10 WILD-TYPE 228 138
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
                3               366 
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
                1               138 
$`TAS2R10 MUTATED`
TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-VQ-A8PK 
       22.68         6.58        17.85 

$`TAS2R10 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
             6.58              0.00 
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
            22.68            122.30 
  TAS2R10 MUTATED TAS2R10 WILD-TYPE 
            17.85             14.22 
[1] "6.6 - 22.7 (17.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1"  
D286V2, 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       1       15       40       30        37        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAS2R10 MUTATED           0          0          1          0        0
  TAS2R10 WILD-TYPE         3         70         52         32       38
D286V3, multiclass
            clus
vv           TAS2R10 MUTATED TAS2R10 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                0                37
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TAS2R10 MUTATED     1   0   3   0
  TAS2R10 WILD-TYPE  21  92 170  97
D286V4, multiclass
    clus
vv   TAS2R10 MUTATED TAS2R10 WILD-TYPE
  T1               1                21
  T2               0                92
  T3               3               170
  T4               0                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
  TAS2R10 MUTATED     0   3   0   1
  TAS2R10 WILD-TYPE 118 101  77  76
D286V5, multiclass
    clus
vv   TAS2R10 MUTATED TAS2R10 WILD-TYPE
  N0               0               118
  N1               3               101
  N2               0                77
  N3               1                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"
D286V6, binary
                   cls
clus                  0   1
  TAS2R10 MUTATED     3   0
  TAS2R10 WILD-TYPE 343  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R10 MUTATED      3    0
  TAS2R10 WILD-TYPE  343   29
   clus
vv  TAS2R10 MUTATED TAS2R10 WILD-TYPE
  0               3               343
  1               0                29
[1] 2 2
[1] FALSE
D286V7, binary
                   cls
clus                  0   1
  TAS2R10 MUTATED     1   3
  TAS2R10 WILD-TYPE 144 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R10 MUTATED      1    3
  TAS2R10 WILD-TYPE  144  245
        clus
vv       TAS2R10 MUTATED TAS2R10 WILD-TYPE
  FEMALE               1               144
  MALE                 3               245
[1] 2 2
[1] FALSE
D286V8, binary
                   cls
clus                  0   1
  TAS2R10 MUTATED     4   0
  TAS2R10 WILD-TYPE 288  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R10 MUTATED      4    0
  TAS2R10 WILD-TYPE  288   59
     clus
vv    TAS2R10 MUTATED TAS2R10 WILD-TYPE
  NO                4               288
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TAS2R10 MUTATED                                          0
  TAS2R10 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TAS2R10 MUTATED                                       2
  TAS2R10 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TAS2R10 MUTATED                                                        1
  TAS2R10 WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TAS2R10 MUTATED                                                   0
  TAS2R10 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TAS2R10 MUTATED                                                                   1
  TAS2R10 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TAS2R10 MUTATED                                                    0
  TAS2R10 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TAS2R10 MUTATED                                                  0
  TAS2R10 WILD-TYPE                                               61
D286V9, multiclass
                                                                   clus
vv                                                                  TAS2R10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  TAS2R10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TAS2R10 MUTATED     3   0   0   0
  TAS2R10 WILD-TYPE 308  14  15  24
D286V10, multiclass
    clus
vv   TAS2R10 MUTATED TAS2R10 WILD-TYPE
  R0               3               308
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TAS2R10 MUTATED       2                         1
  TAS2R10 WILD-TYPE    85                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAS2R10 MUTATED                                           0     1
  TAS2R10 WILD-TYPE                                         1   242
D286V12, multiclass
                                           clus
vv                                          TAS2R10 MUTATED TAS2R10 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   1               242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V13, binary
                   cls
clus                  0   1
  TAS2R10 MUTATED     0   3
  TAS2R10 WILD-TYPE   4 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R10 MUTATED      0    3
  TAS2R10 WILD-TYPE    4  307
                        clus
vv                       TAS2R10 MUTATED TAS2R10 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               3               307
[1] 2 2
[1] FALSE

Clustering(287) Variable = FAM82A1 MUTATION ANALYSIS
D287V1, survival
                   sevent
clus2                 0   1
  FAM82A1 MUTATED     2   2
  FAM82A1 WILD-TYPE 228 137
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
                4               365 
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
                2               137 
$`FAM82A1 MUTATED`
TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 TCGA-F1-A448 
        1.02         6.02        28.96        21.27 

$`FAM82A1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
             1.02              0.00 
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
            28.96            122.30 
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
           13.645            14.270 
[1] "1.0 - 29.0 (13.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.6"
D287V2, 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       2       14       40       30        37        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM82A1 MUTATED           0          0          1          0        2
  FAM82A1 WILD-TYPE         3         70         52         32       36
D287V3, multiclass
            clus
vv           FAM82A1 MUTATED FAM82A1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                0                37
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM82A1 MUTATED     1   0   2   1
  FAM82A1 WILD-TYPE  21  92 171  96
D287V4, multiclass
    clus
vv   FAM82A1 MUTATED FAM82A1 WILD-TYPE
  T1               1                21
  T2               0                92
  T3               2               171
  T4               1                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
  FAM82A1 MUTATED     1   2   1   1
  FAM82A1 WILD-TYPE 117 102  76  76
D287V5, multiclass
    clus
vv   FAM82A1 MUTATED FAM82A1 WILD-TYPE
  N0               1               117
  N1               2               102
  N2               1                76
  N3               1                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"
D287V6, binary
                   cls
clus                  0   1
  FAM82A1 MUTATED     4   1
  FAM82A1 WILD-TYPE 342  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A1 MUTATED      4    1
  FAM82A1 WILD-TYPE  342   28
   clus
vv  FAM82A1 MUTATED FAM82A1 WILD-TYPE
  0               4               342
  1               1                28
[1] 2 2
[1] FALSE
D287V7, binary
                   cls
clus                  0   1
  FAM82A1 MUTATED     1   4
  FAM82A1 WILD-TYPE 144 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A1 MUTATED      1    4
  FAM82A1 WILD-TYPE  144  244
        clus
vv       FAM82A1 MUTATED FAM82A1 WILD-TYPE
  FEMALE               1               144
  MALE                 4               244
[1] 2 2
[1] FALSE
D287V8, binary
                   cls
clus                  0   1
  FAM82A1 MUTATED     1   1
  FAM82A1 WILD-TYPE 291  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A1 MUTATED      1    1
  FAM82A1 WILD-TYPE  291   58
     clus
vv    FAM82A1 MUTATED FAM82A1 WILD-TYPE
  NO                1               291
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM82A1 MUTATED                                          0
  FAM82A1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM82A1 MUTATED                                       0
  FAM82A1 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM82A1 MUTATED                                                        2
  FAM82A1 WILD-TYPE                                                    156
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM82A1 MUTATED                                                   1
  FAM82A1 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM82A1 MUTATED                                                                   2
  FAM82A1 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM82A1 MUTATED                                                    0
  FAM82A1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM82A1 MUTATED                                                  0
  FAM82A1 WILD-TYPE                                               61
D287V9, multiclass
                                                                   clus
vv                                                                  FAM82A1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  FAM82A1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM82A1 MUTATED     3   0   1   1
  FAM82A1 WILD-TYPE 308  14  14  23
D287V10, multiclass
    clus
vv   FAM82A1 MUTATED FAM82A1 WILD-TYPE
  R0               3               308
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM82A1 MUTATED       0                         0
  FAM82A1 WILD-TYPE    87                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM82A1 MUTATED                                           0     2
  FAM82A1 WILD-TYPE                                         1   241
D287V12, multiclass
[1] "Remove cluster labels:" "FAM82A1 MUTATED"       
clus
  FAM82A1 MUTATED FAM82A1 WILD-TYPE 
                2               338 
       TCGA-EQ-A4SO        TCGA-F1-6177        TCGA-FP-A8CX        TCGA-KB-A93G 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-MX-A663        TCGA-B7-5816        TCGA-B7-5818        TCGA-B7-A5TI 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-B7-A5TJ        TCGA-B7-A5TK        TCGA-B7-A5TN        TCGA-BR-4183 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-4184        TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-4201        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-4257        TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-4292        TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4368        TCGA-BR-4369 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452        TCGA-BR-6453 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-7959        TCGA-BR-8058        TCGA-BR-8059        TCGA-BR-8060 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8297        TCGA-BR-8360 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8361        TCGA-BR-8363        TCGA-BR-8364        TCGA-BR-8365 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8366        TCGA-BR-8367        TCGA-BR-8368        TCGA-BR-8369 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8370        TCGA-BR-8371        TCGA-BR-8372        TCGA-BR-8373 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8380        TCGA-BR-8381        TCGA-BR-8382        TCGA-BR-8384 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8483        TCGA-BR-8484        TCGA-BR-8485        TCGA-BR-8486 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8487        TCGA-BR-8588        TCGA-BR-8589        TCGA-BR-8590 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8591        TCGA-BR-8592        TCGA-BR-8676        TCGA-BR-8677 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8678        TCGA-BR-8679        TCGA-BR-8680        TCGA-BR-8682 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-8683        TCGA-BR-8686        TCGA-BR-8687        TCGA-BR-8690 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-A44T        TCGA-BR-A44U        TCGA-BR-A452        TCGA-BR-A453 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-A4CQ        TCGA-BR-A4CR        TCGA-BR-A4CS        TCGA-BR-A4IU 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ        TCGA-BR-A4J1 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J5        TCGA-BR-A4J6 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-A4J7        TCGA-BR-A4J8        TCGA-BR-A4PD        TCGA-BR-A4PE 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-BR-A4QM 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804        TCGA-CD-5813 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-8524        TCGA-CD-8525        TCGA-CD-8526        TCGA-CD-8527 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-8528        TCGA-CD-8529        TCGA-CD-8530        TCGA-CD-8531 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-8532        TCGA-CD-8533        TCGA-CD-8534        TCGA-CD-8535 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-8536        TCGA-CD-A486        TCGA-CD-A487        TCGA-CD-A489 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-A48A        TCGA-CD-A48C        TCGA-CD-A4MG        TCGA-CD-A4MH 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-CD-A4MI        TCGA-CD-A4MJ        TCGA-D7-5577        TCGA-D7-5578 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-8570        TCGA-D7-8572        TCGA-D7-8573        TCGA-D7-8574 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-8575        TCGA-D7-8576        TCGA-D7-8578        TCGA-D7-8579 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-A4YT        TCGA-D7-A4YU        TCGA-D7-A4YV        TCGA-D7-A4YX 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-A4YY        TCGA-D7-A4Z0        TCGA-D7-A6ET        TCGA-D7-A6EV 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-A6EX        TCGA-D7-A6EY        TCGA-D7-A6EZ        TCGA-D7-A6F0 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-A6F2        TCGA-D7-A747        TCGA-D7-A748        TCGA-D7-A74A 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-D7-A74B        TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6874 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-F1-6875        TCGA-F1-A72C        TCGA-FP-7735        TCGA-FP-7829 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631        TCGA-FP-A4BE 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-FP-A4BF        TCGA-FP-A9TM        TCGA-HJ-7597        TCGA-HU-8238 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-8243        TCGA-HU-8244        TCGA-HU-8249        TCGA-HU-8602 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-8604        TCGA-HU-8608        TCGA-HU-8610        TCGA-HU-A4G2 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-A4G3        TCGA-HU-A4G6        TCGA-HU-A4G8        TCGA-HU-A4G9 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-A4GC        TCGA-HU-A4GD        TCGA-HU-A4GF        TCGA-HU-A4GH 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-A4GJ        TCGA-HU-A4GN        TCGA-HU-A4GP        TCGA-HU-A4GQ 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-A4GT        TCGA-HU-A4GU        TCGA-HU-A4GX        TCGA-HU-A4GY 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-A4H0        TCGA-HU-A4H2        TCGA-HU-A4H3        TCGA-HU-A4H4 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-A4H5        TCGA-HU-A4H6        TCGA-HU-A4H8        TCGA-HU-A4HB 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-HU-A4HD        TCGA-IN-7806        TCGA-IN-7808        TCGA-IN-8462 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-IN-8663        TCGA-IN-A6RI        TCGA-IN-A6RJ        TCGA-IN-A6RL 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-IN-A6RN        TCGA-IN-A6RO        TCGA-IN-A6RP        TCGA-IN-A6RR 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-IN-A6RS        TCGA-IN-A7NR        TCGA-IN-A7NT        TCGA-IN-A7NU 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-IN-AB1V        TCGA-IN-AB1X        TCGA-IP-7968        TCGA-KB-A93J 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-MX-A5UG        TCGA-MX-A5UJ        TCGA-MX-A666        TCGA-R5-A7O7 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-R5-A7ZE        TCGA-R5-A7ZF        TCGA-R5-A7ZI        TCGA-R5-A7ZR 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-R5-A804        TCGA-R5-A805        TCGA-RD-A7BS        TCGA-RD-A7BT 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-RD-A7BW        TCGA-RD-A7C1        TCGA-RD-A8MV        TCGA-RD-A8MW 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-RD-A8N0        TCGA-RD-A8N1        TCGA-RD-A8N2        TCGA-RD-A8N4 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-RD-A8N5        TCGA-RD-A8N6        TCGA-RD-A8N9        TCGA-SW-A7EA 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-SW-A7EB        TCGA-VQ-A8DL        TCGA-VQ-A8DU        TCGA-VQ-A8DV 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-VQ-A8DZ        TCGA-VQ-A8E2        TCGA-VQ-A8E7        TCGA-VQ-A8P2 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-VQ-A8P3        TCGA-VQ-A8PE        TCGA-VQ-A8PK        TCGA-VQ-A8PM 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-VQ-A8PQ        TCGA-VQ-A91U        TCGA-VQ-A92D        TCGA-VQ-AA64 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-VQ-AA68        TCGA-VQ-AA69        TCGA-VQ-AA6A        TCGA-VQ-AA6B 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-VQ-AA6F        TCGA-VQ-AA6G        TCGA-VQ-AA6I        TCGA-VQ-AA6J 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
       TCGA-VQ-AA6K        TCGA-ZA-A8F6 
"FAM82A1 WILD-TYPE" "FAM82A1 WILD-TYPE" 
D287V13, binary
                   cls
clus                  0   1
  FAM82A1 MUTATED     1   1
  FAM82A1 WILD-TYPE   3 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A1 MUTATED      1    1
  FAM82A1 WILD-TYPE    3  309
                        clus
vv                       FAM82A1 MUTATED FAM82A1 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               1               309
[1] 2 2
[1] FALSE

Clustering(288) Variable = DYRK4 MUTATION ANALYSIS
D288V1, survival
                 sevent
clus2               0   1
  DYRK4 MUTATED     5   2
  DYRK4 WILD-TYPE 225 137
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              7             362 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              2             137 
$`DYRK4 MUTATED`
TCGA-BR-4256 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8680 TCGA-D7-A4YV TCGA-HF-7132 
        9.34        29.59        31.10        31.96         5.92        77.29 
TCGA-HU-A4H3 
       29.00 

$`DYRK4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  DYRK4 MUTATED DYRK4 WILD-TYPE 
           5.92            0.00 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
          77.29          122.30 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
          29.59           14.12 
[1] "5.9 - 77.3 (29.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.1"
D288V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DYRK4 MUTATED         0        0        0        1         0         2
  DYRK4 WILD-TYPE       2       15       40       29        37        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DYRK4 MUTATED           0          0          0          2        1
  DYRK4 WILD-TYPE         3         70         53         30       37
D288V3, multiclass
            clus
vv           DYRK4 MUTATED DYRK4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DYRK4 MUTATED     1   1   1   4
  DYRK4 WILD-TYPE  21  91 172  93
D288V4, multiclass
    clus
vv   DYRK4 MUTATED DYRK4 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             1             172
  T4             4              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
  DYRK4 MUTATED     1   3   2   1
  DYRK4 WILD-TYPE 117 101  75  76
D288V5, multiclass
    clus
vv   DYRK4 MUTATED DYRK4 WILD-TYPE
  N0             1             117
  N1             3             101
  N2             2              75
  N3             1              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"
D288V6, binary
                 cls
clus                0   1
  DYRK4 MUTATED     7   1
  DYRK4 WILD-TYPE 339  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      7    1
  DYRK4 WILD-TYPE  339   28
   clus
vv  DYRK4 MUTATED DYRK4 WILD-TYPE
  0             7             339
  1             1              28
[1] 2 2
[1] FALSE
D288V7, binary
                 cls
clus                0   1
  DYRK4 MUTATED     5   3
  DYRK4 WILD-TYPE 140 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      5    3
  DYRK4 WILD-TYPE  140  245
        clus
vv       DYRK4 MUTATED DYRK4 WILD-TYPE
  FEMALE             5             140
  MALE               3             245
[1] 2 2
[1] FALSE
D288V8, binary
                 cls
clus                0   1
  DYRK4 MUTATED     5   1
  DYRK4 WILD-TYPE 287  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      5    1
  DYRK4 WILD-TYPE  287   58
     clus
vv    DYRK4 MUTATED DYRK4 WILD-TYPE
  NO              5             287
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DYRK4 MUTATED                                          0
  DYRK4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DYRK4 MUTATED                                       1
  DYRK4 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DYRK4 MUTATED                                                        4
  DYRK4 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DYRK4 MUTATED                                                   1
  DYRK4 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DYRK4 MUTATED                                                                   0
  DYRK4 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DYRK4 MUTATED                                                    0
  DYRK4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DYRK4 MUTATED                                                  2
  DYRK4 WILD-TYPE                                               59
D288V9, multiclass
                                                                   clus
vv                                                                  DYRK4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  DYRK4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DYRK4 MUTATED     6   0   0   2
  DYRK4 WILD-TYPE 305  14  15  22
D288V10, multiclass
    clus
vv   DYRK4 MUTATED DYRK4 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DYRK4 MUTATED       2                         0
  DYRK4 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DYRK4 MUTATED                                           0     5
  DYRK4 WILD-TYPE                                         1   238
D288V12, multiclass
                                           clus
vv                                          DYRK4 MUTATED DYRK4 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V13, binary
                 cls
clus                0   1
  DYRK4 MUTATED     0   7
  DYRK4 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      0    7
  DYRK4 WILD-TYPE    4  303
                        clus
vv                       DYRK4 MUTATED DYRK4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(289) Variable = BTNL3 MUTATION ANALYSIS
D289V1, survival
                 sevent
clus2               0   1
  BTNL3 MUTATED     3   2
  BTNL3 WILD-TYPE 227 137
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              5             364 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              2             137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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           14.12 
[1] "7.0 - 105.1 (29.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D289V2, 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       2       14       40       29        37        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTNL3 MUTATED           0          2          0          0        0
  BTNL3 WILD-TYPE         3         68         53         32       38
D289V3, multiclass
            clus
vv           BTNL3 MUTATED BTNL3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BTNL3 MUTATED     1   1   1   3
  BTNL3 WILD-TYPE  21  91 172  94
D289V4, multiclass
    clus
vv   BTNL3 MUTATED BTNL3 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             1             172
  T4             3              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
  BTNL3 MUTATED     3   3   0   0
  BTNL3 WILD-TYPE 115 101  77  77
D289V5, multiclass
    clus
vv   BTNL3 MUTATED BTNL3 WILD-TYPE
  N0             3             115
  N1             3             101
  N2             0              77
  N3             0              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"
D289V6, binary
                 cls
clus                0   1
  BTNL3 MUTATED     5   0
  BTNL3 WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      5    0
  BTNL3 WILD-TYPE  341   29
   clus
vv  BTNL3 MUTATED BTNL3 WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D289V7, binary
                 cls
clus                0   1
  BTNL3 MUTATED     2   4
  BTNL3 WILD-TYPE 143 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      2    4
  BTNL3 WILD-TYPE  143  244
        clus
vv       BTNL3 MUTATED BTNL3 WILD-TYPE
  FEMALE             2             143
  MALE               4             244
[1] 2 2
[1] FALSE
D289V8, binary
                 cls
clus                0   1
  BTNL3 MUTATED     5   0
  BTNL3 WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      5    0
  BTNL3 WILD-TYPE  287   59
     clus
vv    BTNL3 MUTATED BTNL3 WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BTNL3 MUTATED                                          0
  BTNL3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BTNL3 MUTATED                                       0
  BTNL3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BTNL3 MUTATED                                                        3
  BTNL3 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BTNL3 MUTATED                                                   0
  BTNL3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BTNL3 MUTATED                                                                   3
  BTNL3 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BTNL3 MUTATED                                                    0
  BTNL3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BTNL3 MUTATED                                                  0
  BTNL3 WILD-TYPE                                               61
D289V9, multiclass
                                                                   clus
vv                                                                  BTNL3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  BTNL3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BTNL3 MUTATED     5   0   0   1
  BTNL3 WILD-TYPE 306  14  15  23
D289V10, multiclass
    clus
vv   BTNL3 MUTATED BTNL3 WILD-TYPE
  R0             5             306
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BTNL3 MUTATED       0                         0
  BTNL3 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BTNL3 MUTATED                                           0     4
  BTNL3 WILD-TYPE                                         1   239
D289V12, multiclass
                                           clus
vv                                          BTNL3 MUTATED BTNL3 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V13, binary
                 cls
clus                0   1
  BTNL3 MUTATED     0   4
  BTNL3 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      0    4
  BTNL3 WILD-TYPE    4  306
                        clus
vv                       BTNL3 MUTATED BTNL3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(290) Variable = ADNP MUTATION ANALYSIS
D290V1, survival
                sevent
clus2              0   1
  ADNP MUTATED     7   7
  ADNP WILD-TYPE 223 132
  ADNP MUTATED ADNP WILD-TYPE 
            14            355 
  ADNP MUTATED ADNP WILD-TYPE 
             7            132 
$`ADNP MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MI 
       21.99         6.97        34.68        16.14        12.43        11.77 
TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A4YY TCGA-D7-A6EY TCGA-F1-6874 TCGA-F1-A448 
        6.02        28.96        13.78        11.44        14.47        21.27 
TCGA-HF-A5NB TCGA-IN-A6RR 
       30.51         6.74 

$`ADNP WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-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-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-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 

  ADNP MUTATED ADNP WILD-TYPE 
          6.02           0.00 
  ADNP MUTATED ADNP WILD-TYPE 
         34.68         122.30 
  ADNP MUTATED ADNP WILD-TYPE 
        14.125         14.270 
[1] "6.0 - 34.7 (14.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D290V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADNP MUTATED         0        1        2        1         1         1
  ADNP WILD-TYPE       2       14       38       29        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADNP MUTATED           0          3          4          1        3
  ADNP WILD-TYPE         3         67         49         31       35
D290V3, multiclass
            clus
vv           ADNP MUTATED ADNP WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            4             49
  STAGE IIIC            1             31
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ADNP MUTATED     2   2   9   5
  ADNP WILD-TYPE  20  90 164  92
D290V4, multiclass
    clus
vv   ADNP MUTATED ADNP WILD-TYPE
  T1            2             20
  T2            2             90
  T3            9            164
  T4            5             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
  ADNP MUTATED     6   5   1   5
  ADNP WILD-TYPE 112  99  76  72
D290V5, multiclass
    clus
vv   ADNP MUTATED ADNP WILD-TYPE
  N0            6            112
  N1            5             99
  N2            1             76
  N3            5             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"
D290V6, binary
                cls
clus               0   1
  ADNP MUTATED    16   1
  ADNP WILD-TYPE 330  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADNP MUTATED     16    1
  ADNP WILD-TYPE  330   28
   clus
vv  ADNP MUTATED ADNP WILD-TYPE
  0           16            330
  1            1             28
[1] 2 2
[1] FALSE
D290V7, binary
                cls
clus               0   1
  ADNP MUTATED     7  11
  ADNP WILD-TYPE 138 237
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADNP MUTATED      7   11
  ADNP WILD-TYPE  138  237
        clus
vv       ADNP MUTATED ADNP WILD-TYPE
  FEMALE            7            138
  MALE             11            237
[1] 2 2
[1] FALSE
D290V8, binary
                cls
clus               0   1
  ADNP MUTATED    11   3
  ADNP WILD-TYPE 281  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADNP MUTATED     11    3
  ADNP WILD-TYPE  281   56
     clus
vv    ADNP MUTATED ADNP WILD-TYPE
  NO            11            281
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ADNP MUTATED                                          0
  ADNP WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ADNP MUTATED                                       0
  ADNP WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ADNP MUTATED                                                        9
  ADNP WILD-TYPE                                                    149
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ADNP MUTATED                                                   2
  ADNP WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ADNP MUTATED                                                                   6
  ADNP WILD-TYPE                                                                62
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ADNP MUTATED                                                    0
  ADNP WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ADNP MUTATED                                                  1
  ADNP WILD-TYPE                                               60
D290V9, multiclass
                                                                   clus
vv                                                                  ADNP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  ADNP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ADNP MUTATED    12   1   1   3
  ADNP WILD-TYPE 299  13  14  21
D290V10, multiclass
    clus
vv   ADNP MUTATED ADNP WILD-TYPE
  R0           12            299
  R1            1             13
  R2            1             14
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ADNP MUTATED       2                         0
  ADNP WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ADNP MUTATED                                           0    11
  ADNP WILD-TYPE                                         1   232
D290V12, multiclass
                                           clus
vv                                          ADNP MUTATED ADNP WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V13, binary
                cls
clus               0   1
  ADNP MUTATED     1  12
  ADNP WILD-TYPE   3 298
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADNP MUTATED      1   12
  ADNP WILD-TYPE    3  298
                        clus
vv                       ADNP MUTATED ADNP WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           12            298
[1] 2 2
[1] FALSE

Clustering(291) Variable = ELF3 MUTATION ANALYSIS
D291V1, survival
                sevent
clus2              0   1
  ELF3 MUTATED     8   4
  ELF3 WILD-TYPE 222 135
  ELF3 MUTATED ELF3 WILD-TYPE 
            12            357 
  ELF3 MUTATED ELF3 WILD-TYPE 
             4            135 
$`ELF3 MUTATED`
TCGA-B7-5816 TCGA-BR-6852 TCGA-CD-5813 TCGA-CG-4462 TCGA-CG-4469 TCGA-CG-4477 
       26.70        44.94        12.39         0.00         7.07        30.97 
TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-A4YY TCGA-F1-6874 TCGA-F1-A448 TCGA-HU-A4GT 
        6.02        21.07        13.78        14.47        21.27         6.51 

$`ELF3 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-4465 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         9.01        18.97 
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-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-A72C TCGA-FP-7735 
        7.13         0.62         7.99        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-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 

  ELF3 MUTATED ELF3 WILD-TYPE 
           0.0            0.1 
  ELF3 MUTATED ELF3 WILD-TYPE 
         44.94         122.30 
  ELF3 MUTATED ELF3 WILD-TYPE 
        14.125         14.270 
[1] "0.0 - 44.9 (14.1)"  "0.1 - 122.3 (14.3)"
[1] "hr=" "1.1"
D291V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ELF3 MUTATED         0        0        2        1         2         1
  ELF3 WILD-TYPE       2       15       38       29        35        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ELF3 MUTATED           0          2          2          0        3
  ELF3 WILD-TYPE         3         68         51         32       35
D291V3, multiclass
            clus
vv           ELF3 MUTATED ELF3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            2             51
  STAGE IIIC            0             32
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ELF3 MUTATED     0   3   7   3
  ELF3 WILD-TYPE  22  89 166  94
D291V4, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  T1            0             22
  T2            3             89
  T3            7            166
  T4            3             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
  ELF3 MUTATED     7   1   1   4
  ELF3 WILD-TYPE 111 103  76  73
D291V5, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  N0            7            111
  N1            1            103
  N2            1             76
  N3            4             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"
D291V6, binary
                cls
clus               0   1
  ELF3 MUTATED    12   1
  ELF3 WILD-TYPE 334  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED     12    1
  ELF3 WILD-TYPE  334   28
   clus
vv  ELF3 MUTATED ELF3 WILD-TYPE
  0           12            334
  1            1             28
[1] 2 2
[1] FALSE
D291V7, binary
                cls
clus               0   1
  ELF3 MUTATED     7   6
  ELF3 WILD-TYPE 138 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      7    6
  ELF3 WILD-TYPE  138  242
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  FEMALE            7            138
  MALE              6            242
[1] 2 2
[1] FALSE
D291V8, binary
                cls
clus               0   1
  ELF3 MUTATED     7   3
  ELF3 WILD-TYPE 285  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      7    3
  ELF3 WILD-TYPE  285   56
     clus
vv    ELF3 MUTATED ELF3 WILD-TYPE
  NO             7            285
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ELF3 MUTATED                                          0
  ELF3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ELF3 MUTATED                                       2
  ELF3 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ELF3 MUTATED                                                        3
  ELF3 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ELF3 MUTATED                                                   2
  ELF3 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ELF3 MUTATED                                                                   5
  ELF3 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ELF3 MUTATED                                                    0
  ELF3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ELF3 MUTATED                                                  1
  ELF3 WILD-TYPE                                               60
D291V9, multiclass
                                                                   clus
vv                                                                  ELF3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  ELF3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ELF3 MUTATED     9   1   1   1
  ELF3 WILD-TYPE 302  13  14  23
D291V10, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  R0            9            302
  R1            1             13
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ELF3 MUTATED       2                         0
  ELF3 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ELF3 MUTATED                                           0     6
  ELF3 WILD-TYPE                                         1   237
D291V12, multiclass
                                           clus
vv                                          ELF3 MUTATED ELF3 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V13, binary
                cls
clus               0   1
  ELF3 MUTATED     1   7
  ELF3 WILD-TYPE   3 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      1    7
  ELF3 WILD-TYPE    3  303
                        clus
vv                       ELF3 MUTATED ELF3 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(292) Variable = NID2 MUTATION ANALYSIS
D292V1, survival
                sevent
clus2              0   1
  NID2 MUTATED    11   6
  NID2 WILD-TYPE 219 133
  NID2 MUTATED NID2 WILD-TYPE 
            17            352 
  NID2 MUTATED NID2 WILD-TYPE 
             6            133 
$`NID2 MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8361 
       19.56         6.97        30.90         9.34        34.68        31.10 
TCGA-BR-8368 TCGA-BR-8381 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-5721 TCGA-CG-5733 
        4.31         7.36        11.77        12.62         6.02        21.07 
TCGA-D7-6524 TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4GX 
       17.85        77.29        26.47        29.98        20.25 

$`NID2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-8372 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79        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-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-D7-6525 
       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-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-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 

  NID2 MUTATED NID2 WILD-TYPE 
          4.31           0.00 
  NID2 MUTATED NID2 WILD-TYPE 
         77.29         122.30 
  NID2 MUTATED NID2 WILD-TYPE 
         19.56          14.12 
[1] "4.3 - 77.3 (19.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D292V2, 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       2       15       37       28        35        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NID2 MUTATED           0          3          0          3        1
  NID2 WILD-TYPE         3         67         53         29       37
D292V3, multiclass
            clus
vv           NID2 MUTATED NID2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              3             37
  STAGE II              2             28
  STAGE IIA             2             35
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            0             53
  STAGE IIIC            3             29
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NID2 MUTATED     1   8   4   4
  NID2 WILD-TYPE  21  84 169  93
D292V4, multiclass
    clus
vv   NID2 MUTATED NID2 WILD-TYPE
  T1            1             21
  T2            8             84
  T3            4            169
  T4            4             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
  NID2 MUTATED     4   9   3   1
  NID2 WILD-TYPE 114  95  74  76
D292V5, multiclass
    clus
vv   NID2 MUTATED NID2 WILD-TYPE
  N0            4            114
  N1            9             95
  N2            3             74
  N3            1             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"
D292V6, binary
                cls
clus               0   1
  NID2 MUTATED    17   0
  NID2 WILD-TYPE 329  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED     17    0
  NID2 WILD-TYPE  329   29
   clus
vv  NID2 MUTATED NID2 WILD-TYPE
  0           17            329
  1            0             29
[1] 2 2
[1] FALSE
D292V7, binary
                cls
clus               0   1
  NID2 MUTATED     9  10
  NID2 WILD-TYPE 136 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED      9   10
  NID2 WILD-TYPE  136  238
        clus
vv       NID2 MUTATED NID2 WILD-TYPE
  FEMALE            9            136
  MALE             10            238
[1] 2 2
[1] FALSE
D292V8, binary
                cls
clus               0   1
  NID2 MUTATED    16   1
  NID2 WILD-TYPE 276  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED     16    1
  NID2 WILD-TYPE  276   58
     clus
vv    NID2 MUTATED NID2 WILD-TYPE
  NO            16            276
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NID2 MUTATED                                          1
  NID2 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NID2 MUTATED                                       3
  NID2 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NID2 MUTATED                                                       11
  NID2 WILD-TYPE                                                    147
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NID2 MUTATED                                                   1
  NID2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NID2 MUTATED                                                                   2
  NID2 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NID2 MUTATED                                                    0
  NID2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NID2 MUTATED                                                  1
  NID2 WILD-TYPE                                               60
D292V9, multiclass
                                                                   clus
vv                                                                  NID2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  NID2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NID2 MUTATED    10   1   0   5
  NID2 WILD-TYPE 301  13  15  19
D292V10, multiclass
    clus
vv   NID2 MUTATED NID2 WILD-TYPE
  R0           10            301
  R1            1             13
  R2            0             15
  RX            5             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NID2 MUTATED       4                         0
  NID2 WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NID2 MUTATED                                           0    12
  NID2 WILD-TYPE                                         1   231
D292V12, multiclass
                                           clus
vv                                          NID2 MUTATED NID2 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               12            231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V13, binary
                cls
clus               0   1
  NID2 MUTATED     0  16
  NID2 WILD-TYPE   4 294
[1] "tbl2"
                cls
clus             [,1] [,2]
  NID2 MUTATED      0   16
  NID2 WILD-TYPE    4  294
                        clus
vv                       NID2 MUTATED NID2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           16            294
[1] 2 2
[1] FALSE

Clustering(293) Variable = FBN3 MUTATION ANALYSIS
D293V1, survival
                sevent
clus2              0   1
  FBN3 MUTATED    17  12
  FBN3 WILD-TYPE 213 127
  FBN3 MUTATED FBN3 WILD-TYPE 
            29            340 
  FBN3 MUTATED FBN3 WILD-TYPE 
            12            127 
$`FBN3 MUTATED`
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8078 
        6.61        15.95         9.17        32.78        35.84        29.59 
TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 
       32.25         4.31        31.27        25.05         1.12        31.96 
TCGA-BR-A4CS TCGA-CD-5801 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4469 TCGA-CG-5721 
        1.48        13.18         6.58        15.95         7.07         6.02 
TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-A4YV TCGA-D7-A6EY TCGA-HU-A4G9 TCGA-HU-A4GT 
       28.96        21.07         5.92        11.44        24.20         6.51 
TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-VQ-A8DT TCGA-VQ-A8P2 TCGA-VQ-A8PK 
        6.58        23.80        48.79        38.14        17.85 

$`FBN3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        34.68        13.87        17.29        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       19.33        39.12        26.10        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-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-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-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-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-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-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-D7-6528 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-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-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-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-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-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 

  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          14.12 
[1] "1.1 - 48.8 (15.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D293V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBN3 MUTATED         0        2        4        1         5         6
  FBN3 WILD-TYPE       2       13       36       29        32        46
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBN3 MUTATED           1          4          3          3        3
  FBN3 WILD-TYPE         2         66         50         29       35
D293V3, multiclass
            clus
vv           FBN3 MUTATED FBN3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              2             13
  STAGE IB              4             36
  STAGE II              1             29
  STAGE IIA             5             32
  STAGE IIB             6             46
  STAGE III             1              2
  STAGE IIIA            4             66
  STAGE IIIB            3             50
  STAGE IIIC            3             29
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FBN3 MUTATED     2   8  11  11
  FBN3 WILD-TYPE  20  84 162  86
D293V4, multiclass
    clus
vv   FBN3 MUTATED FBN3 WILD-TYPE
  T1            2             20
  T2            8             84
  T3           11            162
  T4           11             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
  FBN3 MUTATED    15   9   2   7
  FBN3 WILD-TYPE 103  95  75  70
D293V5, multiclass
    clus
vv   FBN3 MUTATED FBN3 WILD-TYPE
  N0           15            103
  N1            9             95
  N2            2             75
  N3            7             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"
D293V6, binary
                cls
clus               0   1
  FBN3 MUTATED    32   1
  FBN3 WILD-TYPE 314  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED     32    1
  FBN3 WILD-TYPE  314   28
   clus
vv  FBN3 MUTATED FBN3 WILD-TYPE
  0           32            314
  1            1             28
[1] 2 2
[1] FALSE
D293V7, binary
                cls
clus               0   1
  FBN3 MUTATED    15  18
  FBN3 WILD-TYPE 130 230
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED     15   18
  FBN3 WILD-TYPE  130  230
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  FEMALE           15            130
  MALE             18            230
[1] 2 2
[1] FALSE
D293V8, binary
                cls
clus               0   1
  FBN3 MUTATED    26   2
  FBN3 WILD-TYPE 266  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED     26    2
  FBN3 WILD-TYPE  266   57
     clus
vv    FBN3 MUTATED FBN3 WILD-TYPE
  NO            26            266
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FBN3 MUTATED                                          0
  FBN3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FBN3 MUTATED                                       2
  FBN3 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBN3 MUTATED                                                       16
  FBN3 WILD-TYPE                                                    142
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FBN3 MUTATED                                                   1
  FBN3 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBN3 MUTATED                                                                   8
  FBN3 WILD-TYPE                                                                60
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FBN3 MUTATED                                                    1
  FBN3 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FBN3 MUTATED                                                  5
  FBN3 WILD-TYPE                                               56
D293V9, multiclass
                                                                   clus
vv                                                                  FBN3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            8
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             5
                                                                   clus
vv                                                                  FBN3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             60
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FBN3 MUTATED    28   1   0   3
  FBN3 WILD-TYPE 283  13  15  21
D293V10, multiclass
    clus
vv   FBN3 MUTATED FBN3 WILD-TYPE
  R0           28            283
  R1            1             13
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FBN3 MUTATED       7                         0
  FBN3 WILD-TYPE    80                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBN3 MUTATED                                           0    19
  FBN3 WILD-TYPE                                         1   224
D293V12, multiclass
                                           clus
vv                                          FBN3 MUTATED FBN3 WILD-TYPE
  ASIAN                                                7             80
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               19            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V13, binary
                cls
clus               0   1
  FBN3 MUTATED     0  24
  FBN3 WILD-TYPE   4 286
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN3 MUTATED      0   24
  FBN3 WILD-TYPE    4  286
                        clus
vv                       FBN3 MUTATED FBN3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           24            286
[1] 2 2
[1] FALSE

Clustering(294) Variable = ABCA6 MUTATION ANALYSIS
D294V1, survival
                 sevent
clus2               0   1
  ABCA6 MUTATED     7   5
  ABCA6 WILD-TYPE 223 134
  ABCA6 MUTATED ABCA6 WILD-TYPE 
             12             357 
  ABCA6 MUTATED ABCA6 WILD-TYPE 
              5             134 
$`ABCA6 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-7704 TCGA-BR-8487 TCGA-BR-8680 
        6.97        34.68        18.05        35.24         1.12        31.96 
TCGA-CG-4465 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HF-7132 TCGA-RD-A7BW TCGA-VQ-A8P2 
        9.01         5.92        11.08        77.29         5.13        38.14 

$`ABCA6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  ABCA6 MUTATED ABCA6 WILD-TYPE 
           1.12            0.00 
  ABCA6 MUTATED ABCA6 WILD-TYPE 
          77.29          122.30 
  ABCA6 MUTATED ABCA6 WILD-TYPE 
         14.565          14.270 
[1] "1.1 - 77.3 (14.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D294V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCA6 MUTATED         0        0        1        2         3         2
  ABCA6 WILD-TYPE       2       15       39       28        34        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABCA6 MUTATED           0          4          0          0        2
  ABCA6 WILD-TYPE         3         66         53         32       36
D294V3, multiclass
            clus
vv           ABCA6 MUTATED ABCA6 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              3              34
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCA6 MUTATED     0   2   7   5
  ABCA6 WILD-TYPE  22  90 166  92
D294V4, multiclass
    clus
vv   ABCA6 MUTATED ABCA6 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             7             166
  T4             5              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
  ABCA6 MUTATED     7   6   1   1
  ABCA6 WILD-TYPE 111  98  76  76
D294V5, multiclass
    clus
vv   ABCA6 MUTATED ABCA6 WILD-TYPE
  N0             7             111
  N1             6              98
  N2             1              76
  N3             1              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"
D294V6, binary
                 cls
clus                0   1
  ABCA6 MUTATED    12   2
  ABCA6 WILD-TYPE 334  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA6 MUTATED     12    2
  ABCA6 WILD-TYPE  334   27
   clus
vv  ABCA6 MUTATED ABCA6 WILD-TYPE
  0            12             334
  1             2              27
[1] 2 2
[1] FALSE
D294V7, binary
                 cls
clus                0   1
  ABCA6 MUTATED     8   7
  ABCA6 WILD-TYPE 137 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA6 MUTATED      8    7
  ABCA6 WILD-TYPE  137  241
        clus
vv       ABCA6 MUTATED ABCA6 WILD-TYPE
  FEMALE             8             137
  MALE               7             241
[1] 2 2
[1] FALSE
D294V8, binary
                 cls
clus                0   1
  ABCA6 MUTATED     8   4
  ABCA6 WILD-TYPE 284  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA6 MUTATED      8    4
  ABCA6 WILD-TYPE  284   55
     clus
vv    ABCA6 MUTATED ABCA6 WILD-TYPE
  NO              8             284
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ABCA6 MUTATED                                          0
  ABCA6 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ABCA6 MUTATED                                       2
  ABCA6 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCA6 MUTATED                                                        7
  ABCA6 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ABCA6 MUTATED                                                   2
  ABCA6 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCA6 MUTATED                                                                   2
  ABCA6 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ABCA6 MUTATED                                                    0
  ABCA6 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ABCA6 MUTATED                                                  2
  ABCA6 WILD-TYPE                                               59
D294V9, multiclass
                                                                   clus
vv                                                                  ABCA6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  ABCA6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCA6 MUTATED    11   0   1   3
  ABCA6 WILD-TYPE 300  14  14  21
D294V10, multiclass
    clus
vv   ABCA6 MUTATED ABCA6 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCA6 MUTATED       1                         1
  ABCA6 WILD-TYPE    86                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCA6 MUTATED                                           0    11
  ABCA6 WILD-TYPE                                         1   232
D294V12, multiclass
                                           clus
vv                                          ABCA6 MUTATED ABCA6 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V13, binary
                 cls
clus                0   1
  ABCA6 MUTATED     0  12
  ABCA6 WILD-TYPE   4 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA6 MUTATED      0   12
  ABCA6 WILD-TYPE    4  298
                        clus
vv                       ABCA6 MUTATED ABCA6 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(295) Variable = IDE MUTATION ANALYSIS
D295V1, survival
               sevent
clus2             0   1
  IDE MUTATED     4   6
  IDE WILD-TYPE 226 133
  IDE MUTATED IDE WILD-TYPE 
           10           359 
  IDE MUTATED IDE WILD-TYPE 
            6           133 
$`IDE MUTATED`
TCGA-BR-7703 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4306 
       36.16        31.96        16.14         6.58        11.77         1.02 
TCGA-HJ-7597 TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4GT 
       26.47        11.77         0.10         6.51 

$`IDE WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         8.98         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 

  IDE MUTATED IDE WILD-TYPE 
          0.1           0.0 
  IDE MUTATED IDE WILD-TYPE 
        36.16        122.30 
  IDE MUTATED IDE WILD-TYPE 
        11.77         14.43 
[1] "0.1 - 36.2 (11.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.9"
D295V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IDE MUTATED         0        2        1        0         2         0
  IDE WILD-TYPE       2       13       39       30        35        52
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IDE MUTATED           0          2          1          1        2
  IDE WILD-TYPE         3         68         52         31       36
D295V3, multiclass
            clus
vv           IDE MUTATED IDE WILD-TYPE
  STAGE I              0             2
  STAGE IA             2            13
  STAGE IB             1            39
  STAGE II             0            30
  STAGE IIA            2            35
  STAGE IIB            0            52
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           1            52
  STAGE IIIC           1            31
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  IDE MUTATED     2   1   5   3
  IDE WILD-TYPE  20  91 168  94
D295V4, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  T1           2            20
  T2           1            91
  T3           5           168
  T4           3            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
  IDE MUTATED     6   1   3   1
  IDE WILD-TYPE 112 103  74  76
D295V5, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  N0           6           112
  N1           1           103
  N2           3            74
  N3           1            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"
D295V6, binary
               cls
clus              0   1
  IDE MUTATED     8   2
  IDE WILD-TYPE 338  27
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      8    2
  IDE WILD-TYPE  338   27
   clus
vv  IDE MUTATED IDE WILD-TYPE
  0           8           338
  1           2            27
[1] 2 2
[1] FALSE
D295V7, binary
               cls
clus              0   1
  IDE MUTATED     4   7
  IDE WILD-TYPE 141 241
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      4    7
  IDE WILD-TYPE  141  241
        clus
vv       IDE MUTATED IDE WILD-TYPE
  FEMALE           4           141
  MALE             7           241
[1] 2 2
[1] FALSE
D295V8, binary
               cls
clus              0   1
  IDE MUTATED     9   0
  IDE WILD-TYPE 283  59
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      9    0
  IDE WILD-TYPE  283   59
     clus
vv    IDE MUTATED IDE WILD-TYPE
  NO            9           283
  YES           0            59
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IDE MUTATED                                          1
  IDE WILD-TYPE                                        7
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IDE MUTATED                                       1
  IDE WILD-TYPE                                    69
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IDE MUTATED                                                        4
  IDE WILD-TYPE                                                    154
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IDE MUTATED                                                   0
  IDE WILD-TYPE                                                21
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IDE MUTATED                                                                   0
  IDE WILD-TYPE                                                                68
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IDE MUTATED                                                    1
  IDE WILD-TYPE                                                  4
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IDE MUTATED                                                  4
  IDE WILD-TYPE                                               57
D295V9, multiclass
                                                                   clus
vv                                                                  IDE MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            4
                                                                   clus
vv                                                                  IDE WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  IDE MUTATED     7   0   1   1
  IDE WILD-TYPE 304  14  14  23
D295V10, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  R0           7           304
  R1           0            14
  R2           1            14
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  IDE MUTATED       6                         0
  IDE WILD-TYPE    81                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IDE MUTATED                                           0     4
  IDE WILD-TYPE                                         1   239
D295V12, multiclass
                                           clus
vv                                          IDE MUTATED IDE WILD-TYPE
  ASIAN                                               6            81
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               4           239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V13, binary
               cls
clus              0   1
  IDE MUTATED     0  10
  IDE WILD-TYPE   4 300
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      0   10
  IDE WILD-TYPE    4  300
                        clus
vv                       IDE MUTATED IDE WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          10           300
[1] 2 2
[1] FALSE

Clustering(296) Variable = BCLAF1 MUTATION ANALYSIS
D296V1, survival
                  sevent
clus2                0   1
  BCLAF1 MUTATED    20   9
  BCLAF1 WILD-TYPE 210 130
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              29              340 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               9              130 
$`BCLAF1 MUTATED`
TCGA-CG-4444 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8289 
       47.05         6.97        34.68        32.25         8.05         2.66 
TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8680 TCGA-BR-A4PE TCGA-CD-8532 
        0.26         4.31        31.27        31.96        20.42        11.64 
TCGA-CD-A48A TCGA-CG-4305 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6526 TCGA-D7-6817 
       12.43        15.95       105.07        21.07        17.19        12.79 
TCGA-D7-6818 TCGA-F1-6874 TCGA-F1-A448 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4G8 
       12.36        14.47        21.27        22.32        22.82        22.68 
TCGA-R5-A7ZI TCGA-SW-A7EB TCGA-VQ-A8P2 TCGA-VQ-A94T TCGA-VQ-AA6G 
       74.53         5.79        38.14        11.24        26.04 

$`BCLAF1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-8285 TCGA-BR-8286 TCGA-BR-8291 
        0.69        29.59         9.60         0.56        29.42        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-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-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-8533 
        7.17        12.33        12.30        12.39        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-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-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85        13.35        10.26        15.22        15.98 
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-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-8608 TCGA-HU-8610 
        1.51         5.92        24.39        28.96        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-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-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-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-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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
            0.26             0.00 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
          105.07           122.30 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
          20.420           14.055 
[1] "0.3 - 105.1 (20.4)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D296V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BCLAF1 MUTATED         0        0        4        3         4         3
  BCLAF1 WILD-TYPE       2       15       36       27        33        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCLAF1 MUTATED           0          8          2          2        3
  BCLAF1 WILD-TYPE         3         62         51         30       35
D296V3, multiclass
            clus
vv           BCLAF1 MUTATED BCLAF1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                4               36
  STAGE II                3               27
  STAGE IIA               4               33
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              8               62
  STAGE IIIB              2               51
  STAGE IIIC              2               30
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BCLAF1 MUTATED     0  10  11   8
  BCLAF1 WILD-TYPE  22  82 162  89
D296V4, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  T1              0               22
  T2             10               82
  T3             11              162
  T4              8               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
  BCLAF1 MUTATED    11   7   6   6
  BCLAF1 WILD-TYPE 107  97  71  71
D296V5, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  N0             11              107
  N1              7               97
  N2              6               71
  N3              6               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"
D296V6, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED    26   3
  BCLAF1 WILD-TYPE 320  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED     26    3
  BCLAF1 WILD-TYPE  320   26
   clus
vv  BCLAF1 MUTATED BCLAF1 WILD-TYPE
  0             26              320
  1              3               26
[1] 2 2
[1] FALSE
D296V7, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED    13  17
  BCLAF1 WILD-TYPE 132 231
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED     13   17
  BCLAF1 WILD-TYPE  132  231
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  FEMALE             13              132
  MALE               17              231
[1] 2 2
[1] FALSE
D296V8, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED    23   6
  BCLAF1 WILD-TYPE 269  53
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED     23    6
  BCLAF1 WILD-TYPE  269   53
     clus
vv    BCLAF1 MUTATED BCLAF1 WILD-TYPE
  NO              23              269
  YES              6               53
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BCLAF1 MUTATED                                          0
  BCLAF1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BCLAF1 MUTATED                                       6
  BCLAF1 WILD-TYPE                                    64
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BCLAF1 MUTATED                                                       12
  BCLAF1 WILD-TYPE                                                    146
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BCLAF1 MUTATED                                                   3
  BCLAF1 WILD-TYPE                                                18
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BCLAF1 MUTATED                                                                   5
  BCLAF1 WILD-TYPE                                                                63
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BCLAF1 MUTATED                                                    0
  BCLAF1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BCLAF1 MUTATED                                                  4
  BCLAF1 WILD-TYPE                                               57
D296V9, multiclass
                                                                   clus
vv                                                                  BCLAF1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  BCLAF1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BCLAF1 MUTATED    26   0   0   2
  BCLAF1 WILD-TYPE 285  14  15  22
D296V10, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  R0             26              285
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  BCLAF1 MUTATED       6                         0
  BCLAF1 WILD-TYPE    81                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BCLAF1 MUTATED                                           0    19
  BCLAF1 WILD-TYPE                                         1   224
D296V12, multiclass
                                           clus
vv                                          BCLAF1 MUTATED BCLAF1 WILD-TYPE
  ASIAN                                                  6               81
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 19              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V13, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED     2  21
  BCLAF1 WILD-TYPE   2 289
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      2   21
  BCLAF1 WILD-TYPE    2  289
                        clus
vv                       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  HISPANIC OR LATINO                  2                2
  NOT HISPANIC OR LATINO             21              289
[1] 2 2
[1] FALSE

Clustering(297) Variable = DLGAP3 MUTATION ANALYSIS
D297V1, survival
                  sevent
clus2                0   1
  DLGAP3 MUTATED    18   2
  DLGAP3 WILD-TYPE 212 137
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              20              349 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
               2              137 
$`DLGAP3 MUTATED`
TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-8078 TCGA-BR-8680 TCGA-BR-A4J7 TCGA-CG-5721 
       30.90        32.78        29.59        31.96        32.52         6.02 
TCGA-CG-5728 TCGA-D7-6822 TCGA-HF-7132 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU 
       65.10        12.33        77.29        29.98         6.51         6.58 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-IN-8462 TCGA-IP-7968 
        0.26        29.00        23.84        14.07        18.81         2.53 
TCGA-VQ-A8P2 TCGA-VQ-A91U 
       38.14         1.71 

$`DLGAP3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-D7-8570 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-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-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 
        8.98         0.10        20.25         2.10        12.95        23.80 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
       21.17        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-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-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 

  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
            0.26             0.00 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
           77.29           122.30 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
           26.42            14.07 
[1] "0.3 - 77.3 (26.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "5"  
D297V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DLGAP3 MUTATED         0        0        3        1         3         5
  DLGAP3 WILD-TYPE       2       15       37       29        34        47
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DLGAP3 MUTATED           0          3          1          1        2
  DLGAP3 WILD-TYPE         3         67         52         31       36
D297V3, multiclass
            clus
vv           DLGAP3 MUTATED DLGAP3 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               5               47
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DLGAP3 MUTATED     1   7   5   7
  DLGAP3 WILD-TYPE  21  85 168  90
D297V4, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  T1              1               21
  T2              7               85
  T3              5              168
  T4              7               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
  DLGAP3 MUTATED     5   9   3   1
  DLGAP3 WILD-TYPE 113  95  74  76
D297V5, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  N0              5              113
  N1              9               95
  N2              3               74
  N3              1               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"
D297V6, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED    18   1
  DLGAP3 WILD-TYPE 328  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED     18    1
  DLGAP3 WILD-TYPE  328   28
   clus
vv  DLGAP3 MUTATED DLGAP3 WILD-TYPE
  0             18              328
  1              1               28
[1] 2 2
[1] FALSE
D297V7, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED     8  12
  DLGAP3 WILD-TYPE 137 236
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED      8   12
  DLGAP3 WILD-TYPE  137  236
        clus
vv       DLGAP3 MUTATED DLGAP3 WILD-TYPE
  FEMALE              8              137
  MALE               12              236
[1] 2 2
[1] FALSE
D297V8, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED    15   2
  DLGAP3 WILD-TYPE 277  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED     15    2
  DLGAP3 WILD-TYPE  277   57
     clus
vv    DLGAP3 MUTATED DLGAP3 WILD-TYPE
  NO              15              277
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DLGAP3 MUTATED                                          0
  DLGAP3 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DLGAP3 MUTATED                                       3
  DLGAP3 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DLGAP3 MUTATED                                                        5
  DLGAP3 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DLGAP3 MUTATED                                                   3
  DLGAP3 WILD-TYPE                                                18
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DLGAP3 MUTATED                                                                   3
  DLGAP3 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DLGAP3 MUTATED                                                    0
  DLGAP3 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DLGAP3 MUTATED                                                  6
  DLGAP3 WILD-TYPE                                               55
D297V9, multiclass
                                                                   clus
vv                                                                  DLGAP3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               6
                                                                   clus
vv                                                                  DLGAP3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DLGAP3 MUTATED    19   0   0   1
  DLGAP3 WILD-TYPE 292  14  15  23
D297V10, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  R0             19              292
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DLGAP3 MUTATED      10                         0
  DLGAP3 WILD-TYPE    77                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DLGAP3 MUTATED                                           0     7
  DLGAP3 WILD-TYPE                                         1   236
D297V12, multiclass
                                           clus
vv                                          DLGAP3 MUTATED DLGAP3 WILD-TYPE
  ASIAN                                                 10               77
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V13, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED     0  15
  DLGAP3 WILD-TYPE   4 295
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED      0   15
  DLGAP3 WILD-TYPE    4  295
                        clus
vv                       DLGAP3 MUTATED DLGAP3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             15              295
[1] 2 2
[1] FALSE

Clustering(298) Variable = ZC3H13 MUTATION ANALYSIS
D298V1, survival
                  sevent
clus2                0   1
  ZC3H13 MUTATED    17   9
  ZC3H13 WILD-TYPE 213 130
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              26              343 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
               9              130 
$`ZC3H13 MUTATED`
TCGA-CG-4460 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6802 TCGA-BR-6852 
       21.99        30.90        34.68        15.95        30.90        44.94 
TCGA-BR-8360 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CD-A4MJ 
        6.18        25.05         1.12        31.96         6.58        12.62 
TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-5723 TCGA-D7-A4YV TCGA-D7-A6EV TCGA-FP-A4BE 
        1.02         4.01       105.07         5.92        11.24        11.08 
TCGA-HF-7132 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-MX-A5UJ 
       77.29        24.20        29.98         0.10         6.58        19.73 
TCGA-SW-A7EA TCGA-VQ-A91Q 
       19.04        20.81 

$`ZC3H13 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-6803 TCGA-BR-7196 TCGA-BR-7197 
       12.16         8.98        40.21        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-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-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-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-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-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-A4YX TCGA-D7-A4YY 
       21.14        20.91        14.27        16.44        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-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-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-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-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-A91U TCGA-VQ-A91V 
       22.19        17.85         1.87        15.65         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 

  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
             0.1              0.0 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
          105.07           122.30 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
          19.385           14.070 
[1] "0.1 - 105.1 (19.4)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D298V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZC3H13 MUTATED         0        1        3        2         8         4
  ZC3H13 WILD-TYPE       2       14       37       28        29        48
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H13 MUTATED           0          3          0          2        5
  ZC3H13 WILD-TYPE         3         67         53         30       33
D298V3, multiclass
            clus
vv           ZC3H13 MUTATED ZC3H13 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                3               37
  STAGE II                2               28
  STAGE IIA               8               29
  STAGE IIB               4               48
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                5               33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZC3H13 MUTATED     2   9  14   6
  ZC3H13 WILD-TYPE  20  83 159  91
D298V4, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  T1              2               20
  T2              9               83
  T3             14              159
  T4              6               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
  ZC3H13 MUTATED    12   7   6   3
  ZC3H13 WILD-TYPE 106  97  71  74
D298V5, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  N0             12              106
  N1              7               97
  N2              6               71
  N3              3               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"
D298V6, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    26   4
  ZC3H13 WILD-TYPE 320  25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     26    4
  ZC3H13 WILD-TYPE  320   25
   clus
vv  ZC3H13 MUTATED ZC3H13 WILD-TYPE
  0             26              320
  1              4               25
[1] 2 2
[1] FALSE
D298V7, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    14  17
  ZC3H13 WILD-TYPE 131 231
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     14   17
  ZC3H13 WILD-TYPE  131  231
        clus
vv       ZC3H13 MUTATED ZC3H13 WILD-TYPE
  FEMALE             14              131
  MALE               17              231
[1] 2 2
[1] FALSE
D298V8, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    22   3
  ZC3H13 WILD-TYPE 270  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     22    3
  ZC3H13 WILD-TYPE  270   56
     clus
vv    ZC3H13 MUTATED ZC3H13 WILD-TYPE
  NO              22              270
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZC3H13 MUTATED                                          0
  ZC3H13 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZC3H13 MUTATED                                       3
  ZC3H13 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZC3H13 MUTATED                                                       15
  ZC3H13 WILD-TYPE                                                    143
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZC3H13 MUTATED                                                   1
  ZC3H13 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZC3H13 MUTATED                                                                   5
  ZC3H13 WILD-TYPE                                                                63
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZC3H13 MUTATED                                                    0
  ZC3H13 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZC3H13 MUTATED                                                  7
  ZC3H13 WILD-TYPE                                               54
D298V9, multiclass
                                                                   clus
vv                                                                  ZC3H13 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               7
                                                                   clus
vv                                                                  ZC3H13 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZC3H13 MUTATED    22   0   3   4
  ZC3H13 WILD-TYPE 289  14  12  20
D298V10, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  R0             22              289
  R1              0               14
  R2              3               12
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZC3H13 MUTATED       7                         1
  ZC3H13 WILD-TYPE    80                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZC3H13 MUTATED                                           0    16
  ZC3H13 WILD-TYPE                                         1   227
D298V12, multiclass
                                           clus
vv                                          ZC3H13 MUTATED ZC3H13 WILD-TYPE
  ASIAN                                                  7               80
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 16              227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V13, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED     0  24
  ZC3H13 WILD-TYPE   4 286
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED      0   24
  ZC3H13 WILD-TYPE    4  286
                        clus
vv                       ZC3H13 MUTATED ZC3H13 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             24              286
[1] 2 2
[1] FALSE

Clustering(299) Variable = RTN2 MUTATION ANALYSIS
D299V1, survival
                sevent
clus2              0   1
  RTN2 MUTATED     7   4
  RTN2 WILD-TYPE 223 135
  RTN2 MUTATED RTN2 WILD-TYPE 
            11            358 
  RTN2 MUTATED RTN2 WILD-TYPE 
             4            135 
$`RTN2 MUTATED`
TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8360 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-5721 
       34.68        32.25         6.18         6.58        15.95         6.02 
TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-6526 TCGA-D7-A4YV TCGA-VQ-A8E2 
       28.96        21.07        17.19         5.92        43.36 

$`RTN2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-D7-6527 
       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-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-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 

  RTN2 MUTATED RTN2 WILD-TYPE 
          5.92           0.00 
  RTN2 MUTATED RTN2 WILD-TYPE 
         43.36         122.30 
  RTN2 MUTATED RTN2 WILD-TYPE 
         17.19          14.12 
[1] "5.9 - 43.4 (17.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D299V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RTN2 MUTATED         1        1        0        1         3         3
  RTN2 WILD-TYPE       1       14       40       29        34        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RTN2 MUTATED           0          3          1          0        1
  RTN2 WILD-TYPE         3         67         52         32       37
D299V3, multiclass
            clus
vv           RTN2 MUTATED RTN2 WILD-TYPE
  STAGE I               1              1
  STAGE IA              1             14
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             3             34
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RTN2 MUTATED     2   2   6   4
  RTN2 WILD-TYPE  20  90 167  93
D299V4, multiclass
    clus
vv   RTN2 MUTATED RTN2 WILD-TYPE
  T1            2             20
  T2            2             90
  T3            6            167
  T4            4             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
  RTN2 MUTATED     7   4   3   0
  RTN2 WILD-TYPE 111 100  74  77
D299V5, multiclass
    clus
vv   RTN2 MUTATED RTN2 WILD-TYPE
  N0            7            111
  N1            4            100
  N2            3             74
  N3            0             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"
D299V6, binary
                cls
clus               0   1
  RTN2 MUTATED    14   0
  RTN2 WILD-TYPE 332  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN2 MUTATED     14    0
  RTN2 WILD-TYPE  332   29
   clus
vv  RTN2 MUTATED RTN2 WILD-TYPE
  0           14            332
  1            0             29
[1] 2 2
[1] FALSE
D299V7, binary
                cls
clus               0   1
  RTN2 MUTATED     7   8
  RTN2 WILD-TYPE 138 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN2 MUTATED      7    8
  RTN2 WILD-TYPE  138  240
        clus
vv       RTN2 MUTATED RTN2 WILD-TYPE
  FEMALE            7            138
  MALE              8            240
[1] 2 2
[1] FALSE
D299V8, binary
                cls
clus               0   1
  RTN2 MUTATED    11   1
  RTN2 WILD-TYPE 281  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN2 MUTATED     11    1
  RTN2 WILD-TYPE  281   58
     clus
vv    RTN2 MUTATED RTN2 WILD-TYPE
  NO            11            281
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RTN2 MUTATED                                          0
  RTN2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RTN2 MUTATED                                       1
  RTN2 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RTN2 MUTATED                                                        6
  RTN2 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RTN2 MUTATED                                                   0
  RTN2 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RTN2 MUTATED                                                                   5
  RTN2 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RTN2 MUTATED                                                    0
  RTN2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RTN2 MUTATED                                                  3
  RTN2 WILD-TYPE                                               58
D299V9, multiclass
                                                                   clus
vv                                                                  RTN2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  RTN2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RTN2 MUTATED    12   0   0   2
  RTN2 WILD-TYPE 299  14  15  22
D299V10, multiclass
    clus
vv   RTN2 MUTATED RTN2 WILD-TYPE
  R0           12            299
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RTN2 MUTATED       2                         1
  RTN2 WILD-TYPE    85                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RTN2 MUTATED                                           0     8
  RTN2 WILD-TYPE                                         1   235
D299V12, multiclass
                                           clus
vv                                          RTN2 MUTATED RTN2 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V13, binary
                cls
clus               0   1
  RTN2 MUTATED     0  10
  RTN2 WILD-TYPE   4 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN2 MUTATED      0   10
  RTN2 WILD-TYPE    4  300
                        clus
vv                       RTN2 MUTATED RTN2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           10            300
[1] 2 2
[1] FALSE

Clustering(300) Variable = RAI1 MUTATION ANALYSIS
D300V1, survival
                sevent
clus2              0   1
  RAI1 MUTATED    18   5
  RAI1 WILD-TYPE 212 134
  RAI1 MUTATED RAI1 WILD-TYPE 
            23            346 
  RAI1 MUTATED RAI1 WILD-TYPE 
             5            134 
$`RAI1 MUTATED`
TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-8289 TCGA-BR-8483 
       44.94        36.16        35.84        39.78         2.66         5.39 
TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5723 
       28.14        16.14         6.58        11.77         6.02       105.07 
TCGA-D7-A4YT TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4G9 
       14.27        77.29        26.47        22.32        22.68        24.20 
TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-IN-A7NT TCGA-SW-A7EA TCGA-VQ-A8P2 
        6.58        14.07        10.62        19.04        38.14 

$`RAI1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-7704 
       40.21        30.90        31.20        21.90         9.21        35.24 
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-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-8487 TCGA-BR-8588 
        3.72        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-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-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-A4YU 
       17.19        18.21        14.66        21.14        20.91        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-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-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-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-A7NU 
       19.53         6.44         6.74        12.59         6.51        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 

  RAI1 MUTATED RAI1 WILD-TYPE 
          2.66           0.00 
  RAI1 MUTATED RAI1 WILD-TYPE 
        105.07         122.30 
  RAI1 MUTATED RAI1 WILD-TYPE 
         22.32          14.04 
[1] "2.7 - 105.1 (22.3)" "0.0 - 122.3 (14.0)"
[1] "hr=" "2.3"
D300V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAI1 MUTATED         0        2        4        2         2         6
  RAI1 WILD-TYPE       2       13       36       28        35        46
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAI1 MUTATED           0          5          1          1        3
  RAI1 WILD-TYPE         3         65         52         31       35
D300V3, multiclass
            clus
vv           RAI1 MUTATED RAI1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              2             13
  STAGE IB              4             36
  STAGE II              2             28
  STAGE IIA             2             35
  STAGE IIB             6             46
  STAGE III             0              3
  STAGE IIIA            5             65
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RAI1 MUTATED     4   6   9   8
  RAI1 WILD-TYPE  18  86 164  89
D300V4, multiclass
    clus
vv   RAI1 MUTATED RAI1 WILD-TYPE
  T1            4             18
  T2            6             86
  T3            9            164
  T4            8             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
  RAI1 MUTATED    10  11   2   4
  RAI1 WILD-TYPE 108  93  75  73
D300V5, multiclass
    clus
vv   RAI1 MUTATED RAI1 WILD-TYPE
  N0           10            108
  N1           11             93
  N2            2             75
  N3            4             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"
D300V6, binary
                cls
clus               0   1
  RAI1 MUTATED    27   1
  RAI1 WILD-TYPE 319  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED     27    1
  RAI1 WILD-TYPE  319   28
   clus
vv  RAI1 MUTATED RAI1 WILD-TYPE
  0           27            319
  1            1             28
[1] 2 2
[1] FALSE
D300V7, binary
                cls
clus               0   1
  RAI1 MUTATED    15  14
  RAI1 WILD-TYPE 130 234
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED     15   14
  RAI1 WILD-TYPE  130  234
        clus
vv       RAI1 MUTATED RAI1 WILD-TYPE
  FEMALE           15            130
  MALE             14            234
[1] 2 2
[1] FALSE
D300V8, binary
                cls
clus               0   1
  RAI1 MUTATED    22   2
  RAI1 WILD-TYPE 270  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED     22    2
  RAI1 WILD-TYPE  270   57
     clus
vv    RAI1 MUTATED RAI1 WILD-TYPE
  NO            22            270
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RAI1 MUTATED                                          1
  RAI1 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RAI1 MUTATED                                       5
  RAI1 WILD-TYPE                                    65
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RAI1 MUTATED                                                       13
  RAI1 WILD-TYPE                                                    145
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RAI1 MUTATED                                                   2
  RAI1 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RAI1 MUTATED                                                                   4
  RAI1 WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RAI1 MUTATED                                                    1
  RAI1 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RAI1 MUTATED                                                  3
  RAI1 WILD-TYPE                                               58
D300V9, multiclass
                                                                   clus
vv                                                                  RAI1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  RAI1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RAI1 MUTATED    21   0   0   5
  RAI1 WILD-TYPE 290  14  15  19
D300V10, multiclass
    clus
vv   RAI1 MUTATED RAI1 WILD-TYPE
  R0           21            290
  R1            0             14
  R2            0             15
  RX            5             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RAI1 MUTATED       7                         0
  RAI1 WILD-TYPE    80                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAI1 MUTATED                                           0    19
  RAI1 WILD-TYPE                                         1   224
D300V12, multiclass
                                           clus
vv                                          RAI1 MUTATED RAI1 WILD-TYPE
  ASIAN                                                7             80
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               19            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V13, binary
                cls
clus               0   1
  RAI1 MUTATED     0  25
  RAI1 WILD-TYPE   4 285
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      0   25
  RAI1 WILD-TYPE    4  285
                        clus
vv                       RAI1 MUTATED RAI1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           25            285
[1] 2 2
[1] FALSE

Clustering(301) Variable = C6ORF165 MUTATION ANALYSIS
D301V1, survival
                    sevent
clus2                  0   1
  C6ORF165 MUTATED    12   4
  C6ORF165 WILD-TYPE 218 135
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                16                353 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                 4                135 
$`C6ORF165 MUTATED`
TCGA-KB-A93G TCGA-BR-4184 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 
       20.15         6.97        32.25         4.31        31.27        25.05 
TCGA-BR-8680 TCGA-CG-4306 TCGA-CG-5723 TCGA-D7-6818 TCGA-F1-A448 TCGA-HU-8602 
       31.96         1.02       105.07        12.36        21.27        22.32 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-HU-A4H4 
       24.26        22.68        20.25        23.84 

$`C6ORF165 WILD-TYPE`
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-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
       14.04         3.32        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-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-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-D7-6820 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-F1-6874 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-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
        5.59        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-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 

  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
              1.02               0.00 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
            105.07             122.30 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
             22.50              14.04 
[1] "1.0 - 105.1 (22.5)" "0.0 - 122.3 (14.0)"
[1] "hr=" "2"  
D301V2, 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       2       14       38       29        37        48
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF165 MUTATED           0          2          1          3        2
  C6ORF165 WILD-TYPE         3         68         52         29       36
D301V3, multiclass
            clus
vv           C6ORF165 MUTATED C6ORF165 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  2                 38
  STAGE II                  1                 29
  STAGE IIA                 0                 37
  STAGE IIB                 4                 48
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                1                 52
  STAGE IIIC                3                 29
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C6ORF165 MUTATED     1   5   4   6
  C6ORF165 WILD-TYPE  21  87 169  91
D301V4, multiclass
    clus
vv   C6ORF165 MUTATED C6ORF165 WILD-TYPE
  T1                1                 21
  T2                5                 87
  T3                4                169
  T4                6                 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
  C6ORF165 MUTATED     5   3   4   4
  C6ORF165 WILD-TYPE 113 101  73  73
D301V5, multiclass
    clus
vv   C6ORF165 MUTATED C6ORF165 WILD-TYPE
  N0                5                113
  N1                3                101
  N2                4                 73
  N3                4                 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"
D301V6, binary
                    cls
clus                   0   1
  C6ORF165 MUTATED    13   2
  C6ORF165 WILD-TYPE 333  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED     13    2
  C6ORF165 WILD-TYPE  333   27
   clus
vv  C6ORF165 MUTATED C6ORF165 WILD-TYPE
  0               13                333
  1                2                 27
[1] 2 2
[1] FALSE
D301V7, binary
                    cls
clus                   0   1
  C6ORF165 MUTATED     7   9
  C6ORF165 WILD-TYPE 138 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      7    9
  C6ORF165 WILD-TYPE  138  239
        clus
vv       C6ORF165 MUTATED C6ORF165 WILD-TYPE
  FEMALE                7                138
  MALE                  9                239
[1] 2 2
[1] FALSE
D301V8, binary
                    cls
clus                   0   1
  C6ORF165 MUTATED    13   2
  C6ORF165 WILD-TYPE 279  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED     13    2
  C6ORF165 WILD-TYPE  279   57
     clus
vv    C6ORF165 MUTATED C6ORF165 WILD-TYPE
  NO                13                279
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C6ORF165 MUTATED                                          1
  C6ORF165 WILD-TYPE                                        7
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C6ORF165 MUTATED                                       4
  C6ORF165 WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C6ORF165 MUTATED                                                        7
  C6ORF165 WILD-TYPE                                                    151
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C6ORF165 MUTATED                                                   1
  C6ORF165 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C6ORF165 MUTATED                                                                   0
  C6ORF165 WILD-TYPE                                                                68
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C6ORF165 MUTATED                                                    1
  C6ORF165 WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C6ORF165 MUTATED                                                  2
  C6ORF165 WILD-TYPE                                               59
D301V9, multiclass
                                                                   clus
vv                                                                  C6ORF165 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  C6ORF165 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C6ORF165 MUTATED    13   0   1   1
  C6ORF165 WILD-TYPE 298  14  14  23
D301V10, multiclass
    clus
vv   C6ORF165 MUTATED C6ORF165 WILD-TYPE
  R0               13                298
  R1                0                 14
  R2                1                 14
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C6ORF165 MUTATED       6                         0
  C6ORF165 WILD-TYPE    81                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C6ORF165 MUTATED                                           0     8
  C6ORF165 WILD-TYPE                                         1   235
D301V12, multiclass
                                           clus
vv                                          C6ORF165 MUTATED C6ORF165 WILD-TYPE
  ASIAN                                                    6                 81
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    8                235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V13, binary
                    cls
clus                   0   1
  C6ORF165 MUTATED     1  12
  C6ORF165 WILD-TYPE   3 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      1   12
  C6ORF165 WILD-TYPE    3  298
                        clus
vv                       C6ORF165 MUTATED C6ORF165 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               12                298
[1] 2 2
[1] FALSE

Clustering(302) Variable = HIAT1 MUTATION ANALYSIS
D302V1, survival
                 sevent
clus2               0   1
  HIAT1 MUTATED     5   3
  HIAT1 WILD-TYPE 225 136
  HIAT1 MUTATED HIAT1 WILD-TYPE 
              8             361 
  HIAT1 MUTATED HIAT1 WILD-TYPE 
              3             136 
$`HIAT1 MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6566 TCGA-BR-8372 TCGA-BR-8680 
       19.56         6.97         9.34        32.78        31.27        31.96 
TCGA-VQ-A8DL TCGA-VQ-A8P2 
        0.92        38.14 

$`HIAT1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  HIAT1 MUTATED HIAT1 WILD-TYPE 
           0.92            0.00 
  HIAT1 MUTATED HIAT1 WILD-TYPE 
          38.14          122.30 
  HIAT1 MUTATED HIAT1 WILD-TYPE 
         25.415          14.170 
[1] "0.9 - 38.1 (25.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D302V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HIAT1 MUTATED         0        0        0        0         2         0
  HIAT1 WILD-TYPE       2       15       40       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIAT1 MUTATED           0          3          0          2        1
  HIAT1 WILD-TYPE         3         67         53         30       37
D302V3, multiclass
            clus
vv           HIAT1 MUTATED HIAT1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HIAT1 MUTATED     0   0   3   5
  HIAT1 WILD-TYPE  22  92 170  92
D302V4, multiclass
    clus
vv   HIAT1 MUTATED HIAT1 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             3             170
  T4             5              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
  HIAT1 MUTATED     3   3   1   2
  HIAT1 WILD-TYPE 115 101  76  75
D302V5, multiclass
    clus
vv   HIAT1 MUTATED HIAT1 WILD-TYPE
  N0             3             115
  N1             3             101
  N2             1              76
  N3             2              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"
D302V6, binary
                 cls
clus                0   1
  HIAT1 MUTATED     7   1
  HIAT1 WILD-TYPE 339  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIAT1 MUTATED      7    1
  HIAT1 WILD-TYPE  339   28
   clus
vv  HIAT1 MUTATED HIAT1 WILD-TYPE
  0             7             339
  1             1              28
[1] 2 2
[1] FALSE
D302V7, binary
                 cls
clus                0   1
  HIAT1 MUTATED     3   6
  HIAT1 WILD-TYPE 142 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIAT1 MUTATED      3    6
  HIAT1 WILD-TYPE  142  242
        clus
vv       HIAT1 MUTATED HIAT1 WILD-TYPE
  FEMALE             3             142
  MALE               6             242
[1] 2 2
[1] FALSE
D302V8, binary
                 cls
clus                0   1
  HIAT1 MUTATED     7   1
  HIAT1 WILD-TYPE 285  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIAT1 MUTATED      7    1
  HIAT1 WILD-TYPE  285   58
     clus
vv    HIAT1 MUTATED HIAT1 WILD-TYPE
  NO              7             285
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HIAT1 MUTATED                                          0
  HIAT1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HIAT1 MUTATED                                       1
  HIAT1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HIAT1 MUTATED                                                        5
  HIAT1 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HIAT1 MUTATED                                                   1
  HIAT1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HIAT1 MUTATED                                                                   0
  HIAT1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HIAT1 MUTATED                                                    0
  HIAT1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HIAT1 MUTATED                                                  2
  HIAT1 WILD-TYPE                                               59
D302V9, multiclass
                                                                   clus
vv                                                                  HIAT1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  HIAT1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HIAT1 MUTATED     5   0   0   3
  HIAT1 WILD-TYPE 306  14  15  21
D302V10, multiclass
    clus
vv   HIAT1 MUTATED HIAT1 WILD-TYPE
  R0             5             306
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HIAT1 MUTATED       1                         0
  HIAT1 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HIAT1 MUTATED                                           0     8
  HIAT1 WILD-TYPE                                         1   235
D302V12, multiclass
                                           clus
vv                                          HIAT1 MUTATED HIAT1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V13, binary
                 cls
clus                0   1
  HIAT1 MUTATED     0   7
  HIAT1 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIAT1 MUTATED      0    7
  HIAT1 WILD-TYPE    4  303
                        clus
vv                       HIAT1 MUTATED HIAT1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(303) Variable = HSPG2 MUTATION ANALYSIS
D303V1, survival
                 sevent
clus2               0   1
  HSPG2 MUTATED    41  16
  HSPG2 WILD-TYPE 189 123
  HSPG2 MUTATED HSPG2 WILD-TYPE 
             57             312 
  HSPG2 MUTATED HSPG2 WILD-TYPE 
             16             123 
$`HSPG2 MUTATED`
TCGA-CG-4460 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6709 TCGA-BR-6802 TCGA-BR-7197 
       21.99        30.90        34.68        12.16        30.90         9.21 
TCGA-BR-7704 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       35.24        14.43         0.69        29.59        32.25         8.05 
TCGA-BR-8360 TCGA-BR-8591 TCGA-BR-A44U TCGA-BR-A4J2 TCGA-CD-5800 TCGA-CD-8525 
        6.18        28.14        13.87        14.17        13.15        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-8536 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5721 
       12.43         6.58         1.02         9.01        30.97         6.02 
TCGA-CG-5728 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-A6EY 
       65.10        16.80        19.50        17.19        14.66        11.44 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8211 TCGA-FP-A4BE TCGA-HU-8243 TCGA-HU-8244 
       17.06        59.54        13.58        11.08         5.92        24.39 
TCGA-HU-8604 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GP 
       22.82        24.26        22.68        24.20        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H8 
        0.10         6.51         6.58         0.26         2.10        14.07 
TCGA-MX-A5UJ TCGA-VQ-A8DU TCGA-VQ-A8P2 
       19.73         5.46        38.14 

$`HSPG2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-6710 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       19.89         8.98        40.21        31.20        44.94        21.90 
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-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-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-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-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-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-8527 TCGA-CD-8533 
       11.21        12.10        12.39        12.76         7.17        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-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-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
        7.07         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-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       11.31        12.33        24.72        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-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-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A9TM 
       14.07        22.29         5.03         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-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-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GX 
        3.25        22.75        25.81        11.77        21.37        20.25 
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-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 

  HSPG2 MUTATED HSPG2 WILD-TYPE 
            0.1             0.0 
  HSPG2 MUTATED HSPG2 WILD-TYPE 
           65.1           122.3 
  HSPG2 MUTATED HSPG2 WILD-TYPE 
         13.580          14.905 
[1] "0.1 - 65.1 (13.6)"  "0.0 - 122.3 (14.9)"
[1] "hr=" "1.3"
D303V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HSPG2 MUTATED         1        3        5        6        10         8
  HSPG2 WILD-TYPE       1       12       35       24        27        44
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSPG2 MUTATED           1         11          5          5        5
  HSPG2 WILD-TYPE         2         59         48         27       33
D303V3, multiclass
            clus
vv           HSPG2 MUTATED HSPG2 WILD-TYPE
  STAGE I                1               1
  STAGE IA               3              12
  STAGE IB               5              35
  STAGE II               6              24
  STAGE IIA             10              27
  STAGE IIB              8              44
  STAGE III              1               2
  STAGE IIIA            11              59
  STAGE IIIB             5              48
  STAGE IIIC             5              27
  STAGE IV               5              33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HSPG2 MUTATED     6   9  28  19
  HSPG2 WILD-TYPE  16  83 145  78
D303V4, multiclass
    clus
vv   HSPG2 MUTATED HSPG2 WILD-TYPE
  T1             6              16
  T2             9              83
  T3            28             145
  T4            19              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"
                 vv
clus              N0 N1 N2 N3
  HSPG2 MUTATED   28 16  6 10
  HSPG2 WILD-TYPE 90 88 71 67
D303V5, multiclass
    clus
vv   HSPG2 MUTATED HSPG2 WILD-TYPE
  N0            28              90
  N1            16              88
  N2             6              71
  N3            10              67
[1] 4 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
  HSPG2 MUTATED    55   4
  HSPG2 WILD-TYPE 291  25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPG2 MUTATED     55    4
  HSPG2 WILD-TYPE  291   25
   clus
vv  HSPG2 MUTATED HSPG2 WILD-TYPE
  0            55             291
  1             4              25
[1] 2 2
[1] FALSE
D303V7, binary
                 cls
clus                0   1
  HSPG2 MUTATED    29  33
  HSPG2 WILD-TYPE 116 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPG2 MUTATED     29   33
  HSPG2 WILD-TYPE  116  215
        clus
vv       HSPG2 MUTATED HSPG2 WILD-TYPE
  FEMALE            29             116
  MALE              33             215
[1] 2 2
[1] FALSE
D303V8, binary
                 cls
clus                0   1
  HSPG2 MUTATED    45  10
  HSPG2 WILD-TYPE 247  49
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPG2 MUTATED     45   10
  HSPG2 WILD-TYPE  247   49
     clus
vv    HSPG2 MUTATED HSPG2 WILD-TYPE
  NO             45             247
  YES            10              49
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HSPG2 MUTATED                                          0
  HSPG2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HSPG2 MUTATED                                      11
  HSPG2 WILD-TYPE                                    59
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HSPG2 MUTATED                                                       21
  HSPG2 WILD-TYPE                                                    137
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HSPG2 MUTATED                                                   3
  HSPG2 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HSPG2 MUTATED                                                                  12
  HSPG2 WILD-TYPE                                                                56
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HSPG2 MUTATED                                                    2
  HSPG2 WILD-TYPE                                                  3
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HSPG2 MUTATED                                                 13
  HSPG2 WILD-TYPE                                               48
D303V9, multiclass
                                                                   clus
vv                                                                  HSPG2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        11
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       21
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             13
                                                                   clus
vv                                                                  HSPG2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          59
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        137
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              56
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               48
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HSPG2 MUTATED    52   2   3   3
  HSPG2 WILD-TYPE 259  12  12  21
D303V10, multiclass
    clus
vv   HSPG2 MUTATED HSPG2 WILD-TYPE
  R0            52             259
  R1             2              12
  R2             3              12
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HSPG2 MUTATED      25                         2
  HSPG2 WILD-TYPE    62                         7
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HSPG2 MUTATED                                           0    28
  HSPG2 WILD-TYPE                                         1   215
D303V12, multiclass
                                           clus
vv                                          HSPG2 MUTATED HSPG2 WILD-TYPE
  ASIAN                                                25              62
  BLACK OR AFRICAN AMERICAN                             2               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                28             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V13, binary
                 cls
clus                0   1
  HSPG2 MUTATED     0  53
  HSPG2 WILD-TYPE   4 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPG2 MUTATED      0   53
  HSPG2 WILD-TYPE    4  257
                        clus
vv                       HSPG2 MUTATED HSPG2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            53             257
[1] 2 2
[1] FALSE

Clustering(304) Variable = NBN MUTATION ANALYSIS
D304V1, survival
               sevent
clus2             0   1
  NBN MUTATED     9   5
  NBN WILD-TYPE 221 134
  NBN MUTATED NBN WILD-TYPE 
           14           355 
  NBN MUTATED NBN WILD-TYPE 
            5           134 
$`NBN MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4256 TCGA-BR-6801 TCGA-CD-8536 TCGA-CD-A486 
       26.70        19.56         9.34        40.21        12.43         6.31 
TCGA-CD-A48C TCGA-D7-A6EY TCGA-HF-7132 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4GX 
       11.61        11.44        77.29        22.68         0.10        20.25 
TCGA-HU-A4H8 TCGA-IN-A6RI 
       14.07        18.38 

$`NBN WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        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 
       16.225        14.270 
[1] "0.1 - 77.3 (16.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D304V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NBN MUTATED         1        0        1        2         2         3
  NBN WILD-TYPE       1       15       39       28        35        49
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NBN MUTATED           0          0          1          3        0
  NBN WILD-TYPE         3         70         52         29       38
D304V3, multiclass
            clus
vv           NBN MUTATED NBN WILD-TYPE
  STAGE I              1             1
  STAGE IA             0            15
  STAGE IB             1            39
  STAGE II             2            28
  STAGE IIA            2            35
  STAGE IIB            3            49
  STAGE III            0             3
  STAGE IIIA           0            70
  STAGE IIIB           1            52
  STAGE IIIC           3            29
  STAGE IV             0            38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NBN MUTATED     3   1   6   4
  NBN WILD-TYPE  19  91 167  93
D304V4, multiclass
    clus
vv   NBN MUTATED NBN WILD-TYPE
  T1           3            19
  T2           1            91
  T3           6           167
  T4           4            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
  NBN MUTATED     5   5   2   2
  NBN WILD-TYPE 113  99  75  75
D304V5, multiclass
    clus
vv   NBN MUTATED NBN WILD-TYPE
  N0           5           113
  N1           5            99
  N2           2            75
  N3           2            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"
D304V6, binary
               cls
clus              0   1
  NBN MUTATED    15   0
  NBN WILD-TYPE 331  29
[1] "tbl2"
               cls
clus            [,1] [,2]
  NBN MUTATED     15    0
  NBN WILD-TYPE  331   29
   clus
vv  NBN MUTATED NBN WILD-TYPE
  0          15           331
  1           0            29
[1] 2 2
[1] FALSE
D304V7, binary
               cls
clus              0   1
  NBN MUTATED     6   9
  NBN WILD-TYPE 139 239
[1] "tbl2"
               cls
clus            [,1] [,2]
  NBN MUTATED      6    9
  NBN WILD-TYPE  139  239
        clus
vv       NBN MUTATED NBN WILD-TYPE
  FEMALE           6           139
  MALE             9           239
[1] 2 2
[1] FALSE
D304V8, binary
               cls
clus              0   1
  NBN MUTATED    13   1
  NBN WILD-TYPE 279  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  NBN MUTATED     13    1
  NBN WILD-TYPE  279   58
     clus
vv    NBN MUTATED NBN WILD-TYPE
  NO           13           279
  YES           1            58
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NBN MUTATED                                          0
  NBN WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NBN MUTATED                                       4
  NBN WILD-TYPE                                    66
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NBN MUTATED                                                        7
  NBN WILD-TYPE                                                    151
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NBN MUTATED                                                   1
  NBN WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NBN MUTATED                                                                   0
  NBN WILD-TYPE                                                                68
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NBN MUTATED                                                    0
  NBN WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NBN MUTATED                                                  3
  NBN WILD-TYPE                                               58
D304V9, multiclass
                                                                   clus
vv                                                                  NBN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            3
                                                                   clus
vv                                                                  NBN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  NBN MUTATED     9   0   0   2
  NBN WILD-TYPE 302  14  15  22
D304V10, multiclass
    clus
vv   NBN MUTATED NBN WILD-TYPE
  R0           9           302
  R1           0            14
  R2           0            15
  RX           2            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  NBN MUTATED       7                         0
  NBN WILD-TYPE    80                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NBN MUTATED                                           0     7
  NBN WILD-TYPE                                         1   236
D304V12, multiclass
                                           clus
vv                                          NBN MUTATED NBN WILD-TYPE
  ASIAN                                               7            80
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               7           236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V13, binary
               cls
clus              0   1
  NBN MUTATED     0  14
  NBN WILD-TYPE   4 296
[1] "tbl2"
               cls
clus            [,1] [,2]
  NBN MUTATED      0   14
  NBN WILD-TYPE    4  296
                        clus
vv                       NBN MUTATED NBN WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          14           296
[1] 2 2
[1] FALSE

Clustering(305) Variable = ERBB3 MUTATION ANALYSIS
D305V1, survival
                 sevent
clus2               0   1
  ERBB3 MUTATED    16  14
  ERBB3 WILD-TYPE 214 125
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             30             339 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             14             125 
$`ERBB3 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-4267 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         4.08         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-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-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-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-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-CD-5798 
       13.51        20.65        20.42         1.15        21.44        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-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91        14.27        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-F1-6874 TCGA-F1-6875 
        4.34        19.96         7.13         0.62        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-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-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-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-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-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 

  ERBB3 MUTATED ERBB3 WILD-TYPE 
           0.26            0.00 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          77.29          122.30 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
         15.285          14.170 
[1] "0.3 - 77.3 (15.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D305V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERBB3 MUTATED         0        2        6        3         2         7
  ERBB3 WILD-TYPE       2       13       34       27        35        45
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERBB3 MUTATED           1          5          3          1        1
  ERBB3 WILD-TYPE         2         65         50         31       37
D305V3, multiclass
            clus
vv           ERBB3 MUTATED ERBB3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               6              34
  STAGE II               3              27
  STAGE IIA              2              35
  STAGE IIB              7              45
  STAGE III              1               2
  STAGE IIIA             5              65
  STAGE IIIB             3              50
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERBB3 MUTATED     3   8  13   7
  ERBB3 WILD-TYPE  19  84 160  90
D305V4, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  T1             3              19
  T2             8              84
  T3            13             160
  T4             7              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
  ERBB3 MUTATED    12  16   1   4
  ERBB3 WILD-TYPE 106  88  76  73
D305V5, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  N0            12             106
  N1            16              88
  N2             1              76
  N3             4              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"
D305V6, binary
                 cls
clus                0   1
  ERBB3 MUTATED    32   0
  ERBB3 WILD-TYPE 314  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     32    0
  ERBB3 WILD-TYPE  314   29
   clus
vv  ERBB3 MUTATED ERBB3 WILD-TYPE
  0            32             314
  1             0              29
[1] 2 2
[1] FALSE
D305V7, binary
                 cls
clus                0   1
  ERBB3 MUTATED    16  19
  ERBB3 WILD-TYPE 129 229
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     16   19
  ERBB3 WILD-TYPE  129  229
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  FEMALE            16             129
  MALE              19             229
[1] 2 2
[1] FALSE
D305V8, binary
                 cls
clus                0   1
  ERBB3 MUTATED    25   4
  ERBB3 WILD-TYPE 267  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     25    4
  ERBB3 WILD-TYPE  267   55
     clus
vv    ERBB3 MUTATED ERBB3 WILD-TYPE
  NO             25             267
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ERBB3 MUTATED                                          0
  ERBB3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ERBB3 MUTATED                                       4
  ERBB3 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ERBB3 MUTATED                                                       17
  ERBB3 WILD-TYPE                                                    141
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ERBB3 MUTATED                                                   2
  ERBB3 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ERBB3 MUTATED                                                                   6
  ERBB3 WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ERBB3 MUTATED                                                    0
  ERBB3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ERBB3 MUTATED                                                  6
  ERBB3 WILD-TYPE                                               55
D305V9, multiclass
                                                                   clus
vv                                                                  ERBB3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       17
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              6
                                                                   clus
vv                                                                  ERBB3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        141
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ERBB3 MUTATED    28   0   0   6
  ERBB3 WILD-TYPE 283  14  15  18
D305V10, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  R0            28             283
  R1             0              14
  R2             0              15
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ERBB3 MUTATED       5                         1
  ERBB3 WILD-TYPE    82                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ERBB3 MUTATED                                           0    25
  ERBB3 WILD-TYPE                                         1   218
D305V12, multiclass
                                           clus
vv                                          ERBB3 MUTATED ERBB3 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                25             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V13, binary
                 cls
clus                0   1
  ERBB3 MUTATED     0  28
  ERBB3 WILD-TYPE   4 282
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      0   28
  ERBB3 WILD-TYPE    4  282
                        clus
vv                       ERBB3 MUTATED ERBB3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            28             282
[1] 2 2
[1] FALSE

Clustering(306) Variable = IPO5 MUTATION ANALYSIS
D306V1, survival
                sevent
clus2              0   1
  IPO5 MUTATED    12   6
  IPO5 WILD-TYPE 218 133
  IPO5 MUTATED IPO5 WILD-TYPE 
            18            351 
  IPO5 MUTATED IPO5 WILD-TYPE 
             6            133 
$`IPO5 MUTATED`
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8367 
        9.34        34.68         0.69        32.25         8.05        26.33 
TCGA-BR-8368 TCGA-BR-A4PF TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8530 
        4.31         1.15        12.76        12.59        12.33        12.39 
TCGA-CD-8532 TCGA-F1-6874 TCGA-FP-8211 TCGA-HU-A4GQ TCGA-VQ-A8P2 TCGA-VQ-AA64 
       11.64        14.47        13.58         0.10        38.14        18.41 

$`IPO5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8078 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       11.44        29.59         9.60         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-8369 TCGA-BR-8370 TCGA-BR-8371 
       22.19        17.52         0.95        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-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-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 
       12.53         7.17        12.30        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-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-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-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-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 

  IPO5 MUTATED IPO5 WILD-TYPE 
           0.1            0.0 
  IPO5 MUTATED IPO5 WILD-TYPE 
         38.14         122.30 
  IPO5 MUTATED IPO5 WILD-TYPE 
         12.49          14.76 
[1] "0.1 - 38.1 (12.5)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.1"
D306V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IPO5 MUTATED         0        0        2        3         1         2
  IPO5 WILD-TYPE       2       15       38       27        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IPO5 MUTATED           0          4          4          2        1
  IPO5 WILD-TYPE         3         66         49         30       37
D306V3, multiclass
            clus
vv           IPO5 MUTATED IPO5 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              3             27
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            4             66
  STAGE IIIB            4             49
  STAGE IIIC            2             30
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IPO5 MUTATED     0   2   8   9
  IPO5 WILD-TYPE  22  90 165  88
D306V4, multiclass
    clus
vv   IPO5 MUTATED IPO5 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            8            165
  T4            9             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
  IPO5 MUTATED     9   5   4   2
  IPO5 WILD-TYPE 109  99  73  75
D306V5, multiclass
    clus
vv   IPO5 MUTATED IPO5 WILD-TYPE
  N0            9            109
  N1            5             99
  N2            4             73
  N3            2             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"
D306V6, binary
                cls
clus               0   1
  IPO5 MUTATED    20   0
  IPO5 WILD-TYPE 326  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO5 MUTATED     20    0
  IPO5 WILD-TYPE  326   29
   clus
vv  IPO5 MUTATED IPO5 WILD-TYPE
  0           20            326
  1            0             29
[1] 2 2
[1] FALSE
D306V7, binary
                cls
clus               0   1
  IPO5 MUTATED    11  10
  IPO5 WILD-TYPE 134 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO5 MUTATED     11   10
  IPO5 WILD-TYPE  134  238
        clus
vv       IPO5 MUTATED IPO5 WILD-TYPE
  FEMALE           11            134
  MALE             10            238
[1] 2 2
[1] FALSE
D306V8, binary
                cls
clus               0   1
  IPO5 MUTATED    11   6
  IPO5 WILD-TYPE 281  53
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO5 MUTATED     11    6
  IPO5 WILD-TYPE  281   53
     clus
vv    IPO5 MUTATED IPO5 WILD-TYPE
  NO            11            281
  YES            6             53
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IPO5 MUTATED                                          0
  IPO5 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IPO5 MUTATED                                       1
  IPO5 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IPO5 MUTATED                                                       12
  IPO5 WILD-TYPE                                                    146
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IPO5 MUTATED                                                   2
  IPO5 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IPO5 MUTATED                                                                   5
  IPO5 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IPO5 MUTATED                                                    0
  IPO5 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IPO5 MUTATED                                                  1
  IPO5 WILD-TYPE                                               60
D306V9, multiclass
                                                                   clus
vv                                                                  IPO5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  IPO5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IPO5 MUTATED    16   1   0   4
  IPO5 WILD-TYPE 295  13  15  20
D306V10, multiclass
    clus
vv   IPO5 MUTATED IPO5 WILD-TYPE
  R0           16            295
  R1            1             13
  R2            0             15
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IPO5 MUTATED       6                         0
  IPO5 WILD-TYPE    81                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IPO5 MUTATED                                           0    15
  IPO5 WILD-TYPE                                         1   228
D306V12, multiclass
                                           clus
vv                                          IPO5 MUTATED IPO5 WILD-TYPE
  ASIAN                                                6             81
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               15            228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V13, binary
                cls
clus               0   1
  IPO5 MUTATED     0  19
  IPO5 WILD-TYPE   4 291
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO5 MUTATED      0   19
  IPO5 WILD-TYPE    4  291
                        clus
vv                       IPO5 MUTATED IPO5 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           19            291
[1] 2 2
[1] FALSE

Clustering(307) Variable = MARVELD3 MUTATION ANALYSIS
D307V1, survival
                    sevent
clus2                  0   1
  MARVELD3 MUTATED     7   4
  MARVELD3 WILD-TYPE 223 135
  MARVELD3 MUTATED MARVELD3 WILD-TYPE 
                11                358 
  MARVELD3 MUTATED MARVELD3 WILD-TYPE 
                 4                135 
$`MARVELD3 MUTATED`
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-5733 
        9.34         9.67        34.68         1.12        16.14        21.07 
TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-VQ-A8E2 
       11.08        30.51        23.84        23.80        43.36 

$`MARVELD3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  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              14.12 
[1] "1.1 - 43.4 (21.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D307V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MARVELD3 MUTATED         1        0        1        0         3         1
  MARVELD3 WILD-TYPE       1       15       39       30        34        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MARVELD3 MUTATED           0          1          2          1        0
  MARVELD3 WILD-TYPE         3         69         51         31       38
D307V3, multiclass
            clus
vv           MARVELD3 MUTATED MARVELD3 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 3                 34
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                2                 51
  STAGE IIIC                1                 31
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  MARVELD3 MUTATED     1   3   5   1
  MARVELD3 WILD-TYPE  21  89 168  96
D307V4, multiclass
    clus
vv   MARVELD3 MUTATED MARVELD3 WILD-TYPE
  T1                1                 21
  T2                3                 89
  T3                5                168
  T4                1                 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
  MARVELD3 MUTATED     4   2   3   2
  MARVELD3 WILD-TYPE 114 102  74  75
D307V5, multiclass
    clus
vv   MARVELD3 MUTATED MARVELD3 WILD-TYPE
  N0                4                114
  N1                2                102
  N2                3                 74
  N3                2                 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"
D307V6, binary
                    cls
clus                   0   1
  MARVELD3 MUTATED    11   0
  MARVELD3 WILD-TYPE 335  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD3 MUTATED     11    0
  MARVELD3 WILD-TYPE  335   29
   clus
vv  MARVELD3 MUTATED MARVELD3 WILD-TYPE
  0               11                335
  1                0                 29
[1] 2 2
[1] FALSE
D307V7, binary
                    cls
clus                   0   1
  MARVELD3 MUTATED     7   5
  MARVELD3 WILD-TYPE 138 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD3 MUTATED      7    5
  MARVELD3 WILD-TYPE  138  243
        clus
vv       MARVELD3 MUTATED MARVELD3 WILD-TYPE
  FEMALE                7                138
  MALE                  5                243
[1] 2 2
[1] FALSE
D307V8, binary
                    cls
clus                   0   1
  MARVELD3 MUTATED     9   3
  MARVELD3 WILD-TYPE 283  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD3 MUTATED      9    3
  MARVELD3 WILD-TYPE  283   56
     clus
vv    MARVELD3 MUTATED MARVELD3 WILD-TYPE
  NO                 9                283
  YES                3                 56
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MARVELD3 MUTATED                                          0
  MARVELD3 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MARVELD3 MUTATED                                       0
  MARVELD3 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MARVELD3 MUTATED                                                        7
  MARVELD3 WILD-TYPE                                                    151
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MARVELD3 MUTATED                                                   1
  MARVELD3 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MARVELD3 MUTATED                                                                   1
  MARVELD3 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MARVELD3 MUTATED                                                    1
  MARVELD3 WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MARVELD3 MUTATED                                                  2
  MARVELD3 WILD-TYPE                                               59
D307V9, multiclass
                                                                   clus
vv                                                                  MARVELD3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  MARVELD3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  MARVELD3 MUTATED     9   1   0   2
  MARVELD3 WILD-TYPE 302  13  15  22
D307V10, multiclass
    clus
vv   MARVELD3 MUTATED MARVELD3 WILD-TYPE
  R0                9                302
  R1                1                 13
  R2                0                 15
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  MARVELD3 MUTATED       3                         2
  MARVELD3 WILD-TYPE    84                         7
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MARVELD3 MUTATED                                           0     5
  MARVELD3 WILD-TYPE                                         1   238
D307V12, multiclass
                                           clus
vv                                          MARVELD3 MUTATED MARVELD3 WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                2                  7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V13, binary
                    cls
clus                   0   1
  MARVELD3 MUTATED     0   9
  MARVELD3 WILD-TYPE   4 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD3 MUTATED      0    9
  MARVELD3 WILD-TYPE    4  301
                        clus
vv                       MARVELD3 MUTATED MARVELD3 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                9                301
[1] 2 2
[1] FALSE

Clustering(308) Variable = NOS3 MUTATION ANALYSIS
D308V1, survival
                sevent
clus2              0   1
  NOS3 MUTATED    10   3
  NOS3 WILD-TYPE 220 136
  NOS3 MUTATED NOS3 WILD-TYPE 
            13            356 
  NOS3 MUTATED NOS3 WILD-TYPE 
             3            136 
$`NOS3 MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-BR-4257 TCGA-BR-8078 TCGA-BR-8284 TCGA-CD-8526 
       47.05        21.99         9.67        29.59         8.05        12.53 
TCGA-CG-5723 TCGA-F1-6874 TCGA-FP-7829 TCGA-HF-A5NB TCGA-HU-A4GT TCGA-HU-A4H3 
      105.07        14.47        19.53        30.51         6.51        29.00 
TCGA-R5-A7ZI 
       74.53 

$`NOS3 WILD-TYPE`
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-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 
          6.51           0.00 
  NOS3 MUTATED NOS3 WILD-TYPE 
        105.07         122.30 
  NOS3 MUTATED NOS3 WILD-TYPE 
         21.99          14.07 
[1] "6.5 - 105.1 (22.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.4"
D308V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOS3 MUTATED         1        0        2        1         1         2
  NOS3 WILD-TYPE       1       15       38       29        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOS3 MUTATED           0          2          0          3        2
  NOS3 WILD-TYPE         3         68         53         29       36
D308V3, multiclass
            clus
vv           NOS3 MUTATED NOS3 WILD-TYPE
  STAGE I               1              1
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            3             29
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOS3 MUTATED     1   4   3   6
  NOS3 WILD-TYPE  21  88 170  91
D308V4, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  T1            1             21
  T2            4             88
  T3            3            170
  T4            6             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
  NOS3 MUTATED     4   6   1   3
  NOS3 WILD-TYPE 114  98  76  74
D308V5, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  N0            4            114
  N1            6             98
  N2            1             76
  N3            3             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"
D308V6, binary
                cls
clus               0   1
  NOS3 MUTATED    12   2
  NOS3 WILD-TYPE 334  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED     12    2
  NOS3 WILD-TYPE  334   27
   clus
vv  NOS3 MUTATED NOS3 WILD-TYPE
  0           12            334
  1            2             27
[1] 2 2
[1] FALSE
D308V7, binary
                cls
clus               0   1
  NOS3 MUTATED     9   6
  NOS3 WILD-TYPE 136 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED      9    6
  NOS3 WILD-TYPE  136  242
        clus
vv       NOS3 MUTATED NOS3 WILD-TYPE
  FEMALE            9            136
  MALE              6            242
[1] 2 2
[1] FALSE
D308V8, binary
                cls
clus               0   1
  NOS3 MUTATED    10   3
  NOS3 WILD-TYPE 282  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED     10    3
  NOS3 WILD-TYPE  282   56
     clus
vv    NOS3 MUTATED NOS3 WILD-TYPE
  NO            10            282
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NOS3 MUTATED                                          0
  NOS3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NOS3 MUTATED                                       3
  NOS3 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NOS3 MUTATED                                                        4
  NOS3 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NOS3 MUTATED                                                   2
  NOS3 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NOS3 MUTATED                                                                   5
  NOS3 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NOS3 MUTATED                                                    0
  NOS3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NOS3 MUTATED                                                  1
  NOS3 WILD-TYPE                                               60
D308V9, multiclass
                                                                   clus
vv                                                                  NOS3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  NOS3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NOS3 MUTATED    12   1   1   1
  NOS3 WILD-TYPE 299  13  14  23
D308V10, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  R0           12            299
  R1            1             13
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NOS3 MUTATED       3                         1
  NOS3 WILD-TYPE    84                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOS3 MUTATED                                           0     6
  NOS3 WILD-TYPE                                         1   237
D308V12, multiclass
                                           clus
vv                                          NOS3 MUTATED NOS3 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V13, binary
                cls
clus               0   1
  NOS3 MUTATED     1   9
  NOS3 WILD-TYPE   3 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED      1    9
  NOS3 WILD-TYPE    3  301
                        clus
vv                       NOS3 MUTATED NOS3 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(309) Variable = TAS2R42 MUTATION ANALYSIS
D309V1, survival
                   sevent
clus2                 0   1
  TAS2R42 MUTATED     4   2
  TAS2R42 WILD-TYPE 226 137
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
                6               363 
  TAS2R42 MUTATED TAS2R42 WILD-TYPE 
                2               137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        25.81        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-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 

  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             14.43 
[1] "0.3 - 32.2 (12.4)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1"  
D309V2, 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       2       14       39       30        37        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAS2R42 MUTATED           0          0          2          0        0
  TAS2R42 WILD-TYPE         3         70         51         32       38
D309V3, multiclass
            clus
vv           TAS2R42 MUTATED TAS2R42 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                0                37
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               2                51
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TAS2R42 MUTATED     1   1   3   1
  TAS2R42 WILD-TYPE  21  91 170  96
D309V4, multiclass
    clus
vv   TAS2R42 MUTATED TAS2R42 WILD-TYPE
  T1               1                21
  T2               1                91
  T3               3               170
  T4               1                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
  TAS2R42 MUTATED     3   1   0   2
  TAS2R42 WILD-TYPE 115 103  77  75
D309V5, multiclass
    clus
vv   TAS2R42 MUTATED TAS2R42 WILD-TYPE
  N0               3               115
  N1               1               103
  N2               0                77
  N3               2                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"
D309V6, binary
                   cls
clus                  0   1
  TAS2R42 MUTATED     6   0
  TAS2R42 WILD-TYPE 340  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R42 MUTATED      6    0
  TAS2R42 WILD-TYPE  340   29
   clus
vv  TAS2R42 MUTATED TAS2R42 WILD-TYPE
  0               6               340
  1               0                29
[1] 2 2
[1] FALSE
D309V7, binary
                   cls
clus                  0   1
  TAS2R42 MUTATED     4   2
  TAS2R42 WILD-TYPE 141 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R42 MUTATED      4    2
  TAS2R42 WILD-TYPE  141  246
        clus
vv       TAS2R42 MUTATED TAS2R42 WILD-TYPE
  FEMALE               4               141
  MALE                 2               246
[1] 2 2
[1] FALSE
D309V8, binary
                   cls
clus                  0   1
  TAS2R42 MUTATED     6   0
  TAS2R42 WILD-TYPE 286  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R42 MUTATED      6    0
  TAS2R42 WILD-TYPE  286   59
     clus
vv    TAS2R42 MUTATED TAS2R42 WILD-TYPE
  NO                6               286
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TAS2R42 MUTATED                                          0
  TAS2R42 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TAS2R42 MUTATED                                       0
  TAS2R42 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TAS2R42 MUTATED                                                        2
  TAS2R42 WILD-TYPE                                                    156
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TAS2R42 MUTATED                                                   0
  TAS2R42 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TAS2R42 MUTATED                                                                   0
  TAS2R42 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TAS2R42 MUTATED                                                    0
  TAS2R42 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TAS2R42 MUTATED                                                  4
  TAS2R42 WILD-TYPE                                               57
D309V9, multiclass
                                                                   clus
vv                                                                  TAS2R42 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                4
                                                                   clus
vv                                                                  TAS2R42 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TAS2R42 MUTATED     6   0   0   0
  TAS2R42 WILD-TYPE 305  14  15  24
D309V10, multiclass
    clus
vv   TAS2R42 MUTATED TAS2R42 WILD-TYPE
  R0               6               305
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TAS2R42 MUTATED       3                         0
  TAS2R42 WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAS2R42 MUTATED                                           0     3
  TAS2R42 WILD-TYPE                                         1   240
D309V12, multiclass
                                           clus
vv                                          TAS2R42 MUTATED TAS2R42 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V13, binary
                   cls
clus                  0   1
  TAS2R42 MUTATED     0   6
  TAS2R42 WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R42 MUTATED      0    6
  TAS2R42 WILD-TYPE    4  304
                        clus
vv                       TAS2R42 MUTATED TAS2R42 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(310) Variable = ANKRD20A4 MUTATION ANALYSIS
D310V1, survival
                     sevent
clus2                   0   1
  ANKRD20A4 MUTATED     7   0
  ANKRD20A4 WILD-TYPE 223 139
  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
                  7                 362 
  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
                  0                 139 
$`ANKRD20A4 MUTATED`
TCGA-BR-8369 TCGA-BR-8372 TCGA-BR-A4PF TCGA-D7-A6F2 TCGA-F1-A448 TCGA-HU-A4GT 
       14.04        31.27         1.15        15.65        21.27         6.51 
TCGA-VQ-A8P2 
       38.14 

$`ANKRD20A4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
               1.15                0.00 
  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
              38.14              122.30 
  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE 
              15.65               14.22 
[1] "1.1 - 38.1 (15.7)"  "0.0 - 122.3 (14.2)"
[1] "hr="     "9200000"
D310V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKRD20A4 MUTATED         0        0        1        0         1         0
  ANKRD20A4 WILD-TYPE       2       15       39       30        36        52
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD20A4 MUTATED           0          1          3          1        0
  ANKRD20A4 WILD-TYPE         3         69         50         31       38
D310V3, multiclass
            clus
vv           ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  STAGE I                    0                   2
  STAGE IA                   0                  15
  STAGE IB                   1                  39
  STAGE II                   0                  30
  STAGE IIA                  1                  36
  STAGE IIB                  0                  52
  STAGE III                  0                   3
  STAGE IIIA                 1                  69
  STAGE IIIB                 3                  50
  STAGE IIIC                 1                  31
  STAGE IV                   0                  38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  ANKRD20A4 MUTATED     0   1   3   3
  ANKRD20A4 WILD-TYPE  22  91 170  94
D310V4, multiclass
    clus
vv   ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  T1                 0                  22
  T2                 1                  91
  T3                 3                 170
  T4                 3                  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
  ANKRD20A4 MUTATED     2   1   1   3
  ANKRD20A4 WILD-TYPE 116 103  76  74
D310V5, multiclass
    clus
vv   ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  N0                 2                 116
  N1                 1                 103
  N2                 1                  76
  N3                 3                  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"
D310V6, binary
                     cls
clus                    0   1
  ANKRD20A4 MUTATED     7   0
  ANKRD20A4 WILD-TYPE 339  29
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ANKRD20A4 MUTATED      7    0
  ANKRD20A4 WILD-TYPE  339   29
   clus
vv  ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  0                 7                 339
  1                 0                  29
[1] 2 2
[1] FALSE
D310V7, binary
                     cls
clus                    0   1
  ANKRD20A4 MUTATED     2   5
  ANKRD20A4 WILD-TYPE 143 243
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ANKRD20A4 MUTATED      2    5
  ANKRD20A4 WILD-TYPE  143  243
        clus
vv       ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  FEMALE                 2                 143
  MALE                   5                 243
[1] 2 2
[1] FALSE
D310V8, binary
                     cls
clus                    0   1
  ANKRD20A4 MUTATED     5   2
  ANKRD20A4 WILD-TYPE 287  57
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ANKRD20A4 MUTATED      5    2
  ANKRD20A4 WILD-TYPE  287   57
     clus
vv    ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  NO                  5                 287
  YES                 2                  57
[1] 2 2
[1] FALSE
                     vv
clus                  STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ANKRD20A4 MUTATED                                          0
  ANKRD20A4 WILD-TYPE                                        8
                     vv
clus                  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ANKRD20A4 MUTATED                                       0
  ANKRD20A4 WILD-TYPE                                    70
                     vv
clus                  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANKRD20A4 MUTATED                                                        3
  ANKRD20A4 WILD-TYPE                                                    155
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ANKRD20A4 MUTATED                                                   2
  ANKRD20A4 WILD-TYPE                                                19
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANKRD20A4 MUTATED                                                                   0
  ANKRD20A4 WILD-TYPE                                                                68
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ANKRD20A4 MUTATED                                                    0
  ANKRD20A4 WILD-TYPE                                                  5
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ANKRD20A4 MUTATED                                                  2
  ANKRD20A4 WILD-TYPE                                               59
D310V9, multiclass
                                                                   clus
vv                                                                  ANKRD20A4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  2
                                                                   clus
vv                                                                  ANKRD20A4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                            8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                              70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                  19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                  5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                   59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  ANKRD20A4 MUTATED     7   0   0   0
  ANKRD20A4 WILD-TYPE 304  14  15  24
D310V10, multiclass
    clus
vv   ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  R0                 7                 304
  R1                 0                  14
  R2                 0                  15
  RX                 0                  24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN
  ANKRD20A4 MUTATED       1                         0
  ANKRD20A4 WILD-TYPE    86                         9
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANKRD20A4 MUTATED                                           0     6
  ANKRD20A4 WILD-TYPE                                         1   237
D310V12, multiclass
                                           clus
vv                                          ANKRD20A4 MUTATED
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                     6
                                           clus
vv                                          ANKRD20A4 WILD-TYPE
  ASIAN                                                      86
  BLACK OR AFRICAN AMERICAN                                   9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   1
  WHITE                                                     237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V13, binary
                     cls
clus                    0   1
  ANKRD20A4 MUTATED     1   5
  ANKRD20A4 WILD-TYPE   3 305
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ANKRD20A4 MUTATED      1    5
  ANKRD20A4 WILD-TYPE    3  305
                        clus
vv                       ANKRD20A4 MUTATED ANKRD20A4 WILD-TYPE
  HISPANIC OR LATINO                     1                   3
  NOT HISPANIC OR LATINO                 5                 305
[1] 2 2
[1] FALSE

Clustering(311) Variable = UGP2 MUTATION ANALYSIS
D311V1, survival
                sevent
clus2              0   1
  UGP2 MUTATED     7   1
  UGP2 WILD-TYPE 223 138
  UGP2 MUTATED UGP2 WILD-TYPE 
             8            361 
  UGP2 MUTATED UGP2 WILD-TYPE 
             1            138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  UGP2 MUTATED UGP2 WILD-TYPE 
         12.43           0.00 
  UGP2 MUTATED UGP2 WILD-TYPE 
        105.07         122.30 
  UGP2 MUTATED UGP2 WILD-TYPE 
         36.99          14.07 
[1] "12.4 - 105.1 (37.0)" "0.0 - 122.3 (14.1)" 
[1] "hr=" "5.6"
D311V2, 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       2       14       38       28        37        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGP2 MUTATED           0          1          1          1        0
  UGP2 WILD-TYPE         3         69         52         31       38
D311V3, multiclass
            clus
vv           UGP2 MUTATED UGP2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              2             38
  STAGE II              2             28
  STAGE IIA             0             37
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  UGP2 MUTATED     1   3   2   2
  UGP2 WILD-TYPE  21  89 171  95
D311V4, multiclass
    clus
vv   UGP2 MUTATED UGP2 WILD-TYPE
  T1            1             21
  T2            3             89
  T3            2            171
  T4            2             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
  UGP2 MUTATED     4   3   0   2
  UGP2 WILD-TYPE 114 101  77  75
D311V5, multiclass
    clus
vv   UGP2 MUTATED UGP2 WILD-TYPE
  N0            4            114
  N1            3            101
  N2            0             77
  N3            2             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"
D311V6, binary
                cls
clus               0   1
  UGP2 MUTATED     9   0
  UGP2 WILD-TYPE 337  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      9    0
  UGP2 WILD-TYPE  337   29
   clus
vv  UGP2 MUTATED UGP2 WILD-TYPE
  0            9            337
  1            0             29
[1] 2 2
[1] FALSE
D311V7, binary
                cls
clus               0   1
  UGP2 MUTATED     4   5
  UGP2 WILD-TYPE 141 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      4    5
  UGP2 WILD-TYPE  141  243
        clus
vv       UGP2 MUTATED UGP2 WILD-TYPE
  FEMALE            4            141
  MALE              5            243
[1] 2 2
[1] FALSE
D311V8, binary
                cls
clus               0   1
  UGP2 MUTATED     6   1
  UGP2 WILD-TYPE 286  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      6    1
  UGP2 WILD-TYPE  286   58
     clus
vv    UGP2 MUTATED UGP2 WILD-TYPE
  NO             6            286
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  UGP2 MUTATED                                          0
  UGP2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  UGP2 MUTATED                                       0
  UGP2 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UGP2 MUTATED                                                        6
  UGP2 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  UGP2 MUTATED                                                   1
  UGP2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UGP2 MUTATED                                                                   2
  UGP2 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  UGP2 MUTATED                                                    0
  UGP2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  UGP2 MUTATED                                                  0
  UGP2 WILD-TYPE                                               61
D311V9, multiclass
                                                                   clus
vv                                                                  UGP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  UGP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  UGP2 MUTATED     8   0   0   1
  UGP2 WILD-TYPE 303  14  15  23
D311V10, multiclass
    clus
vv   UGP2 MUTATED UGP2 WILD-TYPE
  R0            8            303
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  UGP2 MUTATED       1                         0
  UGP2 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UGP2 MUTATED                                           0     5
  UGP2 WILD-TYPE                                         1   238
D311V12, multiclass
                                           clus
vv                                          UGP2 MUTATED UGP2 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V13, binary
                cls
clus               0   1
  UGP2 MUTATED     0   5
  UGP2 WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      0    5
  UGP2 WILD-TYPE    4  305
                        clus
vv                       UGP2 MUTATED UGP2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(312) Variable = KLHDC8B MUTATION ANALYSIS
D312V1, survival
                   sevent
clus2                 0   1
  KLHDC8B MUTATED     6   3
  KLHDC8B WILD-TYPE 224 136
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
                9               360 
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
                3               136 
$`KLHDC8B MUTATED`
TCGA-B7-A5TI TCGA-BR-8081 TCGA-BR-8363 TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5728 
       19.56        32.25         0.26        12.43        11.77        65.10 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4GU 
       30.51        26.47         6.58 

$`KLHDC8B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
             0.26              0.00 
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
             65.1             122.3 
  KLHDC8B MUTATED KLHDC8B WILD-TYPE 
            19.56             14.22 
[1] "0.3 - 65.1 (19.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D312V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLHDC8B MUTATED         0        0        3        1         0         2
  KLHDC8B WILD-TYPE       2       15       37       29        37        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLHDC8B MUTATED           0          1          0          2        0
  KLHDC8B WILD-TYPE         3         69         53         30       38
D312V3, multiclass
            clus
vv           KLHDC8B MUTATED KLHDC8B WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 3                37
  STAGE II                 1                29
  STAGE IIA                0                37
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               2                30
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  KLHDC8B MUTATED     0   3   3   3
  KLHDC8B WILD-TYPE  22  89 170  94
D312V4, multiclass
    clus
vv   KLHDC8B MUTATED KLHDC8B WILD-TYPE
  T1               0                22
  T2               3                89
  T3               3               170
  T4               3                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
  KLHDC8B MUTATED     5   2   0   2
  KLHDC8B WILD-TYPE 113 102  77  75
D312V5, multiclass
    clus
vv   KLHDC8B MUTATED KLHDC8B WILD-TYPE
  N0               5               113
  N1               2               102
  N2               0                77
  N3               2                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"
D312V6, binary
                   cls
clus                  0   1
  KLHDC8B MUTATED     9   0
  KLHDC8B WILD-TYPE 337  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KLHDC8B MUTATED      9    0
  KLHDC8B WILD-TYPE  337   29
   clus
vv  KLHDC8B MUTATED KLHDC8B WILD-TYPE
  0               9               337
  1               0                29
[1] 2 2
[1] FALSE
D312V7, binary
                   cls
clus                  0   1
  KLHDC8B MUTATED     5   5
  KLHDC8B WILD-TYPE 140 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KLHDC8B MUTATED      5    5
  KLHDC8B WILD-TYPE  140  243
        clus
vv       KLHDC8B MUTATED KLHDC8B WILD-TYPE
  FEMALE               5               140
  MALE                 5               243
[1] 2 2
[1] FALSE
D312V8, binary
                   cls
clus                  0   1
  KLHDC8B MUTATED     7   1
  KLHDC8B WILD-TYPE 285  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KLHDC8B MUTATED      7    1
  KLHDC8B WILD-TYPE  285   58
     clus
vv    KLHDC8B MUTATED KLHDC8B WILD-TYPE
  NO                7               285
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KLHDC8B MUTATED                                          1
  KLHDC8B WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KLHDC8B MUTATED                                       2
  KLHDC8B WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KLHDC8B MUTATED                                                        5
  KLHDC8B WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KLHDC8B MUTATED                                                   1
  KLHDC8B WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KLHDC8B MUTATED                                                                   1
  KLHDC8B WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KLHDC8B MUTATED                                                    0
  KLHDC8B WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KLHDC8B MUTATED                                                  0
  KLHDC8B WILD-TYPE                                               61
D312V9, multiclass
                                                                   clus
vv                                                                  KLHDC8B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  KLHDC8B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  KLHDC8B MUTATED     6   1   0   1
  KLHDC8B WILD-TYPE 305  13  15  23
D312V10, multiclass
    clus
vv   KLHDC8B MUTATED KLHDC8B WILD-TYPE
  R0               6               305
  R1               1                13
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  KLHDC8B MUTATED       3                         0
  KLHDC8B WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLHDC8B MUTATED                                           0     5
  KLHDC8B WILD-TYPE                                         1   238
D312V12, multiclass
                                           clus
vv                                          KLHDC8B MUTATED KLHDC8B WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V13, binary
                   cls
clus                  0   1
  KLHDC8B MUTATED     0   8
  KLHDC8B WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KLHDC8B MUTATED      0    8
  KLHDC8B WILD-TYPE    4  302
                        clus
vv                       KLHDC8B MUTATED KLHDC8B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(313) Variable = ABCB6 MUTATION ANALYSIS
D313V1, survival
                 sevent
clus2               0   1
  ABCB6 MUTATED     8   4
  ABCB6 WILD-TYPE 222 135
  ABCB6 MUTATED ABCB6 WILD-TYPE 
             12             357 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              4             135 
$`ABCB6 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  ABCB6 MUTATED ABCB6 WILD-TYPE 
           1.02            0.00 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
          74.53          122.30 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
         20.695          14.070 
[1] "1.0 - 74.5 (20.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D313V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCB6 MUTATED         0        0        3        0         2         0
  ABCB6 WILD-TYPE       2       15       37       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABCB6 MUTATED           0          2          1          0        3
  ABCB6 WILD-TYPE         3         68         52         32       35
D313V3, multiclass
            clus
vv           ABCB6 MUTATED ABCB6 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCB6 MUTATED     0   5   4   3
  ABCB6 WILD-TYPE  22  87 169  94
D313V4, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  T1             0              22
  T2             5              87
  T3             4             169
  T4             3              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
  ABCB6 MUTATED     6   2   3   0
  ABCB6 WILD-TYPE 112 102  74  77
D313V5, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  N0             6             112
  N1             2             102
  N2             3              74
  N3             0              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"
D313V6, binary
                 cls
clus                0   1
  ABCB6 MUTATED    10   2
  ABCB6 WILD-TYPE 336  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED     10    2
  ABCB6 WILD-TYPE  336   27
   clus
vv  ABCB6 MUTATED ABCB6 WILD-TYPE
  0            10             336
  1             2              27
[1] 2 2
[1] FALSE
D313V7, binary
                 cls
clus                0   1
  ABCB6 MUTATED     6   6
  ABCB6 WILD-TYPE 139 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      6    6
  ABCB6 WILD-TYPE  139  242
        clus
vv       ABCB6 MUTATED ABCB6 WILD-TYPE
  FEMALE             6             139
  MALE               6             242
[1] 2 2
[1] FALSE
D313V8, binary
                 cls
clus                0   1
  ABCB6 MUTATED    11   0
  ABCB6 WILD-TYPE 281  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED     11    0
  ABCB6 WILD-TYPE  281   59
     clus
vv    ABCB6 MUTATED ABCB6 WILD-TYPE
  NO             11             281
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ABCB6 MUTATED                                          0
  ABCB6 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ABCB6 MUTATED                                       1
  ABCB6 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCB6 MUTATED                                                        6
  ABCB6 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ABCB6 MUTATED                                                   0
  ABCB6 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCB6 MUTATED                                                                   5
  ABCB6 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ABCB6 MUTATED                                                    0
  ABCB6 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ABCB6 MUTATED                                                  0
  ABCB6 WILD-TYPE                                               61
D313V9, multiclass
                                                                   clus
vv                                                                  ABCB6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  ABCB6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCB6 MUTATED    10   0   1   1
  ABCB6 WILD-TYPE 301  14  14  23
D313V10, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCB6 MUTATED       0                         0
  ABCB6 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCB6 MUTATED                                           0     9
  ABCB6 WILD-TYPE                                         1   234
D313V12, multiclass
                                           clus
vv                                          ABCB6 MUTATED ABCB6 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V13, binary
                 cls
clus                0   1
  ABCB6 MUTATED     1   8
  ABCB6 WILD-TYPE   3 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      1    8
  ABCB6 WILD-TYPE    3  302
                        clus
vv                       ABCB6 MUTATED ABCB6 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(314) Variable = TMC4 MUTATION ANALYSIS
D314V1, survival
                sevent
clus2              0   1
  TMC4 MUTATED    10   5
  TMC4 WILD-TYPE 220 134
  TMC4 MUTATED TMC4 WILD-TYPE 
            15            354 
  TMC4 MUTATED TMC4 WILD-TYPE 
             5            134 
$`TMC4 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8367 
        6.97        34.68        14.43        29.59         6.18        26.33 
TCGA-BR-8370 TCGA-BR-8371 TCGA-CD-8530 TCGA-CG-5723 TCGA-D7-8572 TCGA-D7-8574 
        3.32        11.80        12.39       105.07        16.80        17.19 
TCGA-D7-8576 TCGA-RD-A8N1 TCGA-VQ-A8P2 
       14.66       115.69        38.14 

$`TMC4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
         16.80          14.07 
[1] "3.3 - 115.7 (16.8)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D314V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMC4 MUTATED         0        0        0        2         2         2
  TMC4 WILD-TYPE       2       15       40       28        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMC4 MUTATED           1          3          5          0        0
  TMC4 WILD-TYPE         2         67         48         32       38
D314V3, multiclass
            clus
vv           TMC4 MUTATED TMC4 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              2             28
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             1              2
  STAGE IIIA            3             67
  STAGE IIIB            5             48
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TMC4 MUTATED     0   3   9   3
  TMC4 WILD-TYPE  22  89 164  94
D314V4, multiclass
    clus
vv   TMC4 MUTATED TMC4 WILD-TYPE
  T1            0             22
  T2            3             89
  T3            9            164
  T4            3             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
  TMC4 MUTATED     4   4   2   5
  TMC4 WILD-TYPE 114 100  75  72
D314V5, multiclass
    clus
vv   TMC4 MUTATED TMC4 WILD-TYPE
  N0            4            114
  N1            4            100
  N2            2             75
  N3            5             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"
D314V6, binary
                cls
clus               0   1
  TMC4 MUTATED    14   0
  TMC4 WILD-TYPE 332  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED     14    0
  TMC4 WILD-TYPE  332   29
   clus
vv  TMC4 MUTATED TMC4 WILD-TYPE
  0           14            332
  1            0             29
[1] 2 2
[1] FALSE
D314V7, binary
                cls
clus               0   1
  TMC4 MUTATED     3  12
  TMC4 WILD-TYPE 142 236
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED      3   12
  TMC4 WILD-TYPE  142  236
        clus
vv       TMC4 MUTATED TMC4 WILD-TYPE
  FEMALE            3            142
  MALE             12            236
[1] 2 2
[1] FALSE
D314V8, binary
                cls
clus               0   1
  TMC4 MUTATED    12   3
  TMC4 WILD-TYPE 280  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED     12    3
  TMC4 WILD-TYPE  280   56
     clus
vv    TMC4 MUTATED TMC4 WILD-TYPE
  NO            12            280
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TMC4 MUTATED                                          0
  TMC4 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TMC4 MUTATED                                       3
  TMC4 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMC4 MUTATED                                                        8
  TMC4 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TMC4 MUTATED                                                   1
  TMC4 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMC4 MUTATED                                                                   2
  TMC4 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TMC4 MUTATED                                                    0
  TMC4 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TMC4 MUTATED                                                  1
  TMC4 WILD-TYPE                                               60
D314V9, multiclass
                                                                   clus
vv                                                                  TMC4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  TMC4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TMC4 MUTATED    13   1   0   1
  TMC4 WILD-TYPE 298  13  15  23
D314V10, multiclass
    clus
vv   TMC4 MUTATED TMC4 WILD-TYPE
  R0           13            298
  R1            1             13
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TMC4 MUTATED       1                         0
  TMC4 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMC4 MUTATED                                           0    13
  TMC4 WILD-TYPE                                         1   230
D314V12, multiclass
                                           clus
vv                                          TMC4 MUTATED TMC4 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V13, binary
                cls
clus               0   1
  TMC4 MUTATED     0  13
  TMC4 WILD-TYPE   4 297
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED      0   13
  TMC4 WILD-TYPE    4  297
                        clus
vv                       TMC4 MUTATED TMC4 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           13            297
[1] 2 2
[1] FALSE

Clustering(315) Variable = TM6SF1 MUTATION ANALYSIS
D315V1, survival
                  sevent
clus2                0   1
  TM6SF1 MUTATED     5   2
  TM6SF1 WILD-TYPE 225 137
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
               7              362 
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
               2              137 
$`TM6SF1 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8591 TCGA-CD-A4MJ TCGA-CG-4465 TCGA-CG-5728 
       26.70        34.68        28.14        12.62         9.01        65.10 
TCGA-D7-A6EY 
       11.44 

$`TM6SF1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
            9.01             0.00 
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
            65.1            122.3 
  TM6SF1 MUTATED TM6SF1 WILD-TYPE 
           26.70            14.22 
[1] "9.0 - 65.1 (26.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.8"
D315V2, 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       2       15       38       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TM6SF1 MUTATED           0          0          1          1        1
  TM6SF1 WILD-TYPE         3         70         52         31       37
D315V3, multiclass
            clus
vv           TM6SF1 MUTATED TM6SF1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TM6SF1 MUTATED     1   2   2   3
  TM6SF1 WILD-TYPE  21  90 171  94
D315V4, multiclass
    clus
vv   TM6SF1 MUTATED TM6SF1 WILD-TYPE
  T1              1               21
  T2              2               90
  T3              2              171
  T4              3               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
  TM6SF1 MUTATED     4   0   0   3
  TM6SF1 WILD-TYPE 114 104  77  74
D315V5, multiclass
    clus
vv   TM6SF1 MUTATED TM6SF1 WILD-TYPE
  N0              4              114
  N1              0              104
  N2              0               77
  N3              3               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"
D315V6, binary
                  cls
clus                 0   1
  TM6SF1 MUTATED     7   1
  TM6SF1 WILD-TYPE 339  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM6SF1 MUTATED      7    1
  TM6SF1 WILD-TYPE  339   28
   clus
vv  TM6SF1 MUTATED TM6SF1 WILD-TYPE
  0              7              339
  1              1               28
[1] 2 2
[1] FALSE
D315V7, binary
                  cls
clus                 0   1
  TM6SF1 MUTATED     6   2
  TM6SF1 WILD-TYPE 139 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM6SF1 MUTATED      6    2
  TM6SF1 WILD-TYPE  139  246
        clus
vv       TM6SF1 MUTATED TM6SF1 WILD-TYPE
  FEMALE              6              139
  MALE                2              246
[1] 2 2
[1] FALSE
D315V8, binary
                  cls
clus                 0   1
  TM6SF1 MUTATED     5   0
  TM6SF1 WILD-TYPE 287  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM6SF1 MUTATED      5    0
  TM6SF1 WILD-TYPE  287   59
     clus
vv    TM6SF1 MUTATED TM6SF1 WILD-TYPE
  NO               5              287
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TM6SF1 MUTATED                                          0
  TM6SF1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TM6SF1 MUTATED                                       2
  TM6SF1 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TM6SF1 MUTATED                                                        4
  TM6SF1 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TM6SF1 MUTATED                                                   0
  TM6SF1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TM6SF1 MUTATED                                                                   1
  TM6SF1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TM6SF1 MUTATED                                                    0
  TM6SF1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TM6SF1 MUTATED                                                  1
  TM6SF1 WILD-TYPE                                               60
D315V9, multiclass
                                                                   clus
vv                                                                  TM6SF1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  TM6SF1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TM6SF1 MUTATED     5   0   1   1
  TM6SF1 WILD-TYPE 306  14  14  23
D315V10, multiclass
    clus
vv   TM6SF1 MUTATED TM6SF1 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TM6SF1 MUTATED       1                         0
  TM6SF1 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TM6SF1 MUTATED                                           0     5
  TM6SF1 WILD-TYPE                                         1   238
D315V12, multiclass
                                           clus
vv                                          TM6SF1 MUTATED TM6SF1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V13, binary
                  cls
clus                 0   1
  TM6SF1 MUTATED     0   6
  TM6SF1 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM6SF1 MUTATED      0    6
  TM6SF1 WILD-TYPE    4  304
                        clus
vv                       TM6SF1 MUTATED TM6SF1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(316) Variable = ARID1B MUTATION ANALYSIS
D316V1, survival
                  sevent
clus2                0   1
  ARID1B MUTATED    14   7
  ARID1B WILD-TYPE 216 132
  ARID1B MUTATED ARID1B WILD-TYPE 
              21              348 
  ARID1B MUTATED ARID1B WILD-TYPE 
               7              132 
$`ARID1B MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8284 
        6.97        30.90         9.34        34.68        32.25         8.05 
TCGA-BR-8361 TCGA-BR-8591 TCGA-BR-A4J4 TCGA-BR-A4QL TCGA-CG-4465 TCGA-CG-5721 
       31.10        28.14         0.53        16.14         9.01         6.02 
TCGA-CG-5723 TCGA-CG-5728 TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GX 
      105.07        65.10        11.08        22.32        22.68        20.25 
TCGA-HU-A4H3 TCGA-VQ-A8DL TCGA-VQ-AA68 
       29.00         0.92        43.66 

$`ARID1B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
           22.32            14.07 
[1] "0.5 - 105.1 (22.3)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D316V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID1B MUTATED         0        0        1        1         3         3
  ARID1B WILD-TYPE       2       15       39       29        34        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID1B MUTATED           0          1          2          6        3
  ARID1B WILD-TYPE         3         69         51         26       35
D316V3, multiclass
            clus
vv           ARID1B MUTATED ARID1B WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              2               51
  STAGE IIIC              6               26
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID1B MUTATED     0   3   7  12
  ARID1B WILD-TYPE  22  89 166  85
D316V4, multiclass
    clus
vv   ARID1B MUTATED ARID1B WILD-TYPE
  T1              0               22
  T2              3               89
  T3              7              166
  T4             12               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
  ARID1B MUTATED     6   6   4   6
  ARID1B WILD-TYPE 112  98  73  71
D316V5, multiclass
    clus
vv   ARID1B MUTATED ARID1B WILD-TYPE
  N0              6              112
  N1              6               98
  N2              4               73
  N3              6               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"
D316V6, binary
                  cls
clus                 0   1
  ARID1B MUTATED    23   1
  ARID1B WILD-TYPE 323  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED     23    1
  ARID1B WILD-TYPE  323   28
   clus
vv  ARID1B MUTATED ARID1B WILD-TYPE
  0             23              323
  1              1               28
[1] 2 2
[1] FALSE
D316V7, binary
                  cls
clus                 0   1
  ARID1B MUTATED    18   8
  ARID1B WILD-TYPE 127 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED     18    8
  ARID1B WILD-TYPE  127  240
        clus
vv       ARID1B MUTATED ARID1B WILD-TYPE
  FEMALE             18              127
  MALE                8              240
[1] 2 2
[1] FALSE
D316V8, binary
                  cls
clus                 0   1
  ARID1B MUTATED    15   2
  ARID1B WILD-TYPE 277  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED     15    2
  ARID1B WILD-TYPE  277   57
     clus
vv    ARID1B MUTATED ARID1B WILD-TYPE
  NO              15              277
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARID1B MUTATED                                          0
  ARID1B WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARID1B MUTATED                                       5
  ARID1B WILD-TYPE                                    65
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARID1B MUTATED                                                       16
  ARID1B WILD-TYPE                                                    142
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARID1B MUTATED                                                   0
  ARID1B WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARID1B MUTATED                                                                   3
  ARID1B WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARID1B MUTATED                                                    0
  ARID1B WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARID1B MUTATED                                                  2
  ARID1B WILD-TYPE                                               59
D316V9, multiclass
                                                                   clus
vv                                                                  ARID1B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  ARID1B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARID1B MUTATED    16   0   1   8
  ARID1B WILD-TYPE 295  14  14  16
D316V10, multiclass
    clus
vv   ARID1B MUTATED ARID1B WILD-TYPE
  R0             16              295
  R1              0               14
  R2              1               14
  RX              8               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ARID1B MUTATED       5                         1
  ARID1B WILD-TYPE    82                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID1B MUTATED                                           0    16
  ARID1B WILD-TYPE                                         1   227
D316V12, multiclass
                                           clus
vv                                          ARID1B MUTATED ARID1B WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 16              227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V13, binary
                  cls
clus                 0   1
  ARID1B MUTATED     0  20
  ARID1B WILD-TYPE   4 290
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1B MUTATED      0   20
  ARID1B WILD-TYPE    4  290
                        clus
vv                       ARID1B MUTATED ARID1B WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             20              290
[1] 2 2
[1] FALSE

Clustering(317) Variable = TNKS1BP1 MUTATION ANALYSIS
D317V1, survival
                    sevent
clus2                  0   1
  TNKS1BP1 MUTATED    14  11
  TNKS1BP1 WILD-TYPE 216 128
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
                25                344 
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
                11                128 
$`TNKS1BP1 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8284 TCGA-BR-8370 
       21.99         6.97        30.90        34.68         8.05         3.32 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-A452 TCGA-BR-A4QL TCGA-CD-8526 TCGA-CD-8529 
       31.27        25.05         7.53        16.14        12.53        12.30 
TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-5721 
       11.64        12.43         6.58         1.02         8.05         6.02 
TCGA-CG-5723 TCGA-D7-8573 TCGA-FP-A4BE TCGA-HU-A4G8 TCGA-R5-A7ZI TCGA-VQ-A8P2 
      105.07        19.50        11.08        22.68        74.53        38.14 
TCGA-VQ-A91Q 
       20.81 

$`TNKS1BP1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-8369 
       22.19        17.52         0.95        26.33         4.31        14.04 
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-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         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-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 
        7.17        12.33        12.39        12.59        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-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       15.95         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-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-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-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-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-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 

  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
              1.02               0.00 
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
            105.07             122.30 
  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE 
             12.53              14.35 
[1] "1.0 - 105.1 (12.5)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D317V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNKS1BP1 MUTATED         0        0        0        4         4         2
  TNKS1BP1 WILD-TYPE       2       15       40       26        33        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNKS1BP1 MUTATED           0          5          2          3        6
  TNKS1BP1 WILD-TYPE         3         65         51         29       32
D317V3, multiclass
            clus
vv           TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  4                 26
  STAGE IIA                 4                 33
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                5                 65
  STAGE IIIB                2                 51
  STAGE IIIC                3                 29
  STAGE IV                  6                 32
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TNKS1BP1 MUTATED     0   3  13  11
  TNKS1BP1 WILD-TYPE  22  89 160  86
D317V4, multiclass
    clus
vv   TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  T1                0                 22
  T2                3                 89
  T3               13                160
  T4               11                 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
  TNKS1BP1 MUTATED     9  10   1   6
  TNKS1BP1 WILD-TYPE 109  94  76  71
D317V5, multiclass
    clus
vv   TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  N0                9                109
  N1               10                 94
  N2                1                 76
  N3                6                 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"
D317V6, binary
                    cls
clus                   0   1
  TNKS1BP1 MUTATED    22   4
  TNKS1BP1 WILD-TYPE 324  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNKS1BP1 MUTATED     22    4
  TNKS1BP1 WILD-TYPE  324   25
   clus
vv  TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  0               22                324
  1                4                 25
[1] 2 2
[1] FALSE
D317V7, binary
                    cls
clus                   0   1
  TNKS1BP1 MUTATED    10  17
  TNKS1BP1 WILD-TYPE 135 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNKS1BP1 MUTATED     10   17
  TNKS1BP1 WILD-TYPE  135  231
        clus
vv       TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  FEMALE               10                135
  MALE                 17                231
[1] 2 2
[1] FALSE
D317V8, binary
                    cls
clus                   0   1
  TNKS1BP1 MUTATED    21   4
  TNKS1BP1 WILD-TYPE 271  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNKS1BP1 MUTATED     21    4
  TNKS1BP1 WILD-TYPE  271   55
     clus
vv    TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  NO                21                271
  YES                4                 55
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TNKS1BP1 MUTATED                                          0
  TNKS1BP1 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TNKS1BP1 MUTATED                                       4
  TNKS1BP1 WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNKS1BP1 MUTATED                                                       12
  TNKS1BP1 WILD-TYPE                                                    146
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TNKS1BP1 MUTATED                                                   2
  TNKS1BP1 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNKS1BP1 MUTATED                                                                   6
  TNKS1BP1 WILD-TYPE                                                                62
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TNKS1BP1 MUTATED                                                    0
  TNKS1BP1 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TNKS1BP1 MUTATED                                                  3
  TNKS1BP1 WILD-TYPE                                               58
D317V9, multiclass
                                                                   clus
vv                                                                  TNKS1BP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 3
                                                                   clus
vv                                                                  TNKS1BP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  TNKS1BP1 MUTATED    20   0   2   3
  TNKS1BP1 WILD-TYPE 291  14  13  21
D317V10, multiclass
    clus
vv   TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  R0               20                291
  R1                0                 14
  R2                2                 13
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  TNKS1BP1 MUTATED       7                         1
  TNKS1BP1 WILD-TYPE    80                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNKS1BP1 MUTATED                                           0    13
  TNKS1BP1 WILD-TYPE                                         1   230
D317V12, multiclass
                                           clus
vv                                          TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  ASIAN                                                    7                 80
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   13                230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V13, binary
                    cls
clus                   0   1
  TNKS1BP1 MUTATED     1  19
  TNKS1BP1 WILD-TYPE   3 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TNKS1BP1 MUTATED      1   19
  TNKS1BP1 WILD-TYPE    3  291
                        clus
vv                       TNKS1BP1 MUTATED TNKS1BP1 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               19                291
[1] 2 2
[1] FALSE

Clustering(318) Variable = ERBB2 MUTATION ANALYSIS
D318V1, survival
                 sevent
clus2               0   1
  ERBB2 MUTATED    14   4
  ERBB2 WILD-TYPE 216 135
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             18             351 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              4             135 
$`ERBB2 MUTATED`
TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8381 TCGA-BR-8487 
       30.90        32.78        30.90        44.94         7.36         1.12 
TCGA-BR-8588 TCGA-CG-4469 TCGA-CG-5730 TCGA-D7-8570 TCGA-D7-A6EY TCGA-HF-7132 
       12.79         7.07         4.01        24.72        11.44        77.29 
TCGA-HU-A4H0 TCGA-HU-A4H8 TCGA-IN-8663 TCGA-MX-A5UJ TCGA-VQ-A8DT TCGA-VQ-A8P2 
        2.10        14.07         3.39        19.73        48.79        38.14 

$`ERBB2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
          16.90           14.27 
[1] "1.1 - 77.3 (16.9)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2"  
D318V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERBB2 MUTATED         0        0        1        1         3         3
  ERBB2 WILD-TYPE       2       15       39       29        34        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERBB2 MUTATED           0          3          3          1        2
  ERBB2 WILD-TYPE         3         67         50         31       36
D318V3, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             3              50
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERBB2 MUTATED     1   4  10   3
  ERBB2 WILD-TYPE  21  88 163  94
D318V4, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  T1             1              21
  T2             4              88
  T3            10             163
  T4             3              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
  ERBB2 MUTATED     4   5   3   5
  ERBB2 WILD-TYPE 114  99  74  72
D318V5, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0             4             114
  N1             5              99
  N2             3              74
  N3             5              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"
D318V6, binary
                 cls
clus                0   1
  ERBB2 MUTATED    18   1
  ERBB2 WILD-TYPE 328  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     18    1
  ERBB2 WILD-TYPE  328   28
   clus
vv  ERBB2 MUTATED ERBB2 WILD-TYPE
  0            18             328
  1             1              28
[1] 2 2
[1] FALSE
D318V7, binary
                 cls
clus                0   1
  ERBB2 MUTATED     9  10
  ERBB2 WILD-TYPE 136 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      9   10
  ERBB2 WILD-TYPE  136  238
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE             9             136
  MALE              10             238
[1] 2 2
[1] FALSE
D318V8, binary
                 cls
clus                0   1
  ERBB2 MUTATED    13   3
  ERBB2 WILD-TYPE 279  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     13    3
  ERBB2 WILD-TYPE  279   56
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  NO             13             279
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ERBB2 MUTATED                                          0
  ERBB2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ERBB2 MUTATED                                       1
  ERBB2 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ERBB2 MUTATED                                                        9
  ERBB2 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ERBB2 MUTATED                                                   2
  ERBB2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ERBB2 MUTATED                                                                   3
  ERBB2 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ERBB2 MUTATED                                                    0
  ERBB2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ERBB2 MUTATED                                                  4
  ERBB2 WILD-TYPE                                               57
D318V9, multiclass
                                                                   clus
vv                                                                  ERBB2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  ERBB2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ERBB2 MUTATED    15   1   1   2
  ERBB2 WILD-TYPE 296  13  14  22
D318V10, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0            15             296
  R1             1              13
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ERBB2 MUTATED       2                         0
  ERBB2 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ERBB2 MUTATED                                           0    13
  ERBB2 WILD-TYPE                                         1   230
D318V12, multiclass
                                           clus
vv                                          ERBB2 MUTATED ERBB2 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V13, binary
                 cls
clus                0   1
  ERBB2 MUTATED     0  14
  ERBB2 WILD-TYPE   4 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      0   14
  ERBB2 WILD-TYPE    4  296
                        clus
vv                       ERBB2 MUTATED ERBB2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(319) Variable = FAM70B MUTATION ANALYSIS
D319V1, survival
                  sevent
clus2                0   1
  FAM70B MUTATED     7   4
  FAM70B WILD-TYPE 223 135
  FAM70B MUTATED FAM70B WILD-TYPE 
              11              358 
  FAM70B MUTATED FAM70B WILD-TYPE 
               4              135 
$`FAM70B MUTATED`
TCGA-BR-4256 TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4PF TCGA-CD-A4MG 
        9.34         6.18         1.12        31.96         1.15         6.58 
TCGA-CD-A4MI TCGA-CG-4465 TCGA-CG-5721 TCGA-F1-A448 TCGA-HU-A4G9 
       11.77         9.01         6.02        21.27        24.20 

$`FAM70B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  FAM70B MUTATED FAM70B WILD-TYPE 
            1.12             0.00 
  FAM70B MUTATED FAM70B WILD-TYPE 
           31.96           122.30 
  FAM70B MUTATED FAM70B WILD-TYPE 
           9.010           14.565 
[1] "1.1 - 32.0 (9.0)"   "0.0 - 122.3 (14.6)"
[1] "hr=" "1.5"
D319V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM70B MUTATED         0        1        1        0         3         0
  FAM70B WILD-TYPE       2       14       39       30        34        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM70B MUTATED           0          1          2          0        3
  FAM70B WILD-TYPE         3         69         51         32       35
D319V3, multiclass
            clus
vv           FAM70B MUTATED FAM70B WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              2               51
  STAGE IIIC              0               32
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM70B MUTATED     1   1   5   4
  FAM70B WILD-TYPE  21  91 168  93
D319V4, multiclass
    clus
vv   FAM70B MUTATED FAM70B WILD-TYPE
  T1              1               21
  T2              1               91
  T3              5              168
  T4              4               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
  FAM70B MUTATED     5   4   2   2
  FAM70B WILD-TYPE 113 100  75  75
D319V5, multiclass
    clus
vv   FAM70B MUTATED FAM70B WILD-TYPE
  N0              5              113
  N1              4              100
  N2              2               75
  N3              2               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"
D319V6, binary
                  cls
clus                 0   1
  FAM70B MUTATED    11   2
  FAM70B WILD-TYPE 335  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70B MUTATED     11    2
  FAM70B WILD-TYPE  335   27
   clus
vv  FAM70B MUTATED FAM70B WILD-TYPE
  0             11              335
  1              2               27
[1] 2 2
[1] FALSE
D319V7, binary
                  cls
clus                 0   1
  FAM70B MUTATED     4   9
  FAM70B WILD-TYPE 141 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70B MUTATED      4    9
  FAM70B WILD-TYPE  141  239
        clus
vv       FAM70B MUTATED FAM70B WILD-TYPE
  FEMALE              4              141
  MALE                9              239
[1] 2 2
[1] FALSE
D319V8, binary
                  cls
clus                 0   1
  FAM70B MUTATED     9   1
  FAM70B WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70B MUTATED      9    1
  FAM70B WILD-TYPE  283   58
     clus
vv    FAM70B MUTATED FAM70B WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM70B MUTATED                                          0
  FAM70B WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM70B MUTATED                                       2
  FAM70B WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM70B MUTATED                                                        5
  FAM70B WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM70B MUTATED                                                   1
  FAM70B WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM70B MUTATED                                                                   3
  FAM70B WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM70B MUTATED                                                    0
  FAM70B WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM70B MUTATED                                                  2
  FAM70B WILD-TYPE                                               59
D319V9, multiclass
                                                                   clus
vv                                                                  FAM70B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  FAM70B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAM70B MUTATED     8   0   1   2
  FAM70B WILD-TYPE 303  14  14  22
D319V10, multiclass
    clus
vv   FAM70B MUTATED FAM70B WILD-TYPE
  R0              8              303
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAM70B MUTATED       4                         0
  FAM70B WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM70B MUTATED                                           0     6
  FAM70B WILD-TYPE                                         1   237
D319V12, multiclass
                                           clus
vv                                          FAM70B MUTATED FAM70B WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V13, binary
                  cls
clus                 0   1
  FAM70B MUTATED     1   9
  FAM70B WILD-TYPE   3 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70B MUTATED      1    9
  FAM70B WILD-TYPE    3  301
                        clus
vv                       FAM70B MUTATED FAM70B WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(320) Variable = MYEOV MUTATION ANALYSIS
D320V1, survival
                 sevent
clus2               0   1
  MYEOV MUTATED     5   2
  MYEOV WILD-TYPE 225 137
  MYEOV MUTATED MYEOV WILD-TYPE 
              7             362 
  MYEOV MUTATED MYEOV WILD-TYPE 
              2             137 
$`MYEOV MUTATED`
TCGA-BR-8078 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-8536 TCGA-CD-A4MG 
       29.59        25.05        28.14        31.96        12.43         6.58 
TCGA-HU-A4G9 
       24.20 

$`MYEOV WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  MYEOV MUTATED MYEOV WILD-TYPE 
           6.58            0.00 
  MYEOV MUTATED MYEOV WILD-TYPE 
          31.96          122.30 
  MYEOV MUTATED MYEOV WILD-TYPE 
          25.05           14.12 
[1] "6.6 - 32.0 (25.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D320V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYEOV MUTATED         1        1        0        1         1         1
  MYEOV WILD-TYPE       1       14       40       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MYEOV MUTATED           0          0          0          2        1
  MYEOV WILD-TYPE         3         70         53         30       37
D320V3, multiclass
            clus
vv           MYEOV MUTATED MYEOV WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYEOV MUTATED     3   0   2   4
  MYEOV WILD-TYPE  19  92 171  93
D320V4, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  T1             3              19
  T2             0              92
  T3             2             171
  T4             4              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
  MYEOV MUTATED     4   1   1   2
  MYEOV WILD-TYPE 114 103  76  75
D320V5, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  N0             4             114
  N1             1             103
  N2             1              76
  N3             2              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"
D320V6, binary
                 cls
clus                0   1
  MYEOV MUTATED     7   1
  MYEOV WILD-TYPE 339  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      7    1
  MYEOV WILD-TYPE  339   28
   clus
vv  MYEOV MUTATED MYEOV WILD-TYPE
  0             7             339
  1             1              28
[1] 2 2
[1] FALSE
D320V7, binary
                 cls
clus                0   1
  MYEOV MUTATED     4   5
  MYEOV WILD-TYPE 141 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      4    5
  MYEOV WILD-TYPE  141  243
        clus
vv       MYEOV MUTATED MYEOV WILD-TYPE
  FEMALE             4             141
  MALE               5             243
[1] 2 2
[1] FALSE
D320V8, binary
                 cls
clus                0   1
  MYEOV MUTATED     8   0
  MYEOV WILD-TYPE 284  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      8    0
  MYEOV WILD-TYPE  284   59
     clus
vv    MYEOV MUTATED MYEOV WILD-TYPE
  NO              8             284
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MYEOV MUTATED                                          0
  MYEOV WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MYEOV MUTATED                                       1
  MYEOV WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MYEOV MUTATED                                                        6
  MYEOV WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MYEOV MUTATED                                                   0
  MYEOV WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MYEOV MUTATED                                                                   0
  MYEOV WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MYEOV MUTATED                                                    0
  MYEOV WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MYEOV MUTATED                                                  2
  MYEOV WILD-TYPE                                               59
D320V9, multiclass
                                                                   clus
vv                                                                  MYEOV MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  MYEOV WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYEOV MUTATED     7   0   0   1
  MYEOV WILD-TYPE 304  14  15  23
D320V10, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  R0             7             304
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MYEOV MUTATED       4                         1
  MYEOV WILD-TYPE    83                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MYEOV MUTATED                                           0     4
  MYEOV WILD-TYPE                                         1   239
D320V12, multiclass
                                           clus
vv                                          MYEOV MUTATED MYEOV WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V13, binary
                 cls
clus                0   1
  MYEOV MUTATED     0   9
  MYEOV WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      0    9
  MYEOV WILD-TYPE    4  301
                        clus
vv                       MYEOV MUTATED MYEOV WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(321) Variable = IRS1 MUTATION ANALYSIS
D321V1, survival
                sevent
clus2              0   1
  IRS1 MUTATED    13   5
  IRS1 WILD-TYPE 217 134
  IRS1 MUTATED IRS1 WILD-TYPE 
            18            351 
  IRS1 MUTATED IRS1 WILD-TYPE 
             5            134 
$`IRS1 MUTATED`
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8680 
        9.34        34.68        29.59         0.26         1.12        31.96 
TCGA-BR-A4QL TCGA-CD-5804 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A4YY 
       16.14        12.10         6.02       105.07        28.96        13.78 
TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-VQ-A8P2 
       77.29        26.47        29.98         6.51        29.00        38.14 

$`IRS1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
        27.715         14.070 
[1] "0.3 - 105.1 (27.7)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D321V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IRS1 MUTATED         0        1        2        2         4         2
  IRS1 WILD-TYPE       2       14       38       28        33        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IRS1 MUTATED           0          2          2          1        2
  IRS1 WILD-TYPE         3         68         51         31       36
D321V3, multiclass
            clus
vv           IRS1 MUTATED IRS1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              2             38
  STAGE II              2             28
  STAGE IIA             4             33
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            2             51
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IRS1 MUTATED     1   5   6   7
  IRS1 WILD-TYPE  21  87 167  90
D321V4, multiclass
    clus
vv   IRS1 MUTATED IRS1 WILD-TYPE
  T1            1             21
  T2            5             87
  T3            6            167
  T4            7             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
  IRS1 MUTATED     9   8   1   3
  IRS1 WILD-TYPE 109  96  76  74
D321V5, multiclass
    clus
vv   IRS1 MUTATED IRS1 WILD-TYPE
  N0            9            109
  N1            8             96
  N2            1             76
  N3            3             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"
D321V6, binary
                cls
clus               0   1
  IRS1 MUTATED    19   1
  IRS1 WILD-TYPE 327  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED     19    1
  IRS1 WILD-TYPE  327   28
   clus
vv  IRS1 MUTATED IRS1 WILD-TYPE
  0           19            327
  1            1             28
[1] 2 2
[1] FALSE
D321V7, binary
                cls
clus               0   1
  IRS1 MUTATED    10  11
  IRS1 WILD-TYPE 135 237
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED     10   11
  IRS1 WILD-TYPE  135  237
        clus
vv       IRS1 MUTATED IRS1 WILD-TYPE
  FEMALE           10            135
  MALE             11            237
[1] 2 2
[1] FALSE
D321V8, binary
                cls
clus               0   1
  IRS1 MUTATED    14   3
  IRS1 WILD-TYPE 278  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED     14    3
  IRS1 WILD-TYPE  278   56
     clus
vv    IRS1 MUTATED IRS1 WILD-TYPE
  NO            14            278
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IRS1 MUTATED                                          1
  IRS1 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IRS1 MUTATED                                       1
  IRS1 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IRS1 MUTATED                                                       11
  IRS1 WILD-TYPE                                                    147
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IRS1 MUTATED                                                   2
  IRS1 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IRS1 MUTATED                                                                   3
  IRS1 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IRS1 MUTATED                                                    0
  IRS1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IRS1 MUTATED                                                  3
  IRS1 WILD-TYPE                                               58
D321V9, multiclass
                                                                   clus
vv                                                                  IRS1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  IRS1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IRS1 MUTATED    18   0   0   3
  IRS1 WILD-TYPE 293  14  15  21
D321V10, multiclass
    clus
vv   IRS1 MUTATED IRS1 WILD-TYPE
  R0           18            293
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IRS1 MUTATED       5                         0
  IRS1 WILD-TYPE    82                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IRS1 MUTATED                                           0    12
  IRS1 WILD-TYPE                                         1   231
D321V12, multiclass
                                           clus
vv                                          IRS1 MUTATED IRS1 WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               12            231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V13, binary
                cls
clus               0   1
  IRS1 MUTATED     0  16
  IRS1 WILD-TYPE   4 294
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED      0   16
  IRS1 WILD-TYPE    4  294
                        clus
vv                       IRS1 MUTATED IRS1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           16            294
[1] 2 2
[1] FALSE

Clustering(322) Variable = WDR5 MUTATION ANALYSIS
D322V1, survival
                sevent
clus2              0   1
  WDR5 MUTATED     1   2
  WDR5 WILD-TYPE 229 137
  WDR5 MUTATED WDR5 WILD-TYPE 
             3            366 
  WDR5 MUTATED WDR5 WILD-TYPE 
             2            137 
$`WDR5 MUTATED`
TCGA-BR-4256 TCGA-BR-7703 TCGA-CG-5718 
        9.34        36.16        36.00 

$`WDR5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  WDR5 MUTATED WDR5 WILD-TYPE 
          9.34           0.00 
  WDR5 MUTATED WDR5 WILD-TYPE 
         36.16         122.30 
  WDR5 MUTATED WDR5 WILD-TYPE 
         36.00          14.22 
[1] "9.3 - 36.2 (36.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D322V2, 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       2       14       40       29        37        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WDR5 MUTATED           0          0          0          0        1
  WDR5 WILD-TYPE         3         70         53         32       37
D322V3, multiclass
            clus
vv           WDR5 MUTATED WDR5 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             0             37
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WDR5 MUTATED     1   1   1   1
  WDR5 WILD-TYPE  21  91 172  96
D322V4, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  T1            1             21
  T2            1             91
  T3            1            172
  T4            1             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
  WDR5 MUTATED     1   2   1   0
  WDR5 WILD-TYPE 117 102  76  77
D322V5, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  N0            1            117
  N1            2            102
  N2            1             76
  N3            0             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"
D322V6, binary
                cls
clus               0   1
  WDR5 MUTATED     4   0
  WDR5 WILD-TYPE 342  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      4    0
  WDR5 WILD-TYPE  342   29
   clus
vv  WDR5 MUTATED WDR5 WILD-TYPE
  0            4            342
  1            0             29
[1] 2 2
[1] FALSE
D322V7, binary
                cls
clus               0   1
  WDR5 MUTATED     3   2
  WDR5 WILD-TYPE 142 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      3    2
  WDR5 WILD-TYPE  142  246
        clus
vv       WDR5 MUTATED WDR5 WILD-TYPE
  FEMALE            3            142
  MALE              2            246
[1] 2 2
[1] FALSE
D322V8, binary
                cls
clus               0   1
  WDR5 MUTATED     3   0
  WDR5 WILD-TYPE 289  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      3    0
  WDR5 WILD-TYPE  289   59
     clus
vv    WDR5 MUTATED WDR5 WILD-TYPE
  NO             3            289
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  WDR5 MUTATED                                          0
  WDR5 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  WDR5 MUTATED                                       0
  WDR5 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WDR5 MUTATED                                                        3
  WDR5 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  WDR5 MUTATED                                                   0
  WDR5 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WDR5 MUTATED                                                                   1
  WDR5 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  WDR5 MUTATED                                                    1
  WDR5 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  WDR5 MUTATED                                                  0
  WDR5 WILD-TYPE                                               61
D322V9, multiclass
                                                                   clus
vv                                                                  WDR5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  WDR5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WDR5 MUTATED     2   0   0   3
  WDR5 WILD-TYPE 309  14  15  21
D322V10, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  R0            2            309
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  WDR5 MUTATED       0                         0
  WDR5 WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WDR5 MUTATED                                           0     4
  WDR5 WILD-TYPE                                         1   239
D322V12, multiclass
                                           clus
vv                                          WDR5 MUTATED WDR5 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V13, binary
                cls
clus               0   1
  WDR5 MUTATED     0   4
  WDR5 WILD-TYPE   4 306
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      0    4
  WDR5 WILD-TYPE    4  306
                        clus
vv                       WDR5 MUTATED WDR5 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            4            306
[1] 2 2
[1] FALSE

Clustering(323) Variable = RPL22 MUTATION ANALYSIS
D323V1, survival
                 sevent
clus2               0   1
  RPL22 MUTATED     6   2
  RPL22 WILD-TYPE 224 137
  RPL22 MUTATED RPL22 WILD-TYPE 
              8             361 
  RPL22 MUTATED RPL22 WILD-TYPE 
              2             137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 
        9.34        28.14         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-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-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-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-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 

  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          14.170 
[1] "6.3 - 65.1 (31.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.2"
D323V2, 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       2       15       38       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPL22 MUTATED           0          1          1          1        1
  RPL22 WILD-TYPE         3         69         52         31       37
D323V3, multiclass
            clus
vv           RPL22 MUTATED RPL22 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RPL22 MUTATED     1   1   2   4
  RPL22 WILD-TYPE  21  91 171  93
D323V4, multiclass
    clus
vv   RPL22 MUTATED RPL22 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             2             171
  T4             4              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
  RPL22 MUTATED     2   5   1   1
  RPL22 WILD-TYPE 116  99  76  76
D323V5, multiclass
    clus
vv   RPL22 MUTATED RPL22 WILD-TYPE
  N0             2             116
  N1             5              99
  N2             1              76
  N3             1              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"
D323V6, binary
                 cls
clus                0   1
  RPL22 MUTATED     7   1
  RPL22 WILD-TYPE 339  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED      7    1
  RPL22 WILD-TYPE  339   28
   clus
vv  RPL22 MUTATED RPL22 WILD-TYPE
  0             7             339
  1             1              28
[1] 2 2
[1] FALSE
D323V7, binary
                 cls
clus                0   1
  RPL22 MUTATED     6   3
  RPL22 WILD-TYPE 139 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED      6    3
  RPL22 WILD-TYPE  139  245
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  FEMALE             6             139
  MALE               3             245
[1] 2 2
[1] FALSE
D323V8, binary
                 cls
clus                0   1
  RPL22 MUTATED     4   3
  RPL22 WILD-TYPE 288  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED      4    3
  RPL22 WILD-TYPE  288   56
     clus
vv    RPL22 MUTATED RPL22 WILD-TYPE
  NO              4             288
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RPL22 MUTATED                                          0
  RPL22 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RPL22 MUTATED                                       1
  RPL22 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RPL22 MUTATED                                                        2
  RPL22 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RPL22 MUTATED                                                   2
  RPL22 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RPL22 MUTATED                                                                   2
  RPL22 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RPL22 MUTATED                                                    0
  RPL22 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RPL22 MUTATED                                                  2
  RPL22 WILD-TYPE                                               59
D323V9, multiclass
                                                                   clus
vv                                                                  RPL22 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  RPL22 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RPL22 MUTATED     6   1   0   1
  RPL22 WILD-TYPE 305  13  15  23
D323V10, multiclass
    clus
vv   RPL22 MUTATED RPL22 WILD-TYPE
  R0             6             305
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RPL22 MUTATED       2                         0
  RPL22 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RPL22 MUTATED                                           0     5
  RPL22 WILD-TYPE                                         1   238
D323V12, multiclass
                                           clus
vv                                          RPL22 MUTATED RPL22 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V13, binary
                 cls
clus                0   1
  RPL22 MUTATED     0   6
  RPL22 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED      0    6
  RPL22 WILD-TYPE    4  304
                        clus
vv                       RPL22 MUTATED RPL22 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(324) Variable = DDX26B MUTATION ANALYSIS
D324V1, survival
                  sevent
clus2                0   1
  DDX26B MUTATED     8   2
  DDX26B WILD-TYPE 222 137
  DDX26B MUTATED DDX26B WILD-TYPE 
              10              359 
  DDX26B MUTATED DDX26B WILD-TYPE 
               2              137 
$`DDX26B MUTATED`
TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8487 TCGA-CD-8525 TCGA-CG-5728 
       35.84        31.10         0.26         1.12        12.59        65.10 
TCGA-HU-A4GP TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-VQ-AA64 
        8.98        23.80        14.07        18.41 

$`DDX26B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  DDX26B MUTATED DDX26B WILD-TYPE 
            0.26             0.00 
  DDX26B MUTATED DDX26B WILD-TYPE 
            65.1            122.3 
  DDX26B MUTATED DDX26B WILD-TYPE 
           16.24            14.27 
[1] "0.3 - 65.1 (16.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2"  
D324V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX26B MUTATED         1        0        5        0         2         0
  DDX26B WILD-TYPE       1       15       35       30        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDX26B MUTATED           0          1          1          1        0
  DDX26B WILD-TYPE         3         69         52         31       38
D324V3, multiclass
            clus
vv           DDX26B MUTATED DDX26B WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                5               35
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DDX26B MUTATED     2   5   3   1
  DDX26B WILD-TYPE  20  87 170  96
D324V4, multiclass
    clus
vv   DDX26B MUTATED DDX26B WILD-TYPE
  T1              2               20
  T2              5               87
  T3              3              170
  T4              1               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
  DDX26B MUTATED     5   4   2   0
  DDX26B WILD-TYPE 113 100  75  77
D324V5, multiclass
    clus
vv   DDX26B MUTATED DDX26B WILD-TYPE
  N0              5              113
  N1              4              100
  N2              2               75
  N3              0               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"
D324V6, binary
                  cls
clus                 0   1
  DDX26B MUTATED    11   0
  DDX26B WILD-TYPE 335  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED     11    0
  DDX26B WILD-TYPE  335   29
   clus
vv  DDX26B MUTATED DDX26B WILD-TYPE
  0             11              335
  1              0               29
[1] 2 2
[1] FALSE
D324V7, binary
                  cls
clus                 0   1
  DDX26B MUTATED     8   4
  DDX26B WILD-TYPE 137 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED      8    4
  DDX26B WILD-TYPE  137  244
        clus
vv       DDX26B MUTATED DDX26B WILD-TYPE
  FEMALE              8              137
  MALE                4              244
[1] 2 2
[1] FALSE
D324V8, binary
                  cls
clus                 0   1
  DDX26B MUTATED     8   2
  DDX26B WILD-TYPE 284  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED      8    2
  DDX26B WILD-TYPE  284   57
     clus
vv    DDX26B MUTATED DDX26B WILD-TYPE
  NO               8              284
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DDX26B MUTATED                                          0
  DDX26B WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DDX26B MUTATED                                       1
  DDX26B WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DDX26B MUTATED                                                        6
  DDX26B WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DDX26B MUTATED                                                   1
  DDX26B WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DDX26B MUTATED                                                                   2
  DDX26B WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DDX26B MUTATED                                                    1
  DDX26B WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DDX26B MUTATED                                                  1
  DDX26B WILD-TYPE                                               60
D324V9, multiclass
                                                                   clus
vv                                                                  DDX26B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  DDX26B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DDX26B MUTATED    11   0   0   1
  DDX26B WILD-TYPE 300  14  15  23
D324V10, multiclass
    clus
vv   DDX26B MUTATED DDX26B WILD-TYPE
  R0             11              300
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DDX26B MUTATED       4                         1
  DDX26B WILD-TYPE    83                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDX26B MUTATED                                           0     6
  DDX26B WILD-TYPE                                         1   237
D324V12, multiclass
                                           clus
vv                                          DDX26B MUTATED DDX26B WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V13, binary
                  cls
clus                 0   1
  DDX26B MUTATED     0  10
  DDX26B WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED      0   10
  DDX26B WILD-TYPE    4  300
                        clus
vv                       DDX26B MUTATED DDX26B WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(325) Variable = EPHX1 MUTATION ANALYSIS
D325V1, survival
                 sevent
clus2               0   1
  EPHX1 MUTATED     6   3
  EPHX1 WILD-TYPE 224 136
  EPHX1 MUTATED EPHX1 WILD-TYPE 
              9             360 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
              3             136 
$`EPHX1 MUTATED`
TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8360 TCGA-CD-A4MG TCGA-CG-5723 
        6.97         9.67        34.68         6.18         6.58       105.07 
TCGA-F1-6874 TCGA-HU-A4G8 TCGA-R5-A7ZI 
       14.47        22.68        74.53 

$`EPHX1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-D7-8573 
       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-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-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 

  EPHX1 MUTATED EPHX1 WILD-TYPE 
           6.18            0.00 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
         105.07          122.30 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
          14.47           14.22 
[1] "6.2 - 105.1 (14.5)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.5"
D325V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPHX1 MUTATED         0        0        1        1         3         1
  EPHX1 WILD-TYPE       2       15       39       29        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPHX1 MUTATED           0          1          0          0        1
  EPHX1 WILD-TYPE         3         69         53         32       37
D325V3, multiclass
            clus
vv           EPHX1 MUTATED EPHX1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHX1 MUTATED     1   2   5   1
  EPHX1 WILD-TYPE  21  90 168  96
D325V4, multiclass
    clus
vv   EPHX1 MUTATED EPHX1 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             5             168
  T4             1              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
  EPHX1 MUTATED     4   4   0   0
  EPHX1 WILD-TYPE 114 100  77  77
D325V5, multiclass
    clus
vv   EPHX1 MUTATED EPHX1 WILD-TYPE
  N0             4             114
  N1             4             100
  N2             0              77
  N3             0              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"
D325V6, binary
                 cls
clus                0   1
  EPHX1 MUTATED     8   1
  EPHX1 WILD-TYPE 338  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED      8    1
  EPHX1 WILD-TYPE  338   28
   clus
vv  EPHX1 MUTATED EPHX1 WILD-TYPE
  0             8             338
  1             1              28
[1] 2 2
[1] FALSE
D325V7, binary
                 cls
clus                0   1
  EPHX1 MUTATED     5   5
  EPHX1 WILD-TYPE 140 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED      5    5
  EPHX1 WILD-TYPE  140  243
        clus
vv       EPHX1 MUTATED EPHX1 WILD-TYPE
  FEMALE             5             140
  MALE               5             243
[1] 2 2
[1] FALSE
D325V8, binary
                 cls
clus                0   1
  EPHX1 MUTATED     9   0
  EPHX1 WILD-TYPE 283  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED      9    0
  EPHX1 WILD-TYPE  283   59
     clus
vv    EPHX1 MUTATED EPHX1 WILD-TYPE
  NO              9             283
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EPHX1 MUTATED                                          0
  EPHX1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EPHX1 MUTATED                                       3
  EPHX1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPHX1 MUTATED                                                        5
  EPHX1 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EPHX1 MUTATED                                                   0
  EPHX1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPHX1 MUTATED                                                                   2
  EPHX1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EPHX1 MUTATED                                                    0
  EPHX1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EPHX1 MUTATED                                                  0
  EPHX1 WILD-TYPE                                               61
D325V9, multiclass
                                                                   clus
vv                                                                  EPHX1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  EPHX1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EPHX1 MUTATED     5   0   0   3
  EPHX1 WILD-TYPE 306  14  15  21
D325V10, multiclass
    clus
vv   EPHX1 MUTATED EPHX1 WILD-TYPE
  R0             5             306
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EPHX1 MUTATED       2                         0
  EPHX1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPHX1 MUTATED                                           0     7
  EPHX1 WILD-TYPE                                         1   236
D325V12, multiclass
                                           clus
vv                                          EPHX1 MUTATED EPHX1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V13, binary
                 cls
clus                0   1
  EPHX1 MUTATED     1   8
  EPHX1 WILD-TYPE   3 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED      1    8
  EPHX1 WILD-TYPE    3  302
                        clus
vv                       EPHX1 MUTATED EPHX1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(326) Variable = CLMN MUTATION ANALYSIS
D326V1, survival
                sevent
clus2              0   1
  CLMN MUTATED     5   6
  CLMN WILD-TYPE 225 133
  CLMN MUTATED CLMN WILD-TYPE 
            11            358 
  CLMN MUTATED CLMN WILD-TYPE 
             6            133 
$`CLMN MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8382 
        6.97         9.34         9.67        32.78        35.84        25.05 
TCGA-BR-8680 TCGA-CD-A4MG TCGA-D7-A4YV TCGA-HU-A4G8 TCGA-HU-A4GX 
       31.96         6.58         5.92        22.68        20.25 

$`CLMN WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  CLMN MUTATED CLMN WILD-TYPE 
          5.92           0.00 
  CLMN MUTATED CLMN WILD-TYPE 
         35.84         122.30 
  CLMN MUTATED CLMN WILD-TYPE 
         20.25          14.22 
[1] "5.9 - 35.8 (20.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D326V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CLMN MUTATED         0        0        2        0         2         3
  CLMN WILD-TYPE       2       15       38       30        35        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLMN MUTATED           0          1          0          2        1
  CLMN WILD-TYPE         3         69         53         30       37
D326V3, multiclass
            clus
vv           CLMN MUTATED CLMN WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CLMN MUTATED     0   2   5   4
  CLMN WILD-TYPE  22  90 168  93
D326V4, multiclass
    clus
vv   CLMN MUTATED CLMN WILD-TYPE
  T1            0             22
  T2            2             90
  T3            5            168
  T4            4             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
  CLMN MUTATED     5   4   2   1
  CLMN WILD-TYPE 113 100  75  76
D326V5, multiclass
    clus
vv   CLMN MUTATED CLMN WILD-TYPE
  N0            5            113
  N1            4            100
  N2            2             75
  N3            1             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"
D326V6, binary
                cls
clus               0   1
  CLMN MUTATED    12   1
  CLMN WILD-TYPE 334  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLMN MUTATED     12    1
  CLMN WILD-TYPE  334   28
   clus
vv  CLMN MUTATED CLMN WILD-TYPE
  0           12            334
  1            1             28
[1] 2 2
[1] FALSE
D326V7, binary
                cls
clus               0   1
  CLMN MUTATED     8   6
  CLMN WILD-TYPE 137 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLMN MUTATED      8    6
  CLMN WILD-TYPE  137  242
        clus
vv       CLMN MUTATED CLMN WILD-TYPE
  FEMALE            8            137
  MALE              6            242
[1] 2 2
[1] FALSE
D326V8, binary
                cls
clus               0   1
  CLMN MUTATED    12   0
  CLMN WILD-TYPE 280  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLMN MUTATED     12    0
  CLMN WILD-TYPE  280   59
     clus
vv    CLMN MUTATED CLMN WILD-TYPE
  NO            12            280
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CLMN MUTATED                                          0
  CLMN WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CLMN MUTATED                                       3
  CLMN WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CLMN MUTATED                                                        7
  CLMN WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CLMN MUTATED                                                   0
  CLMN WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CLMN MUTATED                                                                   2
  CLMN WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CLMN MUTATED                                                    0
  CLMN WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CLMN MUTATED                                                  2
  CLMN WILD-TYPE                                               59
D326V9, multiclass
                                                                   clus
vv                                                                  CLMN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  CLMN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CLMN MUTATED     8   0   0   4
  CLMN WILD-TYPE 303  14  15  20
D326V10, multiclass
    clus
vv   CLMN MUTATED CLMN WILD-TYPE
  R0            8            303
  R1            0             14
  R2            0             15
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CLMN MUTATED       4                         0
  CLMN WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CLMN MUTATED                                           0     9
  CLMN WILD-TYPE                                         1   234
D326V12, multiclass
                                           clus
vv                                          CLMN MUTATED CLMN WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V13, binary
                cls
clus               0   1
  CLMN MUTATED     0  13
  CLMN WILD-TYPE   4 297
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLMN MUTATED      0   13
  CLMN WILD-TYPE    4  297
                        clus
vv                       CLMN MUTATED CLMN WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           13            297
[1] 2 2
[1] FALSE

Clustering(327) Variable = TRAM1L1 MUTATION ANALYSIS
D327V1, survival
                   sevent
clus2                 0   1
  TRAM1L1 MUTATED     7   4
  TRAM1L1 WILD-TYPE 223 135
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
               11               358 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
                4               135 
$`TRAM1L1 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-D7-8570 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-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-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 

  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             14.35 
[1] "0.1 - 74.5 (12.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D327V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRAM1L1 MUTATED         1        0        3        1         2         1
  TRAM1L1 WILD-TYPE       1       15       37       29        35        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRAM1L1 MUTATED           0          2          0          2        2
  TRAM1L1 WILD-TYPE         3         68         53         30       36
D327V3, multiclass
            clus
vv           TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 3                37
  STAGE II                 1                29
  STAGE IIA                2                35
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               2                30
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TRAM1L1 MUTATED     1   4   3   6
  TRAM1L1 WILD-TYPE  21  88 170  91
D327V4, multiclass
    clus
vv   TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  T1               1                21
  T2               4                88
  T3               3               170
  T4               6                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
  TRAM1L1 MUTATED     6   5   3   1
  TRAM1L1 WILD-TYPE 112  99  74  76
D327V5, multiclass
    clus
vv   TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  N0               6               112
  N1               5                99
  N2               3                74
  N3               1                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"
D327V6, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED    13   1
  TRAM1L1 WILD-TYPE 333  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED     13    1
  TRAM1L1 WILD-TYPE  333   28
   clus
vv  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  0              13               333
  1               1                28
[1] 2 2
[1] FALSE
D327V7, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED     7   8
  TRAM1L1 WILD-TYPE 138 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED      7    8
  TRAM1L1 WILD-TYPE  138  240
        clus
vv       TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  FEMALE               7               138
  MALE                 8               240
[1] 2 2
[1] FALSE
D327V8, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED    12   1
  TRAM1L1 WILD-TYPE 280  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED     12    1
  TRAM1L1 WILD-TYPE  280   58
     clus
vv    TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  NO               12               280
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TRAM1L1 MUTATED                                          0
  TRAM1L1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TRAM1L1 MUTATED                                       2
  TRAM1L1 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRAM1L1 MUTATED                                                        6
  TRAM1L1 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TRAM1L1 MUTATED                                                   1
  TRAM1L1 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRAM1L1 MUTATED                                                                   3
  TRAM1L1 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TRAM1L1 MUTATED                                                    0
  TRAM1L1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TRAM1L1 MUTATED                                                  3
  TRAM1L1 WILD-TYPE                                               58
D327V9, multiclass
                                                                   clus
vv                                                                  TRAM1L1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  TRAM1L1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TRAM1L1 MUTATED    12   0   0   2
  TRAM1L1 WILD-TYPE 299  14  15  22
D327V10, multiclass
    clus
vv   TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  R0              12               299
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TRAM1L1 MUTATED       2                         1
  TRAM1L1 WILD-TYPE    85                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRAM1L1 MUTATED                                           0    10
  TRAM1L1 WILD-TYPE                                         1   233
D327V12, multiclass
                                           clus
vv                                          TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V13, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED     1  11
  TRAM1L1 WILD-TYPE   3 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED      1   11
  TRAM1L1 WILD-TYPE    3  299
                        clus
vv                       TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              11               299
[1] 2 2
[1] FALSE

Clustering(328) Variable = EHMT2 MUTATION ANALYSIS
D328V1, survival
                 sevent
clus2               0   1
  EHMT2 MUTATED    14   4
  EHMT2 WILD-TYPE 216 135
  EHMT2 MUTATED EHMT2 WILD-TYPE 
             18             351 
  EHMT2 MUTATED EHMT2 WILD-TYPE 
              4             135 
$`EHMT2 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-7703 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8591 
        6.97        30.90        36.16        29.59        31.10        28.14 
TCGA-CD-8525 TCGA-CG-5721 TCGA-D7-8578 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4G9 
       12.59         6.02        21.14        30.51        22.68        24.20 
TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-R5-A7ZF TCGA-VQ-A8PK TCGA-VQ-AA68 
        8.98        20.25        12.95         8.52        17.85        43.66 

$`EHMT2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       14.66        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-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-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         0.10         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-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-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-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 

  EHMT2 MUTATED EHMT2 WILD-TYPE 
           6.02            0.00 
  EHMT2 MUTATED EHMT2 WILD-TYPE 
          43.66          122.30 
  EHMT2 MUTATED EHMT2 WILD-TYPE 
          21.91           14.07 
[1] "6.0 - 43.7 (21.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.2"
D328V2, 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       2       13       39       30        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EHMT2 MUTATED           0          2          2          5        2
  EHMT2 WILD-TYPE         3         68         51         27       36
D328V3, multiclass
            clus
vv           EHMT2 MUTATED EHMT2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             5              27
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EHMT2 MUTATED     2   3   5   8
  EHMT2 WILD-TYPE  20  89 168  89
D328V4, multiclass
    clus
vv   EHMT2 MUTATED EHMT2 WILD-TYPE
  T1             2              20
  T2             3              89
  T3             5             168
  T4             8              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
  EHMT2 MUTATED     4   6   2   5
  EHMT2 WILD-TYPE 114  98  75  72
D328V5, multiclass
    clus
vv   EHMT2 MUTATED EHMT2 WILD-TYPE
  N0             4             114
  N1             6              98
  N2             2              75
  N3             5              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"
D328V6, binary
                 cls
clus                0   1
  EHMT2 MUTATED    17   1
  EHMT2 WILD-TYPE 329  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHMT2 MUTATED     17    1
  EHMT2 WILD-TYPE  329   28
   clus
vv  EHMT2 MUTATED EHMT2 WILD-TYPE
  0            17             329
  1             1              28
[1] 2 2
[1] FALSE
D328V7, binary
                 cls
clus                0   1
  EHMT2 MUTATED    12   7
  EHMT2 WILD-TYPE 133 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHMT2 MUTATED     12    7
  EHMT2 WILD-TYPE  133  241
        clus
vv       EHMT2 MUTATED EHMT2 WILD-TYPE
  FEMALE            12             133
  MALE               7             241
[1] 2 2
[1] FALSE
D328V8, binary
                 cls
clus                0   1
  EHMT2 MUTATED    15   3
  EHMT2 WILD-TYPE 277  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHMT2 MUTATED     15    3
  EHMT2 WILD-TYPE  277   56
     clus
vv    EHMT2 MUTATED EHMT2 WILD-TYPE
  NO             15             277
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EHMT2 MUTATED                                          0
  EHMT2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EHMT2 MUTATED                                       3
  EHMT2 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EHMT2 MUTATED                                                        7
  EHMT2 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EHMT2 MUTATED                                                   2
  EHMT2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EHMT2 MUTATED                                                                   2
  EHMT2 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EHMT2 MUTATED                                                    1
  EHMT2 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EHMT2 MUTATED                                                  4
  EHMT2 WILD-TYPE                                               57
D328V9, multiclass
                                                                   clus
vv                                                                  EHMT2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  EHMT2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EHMT2 MUTATED    13   1   0   3
  EHMT2 WILD-TYPE 298  13  15  21
D328V10, multiclass
    clus
vv   EHMT2 MUTATED EHMT2 WILD-TYPE
  R0            13             298
  R1             1              13
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EHMT2 MUTATED       6                         1
  EHMT2 WILD-TYPE    81                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EHMT2 MUTATED                                           0    10
  EHMT2 WILD-TYPE                                         1   233
D328V12, multiclass
                                           clus
vv                                          EHMT2 MUTATED EHMT2 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V13, binary
                 cls
clus                0   1
  EHMT2 MUTATED     0  15
  EHMT2 WILD-TYPE   4 295
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHMT2 MUTATED      0   15
  EHMT2 WILD-TYPE    4  295
                        clus
vv                       EHMT2 MUTATED EHMT2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            15             295
[1] 2 2
[1] FALSE

Clustering(329) Variable = GALNTL1 MUTATION ANALYSIS
D329V1, survival
                   sevent
clus2                 0   1
  GALNTL1 MUTATED     2   8
  GALNTL1 WILD-TYPE 228 131
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
               10               359 
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
                8               131 
$`GALNTL1 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8363 TCGA-BR-A4QL 
        6.97        34.68         9.07        14.43         0.26        16.14 
TCGA-CG-5728 TCGA-F1-6875 TCGA-HJ-7597 TCGA-HU-A4GQ 
       65.10        72.23        26.47         0.10 

$`GALNTL1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
        3.45        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-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-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-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 

  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
              0.1               0.0 
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
            72.23            122.30 
  GALNTL1 MUTATED GALNTL1 WILD-TYPE 
           15.285            14.170 
[1] "0.1 - 72.2 (15.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.9"
D329V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GALNTL1 MUTATED         0        1        3        0         1         0
  GALNTL1 WILD-TYPE       2       14       37       30        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GALNTL1 MUTATED           1          1          1          1        1
  GALNTL1 WILD-TYPE         2         69         52         31       37
D329V3, multiclass
            clus
vv           GALNTL1 MUTATED GALNTL1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 3                37
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                1                 2
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GALNTL1 MUTATED     0   4   4   2
  GALNTL1 WILD-TYPE  22  88 169  95
D329V4, multiclass
    clus
vv   GALNTL1 MUTATED GALNTL1 WILD-TYPE
  T1               0                22
  T2               4                88
  T3               4               169
  T4               2                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
  GALNTL1 MUTATED     5   2   1   2
  GALNTL1 WILD-TYPE 113 102  76  75
D329V5, multiclass
    clus
vv   GALNTL1 MUTATED GALNTL1 WILD-TYPE
  N0               5               113
  N1               2               102
  N2               1                76
  N3               2                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"
D329V6, binary
                   cls
clus                  0   1
  GALNTL1 MUTATED     7   1
  GALNTL1 WILD-TYPE 339  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNTL1 MUTATED      7    1
  GALNTL1 WILD-TYPE  339   28
   clus
vv  GALNTL1 MUTATED GALNTL1 WILD-TYPE
  0               7               339
  1               1                28
[1] 2 2
[1] FALSE
D329V7, binary
                   cls
clus                  0   1
  GALNTL1 MUTATED     6   4
  GALNTL1 WILD-TYPE 139 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNTL1 MUTATED      6    4
  GALNTL1 WILD-TYPE  139  244
        clus
vv       GALNTL1 MUTATED GALNTL1 WILD-TYPE
  FEMALE               6               139
  MALE                 4               244
[1] 2 2
[1] FALSE
D329V8, binary
                   cls
clus                  0   1
  GALNTL1 MUTATED     9   0
  GALNTL1 WILD-TYPE 283  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNTL1 MUTATED      9    0
  GALNTL1 WILD-TYPE  283   59
     clus
vv    GALNTL1 MUTATED GALNTL1 WILD-TYPE
  NO                9               283
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GALNTL1 MUTATED                                          1
  GALNTL1 WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GALNTL1 MUTATED                                       0
  GALNTL1 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GALNTL1 MUTATED                                                        5
  GALNTL1 WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GALNTL1 MUTATED                                                   0
  GALNTL1 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GALNTL1 MUTATED                                                                   3
  GALNTL1 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GALNTL1 MUTATED                                                    0
  GALNTL1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GALNTL1 MUTATED                                                  1
  GALNTL1 WILD-TYPE                                               60
D329V9, multiclass
                                                                   clus
vv                                                                  GALNTL1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  GALNTL1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GALNTL1 MUTATED     9   0   0   1
  GALNTL1 WILD-TYPE 302  14  15  23
D329V10, multiclass
    clus
vv   GALNTL1 MUTATED GALNTL1 WILD-TYPE
  R0               9               302
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  GALNTL1 MUTATED       1                         1
  GALNTL1 WILD-TYPE    86                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GALNTL1 MUTATED                                           0     7
  GALNTL1 WILD-TYPE                                         1   236
D329V12, multiclass
                                           clus
vv                                          GALNTL1 MUTATED GALNTL1 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V13, binary
                   cls
clus                  0   1
  GALNTL1 MUTATED     0   9
  GALNTL1 WILD-TYPE   4 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNTL1 MUTATED      0    9
  GALNTL1 WILD-TYPE    4  301
                        clus
vv                       GALNTL1 MUTATED GALNTL1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               9               301
[1] 2 2
[1] FALSE

Clustering(330) Variable = DMXL2 MUTATION ANALYSIS
D330V1, survival
                 sevent
clus2               0   1
  DMXL2 MUTATED    28  12
  DMXL2 WILD-TYPE 202 127
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             40             329 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             12             127 
$`DMXL2 MUTATED`
TCGA-CG-4460 TCGA-BR-4191 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8059 
       21.99        18.35         9.34        34.68        35.84        14.43 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8360 TCGA-BR-8361 
        0.69        29.59        32.25         8.05         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-8524 TCGA-CD-8525 
        0.26         3.72        27.12        31.96        12.76        12.59 
TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-A4MI TCGA-CG-4305 
       12.53        12.30        12.39        12.59        11.77        15.95 
TCGA-D7-8573 TCGA-D7-8576 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-8099 TCGA-FP-8209 
       19.50        14.66        14.47        72.23        17.06        59.54 
TCGA-FP-8211 TCGA-HF-7132 TCGA-HU-8243 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ 
       13.58        77.29         5.92        11.77         8.98         0.10 
TCGA-HU-A4GU TCGA-HU-A4GY TCGA-RD-A8N1 TCGA-VQ-A8P2 
        6.58         0.26       115.69        38.14 

$`DMXL2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-8080 TCGA-BR-8285 TCGA-BR-8286 
       33.21        37.25        11.44         9.60         0.56        29.42 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 
        2.66        19.96         2.20         7.40        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-8483 TCGA-BR-8484 
       31.27        14.79         7.36        25.05         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-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-8528 
       13.35        11.21        12.10        12.39         7.17        12.33 
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-D7-8574 
       12.36        11.31        12.33        24.72        16.80        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-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-8210 TCGA-FP-8631 
        3.48        19.53        14.07        22.29         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-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-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51        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-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 

  DMXL2 MUTATED DMXL2 WILD-TYPE 
            0.1             0.0 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
         115.69          122.30 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
         14.005          14.270 
[1] "0.1 - 115.7 (14.0)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D330V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DMXL2 MUTATED         0        2        4        4         5         4
  DMXL2 WILD-TYPE       2       13       36       26        32        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DMXL2 MUTATED           1          7          4          5        3
  DMXL2 WILD-TYPE         2         63         49         27       35
D330V3, multiclass
            clus
vv           DMXL2 MUTATED DMXL2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               4              36
  STAGE II               4              26
  STAGE IIA              5              32
  STAGE IIB              4              48
  STAGE III              1               2
  STAGE IIIA             7              63
  STAGE IIIB             4              49
  STAGE IIIC             5              27
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DMXL2 MUTATED     1   8  14  16
  DMXL2 WILD-TYPE  21  84 159  81
D330V4, multiclass
    clus
vv   DMXL2 MUTATED DMXL2 WILD-TYPE
  T1             1              21
  T2             8              84
  T3            14             159
  T4            16              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"
                 vv
clus               N0  N1  N2  N3
  DMXL2 MUTATED    16  17   5   3
  DMXL2 WILD-TYPE 102  87  72  74
D330V5, multiclass
    clus
vv   DMXL2 MUTATED DMXL2 WILD-TYPE
  N0            16             102
  N1            17              87
  N2             5              72
  N3             3              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"
D330V6, binary
                 cls
clus                0   1
  DMXL2 MUTATED    36   3
  DMXL2 WILD-TYPE 310  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     36    3
  DMXL2 WILD-TYPE  310   26
   clus
vv  DMXL2 MUTATED DMXL2 WILD-TYPE
  0            36             310
  1             3              26
[1] 2 2
[1] FALSE
D330V7, binary
                 cls
clus                0   1
  DMXL2 MUTATED    17  24
  DMXL2 WILD-TYPE 128 224
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     17   24
  DMXL2 WILD-TYPE  128  224
        clus
vv       DMXL2 MUTATED DMXL2 WILD-TYPE
  FEMALE            17             128
  MALE              24             224
[1] 2 2
[1] FALSE
D330V8, binary
                 cls
clus                0   1
  DMXL2 MUTATED    30   9
  DMXL2 WILD-TYPE 262  50
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     30    9
  DMXL2 WILD-TYPE  262   50
     clus
vv    DMXL2 MUTATED DMXL2 WILD-TYPE
  NO             30             262
  YES             9              50
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DMXL2 MUTATED                                          0
  DMXL2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DMXL2 MUTATED                                       7
  DMXL2 WILD-TYPE                                    63
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DMXL2 MUTATED                                                       16
  DMXL2 WILD-TYPE                                                    142
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DMXL2 MUTATED                                                   4
  DMXL2 WILD-TYPE                                                17
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DMXL2 MUTATED                                                                   8
  DMXL2 WILD-TYPE                                                                60
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DMXL2 MUTATED                                                    0
  DMXL2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DMXL2 MUTATED                                                  6
  DMXL2 WILD-TYPE                                               55
D330V9, multiclass
                                                                   clus
vv                                                                  DMXL2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             8
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              6
                                                                   clus
vv                                                                  DMXL2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          63
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              60
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DMXL2 MUTATED    34   2   1   3
  DMXL2 WILD-TYPE 277  12  14  21
D330V10, multiclass
    clus
vv   DMXL2 MUTATED DMXL2 WILD-TYPE
  R0            34             277
  R1             2              12
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DMXL2 MUTATED      14                         1
  DMXL2 WILD-TYPE    73                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DMXL2 MUTATED                                           0    23
  DMXL2 WILD-TYPE                                         1   220
D330V12, multiclass
                                           clus
vv                                          DMXL2 MUTATED DMXL2 WILD-TYPE
  ASIAN                                                14              73
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                23             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V13, binary
                 cls
clus                0   1
  DMXL2 MUTATED     0  37
  DMXL2 WILD-TYPE   4 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED      0   37
  DMXL2 WILD-TYPE    4  273
                        clus
vv                       DMXL2 MUTATED DMXL2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            37             273
[1] 2 2
[1] FALSE

Clustering(331) Variable = MIA2 MUTATION ANALYSIS
D331V1, survival
                sevent
clus2              0   1
  MIA2 MUTATED     5   3
  MIA2 WILD-TYPE 225 136
  MIA2 MUTATED MIA2 WILD-TYPE 
             8            361 
  MIA2 MUTATED MIA2 WILD-TYPE 
             3            136 
$`MIA2 MUTATED`
TCGA-BR-6566 TCGA-BR-7723 TCGA-BR-8680 TCGA-BR-A452 TCGA-CD-A4MG TCGA-HF-A5NB 
       32.78        28.73        31.96         7.53         6.58        30.51 
TCGA-HU-A4GX TCGA-VQ-A8P2 
       20.25        38.14 

$`MIA2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  MIA2 MUTATED MIA2 WILD-TYPE 
          6.58           0.00 
  MIA2 MUTATED MIA2 WILD-TYPE 
         38.14         122.30 
  MIA2 MUTATED MIA2 WILD-TYPE 
         29.62          14.07 
[1] "6.6 - 38.1 (29.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D331V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MIA2 MUTATED         0        0        0        0         2         0
  MIA2 WILD-TYPE       2       15       40       30        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MIA2 MUTATED           0          2          1          2        1
  MIA2 WILD-TYPE         3         68         52         30       37
D331V3, multiclass
            clus
vv           MIA2 MUTATED MIA2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            2             30
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MIA2 MUTATED     1   0   3   5
  MIA2 WILD-TYPE  21  92 170  92
D331V4, multiclass
    clus
vv   MIA2 MUTATED MIA2 WILD-TYPE
  T1            1             21
  T2            0             92
  T3            3            170
  T4            5             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
  MIA2 MUTATED     2   3   2   2
  MIA2 WILD-TYPE 116 101  75  75
D331V5, multiclass
    clus
vv   MIA2 MUTATED MIA2 WILD-TYPE
  N0            2            116
  N1            3            101
  N2            2             75
  N3            2             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"
D331V6, binary
                cls
clus               0   1
  MIA2 MUTATED     9   1
  MIA2 WILD-TYPE 337  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      9    1
  MIA2 WILD-TYPE  337   28
   clus
vv  MIA2 MUTATED MIA2 WILD-TYPE
  0            9            337
  1            1             28
[1] 2 2
[1] FALSE
D331V7, binary
                cls
clus               0   1
  MIA2 MUTATED     5   5
  MIA2 WILD-TYPE 140 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      5    5
  MIA2 WILD-TYPE  140  243
        clus
vv       MIA2 MUTATED MIA2 WILD-TYPE
  FEMALE            5            140
  MALE              5            243
[1] 2 2
[1] FALSE
D331V8, binary
                cls
clus               0   1
  MIA2 MUTATED     6   2
  MIA2 WILD-TYPE 286  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      6    2
  MIA2 WILD-TYPE  286   57
     clus
vv    MIA2 MUTATED MIA2 WILD-TYPE
  NO             6            286
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MIA2 MUTATED                                          0
  MIA2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MIA2 MUTATED                                       2
  MIA2 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MIA2 MUTATED                                                        4
  MIA2 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MIA2 MUTATED                                                   2
  MIA2 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MIA2 MUTATED                                                                   0
  MIA2 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MIA2 MUTATED                                                    0
  MIA2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MIA2 MUTATED                                                  2
  MIA2 WILD-TYPE                                               59
D331V9, multiclass
                                                                   clus
vv                                                                  MIA2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  MIA2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MIA2 MUTATED     6   1   0   2
  MIA2 WILD-TYPE 305  13  15  22
D331V10, multiclass
    clus
vv   MIA2 MUTATED MIA2 WILD-TYPE
  R0            6            305
  R1            1             13
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MIA2 MUTATED       4                         0
  MIA2 WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MIA2 MUTATED                                           0     5
  MIA2 WILD-TYPE                                         1   238
D331V12, multiclass
                                           clus
vv                                          MIA2 MUTATED MIA2 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V13, binary
                cls
clus               0   1
  MIA2 MUTATED     0   8
  MIA2 WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      0    8
  MIA2 WILD-TYPE    4  302
                        clus
vv                       MIA2 MUTATED MIA2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(332) Variable = NT5DC1 MUTATION ANALYSIS
D332V1, survival
                  sevent
clus2                0   1
  NT5DC1 MUTATED     5   3
  NT5DC1 WILD-TYPE 225 136
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
               8              361 
  NT5DC1 MUTATED NT5DC1 WILD-TYPE 
               3              136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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           14.430 
[1] "0.3 - 38.1 (9.5)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.3"
D332V2, 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       2       15       39       29        34        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NT5DC1 MUTATED           0          2          0          0        0
  NT5DC1 WILD-TYPE         3         68         53         32       38
D332V3, multiclass
            clus
vv           NT5DC1 MUTATED NT5DC1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NT5DC1 MUTATED     0   1   6   1
  NT5DC1 WILD-TYPE  22  91 167  96
D332V4, multiclass
    clus
vv   NT5DC1 MUTATED NT5DC1 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              6              167
  T4              1               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
  NT5DC1 MUTATED     5   2   1   0
  NT5DC1 WILD-TYPE 113 102  76  77
D332V5, multiclass
    clus
vv   NT5DC1 MUTATED NT5DC1 WILD-TYPE
  N0              5              113
  N1              2              102
  N2              1               76
  N3              0               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"
D332V6, binary
                  cls
clus                 0   1
  NT5DC1 MUTATED     8   0
  NT5DC1 WILD-TYPE 338  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC1 MUTATED      8    0
  NT5DC1 WILD-TYPE  338   29
   clus
vv  NT5DC1 MUTATED NT5DC1 WILD-TYPE
  0              8              338
  1              0               29
[1] 2 2
[1] FALSE
D332V7, binary
                  cls
clus                 0   1
  NT5DC1 MUTATED     5   3
  NT5DC1 WILD-TYPE 140 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC1 MUTATED      5    3
  NT5DC1 WILD-TYPE  140  245
        clus
vv       NT5DC1 MUTATED NT5DC1 WILD-TYPE
  FEMALE              5              140
  MALE                3              245
[1] 2 2
[1] FALSE
D332V8, binary
                  cls
clus                 0   1
  NT5DC1 MUTATED     7   1
  NT5DC1 WILD-TYPE 285  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC1 MUTATED      7    1
  NT5DC1 WILD-TYPE  285   58
     clus
vv    NT5DC1 MUTATED NT5DC1 WILD-TYPE
  NO               7              285
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NT5DC1 MUTATED                                          0
  NT5DC1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NT5DC1 MUTATED                                       1
  NT5DC1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NT5DC1 MUTATED                                                        4
  NT5DC1 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NT5DC1 MUTATED                                                   1
  NT5DC1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NT5DC1 MUTATED                                                                   0
  NT5DC1 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NT5DC1 MUTATED                                                    0
  NT5DC1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NT5DC1 MUTATED                                                  2
  NT5DC1 WILD-TYPE                                               59
D332V9, multiclass
                                                                   clus
vv                                                                  NT5DC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  NT5DC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NT5DC1 MUTATED     7   0   0   0
  NT5DC1 WILD-TYPE 304  14  15  24
D332V10, multiclass
    clus
vv   NT5DC1 MUTATED NT5DC1 WILD-TYPE
  R0              7              304
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NT5DC1 MUTATED       2                         0
  NT5DC1 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NT5DC1 MUTATED                                           0     6
  NT5DC1 WILD-TYPE                                         1   237
D332V12, multiclass
                                           clus
vv                                          NT5DC1 MUTATED NT5DC1 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V13, binary
                  cls
clus                 0   1
  NT5DC1 MUTATED     0   7
  NT5DC1 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC1 MUTATED      0    7
  NT5DC1 WILD-TYPE    4  303
                        clus
vv                       NT5DC1 MUTATED NT5DC1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(333) Variable = SYCP1 MUTATION ANALYSIS
D333V1, survival
                 sevent
clus2               0   1
  SYCP1 MUTATED    15   6
  SYCP1 WILD-TYPE 215 133
  SYCP1 MUTATED SYCP1 WILD-TYPE 
             21             348 
  SYCP1 MUTATED SYCP1 WILD-TYPE 
              6             133 
$`SYCP1 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-8363 TCGA-BR-8373 
       34.68        44.94        35.84        18.15         0.26        14.79 
TCGA-BR-8382 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-A4IV TCGA-CD-8536 TCGA-CD-A4MG 
       25.05        27.12        28.14        28.57        12.43         6.58 
TCGA-CG-4466 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-6526 TCGA-FP-7735 TCGA-HF-A5NB 
       18.97         6.02       105.07        17.19         3.48        30.51 
TCGA-IN-A6RP TCGA-VQ-A8P2 TCGA-VQ-A92D 
        6.44        38.14        66.81 

$`SYCP1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
          25.05           14.04 
[1] "0.3 - 105.1 (25.1)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.7"
D333V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SYCP1 MUTATED         0        0        5        2         3         0
  SYCP1 WILD-TYPE       2       15       35       28        34        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYCP1 MUTATED           0          3          2          4        2
  SYCP1 WILD-TYPE         3         67         51         28       36
D333V3, multiclass
            clus
vv           SYCP1 MUTATED SYCP1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               5              35
  STAGE II               2              28
  STAGE IIA              3              34
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             4              28
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SYCP1 MUTATED     1   6   6   9
  SYCP1 WILD-TYPE  21  86 167  88
D333V4, multiclass
    clus
vv   SYCP1 MUTATED SYCP1 WILD-TYPE
  T1             1              21
  T2             6              86
  T3             6             167
  T4             9              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
  SYCP1 MUTATED     9   6   2   4
  SYCP1 WILD-TYPE 109  98  75  73
D333V5, multiclass
    clus
vv   SYCP1 MUTATED SYCP1 WILD-TYPE
  N0             9             109
  N1             6              98
  N2             2              75
  N3             4              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"
D333V6, binary
                 cls
clus                0   1
  SYCP1 MUTATED    21   0
  SYCP1 WILD-TYPE 325  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP1 MUTATED     21    0
  SYCP1 WILD-TYPE  325   29
   clus
vv  SYCP1 MUTATED SYCP1 WILD-TYPE
  0            21             325
  1             0              29
[1] 2 2
[1] FALSE
D333V7, binary
                 cls
clus                0   1
  SYCP1 MUTATED    10  13
  SYCP1 WILD-TYPE 135 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP1 MUTATED     10   13
  SYCP1 WILD-TYPE  135  235
        clus
vv       SYCP1 MUTATED SYCP1 WILD-TYPE
  FEMALE            10             135
  MALE              13             235
[1] 2 2
[1] FALSE
D333V8, binary
                 cls
clus                0   1
  SYCP1 MUTATED    18   3
  SYCP1 WILD-TYPE 274  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP1 MUTATED     18    3
  SYCP1 WILD-TYPE  274   56
     clus
vv    SYCP1 MUTATED SYCP1 WILD-TYPE
  NO             18             274
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SYCP1 MUTATED                                          0
  SYCP1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SYCP1 MUTATED                                       2
  SYCP1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SYCP1 MUTATED                                                       14
  SYCP1 WILD-TYPE                                                    144
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SYCP1 MUTATED                                                   2
  SYCP1 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SYCP1 MUTATED                                                                   3
  SYCP1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SYCP1 MUTATED                                                    0
  SYCP1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SYCP1 MUTATED                                                  2
  SYCP1 WILD-TYPE                                               59
D333V9, multiclass
                                                                   clus
vv                                                                  SYCP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  SYCP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SYCP1 MUTATED    19   1   0   2
  SYCP1 WILD-TYPE 292  13  15  22
D333V10, multiclass
    clus
vv   SYCP1 MUTATED SYCP1 WILD-TYPE
  R0            19             292
  R1             1              13
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SYCP1 MUTATED       3                         1
  SYCP1 WILD-TYPE    84                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SYCP1 MUTATED                                           0    15
  SYCP1 WILD-TYPE                                         1   228
D333V12, multiclass
                                           clus
vv                                          SYCP1 MUTATED SYCP1 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V13, binary
                 cls
clus                0   1
  SYCP1 MUTATED     0  17
  SYCP1 WILD-TYPE   4 293
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP1 MUTATED      0   17
  SYCP1 WILD-TYPE    4  293
                        clus
vv                       SYCP1 MUTATED SYCP1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            17             293
[1] 2 2
[1] FALSE

Clustering(334) Variable = ZNF878 MUTATION ANALYSIS
D334V1, survival
                  sevent
clus2                0   1
  ZNF878 MUTATED    12   1
  ZNF878 WILD-TYPE 218 138
  ZNF878 MUTATED ZNF878 WILD-TYPE 
              13              356 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
               1              138 
$`ZNF878 MUTATED`
TCGA-BR-4257 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 
        9.67        29.59         6.18        31.27         1.12        31.96 
TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-A4YY TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GU 
      105.07        65.10        13.78        30.51        22.68         6.58 
TCGA-VQ-A8P2 
       38.14 

$`ZNF878 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  ZNF878 MUTATED ZNF878 WILD-TYPE 
            1.12             0.00 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
          105.07           122.30 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
           29.59            14.12 
[1] "1.1 - 105.1 (29.6)" "0.0 - 122.3 (14.1)"
[1] "hr=" "7"  
D334V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF878 MUTATED         0        0        1        1         2         3
  ZNF878 WILD-TYPE       2       15       39       29        35        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF878 MUTATED           0          1          1          2        1
  ZNF878 WILD-TYPE         3         69         52         30       37
D334V3, multiclass
            clus
vv           ZNF878 MUTATED ZNF878 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF878 MUTATED     0   2   5   5
  ZNF878 WILD-TYPE  22  90 168  92
D334V4, multiclass
    clus
vv   ZNF878 MUTATED ZNF878 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              5              168
  T4              5               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
  ZNF878 MUTATED     4   4   1   3
  ZNF878 WILD-TYPE 114 100  76  74
D334V5, multiclass
    clus
vv   ZNF878 MUTATED ZNF878 WILD-TYPE
  N0              4              114
  N1              4              100
  N2              1               76
  N3              3               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"
D334V6, binary
                  cls
clus                 0   1
  ZNF878 MUTATED    12   1
  ZNF878 WILD-TYPE 334  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED     12    1
  ZNF878 WILD-TYPE  334   28
   clus
vv  ZNF878 MUTATED ZNF878 WILD-TYPE
  0             12              334
  1              1               28
[1] 2 2
[1] FALSE
D334V7, binary
                  cls
clus                 0   1
  ZNF878 MUTATED     6   7
  ZNF878 WILD-TYPE 139 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED      6    7
  ZNF878 WILD-TYPE  139  241
        clus
vv       ZNF878 MUTATED ZNF878 WILD-TYPE
  FEMALE              6              139
  MALE                7              241
[1] 2 2
[1] FALSE
D334V8, binary
                  cls
clus                 0   1
  ZNF878 MUTATED     9   3
  ZNF878 WILD-TYPE 283  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED      9    3
  ZNF878 WILD-TYPE  283   56
     clus
vv    ZNF878 MUTATED ZNF878 WILD-TYPE
  NO               9              283
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF878 MUTATED                                          0
  ZNF878 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF878 MUTATED                                       2
  ZNF878 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF878 MUTATED                                                        6
  ZNF878 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF878 MUTATED                                                   2
  ZNF878 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF878 MUTATED                                                                   2
  ZNF878 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF878 MUTATED                                                    0
  ZNF878 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF878 MUTATED                                                  1
  ZNF878 WILD-TYPE                                               60
D334V9, multiclass
                                                                   clus
vv                                                                  ZNF878 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ZNF878 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF878 MUTATED    10   1   0   1
  ZNF878 WILD-TYPE 301  13  15  23
D334V10, multiclass
    clus
vv   ZNF878 MUTATED ZNF878 WILD-TYPE
  R0             10              301
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF878 MUTATED       3                         0
  ZNF878 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF878 MUTATED                                           0     7
  ZNF878 WILD-TYPE                                         1   236
D334V12, multiclass
                                           clus
vv                                          ZNF878 MUTATED ZNF878 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V13, binary
                  cls
clus                 0   1
  ZNF878 MUTATED     0   9
  ZNF878 WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED      0    9
  ZNF878 WILD-TYPE    4  301
                        clus
vv                       ZNF878 MUTATED ZNF878 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(335) Variable = KIAA1009 MUTATION ANALYSIS
D335V1, survival
                    sevent
clus2                  0   1
  KIAA1009 MUTATED    11   5
  KIAA1009 WILD-TYPE 219 134
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
                16                353 
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
                 5                134 
$`KIAA1009 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-8078 TCGA-BR-8289 TCGA-BR-8382 
       30.90        34.68         9.17        29.59         2.66        25.05 
TCGA-CD-A4MG TCGA-CG-5723 TCGA-F1-A448 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU 
        6.58       105.07        21.27        29.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       20.25        29.00        19.73        38.14 

$`KIAA1009 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        8.98         0.10         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-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 

  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
              2.66               0.00 
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
            105.07             122.30 
  KIAA1009 MUTATED KIAA1009 WILD-TYPE 
             23.16              14.07 
[1] "2.7 - 105.1 (23.2)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D335V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1009 MUTATED         0        0        0        1         4         3
  KIAA1009 WILD-TYPE       2       15       40       29        33        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1009 MUTATED           0          2          1          3        1
  KIAA1009 WILD-TYPE         3         68         52         29       37
D335V3, multiclass
            clus
vv           KIAA1009 MUTATED KIAA1009 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  1                 29
  STAGE IIA                 4                 33
  STAGE IIB                 3                 49
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                1                 52
  STAGE IIIC                3                 29
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1009 MUTATED     0   3   6   7
  KIAA1009 WILD-TYPE  22  89 167  90
D335V4, multiclass
    clus
vv   KIAA1009 MUTATED KIAA1009 WILD-TYPE
  T1                0                 22
  T2                3                 89
  T3                6                167
  T4                7                 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
  KIAA1009 MUTATED     5   4   2   4
  KIAA1009 WILD-TYPE 113 100  75  73
D335V5, multiclass
    clus
vv   KIAA1009 MUTATED KIAA1009 WILD-TYPE
  N0                5                113
  N1                4                100
  N2                2                 75
  N3                4                 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"
D335V6, binary
                    cls
clus                   0   1
  KIAA1009 MUTATED    15   1
  KIAA1009 WILD-TYPE 331  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1009 MUTATED     15    1
  KIAA1009 WILD-TYPE  331   28
   clus
vv  KIAA1009 MUTATED KIAA1009 WILD-TYPE
  0               15                331
  1                1                 28
[1] 2 2
[1] FALSE
D335V7, binary
                    cls
clus                   0   1
  KIAA1009 MUTATED     8   8
  KIAA1009 WILD-TYPE 137 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1009 MUTATED      8    8
  KIAA1009 WILD-TYPE  137  240
        clus
vv       KIAA1009 MUTATED KIAA1009 WILD-TYPE
  FEMALE                8                137
  MALE                  8                240
[1] 2 2
[1] FALSE
D335V8, binary
                    cls
clus                   0   1
  KIAA1009 MUTATED    13   2
  KIAA1009 WILD-TYPE 279  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1009 MUTATED     13    2
  KIAA1009 WILD-TYPE  279   57
     clus
vv    KIAA1009 MUTATED KIAA1009 WILD-TYPE
  NO                13                279
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA1009 MUTATED                                          0
  KIAA1009 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA1009 MUTATED                                       4
  KIAA1009 WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1009 MUTATED                                                        6
  KIAA1009 WILD-TYPE                                                    152
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA1009 MUTATED                                                   2
  KIAA1009 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1009 MUTATED                                                                   1
  KIAA1009 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA1009 MUTATED                                                    0
  KIAA1009 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA1009 MUTATED                                                  3
  KIAA1009 WILD-TYPE                                               58
D335V9, multiclass
                                                                   clus
vv                                                                  KIAA1009 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 3
                                                                   clus
vv                                                                  KIAA1009 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1009 MUTATED    14   0   0   1
  KIAA1009 WILD-TYPE 297  14  15  23
D335V10, multiclass
    clus
vv   KIAA1009 MUTATED KIAA1009 WILD-TYPE
  R0               14                297
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1009 MUTATED       6                         0
  KIAA1009 WILD-TYPE    81                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1009 MUTATED                                           0     9
  KIAA1009 WILD-TYPE                                         1   234
D335V12, multiclass
                                           clus
vv                                          KIAA1009 MUTATED KIAA1009 WILD-TYPE
  ASIAN                                                    6                 81
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    9                234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V13, binary
                    cls
clus                   0   1
  KIAA1009 MUTATED     1  13
  KIAA1009 WILD-TYPE   3 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1009 MUTATED      1   13
  KIAA1009 WILD-TYPE    3  297
                        clus
vv                       KIAA1009 MUTATED KIAA1009 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               13                297
[1] 2 2
[1] FALSE

Clustering(336) Variable = SENP3 MUTATION ANALYSIS
D336V1, survival
                 sevent
clus2               0   1
  SENP3 MUTATED     7   4
  SENP3 WILD-TYPE 223 135
  SENP3 MUTATED SENP3 WILD-TYPE 
             11             358 
  SENP3 MUTATED SENP3 WILD-TYPE 
              4             135 
$`SENP3 MUTATED`
TCGA-CG-4460 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5733 
       21.99         1.12        28.14         6.58         6.02        21.07 
TCGA-D7-A4YT TCGA-D7-A748 TCGA-HF-A5NB TCGA-HU-A4H8 TCGA-R5-A7ZI 
       14.27         4.34        30.51        14.07        74.53 

$`SENP3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-A4YU 
       17.19        18.21        14.66        21.14        20.91        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-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-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 

  SENP3 MUTATED SENP3 WILD-TYPE 
           1.12            0.00 
  SENP3 MUTATED SENP3 WILD-TYPE 
          74.53          122.30 
  SENP3 MUTATED SENP3 WILD-TYPE 
          14.27           14.30 
[1] "1.1 - 74.5 (14.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D336V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SENP3 MUTATED         0        0        1        0         2         1
  SENP3 WILD-TYPE       2       15       39       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SENP3 MUTATED           0          2          0          2        5
  SENP3 WILD-TYPE         3         68         53         30       33
D336V3, multiclass
            clus
vv           SENP3 MUTATED SENP3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               5              33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SENP3 MUTATED     1   2   2   8
  SENP3 WILD-TYPE  21  90 171  89
D336V4, multiclass
    clus
vv   SENP3 MUTATED SENP3 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             2             171
  T4             8              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
  SENP3 MUTATED     3   4   2   4
  SENP3 WILD-TYPE 115 100  75  73
D336V5, multiclass
    clus
vv   SENP3 MUTATED SENP3 WILD-TYPE
  N0             3             115
  N1             4             100
  N2             2              75
  N3             4              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"
D336V6, binary
                 cls
clus                0   1
  SENP3 MUTATED    10   3
  SENP3 WILD-TYPE 336  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP3 MUTATED     10    3
  SENP3 WILD-TYPE  336   26
   clus
vv  SENP3 MUTATED SENP3 WILD-TYPE
  0            10             336
  1             3              26
[1] 2 2
[1] FALSE
D336V7, binary
                 cls
clus                0   1
  SENP3 MUTATED     7   6
  SENP3 WILD-TYPE 138 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP3 MUTATED      7    6
  SENP3 WILD-TYPE  138  242
        clus
vv       SENP3 MUTATED SENP3 WILD-TYPE
  FEMALE             7             138
  MALE               6             242
[1] 2 2
[1] FALSE
D336V8, binary
                 cls
clus                0   1
  SENP3 MUTATED    10   2
  SENP3 WILD-TYPE 282  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP3 MUTATED     10    2
  SENP3 WILD-TYPE  282   57
     clus
vv    SENP3 MUTATED SENP3 WILD-TYPE
  NO             10             282
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SENP3 MUTATED                                          0
  SENP3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SENP3 MUTATED                                       3
  SENP3 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SENP3 MUTATED                                                        3
  SENP3 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SENP3 MUTATED                                                   1
  SENP3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SENP3 MUTATED                                                                   4
  SENP3 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SENP3 MUTATED                                                    0
  SENP3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SENP3 MUTATED                                                  2
  SENP3 WILD-TYPE                                               59
D336V9, multiclass
                                                                   clus
vv                                                                  SENP3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  SENP3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SENP3 MUTATED     9   1   1   1
  SENP3 WILD-TYPE 302  13  14  23
D336V10, multiclass
    clus
vv   SENP3 MUTATED SENP3 WILD-TYPE
  R0             9             302
  R1             1              13
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SENP3 MUTATED       2                         0
  SENP3 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SENP3 MUTATED                                           0     7
  SENP3 WILD-TYPE                                         1   236
D336V12, multiclass
                                           clus
vv                                          SENP3 MUTATED SENP3 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V13, binary
                 cls
clus                0   1
  SENP3 MUTATED     1   8
  SENP3 WILD-TYPE   3 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP3 MUTATED      1    8
  SENP3 WILD-TYPE    3  302
                        clus
vv                       SENP3 MUTATED SENP3 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(337) Variable = ERBB4 MUTATION ANALYSIS
D337V1, survival
                 sevent
clus2               0   1
  ERBB4 MUTATED    29  18
  ERBB4 WILD-TYPE 201 121
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             47             322 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             18             121 
$`ERBB4 MUTATED`
TCGA-B7-5816 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6705 
       26.70         9.34         9.67         6.61        34.68        25.61 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8295 
        9.21        36.16         3.45        29.56        14.43         2.20 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8485 TCGA-BR-8590 
       31.10         0.26         3.32        31.27         9.21         9.34 
TCGA-BR-8680 TCGA-BR-A4J8 TCGA-CD-5801 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8536 
       31.96        13.51        13.18        12.39        12.76        12.43 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4469 TCGA-CG-5721 
       12.43         6.58         1.02         7.99         7.07         6.02 
TCGA-D7-6820 TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-F1-6874 TCGA-HF-7134 TCGA-HU-A4GT 
       11.31         5.92        14.76        14.47        52.21         6.51 
TCGA-HU-A4H8 TCGA-IN-8462 TCGA-MX-A5UJ TCGA-R5-A805 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       14.07        18.81        19.73         9.24        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8PK TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-AA68 
       37.22        17.85         1.71        42.64        43.66 

$`ERBB4 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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 
          52.21          122.30 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
          12.76           15.12 
[1] "0.3 - 52.2 (12.8)"  "0.0 - 122.3 (15.1)"
[1] "hr=" "1.1"
D337V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERBB4 MUTATED         0        2        5        4         4         7
  ERBB4 WILD-TYPE       2       13       35       26        33        45
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERBB4 MUTATED           2          6          6          5        5
  ERBB4 WILD-TYPE         1         64         47         27       33
D337V3, multiclass
            clus
vv           ERBB4 MUTATED ERBB4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               5              35
  STAGE II               4              26
  STAGE IIA              4              33
  STAGE IIB              7              45
  STAGE III              2               1
  STAGE IIIA             6              64
  STAGE IIIB             6              47
  STAGE IIIC             5              27
  STAGE IV               5              33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERBB4 MUTATED     4   8  22  13
  ERBB4 WILD-TYPE  18  84 151  84
D337V4, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  T1             4              18
  T2             8              84
  T3            22             151
  T4            13              84
[1] 4 2
[1] TRUE
[1] "dimension of 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    17  14   8   8
  ERBB4 WILD-TYPE 101  90  69  69
D337V5, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  N0            17             101
  N1            14              90
  N2             8              69
  N3             8              69
[1] 4 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
  ERBB4 MUTATED    46   3
  ERBB4 WILD-TYPE 300  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     46    3
  ERBB4 WILD-TYPE  300   26
   clus
vv  ERBB4 MUTATED ERBB4 WILD-TYPE
  0            46             300
  1             3              26
[1] 2 2
[1] FALSE
D337V7, binary
                 cls
clus                0   1
  ERBB4 MUTATED    18  31
  ERBB4 WILD-TYPE 127 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     18   31
  ERBB4 WILD-TYPE  127  217
        clus
vv       ERBB4 MUTATED ERBB4 WILD-TYPE
  FEMALE            18             127
  MALE              31             217
[1] 2 2
[1] FALSE
D337V8, binary
                 cls
clus                0   1
  ERBB4 MUTATED    39   6
  ERBB4 WILD-TYPE 253  53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     39    6
  ERBB4 WILD-TYPE  253   53
     clus
vv    ERBB4 MUTATED ERBB4 WILD-TYPE
  NO             39             253
  YES             6              53
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ERBB4 MUTATED                                          0
  ERBB4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ERBB4 MUTATED                                       3
  ERBB4 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ERBB4 MUTATED                                                       22
  ERBB4 WILD-TYPE                                                    136
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ERBB4 MUTATED                                                   3
  ERBB4 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ERBB4 MUTATED                                                                  10
  ERBB4 WILD-TYPE                                                                58
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ERBB4 MUTATED                                                    1
  ERBB4 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ERBB4 MUTATED                                                 10
  ERBB4 WILD-TYPE                                               51
D337V9, multiclass
                                                                   clus
vv                                                                  ERBB4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            10
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             10
                                                                   clus
vv                                                                  ERBB4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        136
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              58
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               51
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ERBB4 MUTATED    39   1   1   4
  ERBB4 WILD-TYPE 272  13  14  20
D337V10, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  R0            39             272
  R1             1              13
  R2             1              14
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ERBB4 MUTATED      10                         0
  ERBB4 WILD-TYPE    77                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ERBB4 MUTATED                                           0    33
  ERBB4 WILD-TYPE                                         1   210
D337V12, multiclass
                                           clus
vv                                          ERBB4 MUTATED ERBB4 WILD-TYPE
  ASIAN                                                10              77
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                33             210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V13, binary
                 cls
clus                0   1
  ERBB4 MUTATED     0  37
  ERBB4 WILD-TYPE   4 273
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED      0   37
  ERBB4 WILD-TYPE    4  273
                        clus
vv                       ERBB4 MUTATED ERBB4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            37             273
[1] 2 2
[1] FALSE

Clustering(338) Variable = COL12A1 MUTATION ANALYSIS
D338V1, survival
                   sevent
clus2                 0   1
  COL12A1 MUTATED    29  19
  COL12A1 WILD-TYPE 201 120
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               48               321 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
               19               120 
$`COL12A1 MUTATED`
TCGA-CG-4444 TCGA-CG-5727 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 
       47.05        79.07        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-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       21.99        22.98        16.24         0.23        20.15         9.86 
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-6453 TCGA-BR-6456 
        9.34         9.67         6.18         9.57        15.95        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-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-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-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-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-8531 
       12.59        12.53         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-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.30        11.31        12.43        12.20        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-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-D7-6528 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-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-F1-6875 
        8.38         4.34        19.96         7.13         0.62        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-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-A4GQ TCGA-HU-A4GU 
       22.75        25.81        11.77        21.37         0.10         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-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-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-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-A8N9 TCGA-SW-A7EA TCGA-SW-A7EB 
      115.69       116.38        71.38        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-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 

  COL12A1 MUTATED COL12A1 WILD-TYPE 
             0.26              0.00 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
           105.07            122.30 
  COL12A1 MUTATED COL12A1 WILD-TYPE 
            13.97             14.43 
[1] "0.3 - 105.1 (14.0)" "0.0 - 122.3 (14.4)"
[1] "hr=" "1"  
D338V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  COL12A1 MUTATED         1        1        7        6         7         4
  COL12A1 WILD-TYPE       1       14       33       24        30        48
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL12A1 MUTATED           1         10          3          6        6
  COL12A1 WILD-TYPE         2         60         50         26       32
D338V3, multiclass
            clus
vv           COL12A1 MUTATED COL12A1 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 1                14
  STAGE IB                 7                33
  STAGE II                 6                24
  STAGE IIA                7                30
  STAGE IIB                4                48
  STAGE III                1                 2
  STAGE IIIA              10                60
  STAGE IIIB               3                50
  STAGE IIIC               6                26
  STAGE IV                 6                32
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  COL12A1 MUTATED     4  15  22  11
  COL12A1 WILD-TYPE  18  77 151  86
D338V4, multiclass
    clus
vv   COL12A1 MUTATED COL12A1 WILD-TYPE
  T1               4                18
  T2              15                77
  T3              22               151
  T4              11                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
  COL12A1 MUTATED    14  20  12   7
  COL12A1 WILD-TYPE 104  84  65  70
D338V5, multiclass
    clus
vv   COL12A1 MUTATED COL12A1 WILD-TYPE
  N0              14               104
  N1              20                84
  N2              12                65
  N3               7                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"
D338V6, binary
                   cls
clus                  0   1
  COL12A1 MUTATED    46   4
  COL12A1 WILD-TYPE 300  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED     46    4
  COL12A1 WILD-TYPE  300   25
   clus
vv  COL12A1 MUTATED COL12A1 WILD-TYPE
  0              46               300
  1               4                25
[1] 2 2
[1] FALSE
D338V7, binary
                   cls
clus                  0   1
  COL12A1 MUTATED    20  33
  COL12A1 WILD-TYPE 125 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED     20   33
  COL12A1 WILD-TYPE  125  215
        clus
vv       COL12A1 MUTATED COL12A1 WILD-TYPE
  FEMALE              20               125
  MALE                33               215
[1] 2 2
[1] FALSE
D338V8, binary
                   cls
clus                  0   1
  COL12A1 MUTATED    35  10
  COL12A1 WILD-TYPE 257  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED     35   10
  COL12A1 WILD-TYPE  257   49
     clus
vv    COL12A1 MUTATED COL12A1 WILD-TYPE
  NO               35               257
  YES              10                49
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  COL12A1 MUTATED                                          0
  COL12A1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  COL12A1 MUTATED                                      10
  COL12A1 WILD-TYPE                                    60
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  COL12A1 MUTATED                                                       19
  COL12A1 WILD-TYPE                                                    139
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  COL12A1 MUTATED                                                   3
  COL12A1 WILD-TYPE                                                18
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  COL12A1 MUTATED                                                                  11
  COL12A1 WILD-TYPE                                                                57
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  COL12A1 MUTATED                                                    1
  COL12A1 WILD-TYPE                                                  4
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  COL12A1 MUTATED                                                  9
  COL12A1 WILD-TYPE                                               52
D338V9, multiclass
                                                                   clus
vv                                                                  COL12A1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          10
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         19
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              11
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                9
                                                                   clus
vv                                                                  COL12A1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          139
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                57
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 52
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  COL12A1 MUTATED    43   0   2   4
  COL12A1 WILD-TYPE 268  14  13  20
D338V10, multiclass
    clus
vv   COL12A1 MUTATED COL12A1 WILD-TYPE
  R0              43               268
  R1               0                14
  R2               2                13
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  COL12A1 MUTATED      11                         2
  COL12A1 WILD-TYPE    76                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  COL12A1 MUTATED                                           0    28
  COL12A1 WILD-TYPE                                         1   215
D338V12, multiclass
                                           clus
vv                                          COL12A1 MUTATED COL12A1 WILD-TYPE
  ASIAN                                                  11                76
  BLACK OR AFRICAN AMERICAN                               2                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  28               215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V13, binary
                   cls
clus                  0   1
  COL12A1 MUTATED     1  38
  COL12A1 WILD-TYPE   3 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL12A1 MUTATED      1   38
  COL12A1 WILD-TYPE    3  272
                        clus
vv                       COL12A1 MUTATED COL12A1 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              38               272
[1] 2 2
[1] FALSE

Clustering(339) Variable = PANK1 MUTATION ANALYSIS
D339V1, survival
                 sevent
clus2               0   1
  PANK1 MUTATED     5   3
  PANK1 WILD-TYPE 225 136
  PANK1 MUTATED PANK1 WILD-TYPE 
              8             361 
  PANK1 MUTATED PANK1 WILD-TYPE 
              3             136 
$`PANK1 MUTATED`
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-8363 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5723 
       21.90        36.16         0.26         6.58         1.02       105.07 
TCGA-D7-A74A TCGA-HU-8238 
       19.96         1.51 

$`PANK1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-7197 TCGA-BR-7704 
       40.21        30.90        31.20        44.94         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-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-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-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-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34         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-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51        26.47         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 

  PANK1 MUTATED PANK1 WILD-TYPE 
           0.26            0.00 
  PANK1 MUTATED PANK1 WILD-TYPE 
         105.07          122.30 
  PANK1 MUTATED PANK1 WILD-TYPE 
          13.27           14.27 
[1] "0.3 - 105.1 (13.3)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D339V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PANK1 MUTATED         0        1        2        1         1         1
  PANK1 WILD-TYPE       2       14       38       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PANK1 MUTATED           0          1          0          0        2
  PANK1 WILD-TYPE         3         69         53         32       36
D339V3, multiclass
            clus
vv           PANK1 MUTATED PANK1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PANK1 MUTATED     1   3   5   1
  PANK1 WILD-TYPE  21  89 168  96
D339V4, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             5             168
  T4             1              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
  PANK1 MUTATED     5   1   3   1
  PANK1 WILD-TYPE 113 103  74  76
D339V5, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  N0             5             113
  N1             1             103
  N2             3              74
  N3             1              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"
D339V6, binary
                 cls
clus                0   1
  PANK1 MUTATED     8   2
  PANK1 WILD-TYPE 338  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      8    2
  PANK1 WILD-TYPE  338   27
   clus
vv  PANK1 MUTATED PANK1 WILD-TYPE
  0             8             338
  1             2              27
[1] 2 2
[1] FALSE
D339V7, binary
                 cls
clus                0   1
  PANK1 MUTATED     2   8
  PANK1 WILD-TYPE 143 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      2    8
  PANK1 WILD-TYPE  143  240
        clus
vv       PANK1 MUTATED PANK1 WILD-TYPE
  FEMALE             2             143
  MALE               8             240
[1] 2 2
[1] FALSE
D339V8, binary
                 cls
clus                0   1
  PANK1 MUTATED     8   0
  PANK1 WILD-TYPE 284  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      8    0
  PANK1 WILD-TYPE  284   59
     clus
vv    PANK1 MUTATED PANK1 WILD-TYPE
  NO              8             284
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PANK1 MUTATED                                          0
  PANK1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PANK1 MUTATED                                       1
  PANK1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PANK1 MUTATED                                                        4
  PANK1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PANK1 MUTATED                                                   0
  PANK1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PANK1 MUTATED                                                                   2
  PANK1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PANK1 MUTATED                                                    1
  PANK1 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PANK1 MUTATED                                                  2
  PANK1 WILD-TYPE                                               59
D339V9, multiclass
                                                                   clus
vv                                                                  PANK1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  PANK1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PANK1 MUTATED     8   0   1   0
  PANK1 WILD-TYPE 303  14  14  24
D339V10, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PANK1 MUTATED       2                         0
  PANK1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PANK1 MUTATED                                           0     5
  PANK1 WILD-TYPE                                         1   238
D339V12, multiclass
                                           clus
vv                                          PANK1 MUTATED PANK1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V13, binary
                 cls
clus                0   1
  PANK1 MUTATED     0   7
  PANK1 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      0    7
  PANK1 WILD-TYPE    4  303
                        clus
vv                       PANK1 MUTATED PANK1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(340) Variable = SNRNP35 MUTATION ANALYSIS
D340V1, survival
                   sevent
clus2                 0   1
  SNRNP35 MUTATED     4   2
  SNRNP35 WILD-TYPE 226 137
  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
                6               363 
  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
                2               137 
$`SNRNP35 MUTATED`
TCGA-CG-4460 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-4305 TCGA-HU-A4G9 TCGA-HU-A4GT 
       21.99         1.12         6.58        15.95        24.20         6.51 

$`SNRNP35 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
             1.12              0.00 
  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
             24.2             122.3 
  SNRNP35 MUTATED SNRNP35 WILD-TYPE 
           11.265            14.270 
[1] "1.1 - 24.2 (11.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D340V2, 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       2       14       40       29        34        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNRNP35 MUTATED           0          0          0          0        1
  SNRNP35 WILD-TYPE         3         70         53         32       37
D340V3, multiclass
            clus
vv           SNRNP35 MUTATED SNRNP35 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 0                40
  STAGE II                 1                29
  STAGE IIA                3                34
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SNRNP35 MUTATED     1   1   3   1
  SNRNP35 WILD-TYPE  21  91 170  96
D340V4, multiclass
    clus
vv   SNRNP35 MUTATED SNRNP35 WILD-TYPE
  T1               1                21
  T2               1                91
  T3               3               170
  T4               1                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
  SNRNP35 MUTATED     4   2   0   0
  SNRNP35 WILD-TYPE 114 102  77  77
D340V5, multiclass
    clus
vv   SNRNP35 MUTATED SNRNP35 WILD-TYPE
  N0               4               114
  N1               2               102
  N2               0                77
  N3               0                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"
D340V6, binary
                   cls
clus                  0   1
  SNRNP35 MUTATED     5   1
  SNRNP35 WILD-TYPE 341  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SNRNP35 MUTATED      5    1
  SNRNP35 WILD-TYPE  341   28
   clus
vv  SNRNP35 MUTATED SNRNP35 WILD-TYPE
  0               5               341
  1               1                28
[1] 2 2
[1] FALSE
D340V7, binary
                   cls
clus                  0   1
  SNRNP35 MUTATED     4   2
  SNRNP35 WILD-TYPE 141 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SNRNP35 MUTATED      4    2
  SNRNP35 WILD-TYPE  141  246
        clus
vv       SNRNP35 MUTATED SNRNP35 WILD-TYPE
  FEMALE               4               141
  MALE                 2               246
[1] 2 2
[1] FALSE
D340V8, binary
                   cls
clus                  0   1
  SNRNP35 MUTATED     6   0
  SNRNP35 WILD-TYPE 286  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SNRNP35 MUTATED      6    0
  SNRNP35 WILD-TYPE  286   59
     clus
vv    SNRNP35 MUTATED SNRNP35 WILD-TYPE
  NO                6               286
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SNRNP35 MUTATED                                          0
  SNRNP35 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SNRNP35 MUTATED                                       1
  SNRNP35 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SNRNP35 MUTATED                                                        2
  SNRNP35 WILD-TYPE                                                    156
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SNRNP35 MUTATED                                                   0
  SNRNP35 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SNRNP35 MUTATED                                                                   1
  SNRNP35 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SNRNP35 MUTATED                                                    0
  SNRNP35 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SNRNP35 MUTATED                                                  2
  SNRNP35 WILD-TYPE                                               59
D340V9, multiclass
                                                                   clus
vv                                                                  SNRNP35 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  SNRNP35 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SNRNP35 MUTATED     4   0   1   0
  SNRNP35 WILD-TYPE 307  14  14  24
D340V10, multiclass
    clus
vv   SNRNP35 MUTATED SNRNP35 WILD-TYPE
  R0               4               307
  R1               0                14
  R2               1                14
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SNRNP35 MUTATED       3                         0
  SNRNP35 WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SNRNP35 MUTATED                                           0     1
  SNRNP35 WILD-TYPE                                         1   242
D340V12, multiclass
                                           clus
vv                                          SNRNP35 MUTATED SNRNP35 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   1               242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V13, binary
                   cls
clus                  0   1
  SNRNP35 MUTATED     0   4
  SNRNP35 WILD-TYPE   4 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SNRNP35 MUTATED      0    4
  SNRNP35 WILD-TYPE    4  306
                        clus
vv                       SNRNP35 MUTATED SNRNP35 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4               306
[1] 2 2
[1] FALSE

Clustering(341) Variable = PTPN4 MUTATION ANALYSIS
D341V1, survival
                 sevent
clus2               0   1
  PTPN4 MUTATED     4   5
  PTPN4 WILD-TYPE 226 134
  PTPN4 MUTATED PTPN4 WILD-TYPE 
              9             360 
  PTPN4 MUTATED PTPN4 WILD-TYPE 
              5             134 
$`PTPN4 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-8078 TCGA-BR-8680 TCGA-BR-A4QL 
       21.99         6.97         9.67        29.59        31.96        16.14 
TCGA-D7-A6EY TCGA-FP-A4BE TCGA-VQ-AA6J 
       11.44        11.08        27.55 

$`PTPN4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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 
          31.96          122.30 
  PTPN4 MUTATED PTPN4 WILD-TYPE 
          16.14           14.22 
[1] "7.0 - 32.0 (16.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D341V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPN4 MUTATED         0        0        0        0         1         2
  PTPN4 WILD-TYPE       2       15       40       30        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN4 MUTATED           0          2          3          0        3
  PTPN4 WILD-TYPE         3         68         50         32       35
D341V3, multiclass
            clus
vv           PTPN4 MUTATED PTPN4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             3              50
  STAGE IIIC             0              32
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPN4 MUTATED     0   0   4   7
  PTPN4 WILD-TYPE  22  92 169  90
D341V4, multiclass
    clus
vv   PTPN4 MUTATED PTPN4 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             4             169
  T4             7              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
  PTPN4 MUTATED     4   2   3   2
  PTPN4 WILD-TYPE 114 102  74  75
D341V5, multiclass
    clus
vv   PTPN4 MUTATED PTPN4 WILD-TYPE
  N0             4             114
  N1             2             102
  N2             3              74
  N3             2              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"
D341V6, binary
                 cls
clus                0   1
  PTPN4 MUTATED     9   2
  PTPN4 WILD-TYPE 337  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN4 MUTATED      9    2
  PTPN4 WILD-TYPE  337   27
   clus
vv  PTPN4 MUTATED PTPN4 WILD-TYPE
  0             9             337
  1             2              27
[1] 2 2
[1] FALSE
D341V7, binary
                 cls
clus                0   1
  PTPN4 MUTATED     7   5
  PTPN4 WILD-TYPE 138 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN4 MUTATED      7    5
  PTPN4 WILD-TYPE  138  243
        clus
vv       PTPN4 MUTATED PTPN4 WILD-TYPE
  FEMALE             7             138
  MALE               5             243
[1] 2 2
[1] FALSE
D341V8, binary
                 cls
clus                0   1
  PTPN4 MUTATED     9   1
  PTPN4 WILD-TYPE 283  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN4 MUTATED      9    1
  PTPN4 WILD-TYPE  283   58
     clus
vv    PTPN4 MUTATED PTPN4 WILD-TYPE
  NO              9             283
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PTPN4 MUTATED                                          0
  PTPN4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PTPN4 MUTATED                                       0
  PTPN4 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTPN4 MUTATED                                                        7
  PTPN4 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PTPN4 MUTATED                                                   0
  PTPN4 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTPN4 MUTATED                                                                   3
  PTPN4 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PTPN4 MUTATED                                                    0
  PTPN4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PTPN4 MUTATED                                                  2
  PTPN4 WILD-TYPE                                               59
D341V9, multiclass
                                                                   clus
vv                                                                  PTPN4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  PTPN4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTPN4 MUTATED     7   0   1   4
  PTPN4 WILD-TYPE 304  14  14  20
D341V10, multiclass
    clus
vv   PTPN4 MUTATED PTPN4 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             1              14
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PTPN4 MUTATED       1                         2
  PTPN4 WILD-TYPE    86                         7
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPN4 MUTATED                                           0     8
  PTPN4 WILD-TYPE                                         1   235
D341V12, multiclass
                                           clus
vv                                          PTPN4 MUTATED PTPN4 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             2               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V13, binary
                 cls
clus                0   1
  PTPN4 MUTATED     0  10
  PTPN4 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN4 MUTATED      0   10
  PTPN4 WILD-TYPE    4  300
                        clus
vv                       PTPN4 MUTATED PTPN4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(342) Variable = TNFRSF9 MUTATION ANALYSIS
D342V1, survival
                   sevent
clus2                 0   1
  TNFRSF9 MUTATED     6   4
  TNFRSF9 WILD-TYPE 224 135
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
               10               359 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                4               135 
$`TNFRSF9 MUTATED`
TCGA-BR-4184 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QI 
        6.97        30.90        35.84        28.14        31.96        21.44 
TCGA-CG-4441 TCGA-CG-5721 TCGA-D7-A6EY TCGA-HU-A4H3 
       14.01         6.02        11.44        29.00 

$`TNFRSF9 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
             6.02              0.00 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
            35.84            122.30 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
            24.79             14.17 
[1] "6.0 - 35.8 (24.8)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D342V2, 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       2       15       39       30        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFRSF9 MUTATED           0          3          1          2        2
  TNFRSF9 WILD-TYPE         3         67         52         30       36
D342V3, multiclass
            clus
vv           TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               3                67
  STAGE IIIB               1                52
  STAGE IIIC               2                30
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TNFRSF9 MUTATED     0   2   4   4
  TNFRSF9 WILD-TYPE  22  90 169  93
D342V4, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  T1               0                22
  T2               2                90
  T3               4               169
  T4               4                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
  TNFRSF9 MUTATED     2   2   3   3
  TNFRSF9 WILD-TYPE 116 102  74  74
D342V5, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  N0               2               116
  N1               2               102
  N2               3                74
  N3               3                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"
D342V6, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     8   1
  TNFRSF9 WILD-TYPE 338  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      8    1
  TNFRSF9 WILD-TYPE  338   28
   clus
vv  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  0               8               338
  1               1                28
[1] 2 2
[1] FALSE
D342V7, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     4   6
  TNFRSF9 WILD-TYPE 141 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      4    6
  TNFRSF9 WILD-TYPE  141  242
        clus
vv       TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  FEMALE               4               141
  MALE                 6               242
[1] 2 2
[1] FALSE
D342V8, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     8   0
  TNFRSF9 WILD-TYPE 284  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      8    0
  TNFRSF9 WILD-TYPE  284   59
     clus
vv    TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  NO                8               284
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TNFRSF9 MUTATED                                          0
  TNFRSF9 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TNFRSF9 MUTATED                                       1
  TNFRSF9 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNFRSF9 MUTATED                                                        5
  TNFRSF9 WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TNFRSF9 MUTATED                                                   0
  TNFRSF9 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNFRSF9 MUTATED                                                                   2
  TNFRSF9 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TNFRSF9 MUTATED                                                    0
  TNFRSF9 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TNFRSF9 MUTATED                                                  2
  TNFRSF9 WILD-TYPE                                               59
D342V9, multiclass
                                                                   clus
vv                                                                  TNFRSF9 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  TNFRSF9 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TNFRSF9 MUTATED     9   0   0   1
  TNFRSF9 WILD-TYPE 302  14  15  23
D342V10, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  R0               9               302
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TNFRSF9 MUTATED       2                         0
  TNFRSF9 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNFRSF9 MUTATED                                           0     6
  TNFRSF9 WILD-TYPE                                         1   237
D342V12, multiclass
                                           clus
vv                                          TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V13, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     0   8
  TNFRSF9 WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      0    8
  TNFRSF9 WILD-TYPE    4  302
                        clus
vv                       TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(343) Variable = SIGLEC10 MUTATION ANALYSIS
D343V1, survival
                    sevent
clus2                  0   1
  SIGLEC10 MUTATED    10   3
  SIGLEC10 WILD-TYPE 220 136
  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
                13                356 
  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
                 3                136 
$`SIGLEC10 MUTATED`
TCGA-B7-A5TI TCGA-BR-4256 TCGA-BR-7197 TCGA-BR-8078 TCGA-BR-8680 TCGA-CD-A48A 
       19.56         9.34         9.21        29.59        31.96        12.43 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-HU-8610 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GQ 
        6.58         6.02         0.76        22.68        29.98         0.10 
TCGA-IN-8462 
       18.81 

$`SIGLEC10 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        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-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 
       22.82        21.07        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-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-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 

  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
               0.1                0.0 
  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
             31.96             122.30 
  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE 
             12.43              14.35 
[1] "0.1 - 32.0 (12.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D343V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SIGLEC10 MUTATED         0        1        0        1         3         3
  SIGLEC10 WILD-TYPE       2       14       40       29        34        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SIGLEC10 MUTATED           0          0          0          2        2
  SIGLEC10 WILD-TYPE         3         70         53         30       36
D343V3, multiclass
            clus
vv           SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  0                 40
  STAGE II                  1                 29
  STAGE IIA                 3                 34
  STAGE IIB                 3                 49
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                0                 53
  STAGE IIIC                2                 30
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SIGLEC10 MUTATED     1   2   4   5
  SIGLEC10 WILD-TYPE  21  90 169  92
D343V4, multiclass
    clus
vv   SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  T1                1                 21
  T2                2                 90
  T3                4                169
  T4                5                 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
  SIGLEC10 MUTATED     5   5   2   1
  SIGLEC10 WILD-TYPE 113  99  75  76
D343V5, multiclass
    clus
vv   SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  N0                5                113
  N1                5                 99
  N2                2                 75
  N3                1                 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"
D343V6, binary
                    cls
clus                   0   1
  SIGLEC10 MUTATED    12   1
  SIGLEC10 WILD-TYPE 334  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC10 MUTATED     12    1
  SIGLEC10 WILD-TYPE  334   28
   clus
vv  SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  0               12                334
  1                1                 28
[1] 2 2
[1] FALSE
D343V7, binary
                    cls
clus                   0   1
  SIGLEC10 MUTATED     2  11
  SIGLEC10 WILD-TYPE 143 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC10 MUTATED      2   11
  SIGLEC10 WILD-TYPE  143  237
        clus
vv       SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  FEMALE                2                143
  MALE                 11                237
[1] 2 2
[1] FALSE
D343V8, binary
                    cls
clus                   0   1
  SIGLEC10 MUTATED    12   1
  SIGLEC10 WILD-TYPE 280  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC10 MUTATED     12    1
  SIGLEC10 WILD-TYPE  280   58
     clus
vv    SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  NO                12                280
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SIGLEC10 MUTATED                                          0
  SIGLEC10 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SIGLEC10 MUTATED                                       3
  SIGLEC10 WILD-TYPE                                    67
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SIGLEC10 MUTATED                                                        5
  SIGLEC10 WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SIGLEC10 MUTATED                                                   0
  SIGLEC10 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SIGLEC10 MUTATED                                                                   1
  SIGLEC10 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SIGLEC10 MUTATED                                                    0
  SIGLEC10 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SIGLEC10 MUTATED                                                  4
  SIGLEC10 WILD-TYPE                                               57
D343V9, multiclass
                                                                   clus
vv                                                                  SIGLEC10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 4
                                                                   clus
vv                                                                  SIGLEC10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SIGLEC10 MUTATED     8   0   0   1
  SIGLEC10 WILD-TYPE 303  14  15  23
D343V10, multiclass
    clus
vv   SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  R0                8                303
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SIGLEC10 MUTATED       7                         0
  SIGLEC10 WILD-TYPE    80                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SIGLEC10 MUTATED                                           0     5
  SIGLEC10 WILD-TYPE                                         1   238
D343V12, multiclass
                                           clus
vv                                          SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  ASIAN                                                    7                 80
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V13, binary
                    cls
clus                   0   1
  SIGLEC10 MUTATED     0  12
  SIGLEC10 WILD-TYPE   4 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC10 MUTATED      0   12
  SIGLEC10 WILD-TYPE    4  298
                        clus
vv                       SIGLEC10 MUTATED SIGLEC10 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               12                298
[1] 2 2
[1] FALSE

Clustering(344) Variable = HTR7 MUTATION ANALYSIS
D344V1, survival
                sevent
clus2              0   1
  HTR7 MUTATED     7   5
  HTR7 WILD-TYPE 223 134
  HTR7 MUTATED HTR7 WILD-TYPE 
            12            357 
  HTR7 MUTATED HTR7 WILD-TYPE 
             5            134 
$`HTR7 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8360 TCGA-BR-8589 TCGA-CD-A4MI 
        6.61        34.68        35.84         6.18        27.12        11.77 
TCGA-CG-4465 TCGA-D7-6527 TCGA-FP-A9TM TCGA-HU-8602 TCGA-HU-A4H3 TCGA-R5-A7ZE 
        9.01        10.26         6.21        22.32        29.00        18.21 

$`HTR7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-D7-6528 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-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-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-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 

  HTR7 MUTATED HTR7 WILD-TYPE 
          6.18           0.00 
  HTR7 MUTATED HTR7 WILD-TYPE 
         35.84         122.30 
  HTR7 MUTATED HTR7 WILD-TYPE 
         14.99          14.27 
[1] "6.2 - 35.8 (15.0)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D344V2, 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       2       15       39       29        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HTR7 MUTATED           1          2          1          1        1
  HTR7 WILD-TYPE         2         68         52         31       37
D344V3, multiclass
            clus
vv           HTR7 MUTATED HTR7 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             1              2
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HTR7 MUTATED     1   3   4   5
  HTR7 WILD-TYPE  21  89 169  92
D344V4, multiclass
    clus
vv   HTR7 MUTATED HTR7 WILD-TYPE
  T1            1             21
  T2            3             89
  T3            4            169
  T4            5             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
  HTR7 MUTATED     5   6   1   2
  HTR7 WILD-TYPE 113  98  76  75
D344V5, multiclass
    clus
vv   HTR7 MUTATED HTR7 WILD-TYPE
  N0            5            113
  N1            6             98
  N2            1             76
  N3            2             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"
D344V6, binary
                cls
clus               0   1
  HTR7 MUTATED    13   1
  HTR7 WILD-TYPE 333  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED     13    1
  HTR7 WILD-TYPE  333   28
   clus
vv  HTR7 MUTATED HTR7 WILD-TYPE
  0           13            333
  1            1             28
[1] 2 2
[1] FALSE
D344V7, binary
                cls
clus               0   1
  HTR7 MUTATED     8   6
  HTR7 WILD-TYPE 137 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED      8    6
  HTR7 WILD-TYPE  137  242
        clus
vv       HTR7 MUTATED HTR7 WILD-TYPE
  FEMALE            8            137
  MALE              6            242
[1] 2 2
[1] FALSE
D344V8, binary
                cls
clus               0   1
  HTR7 MUTATED     9   2
  HTR7 WILD-TYPE 283  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED      9    2
  HTR7 WILD-TYPE  283   57
     clus
vv    HTR7 MUTATED HTR7 WILD-TYPE
  NO             9            283
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HTR7 MUTATED                                          0
  HTR7 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HTR7 MUTATED                                       3
  HTR7 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HTR7 MUTATED                                                        7
  HTR7 WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HTR7 MUTATED                                                   0
  HTR7 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HTR7 MUTATED                                                                   2
  HTR7 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HTR7 MUTATED                                                    1
  HTR7 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HTR7 MUTATED                                                  1
  HTR7 WILD-TYPE                                               60
D344V9, multiclass
                                                                   clus
vv                                                                  HTR7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  HTR7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HTR7 MUTATED     9   0   1   2
  HTR7 WILD-TYPE 302  14  14  22
D344V10, multiclass
    clus
vv   HTR7 MUTATED HTR7 WILD-TYPE
  R0            9            302
  R1            0             14
  R2            1             14
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  HTR7 MUTATED       3                         0
  HTR7 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HTR7 MUTATED                                           0    10
  HTR7 WILD-TYPE                                         1   233
D344V12, multiclass
                                           clus
vv                                          HTR7 MUTATED HTR7 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V13, binary
                cls
clus               0   1
  HTR7 MUTATED     0  13
  HTR7 WILD-TYPE   4 297
[1] "tbl2"
                cls
clus             [,1] [,2]
  HTR7 MUTATED      0   13
  HTR7 WILD-TYPE    4  297
                        clus
vv                       HTR7 MUTATED HTR7 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           13            297
[1] 2 2
[1] FALSE

Clustering(345) Variable = OBSCN MUTATION ANALYSIS
D345V1, survival
                 sevent
clus2               0   1
  OBSCN MUTATED    55  29
  OBSCN WILD-TYPE 175 110
  OBSCN MUTATED OBSCN WILD-TYPE 
             84             285 
  OBSCN MUTATED OBSCN WILD-TYPE 
             29             110 
$`OBSCN MUTATED`
TCGA-CG-4460 TCGA-MX-A663 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6563 
       21.99         9.86         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-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-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-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
       15.95        17.29        13.68        19.33        26.10         9.17 
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-7703 TCGA-BR-7715 TCGA-BR-7716 
       31.20        44.94        21.90        36.16        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-8080 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
       33.21        37.25         9.60         0.56         2.66        19.96 
TCGA-BR-8295 TCGA-BR-8364 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 
        2.20        22.19        26.33        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-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-A453 TCGA-BR-A4CQ 
       20.88         8.22        10.68        34.13         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-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-8527 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
        7.17        12.39        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-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       12.62         3.02        27.02        15.95         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-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-D7-8574 TCGA-D7-8575 
       12.36        11.31        12.33        24.72        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-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-8210 TCGA-FP-8631 
       19.53        14.07        22.29        17.06         5.03         0.56 
TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7133 TCGA-HF-7134 TCGA-HU-8244 TCGA-HU-8604 
        5.52         6.21        63.06        52.21        24.39        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
       21.07        24.30         5.59        24.26        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GT TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
       22.75        21.37         6.51         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-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-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 
        9.24         8.61         5.13        16.67       122.30        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-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-AA6K TCGA-ZA-A8F6 
       16.14        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 
          14.30           14.27 
[1] "0.1 - 105.1 (14.3)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D345V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OBSCN MUTATED         1        3        9        7        14        12
  OBSCN WILD-TYPE       1       12       31       23        23        40
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OBSCN MUTATED           1         16          9          9        7
  OBSCN WILD-TYPE         2         54         44         23       31
D345V3, multiclass
            clus
vv           OBSCN MUTATED OBSCN WILD-TYPE
  STAGE I                1               1
  STAGE IA               3              12
  STAGE IB               9              31
  STAGE II               7              23
  STAGE IIA             14              23
  STAGE IIB             12              40
  STAGE III              1               2
  STAGE IIIA            16              54
  STAGE IIIB             9              44
  STAGE IIIC             9              23
  STAGE IV               7              31
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OBSCN MUTATED     5  16  40  28
  OBSCN WILD-TYPE  17  76 133  69
D345V4, multiclass
    clus
vv   OBSCN MUTATED OBSCN WILD-TYPE
  T1             5              17
  T2            16              76
  T3            40             133
  T4            28              69
[1] 4 2
[1] TRUE
[1] "dimension of 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   36 26 16 11
  OBSCN WILD-TYPE 82 78 61 66
D345V5, multiclass
    clus
vv   OBSCN MUTATED OBSCN WILD-TYPE
  N0            36              82
  N1            26              78
  N2            16              61
  N3            11              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"
D345V6, binary
                 cls
clus                0   1
  OBSCN MUTATED    81   5
  OBSCN WILD-TYPE 265  24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED     81    5
  OBSCN WILD-TYPE  265   24
   clus
vv  OBSCN MUTATED OBSCN WILD-TYPE
  0            81             265
  1             5              24
[1] 2 2
[1] FALSE
D345V7, binary
                 cls
clus                0   1
  OBSCN MUTATED    41  49
  OBSCN WILD-TYPE 104 199
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED     41   49
  OBSCN WILD-TYPE  104  199
        clus
vv       OBSCN MUTATED OBSCN WILD-TYPE
  FEMALE            41             104
  MALE              49             199
[1] 2 2
[1] FALSE
D345V8, binary
                 cls
clus                0   1
  OBSCN MUTATED    67  13
  OBSCN WILD-TYPE 225  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED     67   13
  OBSCN WILD-TYPE  225   46
     clus
vv    OBSCN MUTATED OBSCN WILD-TYPE
  NO             67             225
  YES            13              46
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OBSCN MUTATED                                          1
  OBSCN WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OBSCN MUTATED                                      16
  OBSCN WILD-TYPE                                    54
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OBSCN MUTATED                                                       35
  OBSCN WILD-TYPE                                                    123
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OBSCN MUTATED                                                   5
  OBSCN WILD-TYPE                                                16
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OBSCN MUTATED                                                                  17
  OBSCN WILD-TYPE                                                                51
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OBSCN MUTATED                                                    0
  OBSCN WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OBSCN MUTATED                                                 16
  OBSCN WILD-TYPE                                               45
D345V9, multiclass
                                                                   clus
vv                                                                  OBSCN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        16
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       35
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            17
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             16
                                                                   clus
vv                                                                  OBSCN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          54
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        123
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              51
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               45
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OBSCN MUTATED    79   2   2   4
  OBSCN WILD-TYPE 232  12  13  20
D345V10, multiclass
    clus
vv   OBSCN MUTATED OBSCN WILD-TYPE
  R0            79             232
  R1             2              12
  R2             2              13
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OBSCN MUTATED      28                         3
  OBSCN WILD-TYPE    59                         6
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OBSCN MUTATED                                           0    48
  OBSCN WILD-TYPE                                         1   195
D345V12, multiclass
                                           clus
vv                                          OBSCN MUTATED OBSCN WILD-TYPE
  ASIAN                                                28              59
  BLACK OR AFRICAN AMERICAN                             3               6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                48             195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V13, binary
                 cls
clus                0   1
  OBSCN MUTATED     1  75
  OBSCN WILD-TYPE   3 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OBSCN MUTATED      1   75
  OBSCN WILD-TYPE    3  235
                        clus
vv                       OBSCN MUTATED OBSCN WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            75             235
[1] 2 2
[1] FALSE

Clustering(346) Variable = GAB2 MUTATION ANALYSIS
D346V1, survival
                sevent
clus2              0   1
  GAB2 MUTATED     6   3
  GAB2 WILD-TYPE 224 136
  GAB2 MUTATED GAB2 WILD-TYPE 
             9            360 
  GAB2 MUTATED GAB2 WILD-TYPE 
             3            136 
$`GAB2 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-A4CS TCGA-CD-A487 
       21.99        26.70         5.39         1.12         1.48        12.30 
TCGA-FP-A4BF TCGA-HU-A4GT TCGA-HU-A4H8 
        5.52         6.51        14.07 

$`GAB2 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-8484 TCGA-BR-8485 
       14.79         7.36        25.05         3.72        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-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-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-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-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 

  GAB2 MUTATED GAB2 WILD-TYPE 
          1.12           0.00 
  GAB2 MUTATED GAB2 WILD-TYPE 
          26.7          122.3 
  GAB2 MUTATED GAB2 WILD-TYPE 
         6.510         14.565 
[1] "1.1 - 26.7 (6.5)"   "0.0 - 122.3 (14.6)"
[1] "hr=" "1.5"
D346V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GAB2 MUTATED         0        0        1        0         2         3
  GAB2 WILD-TYPE       2       15       39       30        35        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GAB2 MUTATED           0          2          0          2        1
  GAB2 WILD-TYPE         3         68         53         30       37
D346V3, multiclass
            clus
vv           GAB2 MUTATED GAB2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GAB2 MUTATED     1   0   5   5
  GAB2 WILD-TYPE  21  92 168  92
D346V4, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  T1            1             21
  T2            0             92
  T3            5            168
  T4            5             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
  GAB2 MUTATED     4   3   2   2
  GAB2 WILD-TYPE 114 101  75  75
D346V5, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  N0            4            114
  N1            3            101
  N2            2             75
  N3            2             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"
D346V6, binary
                cls
clus               0   1
  GAB2 MUTATED    10   1
  GAB2 WILD-TYPE 336  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED     10    1
  GAB2 WILD-TYPE  336   28
   clus
vv  GAB2 MUTATED GAB2 WILD-TYPE
  0           10            336
  1            1             28
[1] 2 2
[1] FALSE
D346V7, binary
                cls
clus               0   1
  GAB2 MUTATED     5   6
  GAB2 WILD-TYPE 140 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      5    6
  GAB2 WILD-TYPE  140  242
        clus
vv       GAB2 MUTATED GAB2 WILD-TYPE
  FEMALE            5            140
  MALE              6            242
[1] 2 2
[1] FALSE
D346V8, binary
                cls
clus               0   1
  GAB2 MUTATED    11   0
  GAB2 WILD-TYPE 281  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED     11    0
  GAB2 WILD-TYPE  281   59
     clus
vv    GAB2 MUTATED GAB2 WILD-TYPE
  NO            11            281
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GAB2 MUTATED                                          1
  GAB2 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GAB2 MUTATED                                       2
  GAB2 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GAB2 MUTATED                                                        3
  GAB2 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GAB2 MUTATED                                                   0
  GAB2 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GAB2 MUTATED                                                                   3
  GAB2 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GAB2 MUTATED                                                    0
  GAB2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GAB2 MUTATED                                                  2
  GAB2 WILD-TYPE                                               59
D346V9, multiclass
                                                                   clus
vv                                                                  GAB2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  GAB2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GAB2 MUTATED     9   1   1   0
  GAB2 WILD-TYPE 302  13  14  24
D346V10, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  R0            9            302
  R1            1             13
  R2            1             14
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GAB2 MUTATED       3                         0
  GAB2 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GAB2 MUTATED                                           0     7
  GAB2 WILD-TYPE                                         1   236
D346V12, multiclass
                                           clus
vv                                          GAB2 MUTATED GAB2 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V13, binary
                cls
clus               0   1
  GAB2 MUTATED     0  10
  GAB2 WILD-TYPE   4 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      0   10
  GAB2 WILD-TYPE    4  300
                        clus
vv                       GAB2 MUTATED GAB2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           10            300
[1] 2 2
[1] FALSE

Clustering(347) Variable = SLC12A7 MUTATION ANALYSIS
D347V1, survival
                   sevent
clus2                 0   1
  SLC12A7 MUTATED    18   4
  SLC12A7 WILD-TYPE 212 135
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
               22               347 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
                4               135 
$`SLC12A7 MUTATED`
TCGA-CG-4460 TCGA-FP-A8CX TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8360 
       21.99         0.23        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-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 
       47.05        22.98        79.07        16.24        20.15         9.86 
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-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-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-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-A486 TCGA-CD-A487 
       11.64        15.39        12.07        12.82         6.31        12.30 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        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-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-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-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-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-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 

  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
             0.23              0.00 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
            38.14            122.30 
  SLC12A7 MUTATED SLC12A7 WILD-TYPE 
            13.25             14.43 
[1] "0.2 - 38.1 (13.2)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "2.1"
D347V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC12A7 MUTATED         0        0        5        1         7         2
  SLC12A7 WILD-TYPE       2       15       35       29        30        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC12A7 MUTATED           0          2          0          3        3
  SLC12A7 WILD-TYPE         3         68         53         29       35
D347V3, multiclass
            clus
vv           SLC12A7 MUTATED SLC12A7 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 5                35
  STAGE II                 1                29
  STAGE IIA                7                30
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               3                29
  STAGE IV                 3                35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC12A7 MUTATED     1   4  11   7
  SLC12A7 WILD-TYPE  21  88 162  90
D347V4, multiclass
    clus
vv   SLC12A7 MUTATED SLC12A7 WILD-TYPE
  T1               1                21
  T2               4                88
  T3              11               162
  T4               7                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
  SLC12A7 MUTATED    13   6   1   3
  SLC12A7 WILD-TYPE 105  98  76  74
D347V5, multiclass
    clus
vv   SLC12A7 MUTATED SLC12A7 WILD-TYPE
  N0              13               105
  N1               6                98
  N2               1                76
  N3               3                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"
D347V6, binary
                   cls
clus                  0   1
  SLC12A7 MUTATED    21   2
  SLC12A7 WILD-TYPE 325  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A7 MUTATED     21    2
  SLC12A7 WILD-TYPE  325   27
   clus
vv  SLC12A7 MUTATED SLC12A7 WILD-TYPE
  0              21               325
  1               2                27
[1] 2 2
[1] FALSE
D347V7, binary
                   cls
clus                  0   1
  SLC12A7 MUTATED    10  14
  SLC12A7 WILD-TYPE 135 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A7 MUTATED     10   14
  SLC12A7 WILD-TYPE  135  234
        clus
vv       SLC12A7 MUTATED SLC12A7 WILD-TYPE
  FEMALE              10               135
  MALE                14               234
[1] 2 2
[1] FALSE
D347V8, binary
                   cls
clus                  0   1
  SLC12A7 MUTATED    16   5
  SLC12A7 WILD-TYPE 276  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A7 MUTATED     16    5
  SLC12A7 WILD-TYPE  276   54
     clus
vv    SLC12A7 MUTATED SLC12A7 WILD-TYPE
  NO               16               276
  YES               5                54
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC12A7 MUTATED                                          1
  SLC12A7 WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC12A7 MUTATED                                       3
  SLC12A7 WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC12A7 MUTATED                                                       10
  SLC12A7 WILD-TYPE                                                    148
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC12A7 MUTATED                                                   3
  SLC12A7 WILD-TYPE                                                18
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC12A7 MUTATED                                                                   4
  SLC12A7 WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC12A7 MUTATED                                                    1
  SLC12A7 WILD-TYPE                                                  4
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC12A7 MUTATED                                                  2
  SLC12A7 WILD-TYPE                                               59
D347V9, multiclass
                                                                   clus
vv                                                                  SLC12A7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  SLC12A7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC12A7 MUTATED    18   1   1   1
  SLC12A7 WILD-TYPE 293  13  14  23
D347V10, multiclass
    clus
vv   SLC12A7 MUTATED SLC12A7 WILD-TYPE
  R0              18               293
  R1               1                13
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC12A7 MUTATED       7                         1
  SLC12A7 WILD-TYPE    80                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC12A7 MUTATED                                           0    12
  SLC12A7 WILD-TYPE                                         1   231
D347V12, multiclass
                                           clus
vv                                          SLC12A7 MUTATED SLC12A7 WILD-TYPE
  ASIAN                                                   7                80
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V13, binary
                   cls
clus                  0   1
  SLC12A7 MUTATED     0  19
  SLC12A7 WILD-TYPE   4 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A7 MUTATED      0   19
  SLC12A7 WILD-TYPE    4  291
                        clus
vv                       SLC12A7 MUTATED SLC12A7 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              19               291
[1] 2 2
[1] FALSE

Clustering(348) Variable = KIAA1522 MUTATION ANALYSIS
D348V1, survival
                    sevent
clus2                  0   1
  KIAA1522 MUTATED     7   4
  KIAA1522 WILD-TYPE 223 135
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
                11                358 
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
                 4                135 
$`KIAA1522 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-6566 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5721 
       21.99        26.70        32.78        16.14         6.58         6.02 
TCGA-CG-5728 TCGA-HU-8602 TCGA-HU-A4GN TCGA-MX-A5UJ TCGA-VQ-A94T 
       65.10        22.32        29.98        19.73        11.24 

$`KIAA1522 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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-AA64 
       15.65        20.81         1.71        42.64        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 

  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
              6.02               0.00 
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
              65.1              122.3 
  KIAA1522 MUTATED KIAA1522 WILD-TYPE 
             21.99              14.07 
[1] "6.0 - 65.1 (22.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D348V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1522 MUTATED         0        0        1        0         3         3
  KIAA1522 WILD-TYPE       2       15       39       30        34        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1522 MUTATED           0          1          2          0        2
  KIAA1522 WILD-TYPE         3         69         51         32       36
D348V3, multiclass
            clus
vv           KIAA1522 MUTATED KIAA1522 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 3                 34
  STAGE IIB                 3                 49
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                2                 51
  STAGE IIIC                0                 32
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1522 MUTATED     0   2   5   5
  KIAA1522 WILD-TYPE  22  90 168  92
D348V4, multiclass
    clus
vv   KIAA1522 MUTATED KIAA1522 WILD-TYPE
  T1                0                 22
  T2                2                 90
  T3                5                168
  T4                5                 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
  KIAA1522 MUTATED     6   3   2   1
  KIAA1522 WILD-TYPE 112 101  75  76
D348V5, multiclass
    clus
vv   KIAA1522 MUTATED KIAA1522 WILD-TYPE
  N0                6                112
  N1                3                101
  N2                2                 75
  N3                1                 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"
D348V6, binary
                    cls
clus                   0   1
  KIAA1522 MUTATED    11   1
  KIAA1522 WILD-TYPE 335  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1522 MUTATED     11    1
  KIAA1522 WILD-TYPE  335   28
   clus
vv  KIAA1522 MUTATED KIAA1522 WILD-TYPE
  0               11                335
  1                1                 28
[1] 2 2
[1] FALSE
D348V7, binary
                    cls
clus                   0   1
  KIAA1522 MUTATED     7   5
  KIAA1522 WILD-TYPE 138 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1522 MUTATED      7    5
  KIAA1522 WILD-TYPE  138  243
        clus
vv       KIAA1522 MUTATED KIAA1522 WILD-TYPE
  FEMALE                7                138
  MALE                  5                243
[1] 2 2
[1] FALSE
D348V8, binary
                    cls
clus                   0   1
  KIAA1522 MUTATED    11   0
  KIAA1522 WILD-TYPE 281  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1522 MUTATED     11    0
  KIAA1522 WILD-TYPE  281   59
     clus
vv    KIAA1522 MUTATED KIAA1522 WILD-TYPE
  NO                11                281
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA1522 MUTATED                                          0
  KIAA1522 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA1522 MUTATED                                       4
  KIAA1522 WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1522 MUTATED                                                        2
  KIAA1522 WILD-TYPE                                                    156
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA1522 MUTATED                                                   0
  KIAA1522 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1522 MUTATED                                                                   4
  KIAA1522 WILD-TYPE                                                                64
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA1522 MUTATED                                                    0
  KIAA1522 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA1522 MUTATED                                                  2
  KIAA1522 WILD-TYPE                                               59
D348V9, multiclass
                                                                   clus
vv                                                                  KIAA1522 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  KIAA1522 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1522 MUTATED    10   0   1   0
  KIAA1522 WILD-TYPE 301  14  14  24
D348V10, multiclass
    clus
vv   KIAA1522 MUTATED KIAA1522 WILD-TYPE
  R0               10                301
  R1                0                 14
  R2                1                 14
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1522 MUTATED       3                         0
  KIAA1522 WILD-TYPE    84                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1522 MUTATED                                           0     5
  KIAA1522 WILD-TYPE                                         1   238
D348V12, multiclass
                                           clus
vv                                          KIAA1522 MUTATED KIAA1522 WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V13, binary
                    cls
clus                   0   1
  KIAA1522 MUTATED     0   8
  KIAA1522 WILD-TYPE   4 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1522 MUTATED      0    8
  KIAA1522 WILD-TYPE    4  302
                        clus
vv                       KIAA1522 MUTATED KIAA1522 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                8                302
[1] 2 2
[1] FALSE

Clustering(349) Variable = FERMT2 MUTATION ANALYSIS
D349V1, survival
                  sevent
clus2                0   1
  FERMT2 MUTATED     8   2
  FERMT2 WILD-TYPE 222 137
  FERMT2 MUTATED FERMT2 WILD-TYPE 
              10              359 
  FERMT2 MUTATED FERMT2 WILD-TYPE 
               2              137 
$`FERMT2 MUTATED`
TCGA-BR-6452 TCGA-BR-7704 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4QL 
       34.68        35.24        31.10         1.12        28.14        16.14 
TCGA-HU-8238 TCGA-HU-8602 TCGA-VQ-A8P2 TCGA-VQ-A91Q 
        1.51        22.32        38.14        20.81 

$`FERMT2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  FERMT2 MUTATED FERMT2 WILD-TYPE 
            1.12             0.00 
  FERMT2 MUTATED FERMT2 WILD-TYPE 
           38.14           122.30 
  FERMT2 MUTATED FERMT2 WILD-TYPE 
           25.23            14.07 
[1] "1.1 - 38.1 (25.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.5"
D349V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FERMT2 MUTATED         0        0        0        1         2         1
  FERMT2 WILD-TYPE       2       15       40       29        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FERMT2 MUTATED           0          2          1          2        1
  FERMT2 WILD-TYPE         3         68         52         30       37
D349V3, multiclass
            clus
vv           FERMT2 MUTATED FERMT2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FERMT2 MUTATED     0   0   7   5
  FERMT2 WILD-TYPE  22  92 166  92
D349V4, multiclass
    clus
vv   FERMT2 MUTATED FERMT2 WILD-TYPE
  T1              0               22
  T2              0               92
  T3              7              166
  T4              5               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
  FERMT2 MUTATED     5   1   2   3
  FERMT2 WILD-TYPE 113 103  75  74
D349V5, multiclass
    clus
vv   FERMT2 MUTATED FERMT2 WILD-TYPE
  N0              5              113
  N1              1              103
  N2              2               75
  N3              3               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"
D349V6, binary
                  cls
clus                 0   1
  FERMT2 MUTATED    11   0
  FERMT2 WILD-TYPE 335  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FERMT2 MUTATED     11    0
  FERMT2 WILD-TYPE  335   29
   clus
vv  FERMT2 MUTATED FERMT2 WILD-TYPE
  0             11              335
  1              0               29
[1] 2 2
[1] FALSE
D349V7, binary
                  cls
clus                 0   1
  FERMT2 MUTATED     8   4
  FERMT2 WILD-TYPE 137 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FERMT2 MUTATED      8    4
  FERMT2 WILD-TYPE  137  244
        clus
vv       FERMT2 MUTATED FERMT2 WILD-TYPE
  FEMALE              8              137
  MALE                4              244
[1] 2 2
[1] FALSE
D349V8, binary
                  cls
clus                 0   1
  FERMT2 MUTATED     8   2
  FERMT2 WILD-TYPE 284  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FERMT2 MUTATED      8    2
  FERMT2 WILD-TYPE  284   57
     clus
vv    FERMT2 MUTATED FERMT2 WILD-TYPE
  NO               8              284
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FERMT2 MUTATED                                          0
  FERMT2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FERMT2 MUTATED                                       1
  FERMT2 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FERMT2 MUTATED                                                        7
  FERMT2 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FERMT2 MUTATED                                                   1
  FERMT2 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FERMT2 MUTATED                                                                   1
  FERMT2 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FERMT2 MUTATED                                                    0
  FERMT2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FERMT2 MUTATED                                                  2
  FERMT2 WILD-TYPE                                               59
D349V9, multiclass
                                                                   clus
vv                                                                  FERMT2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  FERMT2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FERMT2 MUTATED    10   0   0   2
  FERMT2 WILD-TYPE 301  14  15  22
D349V10, multiclass
    clus
vv   FERMT2 MUTATED FERMT2 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FERMT2 MUTATED       2                         0
  FERMT2 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FERMT2 MUTATED                                           0     9
  FERMT2 WILD-TYPE                                         1   234
D349V12, multiclass
                                           clus
vv                                          FERMT2 MUTATED FERMT2 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V13, binary
                  cls
clus                 0   1
  FERMT2 MUTATED     0  10
  FERMT2 WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FERMT2 MUTATED      0   10
  FERMT2 WILD-TYPE    4  300
                        clus
vv                       FERMT2 MUTATED FERMT2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(350) Variable = PPP1R13B MUTATION ANALYSIS
D350V1, survival
                    sevent
clus2                  0   1
  PPP1R13B MUTATED    10   3
  PPP1R13B WILD-TYPE 220 136
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
                13                356 
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
                 3                136 
$`PPP1R13B MUTATED`
TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8487 TCGA-CG-4462 TCGA-CG-4466 
       44.94        14.43        32.25         1.12         0.00        18.97 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A74A TCGA-F1-A448 TCGA-FP-A9TM 
        6.02       105.07        28.96        19.96        21.27         6.21 
TCGA-HF-7132 
       77.29 

$`PPP1R13B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-4465 TCGA-CG-4469 TCGA-CG-4477 
       29.98        19.07        12.03         9.01         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-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-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-HF-7133 TCGA-HF-7134 
       13.58         0.56        11.08         5.52        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 

  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
               0.0                0.1 
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
            105.07             122.30 
  PPP1R13B MUTATED PPP1R13B WILD-TYPE 
             19.96              14.07 
[1] "0.0 - 105.1 (20.0)" "0.1 - 122.3 (14.1)"
[1] "hr=" "2.1"
D350V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPP1R13B MUTATED         0        1        1        2         2         1
  PPP1R13B WILD-TYPE       2       14       39       28        35        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R13B MUTATED           1          1          1          0        2
  PPP1R13B WILD-TYPE         2         69         52         32       36
D350V3, multiclass
            clus
vv           PPP1R13B MUTATED PPP1R13B WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  1                 39
  STAGE II                  2                 28
  STAGE IIA                 2                 35
  STAGE IIB                 1                 51
  STAGE III                 1                  2
  STAGE IIIA                1                 69
  STAGE IIIB                1                 52
  STAGE IIIC                0                 32
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PPP1R13B MUTATED     2   3   5   3
  PPP1R13B WILD-TYPE  20  89 168  94
D350V4, multiclass
    clus
vv   PPP1R13B MUTATED PPP1R13B WILD-TYPE
  T1                2                 20
  T2                3                 89
  T3                5                168
  T4                3                 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
  PPP1R13B MUTATED     5   5   1   2
  PPP1R13B WILD-TYPE 113  99  76  75
D350V5, multiclass
    clus
vv   PPP1R13B MUTATED PPP1R13B WILD-TYPE
  N0                5                113
  N1                5                 99
  N2                1                 76
  N3                2                 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"
D350V6, binary
                    cls
clus                   0   1
  PPP1R13B MUTATED    13   1
  PPP1R13B WILD-TYPE 333  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R13B MUTATED     13    1
  PPP1R13B WILD-TYPE  333   28
   clus
vv  PPP1R13B MUTATED PPP1R13B WILD-TYPE
  0               13                333
  1                1                 28
[1] 2 2
[1] FALSE
D350V7, binary
                    cls
clus                   0   1
  PPP1R13B MUTATED     7   7
  PPP1R13B WILD-TYPE 138 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R13B MUTATED      7    7
  PPP1R13B WILD-TYPE  138  241
        clus
vv       PPP1R13B MUTATED PPP1R13B WILD-TYPE
  FEMALE                7                138
  MALE                  7                241
[1] 2 2
[1] FALSE
D350V8, binary
                    cls
clus                   0   1
  PPP1R13B MUTATED     8   3
  PPP1R13B WILD-TYPE 284  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R13B MUTATED      8    3
  PPP1R13B WILD-TYPE  284   56
     clus
vv    PPP1R13B MUTATED PPP1R13B WILD-TYPE
  NO                 8                284
  YES                3                 56
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PPP1R13B MUTATED                                          0
  PPP1R13B WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PPP1R13B MUTATED                                       1
  PPP1R13B WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPP1R13B MUTATED                                                        6
  PPP1R13B WILD-TYPE                                                    152
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PPP1R13B MUTATED                                                   2
  PPP1R13B WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPP1R13B MUTATED                                                                   4
  PPP1R13B WILD-TYPE                                                                64
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PPP1R13B MUTATED                                                    0
  PPP1R13B WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PPP1R13B MUTATED                                                  1
  PPP1R13B WILD-TYPE                                               60
D350V9, multiclass
                                                                   clus
vv                                                                  PPP1R13B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  PPP1R13B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  PPP1R13B MUTATED    12   0   1   1
  PPP1R13B WILD-TYPE 299  14  14  23
D350V10, multiclass
    clus
vv   PPP1R13B MUTATED PPP1R13B WILD-TYPE
  R0               12                299
  R1                0                 14
  R2                1                 14
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PPP1R13B MUTATED       0                         0
  PPP1R13B WILD-TYPE    87                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPP1R13B MUTATED                                           0     8
  PPP1R13B WILD-TYPE                                         1   235
D350V12, multiclass
                                           clus
vv                                          PPP1R13B MUTATED PPP1R13B WILD-TYPE
  ASIAN                                                    0                 87
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    8                235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V13, binary
                    cls
clus                   0   1
  PPP1R13B MUTATED     1   7
  PPP1R13B WILD-TYPE   3 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R13B MUTATED      1    7
  PPP1R13B WILD-TYPE    3  303
                        clus
vv                       PPP1R13B MUTATED PPP1R13B WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO                7                303
[1] 2 2
[1] FALSE

Clustering(351) Variable = KIAA0240 MUTATION ANALYSIS
D351V1, survival
                    sevent
clus2                  0   1
  KIAA0240 MUTATED     6   3
  KIAA0240 WILD-TYPE 224 136
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 9                360 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 3                136 
$`KIAA0240 MUTATED`
TCGA-BR-8382 TCGA-BR-8487 TCGA-CD-8529 TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-8243 
       25.05         1.12        12.30         6.02       105.07         5.92 
TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GQ 
       24.20        11.77         0.10 

$`KIAA0240 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  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              14.45 
[1] "0.1 - 105.1 (11.8)" "0.0 - 122.3 (14.4)"
[1] "hr=" "1"  
D351V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0240 MUTATED         0        2        0        1         1         1
  KIAA0240 WILD-TYPE       2       13       40       29        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0240 MUTATED           0          1          0          3        2
  KIAA0240 WILD-TYPE         3         69         53         29       36
D351V3, multiclass
            clus
vv           KIAA0240 MUTATED KIAA0240 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 13
  STAGE IB                  0                 40
  STAGE II                  1                 29
  STAGE IIA                 1                 36
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                0                 53
  STAGE IIIC                3                 29
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0240 MUTATED     3   1   1   7
  KIAA0240 WILD-TYPE  19  91 172  90
D351V4, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  T1                3                 19
  T2                1                 91
  T3                1                172
  T4                7                 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
  KIAA0240 MUTATED     6   3   1   2
  KIAA0240 WILD-TYPE 112 101  76  75
D351V5, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  N0                6                112
  N1                3                101
  N2                1                 76
  N3                2                 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"
D351V6, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED    12   1
  KIAA0240 WILD-TYPE 334  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED     12    1
  KIAA0240 WILD-TYPE  334   28
   clus
vv  KIAA0240 MUTATED KIAA0240 WILD-TYPE
  0               12                334
  1                1                 28
[1] 2 2
[1] FALSE
D351V7, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     6   7
  KIAA0240 WILD-TYPE 139 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      6    7
  KIAA0240 WILD-TYPE  139  241
        clus
vv       KIAA0240 MUTATED KIAA0240 WILD-TYPE
  FEMALE                6                139
  MALE                  7                241
[1] 2 2
[1] FALSE
D351V8, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     9   1
  KIAA0240 WILD-TYPE 283  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      9    1
  KIAA0240 WILD-TYPE  283   58
     clus
vv    KIAA0240 MUTATED KIAA0240 WILD-TYPE
  NO                 9                283
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA0240 MUTATED                                          0
  KIAA0240 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA0240 MUTATED                                       0
  KIAA0240 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0240 MUTATED                                                        6
  KIAA0240 WILD-TYPE                                                    152
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA0240 MUTATED                                                   1
  KIAA0240 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0240 MUTATED                                                                   2
  KIAA0240 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA0240 MUTATED                                                    0
  KIAA0240 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA0240 MUTATED                                                  4
  KIAA0240 WILD-TYPE                                               57
D351V9, multiclass
                                                                   clus
vv                                                                  KIAA0240 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 4
                                                                   clus
vv                                                                  KIAA0240 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0240 MUTATED    10   0   0   3
  KIAA0240 WILD-TYPE 301  14  15  21
D351V10, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  R0               10                301
  R1                0                 14
  R2                0                 15
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0240 MUTATED       5                         0
  KIAA0240 WILD-TYPE    82                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0240 MUTATED                                           0     6
  KIAA0240 WILD-TYPE                                         1   237
D351V12, multiclass
                                           clus
vv                                          KIAA0240 MUTATED KIAA0240 WILD-TYPE
  ASIAN                                                    5                 82
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V13, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     0  11
  KIAA0240 WILD-TYPE   4 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      0   11
  KIAA0240 WILD-TYPE    4  299
                        clus
vv                       KIAA0240 MUTATED KIAA0240 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               11                299
[1] 2 2
[1] FALSE

Clustering(352) Variable = TP53BP1 MUTATION ANALYSIS
D352V1, survival
                   sevent
clus2                 0   1
  TP53BP1 MUTATED    15   6
  TP53BP1 WILD-TYPE 215 133
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
               21               348 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                6               133 
$`TP53BP1 MUTATED`
TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8370 TCGA-BR-8589 
       30.90         6.61        34.68        30.90         3.32        27.12 
TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-6525 TCGA-HU-8244 TCGA-HU-8610 
       15.95         6.02       105.07        13.35        24.39         0.76 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX TCGA-KB-A93J TCGA-RD-A7C1 
       22.68        29.98         6.51        20.25        36.95        16.67 
TCGA-VQ-A8DL TCGA-VQ-A8P2 TCGA-VQ-A91U 
        0.92        38.14         1.71 

$`TP53BP1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
            20.25             14.07 
[1] "0.8 - 105.1 (20.2)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D352V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TP53BP1 MUTATED         0        2        1        3         4         1
  TP53BP1 WILD-TYPE       2       13       39       27        33        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TP53BP1 MUTATED           1          4          2          1        2
  TP53BP1 WILD-TYPE         2         66         51         31       36
D352V3, multiclass
            clus
vv           TP53BP1 MUTATED TP53BP1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                13
  STAGE IB                 1                39
  STAGE II                 3                27
  STAGE IIA                4                33
  STAGE IIB                1                51
  STAGE III                1                 2
  STAGE IIIA               4                66
  STAGE IIIB               2                51
  STAGE IIIC               1                31
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TP53BP1 MUTATED     2   8   7   5
  TP53BP1 WILD-TYPE  20  84 166  92
D352V4, multiclass
    clus
vv   TP53BP1 MUTATED TP53BP1 WILD-TYPE
  T1               2                20
  T2               8                84
  T3               7               166
  T4               5                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
  TP53BP1 MUTATED     6  10   4   1
  TP53BP1 WILD-TYPE 112  94  73  76
D352V5, multiclass
    clus
vv   TP53BP1 MUTATED TP53BP1 WILD-TYPE
  N0               6               112
  N1              10                94
  N2               4                73
  N3               1                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"
D352V6, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED    22   0
  TP53BP1 WILD-TYPE 324  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED     22    0
  TP53BP1 WILD-TYPE  324   29
   clus
vv  TP53BP1 MUTATED TP53BP1 WILD-TYPE
  0              22               324
  1               0                29
[1] 2 2
[1] FALSE
D352V7, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED     9  13
  TP53BP1 WILD-TYPE 136 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED      9   13
  TP53BP1 WILD-TYPE  136  235
        clus
vv       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  FEMALE               9               136
  MALE                13               235
[1] 2 2
[1] FALSE
D352V8, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED    19   2
  TP53BP1 WILD-TYPE 273  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED     19    2
  TP53BP1 WILD-TYPE  273   57
     clus
vv    TP53BP1 MUTATED TP53BP1 WILD-TYPE
  NO               19               273
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TP53BP1 MUTATED                                          0
  TP53BP1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TP53BP1 MUTATED                                       6
  TP53BP1 WILD-TYPE                                    64
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TP53BP1 MUTATED                                                        8
  TP53BP1 WILD-TYPE                                                    150
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TP53BP1 MUTATED                                                   1
  TP53BP1 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TP53BP1 MUTATED                                                                   2
  TP53BP1 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TP53BP1 MUTATED                                                    0
  TP53BP1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TP53BP1 MUTATED                                                  5
  TP53BP1 WILD-TYPE                                               56
D352V9, multiclass
                                                                   clus
vv                                                                  TP53BP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                5
                                                                   clus
vv                                                                  TP53BP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TP53BP1 MUTATED    18   0   0   3
  TP53BP1 WILD-TYPE 293  14  15  21
D352V10, multiclass
    clus
vv   TP53BP1 MUTATED TP53BP1 WILD-TYPE
  R0              18               293
  R1               0                14
  R2               0                15
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TP53BP1 MUTATED       7                         0
  TP53BP1 WILD-TYPE    80                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TP53BP1 MUTATED                                           0    12
  TP53BP1 WILD-TYPE                                         1   231
D352V12, multiclass
                                           clus
vv                                          TP53BP1 MUTATED TP53BP1 WILD-TYPE
  ASIAN                                                   7                80
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V13, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED     0  15
  TP53BP1 WILD-TYPE   4 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED      0   15
  TP53BP1 WILD-TYPE    4  295
                        clus
vv                       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              15               295
[1] 2 2
[1] FALSE

Clustering(353) Variable = CHPF2 MUTATION ANALYSIS
D353V1, survival
                 sevent
clus2               0   1
  CHPF2 MUTATED    10   5
  CHPF2 WILD-TYPE 220 134
  CHPF2 MUTATED CHPF2 WILD-TYPE 
             15             354 
  CHPF2 MUTATED CHPF2 WILD-TYPE 
              5             134 
$`CHPF2 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8297 TCGA-BR-8381 
       30.90        34.68        44.94        35.84         7.40         7.36 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-5726 TCGA-HU-8602 TCGA-HU-A4GQ 
        6.58         1.02         8.05        28.96        22.32         0.10 
TCGA-HU-A4GT TCGA-HU-A4H4 TCGA-VQ-A8P2 
        6.51        23.84        38.14 

$`CHPF2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
          22.32           14.22 
[1] "0.1 - 44.9 (22.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D353V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CHPF2 MUTATED         0        1        1        1         4         3
  CHPF2 WILD-TYPE       2       14       39       29        33        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHPF2 MUTATED           0          1          0          2        2
  CHPF2 WILD-TYPE         3         69         53         30       36
D353V3, multiclass
            clus
vv           CHPF2 MUTATED CHPF2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              4              33
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CHPF2 MUTATED     1   4   6   5
  CHPF2 WILD-TYPE  21  88 167  92
D353V4, multiclass
    clus
vv   CHPF2 MUTATED CHPF2 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             6             167
  T4             5              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
  CHPF2 MUTATED     7   3   4   1
  CHPF2 WILD-TYPE 111 101  73  76
D353V5, multiclass
    clus
vv   CHPF2 MUTATED CHPF2 WILD-TYPE
  N0             7             111
  N1             3             101
  N2             4              73
  N3             1              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"
D353V6, binary
                 cls
clus                0   1
  CHPF2 MUTATED    15   1
  CHPF2 WILD-TYPE 331  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHPF2 MUTATED     15    1
  CHPF2 WILD-TYPE  331   28
   clus
vv  CHPF2 MUTATED CHPF2 WILD-TYPE
  0            15             331
  1             1              28
[1] 2 2
[1] FALSE
D353V7, binary
                 cls
clus                0   1
  CHPF2 MUTATED     8   8
  CHPF2 WILD-TYPE 137 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHPF2 MUTATED      8    8
  CHPF2 WILD-TYPE  137  240
        clus
vv       CHPF2 MUTATED CHPF2 WILD-TYPE
  FEMALE             8             137
  MALE               8             240
[1] 2 2
[1] FALSE
D353V8, binary
                 cls
clus                0   1
  CHPF2 MUTATED    12   1
  CHPF2 WILD-TYPE 280  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHPF2 MUTATED     12    1
  CHPF2 WILD-TYPE  280   58
     clus
vv    CHPF2 MUTATED CHPF2 WILD-TYPE
  NO             12             280
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CHPF2 MUTATED                                          0
  CHPF2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CHPF2 MUTATED                                       3
  CHPF2 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CHPF2 MUTATED                                                        7
  CHPF2 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CHPF2 MUTATED                                                   1
  CHPF2 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CHPF2 MUTATED                                                                   2
  CHPF2 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CHPF2 MUTATED                                                    0
  CHPF2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CHPF2 MUTATED                                                  3
  CHPF2 WILD-TYPE                                               58
D353V9, multiclass
                                                                   clus
vv                                                                  CHPF2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  CHPF2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CHPF2 MUTATED    12   0   1   2
  CHPF2 WILD-TYPE 299  14  14  22
D353V10, multiclass
    clus
vv   CHPF2 MUTATED CHPF2 WILD-TYPE
  R0            12             299
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CHPF2 MUTATED       5                         0
  CHPF2 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CHPF2 MUTATED                                           0     8
  CHPF2 WILD-TYPE                                         1   235
D353V12, multiclass
                                           clus
vv                                          CHPF2 MUTATED CHPF2 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V13, binary
                 cls
clus                0   1
  CHPF2 MUTATED     0  12
  CHPF2 WILD-TYPE   4 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHPF2 MUTATED      0   12
  CHPF2 WILD-TYPE    4  298
                        clus
vv                       CHPF2 MUTATED CHPF2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(354) Variable = GPR141 MUTATION ANALYSIS
D354V1, survival
                  sevent
clus2                0   1
  GPR141 MUTATED     6   5
  GPR141 WILD-TYPE 224 134
  GPR141 MUTATED GPR141 WILD-TYPE 
              11              358 
  GPR141 MUTATED GPR141 WILD-TYPE 
               5              134 
$`GPR141 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-7957 TCGA-BR-8363 TCGA-BR-8372 TCGA-D7-6525 
       26.70         6.97         9.07         0.26        31.27        13.35 
TCGA-D7-A4YY TCGA-F1-A448 TCGA-HF-A5NB TCGA-HU-A4GU TCGA-VQ-AA6I 
       13.78        21.27        30.51         6.58        16.14 

$`GPR141 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-D7-6526 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-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-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-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-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        27.55        12.43        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 
           13.78            14.35 
[1] "0.3 - 31.3 (13.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D354V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR141 MUTATED         0        0        1        0         0         2
  GPR141 WILD-TYPE       2       15       39       30        37        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR141 MUTATED           0          2          3          2        1
  GPR141 WILD-TYPE         3         68         50         30       37
D354V3, multiclass
            clus
vv           GPR141 MUTATED GPR141 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              3               50
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR141 MUTATED     0   2   6   3
  GPR141 WILD-TYPE  22  90 167  94
D354V4, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              6              167
  T4              3               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
  GPR141 MUTATED     2   2   1   6
  GPR141 WILD-TYPE 116 102  76  71
D354V5, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  N0              2              116
  N1              2              102
  N2              1               76
  N3              6               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"
D354V6, binary
                  cls
clus                 0   1
  GPR141 MUTATED     9   1
  GPR141 WILD-TYPE 337  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      9    1
  GPR141 WILD-TYPE  337   28
   clus
vv  GPR141 MUTATED GPR141 WILD-TYPE
  0              9              337
  1              1               28
[1] 2 2
[1] FALSE
D354V7, binary
                  cls
clus                 0   1
  GPR141 MUTATED     4   7
  GPR141 WILD-TYPE 141 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      4    7
  GPR141 WILD-TYPE  141  241
        clus
vv       GPR141 MUTATED GPR141 WILD-TYPE
  FEMALE              4              141
  MALE                7              241
[1] 2 2
[1] FALSE
D354V8, binary
                  cls
clus                 0   1
  GPR141 MUTATED     8   3
  GPR141 WILD-TYPE 284  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      8    3
  GPR141 WILD-TYPE  284   56
     clus
vv    GPR141 MUTATED GPR141 WILD-TYPE
  NO               8              284
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GPR141 MUTATED                                          0
  GPR141 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GPR141 MUTATED                                       3
  GPR141 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR141 MUTATED                                                        4
  GPR141 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GPR141 MUTATED                                                   2
  GPR141 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR141 MUTATED                                                                   2
  GPR141 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GPR141 MUTATED                                                    0
  GPR141 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GPR141 MUTATED                                                  0
  GPR141 WILD-TYPE                                               61
D354V9, multiclass
                                                                   clus
vv                                                                  GPR141 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  GPR141 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR141 MUTATED     9   1   0   1
  GPR141 WILD-TYPE 302  13  15  23
D354V10, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  R0              9              302
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GPR141 MUTATED       1                         0
  GPR141 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR141 MUTATED                                           0     9
  GPR141 WILD-TYPE                                         1   234
D354V12, multiclass
                                           clus
vv                                          GPR141 MUTATED GPR141 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V13, binary
                  cls
clus                 0   1
  GPR141 MUTATED     1   8
  GPR141 WILD-TYPE   3 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      1    8
  GPR141 WILD-TYPE    3  302
                        clus
vv                       GPR141 MUTATED GPR141 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(355) Variable = PPP1R15A MUTATION ANALYSIS
D355V1, survival
                    sevent
clus2                  0   1
  PPP1R15A MUTATED     3   1
  PPP1R15A WILD-TYPE 227 138
  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
                 4                365 
  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
                 1                138 
$`PPP1R15A MUTATED`
TCGA-B7-5816 TCGA-BR-A4QL TCGA-F1-6874 TCGA-MX-A5UJ 
       26.70        16.14        14.47        19.73 

$`PPP1R15A WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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 

  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
             14.47               0.00 
  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
              26.7              122.3 
  PPP1R15A MUTATED PPP1R15A WILD-TYPE 
            17.935             14.070 
[1] "14.5 - 26.7 (17.9)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D355V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPP1R15A MUTATED         0        0        1        0         0         1
  PPP1R15A WILD-TYPE       2       15       39       30        37        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R15A MUTATED           0          1          1          0        1
  PPP1R15A WILD-TYPE         3         69         52         32       37
D355V3, multiclass
            clus
vv           PPP1R15A MUTATED PPP1R15A WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 0                 37
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                1                 52
  STAGE IIIC                0                 32
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PPP1R15A MUTATED     0   1   2   2
  PPP1R15A WILD-TYPE  22  91 171  95
D355V4, multiclass
    clus
vv   PPP1R15A MUTATED PPP1R15A WILD-TYPE
  T1                0                 22
  T2                1                 91
  T3                2                171
  T4                2                 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
  PPP1R15A MUTATED     2   0   2   1
  PPP1R15A WILD-TYPE 116 104  75  76
D355V5, multiclass
    clus
vv   PPP1R15A MUTATED PPP1R15A WILD-TYPE
  N0                2                116
  N1                0                104
  N2                2                 75
  N3                1                 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"
D355V6, binary
                    cls
clus                   0   1
  PPP1R15A MUTATED     5   0
  PPP1R15A WILD-TYPE 341  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R15A MUTATED      5    0
  PPP1R15A WILD-TYPE  341   29
   clus
vv  PPP1R15A MUTATED PPP1R15A WILD-TYPE
  0                5                341
  1                0                 29
[1] 2 2
[1] FALSE
D355V7, binary
                    cls
clus                   0   1
  PPP1R15A MUTATED     4   1
  PPP1R15A WILD-TYPE 141 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R15A MUTATED      4    1
  PPP1R15A WILD-TYPE  141  247
        clus
vv       PPP1R15A MUTATED PPP1R15A WILD-TYPE
  FEMALE                4                141
  MALE                  1                247
[1] 2 2
[1] FALSE
D355V8, binary
                    cls
clus                   0   1
  PPP1R15A MUTATED     4   0
  PPP1R15A WILD-TYPE 288  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R15A MUTATED      4    0
  PPP1R15A WILD-TYPE  288   59
     clus
vv    PPP1R15A MUTATED PPP1R15A WILD-TYPE
  NO                 4                288
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PPP1R15A MUTATED                                          0
  PPP1R15A WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PPP1R15A MUTATED                                       1
  PPP1R15A WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPP1R15A MUTATED                                                        2
  PPP1R15A WILD-TYPE                                                    156
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PPP1R15A MUTATED                                                   0
  PPP1R15A WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPP1R15A MUTATED                                                                   1
  PPP1R15A WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PPP1R15A MUTATED                                                    0
  PPP1R15A WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PPP1R15A MUTATED                                                  1
  PPP1R15A WILD-TYPE                                               60
D355V9, multiclass
                                                                   clus
vv                                                                  PPP1R15A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  PPP1R15A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  PPP1R15A MUTATED     4   0   0   1
  PPP1R15A WILD-TYPE 307  14  15  23
D355V10, multiclass
    clus
vv   PPP1R15A MUTATED PPP1R15A WILD-TYPE
  R0                4                307
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PPP1R15A MUTATED       0                         0
  PPP1R15A WILD-TYPE    87                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPP1R15A MUTATED                                           0     5
  PPP1R15A WILD-TYPE                                         1   238
D355V12, multiclass
                                           clus
vv                                          PPP1R15A MUTATED PPP1R15A WILD-TYPE
  ASIAN                                                    0                 87
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V13, binary
                    cls
clus                   0   1
  PPP1R15A MUTATED     0   5
  PPP1R15A WILD-TYPE   4 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R15A MUTATED      0    5
  PPP1R15A WILD-TYPE    4  305
                        clus
vv                       PPP1R15A MUTATED PPP1R15A WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                5                305
[1] 2 2
[1] FALSE

Clustering(356) Variable = KYNU MUTATION ANALYSIS
D356V1, survival
                sevent
clus2              0   1
  KYNU MUTATED     9   1
  KYNU WILD-TYPE 221 138
  KYNU MUTATED KYNU WILD-TYPE 
            10            359 
  KYNU MUTATED KYNU WILD-TYPE 
             1            138 
$`KYNU MUTATED`
TCGA-BR-6852 TCGA-BR-7958 TCGA-BR-8368 TCGA-BR-8680 TCGA-CG-4465 TCGA-CG-5721 
       44.94        29.56         4.31        31.96         9.01         6.02 
TCGA-CG-5723 TCGA-HF-A5NB TCGA-HU-A4H4 TCGA-HU-A4HD 
      105.07        30.51        23.84        33.40 

$`KYNU WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-A4H5 
       20.25         0.26         2.10        12.95        29.00        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-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 

  KYNU MUTATED KYNU WILD-TYPE 
          4.31           0.00 
  KYNU MUTATED KYNU WILD-TYPE 
        105.07         122.30 
  KYNU MUTATED KYNU WILD-TYPE 
        30.035         14.070 
[1] "4.3 - 105.1 (30.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "5.6"
D356V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KYNU MUTATED         0        0        2        1         1         1
  KYNU WILD-TYPE       2       15       38       29        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KYNU MUTATED           0          2          1          1        3
  KYNU WILD-TYPE         3         68         52         31       35
D356V3, multiclass
            clus
vv           KYNU MUTATED KYNU WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KYNU MUTATED     0   4   2   6
  KYNU WILD-TYPE  22  88 171  91
D356V4, multiclass
    clus
vv   KYNU MUTATED KYNU WILD-TYPE
  T1            0             22
  T2            4             88
  T3            2            171
  T4            6             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
  KYNU MUTATED     5   2   3   2
  KYNU WILD-TYPE 113 102  74  75
D356V5, multiclass
    clus
vv   KYNU MUTATED KYNU WILD-TYPE
  N0            5            113
  N1            2            102
  N2            3             74
  N3            2             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"
D356V6, binary
                cls
clus               0   1
  KYNU MUTATED    10   2
  KYNU WILD-TYPE 336  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED     10    2
  KYNU WILD-TYPE  336   27
   clus
vv  KYNU MUTATED KYNU WILD-TYPE
  0           10            336
  1            2             27
[1] 2 2
[1] FALSE
D356V7, binary
                cls
clus               0   1
  KYNU MUTATED     6   6
  KYNU WILD-TYPE 139 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      6    6
  KYNU WILD-TYPE  139  242
        clus
vv       KYNU MUTATED KYNU WILD-TYPE
  FEMALE            6            139
  MALE              6            242
[1] 2 2
[1] FALSE
D356V8, binary
                cls
clus               0   1
  KYNU MUTATED     8   1
  KYNU WILD-TYPE 284  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      8    1
  KYNU WILD-TYPE  284   58
     clus
vv    KYNU MUTATED KYNU WILD-TYPE
  NO             8            284
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KYNU MUTATED                                          0
  KYNU WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KYNU MUTATED                                       1
  KYNU WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KYNU MUTATED                                                        5
  KYNU WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KYNU MUTATED                                                   1
  KYNU WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KYNU MUTATED                                                                   2
  KYNU WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KYNU MUTATED                                                    0
  KYNU WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KYNU MUTATED                                                  3
  KYNU WILD-TYPE                                               58
D356V9, multiclass
                                                                   clus
vv                                                                  KYNU MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  KYNU WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KYNU MUTATED     9   1   1   1
  KYNU WILD-TYPE 302  13  14  23
D356V10, multiclass
    clus
vv   KYNU MUTATED KYNU WILD-TYPE
  R0            9            302
  R1            1             13
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  KYNU MUTATED       3                         0
  KYNU WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KYNU MUTATED                                           0     4
  KYNU WILD-TYPE                                         1   239
D356V12, multiclass
                                           clus
vv                                          KYNU MUTATED KYNU WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V13, binary
                cls
clus               0   1
  KYNU MUTATED     0   7
  KYNU WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      0    7
  KYNU WILD-TYPE    4  303
                        clus
vv                       KYNU MUTATED KYNU WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(357) Variable = RIF1 MUTATION ANALYSIS
D357V1, survival
                sevent
clus2              0   1
  RIF1 MUTATED    15   4
  RIF1 WILD-TYPE 215 135
  RIF1 MUTATED RIF1 WILD-TYPE 
            19            350 
  RIF1 MUTATED RIF1 WILD-TYPE 
             4            135 
$`RIF1 MUTATED`
TCGA-B7-5816 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8368 
       26.70         9.34        34.68        35.84        29.59         4.31 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8529 TCGA-CD-8536 TCGA-CG-5721 TCGA-CG-5726 
       31.96        16.14        12.30        12.43         6.02        28.96 
TCGA-D7-6527 TCGA-HF-7132 TCGA-HU-A4GC TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-VQ-A8P2 
       10.26        77.29         3.25         6.51        29.00        38.14 
TCGA-VQ-AA6J 
       27.55 

$`RIF1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        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-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-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-AA6K TCGA-ZA-A8F6 
       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 
         26.70          14.12 
[1] "3.2 - 77.3 (26.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.3"
D357V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RIF1 MUTATED         0        1        3        3         2         3
  RIF1 WILD-TYPE       2       14       37       27        35        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RIF1 MUTATED           0          1          3          1        3
  RIF1 WILD-TYPE         3         69         50         31       35
D357V3, multiclass
            clus
vv           RIF1 MUTATED RIF1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              3             37
  STAGE II              3             27
  STAGE IIA             2             35
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            3             50
  STAGE IIIC            1             31
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RIF1 MUTATED     1   5   5  10
  RIF1 WILD-TYPE  21  87 168  87
D357V4, multiclass
    clus
vv   RIF1 MUTATED RIF1 WILD-TYPE
  T1            1             21
  T2            5             87
  T3            5            168
  T4           10             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
  RIF1 MUTATED    11   6   3   2
  RIF1 WILD-TYPE 107  98  74  75
D357V5, multiclass
    clus
vv   RIF1 MUTATED RIF1 WILD-TYPE
  N0           11            107
  N1            6             98
  N2            3             74
  N3            2             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"
D357V6, binary
                cls
clus               0   1
  RIF1 MUTATED    21   2
  RIF1 WILD-TYPE 325  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     21    2
  RIF1 WILD-TYPE  325   27
   clus
vv  RIF1 MUTATED RIF1 WILD-TYPE
  0           21            325
  1            2             27
[1] 2 2
[1] FALSE
D357V7, binary
                cls
clus               0   1
  RIF1 MUTATED    11  13
  RIF1 WILD-TYPE 134 235
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     11   13
  RIF1 WILD-TYPE  134  235
        clus
vv       RIF1 MUTATED RIF1 WILD-TYPE
  FEMALE           11            134
  MALE             13            235
[1] 2 2
[1] FALSE
D357V8, binary
                cls
clus               0   1
  RIF1 MUTATED    14   4
  RIF1 WILD-TYPE 278  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     14    4
  RIF1 WILD-TYPE  278   55
     clus
vv    RIF1 MUTATED RIF1 WILD-TYPE
  NO            14            278
  YES            4             55
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RIF1 MUTATED                                          0
  RIF1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RIF1 MUTATED                                       3
  RIF1 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RIF1 MUTATED                                                       10
  RIF1 WILD-TYPE                                                    148
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RIF1 MUTATED                                                   3
  RIF1 WILD-TYPE                                                18
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RIF1 MUTATED                                                                   5
  RIF1 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RIF1 MUTATED                                                    1
  RIF1 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RIF1 MUTATED                                                  2
  RIF1 WILD-TYPE                                               59
D357V9, multiclass
                                                                   clus
vv                                                                  RIF1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  RIF1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RIF1 MUTATED    20   0   0   4
  RIF1 WILD-TYPE 291  14  15  20
D357V10, multiclass
    clus
vv   RIF1 MUTATED RIF1 WILD-TYPE
  R0           20            291
  R1            0             14
  R2            0             15
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RIF1 MUTATED       6                         1
  RIF1 WILD-TYPE    81                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RIF1 MUTATED                                           0    13
  RIF1 WILD-TYPE                                         1   230
D357V12, multiclass
                                           clus
vv                                          RIF1 MUTATED RIF1 WILD-TYPE
  ASIAN                                                6             81
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V13, binary
                cls
clus               0   1
  RIF1 MUTATED     0  18
  RIF1 WILD-TYPE   4 292
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED      0   18
  RIF1 WILD-TYPE    4  292
                        clus
vv                       RIF1 MUTATED RIF1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           18            292
[1] 2 2
[1] FALSE

Clustering(358) Variable = TBC1D10C MUTATION ANALYSIS
D358V1, survival
                    sevent
clus2                  0   1
  TBC1D10C MUTATED     6   1
  TBC1D10C WILD-TYPE 224 138
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 7                362 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 1                138 
$`TBC1D10C MUTATED`
TCGA-BR-6852 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MG TCGA-HU-8602 TCGA-HU-A4G9 
       44.94         1.12        28.14         6.58        22.32        24.20 
TCGA-VQ-A8P2 
       38.14 

$`TBC1D10C WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
              1.12               0.00 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
             44.94             122.30 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
             24.20              14.12 
[1] "1.1 - 44.9 (24.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.4"
D358V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TBC1D10C MUTATED         0        1        0        0         3         2
  TBC1D10C WILD-TYPE       2       14       40       30        34        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBC1D10C MUTATED           0          1          0          1        0
  TBC1D10C WILD-TYPE         3         69         53         31       38
D358V3, multiclass
            clus
vv           TBC1D10C MUTATED TBC1D10C WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 3                 34
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                0                 53
  STAGE IIIC                1                 31
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TBC1D10C MUTATED     1   0   3   4
  TBC1D10C WILD-TYPE  21  92 170  93
D358V4, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  T1                1                 21
  T2                0                 92
  T3                3                170
  T4                4                 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
  TBC1D10C MUTATED     6   2   0   1
  TBC1D10C WILD-TYPE 112 102  77  76
D358V5, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  N0                6                112
  N1                2                102
  N2                0                 77
  N3                1                 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"
D358V6, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     9   0
  TBC1D10C WILD-TYPE 337  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      9    0
  TBC1D10C WILD-TYPE  337   29
   clus
vv  TBC1D10C MUTATED TBC1D10C WILD-TYPE
  0                9                337
  1                0                 29
[1] 2 2
[1] FALSE
D358V7, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     5   4
  TBC1D10C WILD-TYPE 140 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      5    4
  TBC1D10C WILD-TYPE  140  244
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  FEMALE                5                140
  MALE                  4                244
[1] 2 2
[1] FALSE
D358V8, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     7   1
  TBC1D10C WILD-TYPE 285  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      7    1
  TBC1D10C WILD-TYPE  285   58
     clus
vv    TBC1D10C MUTATED TBC1D10C WILD-TYPE
  NO                 7                285
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TBC1D10C MUTATED                                          0
  TBC1D10C WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TBC1D10C MUTATED                                       2
  TBC1D10C WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TBC1D10C MUTATED                                                        4
  TBC1D10C WILD-TYPE                                                    154
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TBC1D10C MUTATED                                                   1
  TBC1D10C WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TBC1D10C MUTATED                                                                   1
  TBC1D10C WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TBC1D10C MUTATED                                                    0
  TBC1D10C WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TBC1D10C MUTATED                                                  1
  TBC1D10C WILD-TYPE                                               60
D358V9, multiclass
                                                                   clus
vv                                                                  TBC1D10C MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  TBC1D10C WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  TBC1D10C MUTATED     7   0   0   1
  TBC1D10C WILD-TYPE 304  14  15  23
D358V10, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  R0                7                304
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  TBC1D10C MUTATED       3                         0
  TBC1D10C WILD-TYPE    84                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TBC1D10C MUTATED                                           0     6
  TBC1D10C WILD-TYPE                                         1   237
D358V12, multiclass
                                           clus
vv                                          TBC1D10C MUTATED TBC1D10C WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V13, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     0   8
  TBC1D10C WILD-TYPE   4 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      0    8
  TBC1D10C WILD-TYPE    4  302
                        clus
vv                       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                8                302
[1] 2 2
[1] FALSE

Clustering(359) Variable = UHRF1BP1 MUTATION ANALYSIS
D359V1, survival
                    sevent
clus2                  0   1
  UHRF1BP1 MUTATED    12   6
  UHRF1BP1 WILD-TYPE 218 133
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                18                351 
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                 6                133 
$`UHRF1BP1 MUTATED`
TCGA-CG-4460 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8363 TCGA-BR-8680 
       21.99        30.90        34.68        32.78         0.26        31.96 
TCGA-CD-A4MI TCGA-CG-5717 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 
       11.77         6.97         0.99       105.07        65.10        21.07 
TCGA-F1-A448 TCGA-HU-A4G3 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-R5-A7ZI 
       21.27         5.59        29.00        23.84        14.07        74.53 

$`UHRF1BP1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-5718 
        0.00         9.01        18.97         7.07        30.97        36.00 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        1.02         0.99         6.02        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-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-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-A4H5 TCGA-HU-A4H6 
       20.25         0.26         2.10        12.95        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-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 

  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             14.040 
[1] "0.3 - 105.1 (22.9)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.6"
D359V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UHRF1BP1 MUTATED         0        0        3        2         2         2
  UHRF1BP1 WILD-TYPE       2       15       37       28        35        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UHRF1BP1 MUTATED           0          2          1          1        4
  UHRF1BP1 WILD-TYPE         3         68         52         31       34
D359V3, multiclass
            clus
vv           UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  3                 37
  STAGE II                  2                 28
  STAGE IIA                 2                 35
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                1                 52
  STAGE IIIC                1                 31
  STAGE IV                  4                 34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  UHRF1BP1 MUTATED     2   8   5   4
  UHRF1BP1 WILD-TYPE  20  84 168  93
D359V4, multiclass
    clus
vv   UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  T1                2                 20
  T2                8                 84
  T3                5                168
  T4                4                 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
  UHRF1BP1 MUTATED     4   6   5   2
  UHRF1BP1 WILD-TYPE 114  98  72  75
D359V5, multiclass
    clus
vv   UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  N0                4                114
  N1                6                 98
  N2                5                 72
  N3                2                 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"
D359V6, binary
                    cls
clus                   0   1
  UHRF1BP1 MUTATED    15   4
  UHRF1BP1 WILD-TYPE 331  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED     15    4
  UHRF1BP1 WILD-TYPE  331   25
   clus
vv  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  0               15                331
  1                4                 25
[1] 2 2
[1] FALSE
D359V7, binary
                    cls
clus                   0   1
  UHRF1BP1 MUTATED    12   7
  UHRF1BP1 WILD-TYPE 133 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED     12    7
  UHRF1BP1 WILD-TYPE  133  241
        clus
vv       UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  FEMALE               12                133
  MALE                  7                241
[1] 2 2
[1] FALSE
D359V8, binary
                    cls
clus                   0   1
  UHRF1BP1 MUTATED    14   1
  UHRF1BP1 WILD-TYPE 278  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED     14    1
  UHRF1BP1 WILD-TYPE  278   58
     clus
vv    UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  NO                14                278
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  UHRF1BP1 MUTATED                                          0
  UHRF1BP1 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  UHRF1BP1 MUTATED                                       2
  UHRF1BP1 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UHRF1BP1 MUTATED                                                        8
  UHRF1BP1 WILD-TYPE                                                    150
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  UHRF1BP1 MUTATED                                                   1
  UHRF1BP1 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UHRF1BP1 MUTATED                                                                   4
  UHRF1BP1 WILD-TYPE                                                                64
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  UHRF1BP1 MUTATED                                                    0
  UHRF1BP1 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  UHRF1BP1 MUTATED                                                  4
  UHRF1BP1 WILD-TYPE                                               57
D359V9, multiclass
                                                                   clus
vv                                                                  UHRF1BP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 4
                                                                   clus
vv                                                                  UHRF1BP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  UHRF1BP1 MUTATED    14   0   2   2
  UHRF1BP1 WILD-TYPE 297  14  13  22
D359V10, multiclass
    clus
vv   UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  R0               14                297
  R1                0                 14
  R2                2                 13
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  UHRF1BP1 MUTATED       6                         0
  UHRF1BP1 WILD-TYPE    81                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UHRF1BP1 MUTATED                                           0     7
  UHRF1BP1 WILD-TYPE                                         1   236
D359V12, multiclass
                                           clus
vv                                          UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  ASIAN                                                    6                 81
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V13, binary
                    cls
clus                   0   1
  UHRF1BP1 MUTATED     2  11
  UHRF1BP1 WILD-TYPE   2 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED      2   11
  UHRF1BP1 WILD-TYPE    2  299
                        clus
vv                       UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  HISPANIC OR LATINO                    2                  2
  NOT HISPANIC OR LATINO               11                299
[1] 2 2
[1] FALSE

Clustering(360) Variable = DLAT MUTATION ANALYSIS
D360V1, survival
                sevent
clus2              0   1
  DLAT MUTATED     5   1
  DLAT WILD-TYPE 225 138
  DLAT MUTATED DLAT WILD-TYPE 
             6            363 
  DLAT MUTATED DLAT WILD-TYPE 
             1            138 
$`DLAT MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-8360 TCGA-HF-A5NB TCGA-HU-A4G9 TCGA-MX-A5UJ 
       26.70        30.90         6.18        30.51        24.20        19.73 

$`DLAT WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  DLAT MUTATED DLAT WILD-TYPE 
          6.18           0.00 
  DLAT MUTATED DLAT WILD-TYPE 
          30.9          122.3 
  DLAT MUTATED DLAT WILD-TYPE 
         25.45          14.07 
[1] "6.2 - 30.9 (25.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.1"
D360V2, 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       1       14       40       30        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DLAT MUTATED           0          2          0          1        0
  DLAT WILD-TYPE         3         68         53         31       38
D360V3, multiclass
            clus
vv           DLAT MUTATED DLAT WILD-TYPE
  STAGE I               1              1
  STAGE IA              1             14
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DLAT MUTATED     2   1   2   3
  DLAT WILD-TYPE  20  91 171  94
D360V4, multiclass
    clus
vv   DLAT MUTATED DLAT WILD-TYPE
  T1            2             20
  T2            1             91
  T3            2            171
  T4            3             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
  DLAT MUTATED     4   1   1   1
  DLAT WILD-TYPE 114 103  76  76
D360V5, multiclass
    clus
vv   DLAT MUTATED DLAT WILD-TYPE
  N0            4            114
  N1            1            103
  N2            1             76
  N3            1             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"
D360V6, binary
                cls
clus               0   1
  DLAT MUTATED     7   0
  DLAT WILD-TYPE 339  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLAT MUTATED      7    0
  DLAT WILD-TYPE  339   29
   clus
vv  DLAT MUTATED DLAT WILD-TYPE
  0            7            339
  1            0             29
[1] 2 2
[1] FALSE
D360V7, binary
                cls
clus               0   1
  DLAT MUTATED     6   2
  DLAT WILD-TYPE 139 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLAT MUTATED      6    2
  DLAT WILD-TYPE  139  246
        clus
vv       DLAT MUTATED DLAT WILD-TYPE
  FEMALE            6            139
  MALE              2            246
[1] 2 2
[1] FALSE
D360V8, binary
                cls
clus               0   1
  DLAT MUTATED     6   1
  DLAT WILD-TYPE 286  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLAT MUTATED      6    1
  DLAT WILD-TYPE  286   58
     clus
vv    DLAT MUTATED DLAT WILD-TYPE
  NO             6            286
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DLAT MUTATED                                          0
  DLAT WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DLAT MUTATED                                       1
  DLAT WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DLAT MUTATED                                                        3
  DLAT WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DLAT MUTATED                                                   1
  DLAT WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DLAT MUTATED                                                                   1
  DLAT WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DLAT MUTATED                                                    0
  DLAT WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DLAT MUTATED                                                  2
  DLAT WILD-TYPE                                               59
D360V9, multiclass
                                                                   clus
vv                                                                  DLAT MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  DLAT WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DLAT MUTATED     5   1   0   2
  DLAT WILD-TYPE 306  13  15  22
D360V10, multiclass
    clus
vv   DLAT MUTATED DLAT WILD-TYPE
  R0            5            306
  R1            1             13
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DLAT MUTATED       1                         1
  DLAT WILD-TYPE    86                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DLAT MUTATED                                           0     5
  DLAT WILD-TYPE                                         1   238
D360V12, multiclass
                                           clus
vv                                          DLAT MUTATED DLAT WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V13, binary
                cls
clus               0   1
  DLAT MUTATED     0   7
  DLAT WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLAT MUTATED      0    7
  DLAT WILD-TYPE    4  303
                        clus
vv                       DLAT MUTATED DLAT WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(361) Variable = CD93 MUTATION ANALYSIS
D361V1, survival
                sevent
clus2              0   1
  CD93 MUTATED     9   6
  CD93 WILD-TYPE 221 133
  CD93 MUTATED CD93 WILD-TYPE 
            15            354 
  CD93 MUTATED CD93 WILD-TYPE 
             6            133 
$`CD93 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8360 
       21.99         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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-8680 TCGA-BR-8682 
       28.14         6.28         7.53        26.73        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-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-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        0.10        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-AA6K TCGA-ZA-A8F6 
       32.94        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 
         21.99          14.22 
[1] "0.3 - 36.2 (22.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D361V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD93 MUTATED         0        2        2        0         3         2
  CD93 WILD-TYPE       2       13       38       30        34        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CD93 MUTATED           0          1          1          3        1
  CD93 WILD-TYPE         3         69         52         29       37
D361V3, multiclass
            clus
vv           CD93 MUTATED CD93 WILD-TYPE
  STAGE I               0              2
  STAGE IA              2             13
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             3             34
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            3             29
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD93 MUTATED     2   2   6   5
  CD93 WILD-TYPE  20  90 167  92
D361V4, multiclass
    clus
vv   CD93 MUTATED CD93 WILD-TYPE
  T1            2             20
  T2            2             90
  T3            6            167
  T4            5             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
  CD93 MUTATED     7   6   1   3
  CD93 WILD-TYPE 111  98  76  74
D361V5, multiclass
    clus
vv   CD93 MUTATED CD93 WILD-TYPE
  N0            7            111
  N1            6             98
  N2            1             76
  N3            3             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"
D361V6, binary
                cls
clus               0   1
  CD93 MUTATED    16   1
  CD93 WILD-TYPE 330  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED     16    1
  CD93 WILD-TYPE  330   28
   clus
vv  CD93 MUTATED CD93 WILD-TYPE
  0           16            330
  1            1             28
[1] 2 2
[1] FALSE
D361V7, binary
                cls
clus               0   1
  CD93 MUTATED    10   8
  CD93 WILD-TYPE 135 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED     10    8
  CD93 WILD-TYPE  135  240
        clus
vv       CD93 MUTATED CD93 WILD-TYPE
  FEMALE           10            135
  MALE              8            240
[1] 2 2
[1] FALSE
D361V8, binary
                cls
clus               0   1
  CD93 MUTATED    13   2
  CD93 WILD-TYPE 279  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED     13    2
  CD93 WILD-TYPE  279   57
     clus
vv    CD93 MUTATED CD93 WILD-TYPE
  NO            13            279
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CD93 MUTATED                                          0
  CD93 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CD93 MUTATED                                       2
  CD93 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD93 MUTATED                                                        9
  CD93 WILD-TYPE                                                    149
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CD93 MUTATED                                                   1
  CD93 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD93 MUTATED                                                                   3
  CD93 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CD93 MUTATED                                                    1
  CD93 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CD93 MUTATED                                                  2
  CD93 WILD-TYPE                                               59
D361V9, multiclass
                                                                   clus
vv                                                                  CD93 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  CD93 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CD93 MUTATED    12   1   1   4
  CD93 WILD-TYPE 299  13  14  20
D361V10, multiclass
    clus
vv   CD93 MUTATED CD93 WILD-TYPE
  R0           12            299
  R1            1             13
  R2            1             14
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CD93 MUTATED       4                         1
  CD93 WILD-TYPE    83                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD93 MUTATED                                           0    11
  CD93 WILD-TYPE                                         1   232
D361V12, multiclass
                                           clus
vv                                          CD93 MUTATED CD93 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V13, binary
                cls
clus               0   1
  CD93 MUTATED     0  15
  CD93 WILD-TYPE   4 295
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED      0   15
  CD93 WILD-TYPE    4  295
                        clus
vv                       CD93 MUTATED CD93 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           15            295
[1] 2 2
[1] FALSE

Clustering(362) Variable = SGOL2 MUTATION ANALYSIS
D362V1, survival
                 sevent
clus2               0   1
  SGOL2 MUTATED     8   3
  SGOL2 WILD-TYPE 222 136
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             11             358 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              3             136 
$`SGOL2 MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8363 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-5801 
       34.68        36.16         0.26        28.14        31.96        13.18 
TCGA-CG-4306 TCGA-CG-5728 TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-MX-A5UJ 
        1.02        65.10        20.25        29.00        19.73 

$`SGOL2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-D7-5579 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-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-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 

  SGOL2 MUTATED SGOL2 WILD-TYPE 
           0.26            0.00 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
           65.1           122.3 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
          28.14           14.07 
[1] "0.3 - 65.1 (28.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D362V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SGOL2 MUTATED         0        1        3        0         1         0
  SGOL2 WILD-TYPE       2       14       37       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SGOL2 MUTATED           0          2          0          3        2
  SGOL2 WILD-TYPE         3         68         53         29       36
D362V3, multiclass
            clus
vv           SGOL2 MUTATED SGOL2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SGOL2 MUTATED     1   3   4   4
  SGOL2 WILD-TYPE  21  89 169  93
D362V4, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             4             169
  T4             4              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
  SGOL2 MUTATED     5   2   4   2
  SGOL2 WILD-TYPE 113 102  73  75
D362V5, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  N0             5             113
  N1             2             102
  N2             4              73
  N3             2              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"
D362V6, binary
                 cls
clus                0   1
  SGOL2 MUTATED    11   2
  SGOL2 WILD-TYPE 335  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED     11    2
  SGOL2 WILD-TYPE  335   27
   clus
vv  SGOL2 MUTATED SGOL2 WILD-TYPE
  0            11             335
  1             2              27
[1] 2 2
[1] FALSE
D362V7, binary
                 cls
clus                0   1
  SGOL2 MUTATED     7   6
  SGOL2 WILD-TYPE 138 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      7    6
  SGOL2 WILD-TYPE  138  242
        clus
vv       SGOL2 MUTATED SGOL2 WILD-TYPE
  FEMALE             7             138
  MALE               6             242
[1] 2 2
[1] FALSE
D362V8, binary
                 cls
clus                0   1
  SGOL2 MUTATED     8   0
  SGOL2 WILD-TYPE 284  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      8    0
  SGOL2 WILD-TYPE  284   59
     clus
vv    SGOL2 MUTATED SGOL2 WILD-TYPE
  NO              8             284
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SGOL2 MUTATED                                          0
  SGOL2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SGOL2 MUTATED                                       2
  SGOL2 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SGOL2 MUTATED                                                        6
  SGOL2 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SGOL2 MUTATED                                                   0
  SGOL2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SGOL2 MUTATED                                                                   2
  SGOL2 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SGOL2 MUTATED                                                    1
  SGOL2 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SGOL2 MUTATED                                                  2
  SGOL2 WILD-TYPE                                               59
D362V9, multiclass
                                                                   clus
vv                                                                  SGOL2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  SGOL2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SGOL2 MUTATED    11   0   1   1
  SGOL2 WILD-TYPE 300  14  14  23
D362V10, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SGOL2 MUTATED       4                         0
  SGOL2 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SGOL2 MUTATED                                           0     6
  SGOL2 WILD-TYPE                                         1   237
D362V12, multiclass
                                           clus
vv                                          SGOL2 MUTATED SGOL2 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V13, binary
                 cls
clus                0   1
  SGOL2 MUTATED     0  10
  SGOL2 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      0   10
  SGOL2 WILD-TYPE    4  300
                        clus
vv                       SGOL2 MUTATED SGOL2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(363) Variable = ADNP2 MUTATION ANALYSIS
D363V1, survival
                 sevent
clus2               0   1
  ADNP2 MUTATED    15   3
  ADNP2 WILD-TYPE 215 136
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             18             351 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
              3             136 
$`ADNP2 MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8078 
       11.70         6.97        34.68        44.94        36.16        29.59 
TCGA-BR-8360 TCGA-BR-8487 TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-5726 TCGA-D7-A4YY 
        6.18         1.12        12.43        15.95        28.96        13.78 
TCGA-EQ-8122 TCGA-F1-A448 TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-VQ-A8P2 
        7.99        21.27         6.51        20.25         2.10        38.14 

$`ADNP2 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-F1-6874 
        8.38         4.34        19.96         7.13         0.62        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-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-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 

  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          14.270 
[1] "1.1 - 44.9 (14.9)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.4"
D363V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADNP2 MUTATED         0        2        1        2         5         2
  ADNP2 WILD-TYPE       2       13       39       28        32        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADNP2 MUTATED           0          3          2          2        0
  ADNP2 WILD-TYPE         3         67         51         30       38
D363V3, multiclass
            clus
vv           ADNP2 MUTATED ADNP2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              5              32
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ADNP2 MUTATED     2   2  10   5
  ADNP2 WILD-TYPE  20  90 163  92
D363V4, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  T1             2              20
  T2             2              90
  T3            10             163
  T4             5              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
  ADNP2 MUTATED    11   4   1   3
  ADNP2 WILD-TYPE 107 100  76  74
D363V5, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  N0            11             107
  N1             4             100
  N2             1              76
  N3             3              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"
D363V6, binary
                 cls
clus                0   1
  ADNP2 MUTATED    17   0
  ADNP2 WILD-TYPE 329  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     17    0
  ADNP2 WILD-TYPE  329   29
   clus
vv  ADNP2 MUTATED ADNP2 WILD-TYPE
  0            17             329
  1             0              29
[1] 2 2
[1] FALSE
D363V7, binary
                 cls
clus                0   1
  ADNP2 MUTATED     8  11
  ADNP2 WILD-TYPE 137 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED      8   11
  ADNP2 WILD-TYPE  137  237
        clus
vv       ADNP2 MUTATED ADNP2 WILD-TYPE
  FEMALE             8             137
  MALE              11             237
[1] 2 2
[1] FALSE
D363V8, binary
                 cls
clus                0   1
  ADNP2 MUTATED    13   4
  ADNP2 WILD-TYPE 279  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     13    4
  ADNP2 WILD-TYPE  279   55
     clus
vv    ADNP2 MUTATED ADNP2 WILD-TYPE
  NO             13             279
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ADNP2 MUTATED                                          0
  ADNP2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ADNP2 MUTATED                                       3
  ADNP2 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ADNP2 MUTATED                                                        9
  ADNP2 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ADNP2 MUTATED                                                   2
  ADNP2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ADNP2 MUTATED                                                                   3
  ADNP2 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ADNP2 MUTATED                                                    1
  ADNP2 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ADNP2 MUTATED                                                  1
  ADNP2 WILD-TYPE                                               60
D363V9, multiclass
                                                                   clus
vv                                                                  ADNP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  ADNP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ADNP2 MUTATED    16   0   0   2
  ADNP2 WILD-TYPE 295  14  15  22
D363V10, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  R0            16             295
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ADNP2 MUTATED       4                         0
  ADNP2 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ADNP2 MUTATED                                           0    13
  ADNP2 WILD-TYPE                                         1   230
D363V12, multiclass
                                           clus
vv                                          ADNP2 MUTATED ADNP2 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V13, binary
                 cls
clus                0   1
  ADNP2 MUTATED     1  15
  ADNP2 WILD-TYPE   3 295
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED      1   15
  ADNP2 WILD-TYPE    3  295
                        clus
vv                       ADNP2 MUTATED ADNP2 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            15             295
[1] 2 2
[1] FALSE

Clustering(364) Variable = DPP7 MUTATION ANALYSIS
D364V1, survival
                sevent
clus2              0   1
  DPP7 MUTATED     5   2
  DPP7 WILD-TYPE 225 137
  DPP7 MUTATED DPP7 WILD-TYPE 
             7            362 
  DPP7 MUTATED DPP7 WILD-TYPE 
             2            137 
$`DPP7 MUTATED`
TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8591 TCGA-CG-5726 TCGA-D7-A6EY 
       35.84        29.59         4.31        28.14        28.96        11.44 
TCGA-HF-A5NB 
       30.51 

$`DPP7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  DPP7 MUTATED DPP7 WILD-TYPE 
          4.31           0.00 
  DPP7 MUTATED DPP7 WILD-TYPE 
         35.84         122.30 
  DPP7 MUTATED DPP7 WILD-TYPE 
         28.96          14.12 
[1] "4.3 - 35.8 (29.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D364V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DPP7 MUTATED         0        1        2        0         0         1
  DPP7 WILD-TYPE       2       14       38       30        37        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DPP7 MUTATED           0          0          1          2        1
  DPP7 WILD-TYPE         3         70         52         30       37
D364V3, multiclass
            clus
vv           DPP7 MUTATED DPP7 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            2             30
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DPP7 MUTATED     1   2   1   4
  DPP7 WILD-TYPE  21  90 172  93
D364V4, multiclass
    clus
vv   DPP7 MUTATED DPP7 WILD-TYPE
  T1            1             21
  T2            2             90
  T3            1            172
  T4            4             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
  DPP7 MUTATED     4   1   1   3
  DPP7 WILD-TYPE 114 103  76  74
D364V5, multiclass
    clus
vv   DPP7 MUTATED DPP7 WILD-TYPE
  N0            4            114
  N1            1            103
  N2            1             76
  N3            3             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"
D364V6, binary
                cls
clus               0   1
  DPP7 MUTATED     9   0
  DPP7 WILD-TYPE 337  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP7 MUTATED      9    0
  DPP7 WILD-TYPE  337   29
   clus
vv  DPP7 MUTATED DPP7 WILD-TYPE
  0            9            337
  1            0             29
[1] 2 2
[1] FALSE
D364V7, binary
                cls
clus               0   1
  DPP7 MUTATED     7   2
  DPP7 WILD-TYPE 138 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP7 MUTATED      7    2
  DPP7 WILD-TYPE  138  246
        clus
vv       DPP7 MUTATED DPP7 WILD-TYPE
  FEMALE            7            138
  MALE              2            246
[1] 2 2
[1] FALSE
D364V8, binary
                cls
clus               0   1
  DPP7 MUTATED     5   1
  DPP7 WILD-TYPE 287  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP7 MUTATED      5    1
  DPP7 WILD-TYPE  287   58
     clus
vv    DPP7 MUTATED DPP7 WILD-TYPE
  NO             5            287
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DPP7 MUTATED                                          0
  DPP7 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DPP7 MUTATED                                       0
  DPP7 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DPP7 MUTATED                                                        6
  DPP7 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DPP7 MUTATED                                                   1
  DPP7 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DPP7 MUTATED                                                                   1
  DPP7 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DPP7 MUTATED                                                    0
  DPP7 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DPP7 MUTATED                                                  1
  DPP7 WILD-TYPE                                               60
D364V9, multiclass
                                                                   clus
vv                                                                  DPP7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  DPP7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DPP7 MUTATED     6   1   0   2
  DPP7 WILD-TYPE 305  13  15  22
D364V10, multiclass
    clus
vv   DPP7 MUTATED DPP7 WILD-TYPE
  R0            6            305
  R1            1             13
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DPP7 MUTATED       0                         0
  DPP7 WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DPP7 MUTATED                                           0     7
  DPP7 WILD-TYPE                                         1   236
D364V12, multiclass
                                           clus
vv                                          DPP7 MUTATED DPP7 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V13, binary
                cls
clus               0   1
  DPP7 MUTATED     0   7
  DPP7 WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP7 MUTATED      0    7
  DPP7 WILD-TYPE    4  303
                        clus
vv                       DPP7 MUTATED DPP7 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(365) Variable = CSGALNACT1 MUTATION ANALYSIS
D365V1, survival
                      sevent
clus2                    0   1
  CSGALNACT1 MUTATED    10   8
  CSGALNACT1 WILD-TYPE 220 131
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                  18                  351 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                   8                  131 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       33.21        37.25         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-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-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-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        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-A748 TCGA-D7-A74A 
       11.31        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-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-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-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 

  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               14.070 
[1] "3.3 - 105.1 (20.8)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D365V2, 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       2       15       37       29        36        50
                      vv
clus                   STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSGALNACT1 MUTATED           1          3          3          3        1
  CSGALNACT1 WILD-TYPE         2         67         50         29       37
D365V3, multiclass
            clus
vv           CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  STAGE I                     0                    2
  STAGE IA                    0                   15
  STAGE IB                    3                   37
  STAGE II                    1                   29
  STAGE IIA                   1                   36
  STAGE IIB                   2                   50
  STAGE III                   1                    2
  STAGE IIIA                  3                   67
  STAGE IIIB                  3                   50
  STAGE IIIC                  3                   29
  STAGE IV                    1                   37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    T1  T2  T3  T4
  CSGALNACT1 MUTATED     1   4   6   7
  CSGALNACT1 WILD-TYPE  21  88 167  90
D365V4, multiclass
    clus
vv   CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  T1                  1                   21
  T2                  4                   88
  T3                  6                  167
  T4                  7                   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
  CSGALNACT1 MUTATED     4   7   2   5
  CSGALNACT1 WILD-TYPE 114  97  75  72
D365V5, multiclass
    clus
vv   CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  N0                  4                  114
  N1                  7                   97
  N2                  2                   75
  N3                  5                   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"
D365V6, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED    17   1
  CSGALNACT1 WILD-TYPE 329  28
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED     17    1
  CSGALNACT1 WILD-TYPE  329   28
   clus
vv  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  0                 17                  329
  1                  1                   28
[1] 2 2
[1] FALSE
D365V7, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED     9  10
  CSGALNACT1 WILD-TYPE 136 238
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED      9   10
  CSGALNACT1 WILD-TYPE  136  238
        clus
vv       CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  FEMALE                  9                  136
  MALE                   10                  238
[1] 2 2
[1] FALSE
D365V8, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED    15   2
  CSGALNACT1 WILD-TYPE 277  57
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED     15    2
  CSGALNACT1 WILD-TYPE  277   57
     clus
vv    CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  NO                  15                  277
  YES                  2                   57
[1] 2 2
[1] FALSE
                      vv
clus                   STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CSGALNACT1 MUTATED                                          0
  CSGALNACT1 WILD-TYPE                                        8
                      vv
clus                   STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CSGALNACT1 MUTATED                                       3
  CSGALNACT1 WILD-TYPE                                    67
                      vv
clus                   STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CSGALNACT1 MUTATED                                                        9
  CSGALNACT1 WILD-TYPE                                                    149
                      vv
clus                   STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CSGALNACT1 MUTATED                                                   1
  CSGALNACT1 WILD-TYPE                                                20
                      vv
clus                   STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CSGALNACT1 MUTATED                                                                   4
  CSGALNACT1 WILD-TYPE                                                                64
                      vv
clus                   STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CSGALNACT1 MUTATED                                                    0
  CSGALNACT1 WILD-TYPE                                                  5
                      vv
clus                   STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CSGALNACT1 MUTATED                                                  2
  CSGALNACT1 WILD-TYPE                                               59
D365V9, multiclass
                                                                   clus
vv                                                                  CSGALNACT1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                              3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                  1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                   2
                                                                   clus
vv                                                                  CSGALNACT1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                             8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                               67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                             149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                   20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                   64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                   5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                    59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    R0  R1  R2  RX
  CSGALNACT1 MUTATED    14   0   1   3
  CSGALNACT1 WILD-TYPE 297  14  14  21
D365V10, multiclass
    clus
vv   CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  R0                 14                  297
  R1                  0                   14
  R2                  1                   14
  RX                  3                   21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V11, continuous
                      vv
clus                   ASIAN BLACK OR AFRICAN AMERICAN
  CSGALNACT1 MUTATED       1                         0
  CSGALNACT1 WILD-TYPE    86                         9
                      vv
clus                   NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CSGALNACT1 MUTATED                                           0    14
  CSGALNACT1 WILD-TYPE                                         1   229
D365V12, 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                                                       86
  BLACK OR AFRICAN AMERICAN                                    9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                    1
  WHITE                                                      229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V13, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED     0  14
  CSGALNACT1 WILD-TYPE   4 296
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED      0   14
  CSGALNACT1 WILD-TYPE    4  296
                        clus
vv                       CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  HISPANIC OR LATINO                      0                    4
  NOT HISPANIC OR LATINO                 14                  296
[1] 2 2
[1] FALSE

Clustering(366) Variable = CNNM1 MUTATION ANALYSIS
D366V1, survival
                 sevent
clus2               0   1
  CNNM1 MUTATED     7   4
  CNNM1 WILD-TYPE 223 135
  CNNM1 MUTATED CNNM1 WILD-TYPE 
             11             358 
  CNNM1 MUTATED CNNM1 WILD-TYPE 
              4             135 
$`CNNM1 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-A4QL 
       34.68        44.94        32.25        31.10         1.12        16.14 
TCGA-CD-5813 TCGA-CG-4465 TCGA-D7-A6EZ TCGA-HF-A5NB TCGA-R5-A7ZI 
       12.39         9.01        20.32        30.51        74.53 

$`CNNM1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  CNNM1 MUTATED CNNM1 WILD-TYPE 
           1.12            0.00 
  CNNM1 MUTATED CNNM1 WILD-TYPE 
          74.53          122.30 
  CNNM1 MUTATED CNNM1 WILD-TYPE 
          30.51           14.07 
[1] "1.1 - 74.5 (30.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D366V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNNM1 MUTATED         0        0        0        1         3         1
  CNNM1 WILD-TYPE       2       15       40       29        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNNM1 MUTATED           0          1          1          2        2
  CNNM1 WILD-TYPE         3         69         52         30       36
D366V3, multiclass
            clus
vv           CNNM1 MUTATED CNNM1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CNNM1 MUTATED     1   0   6   5
  CNNM1 WILD-TYPE  21  92 167  92
D366V4, multiclass
    clus
vv   CNNM1 MUTATED CNNM1 WILD-TYPE
  T1             1              21
  T2             0              92
  T3             6             167
  T4             5              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
  CNNM1 MUTATED     5   1   2   3
  CNNM1 WILD-TYPE 113 103  75  74
D366V5, multiclass
    clus
vv   CNNM1 MUTATED CNNM1 WILD-TYPE
  N0             5             113
  N1             1             103
  N2             2              75
  N3             3              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"
D366V6, binary
                 cls
clus                0   1
  CNNM1 MUTATED    10   2
  CNNM1 WILD-TYPE 336  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM1 MUTATED     10    2
  CNNM1 WILD-TYPE  336   27
   clus
vv  CNNM1 MUTATED CNNM1 WILD-TYPE
  0            10             336
  1             2              27
[1] 2 2
[1] FALSE
D366V7, binary
                 cls
clus                0   1
  CNNM1 MUTATED    10   2
  CNNM1 WILD-TYPE 135 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM1 MUTATED     10    2
  CNNM1 WILD-TYPE  135  246
        clus
vv       CNNM1 MUTATED CNNM1 WILD-TYPE
  FEMALE            10             135
  MALE               2             246
[1] 2 2
[1] FALSE
D366V8, binary
                 cls
clus                0   1
  CNNM1 MUTATED     9   1
  CNNM1 WILD-TYPE 283  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM1 MUTATED      9    1
  CNNM1 WILD-TYPE  283   58
     clus
vv    CNNM1 MUTATED CNNM1 WILD-TYPE
  NO              9             283
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CNNM1 MUTATED                                          0
  CNNM1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CNNM1 MUTATED                                       2
  CNNM1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CNNM1 MUTATED                                                        7
  CNNM1 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CNNM1 MUTATED                                                   2
  CNNM1 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CNNM1 MUTATED                                                                   1
  CNNM1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CNNM1 MUTATED                                                    0
  CNNM1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CNNM1 MUTATED                                                  0
  CNNM1 WILD-TYPE                                               61
D366V9, multiclass
                                                                   clus
vv                                                                  CNNM1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  CNNM1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CNNM1 MUTATED     8   1   1   1
  CNNM1 WILD-TYPE 303  13  14  23
D366V10, multiclass
    clus
vv   CNNM1 MUTATED CNNM1 WILD-TYPE
  R0             8             303
  R1             1              13
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CNNM1 MUTATED       1                         0
  CNNM1 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CNNM1 MUTATED                                           0     9
  CNNM1 WILD-TYPE                                         1   234
D366V12, multiclass
                                           clus
vv                                          CNNM1 MUTATED CNNM1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V13, binary
                 cls
clus                0   1
  CNNM1 MUTATED     1   9
  CNNM1 WILD-TYPE   3 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNNM1 MUTATED      1    9
  CNNM1 WILD-TYPE    3  301
                        clus
vv                       CNNM1 MUTATED CNNM1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(367) Variable = IFRD1 MUTATION ANALYSIS
D367V1, survival
                 sevent
clus2               0   1
  IFRD1 MUTATED     2   6
  IFRD1 WILD-TYPE 228 133
  IFRD1 MUTATED IFRD1 WILD-TYPE 
              8             361 
  IFRD1 MUTATED IFRD1 WILD-TYPE 
              6             133 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  IFRD1 MUTATED IFRD1 WILD-TYPE 
           0.26            0.00 
  IFRD1 MUTATED IFRD1 WILD-TYPE 
          44.94          122.30 
  IFRD1 MUTATED IFRD1 WILD-TYPE 
          13.61           14.43 
[1] "0.3 - 44.9 (13.6)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "2.1"
D367V2, 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       1       15       39       30        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFRD1 MUTATED           0          2          0          0        0
  IFRD1 WILD-TYPE         3         68         53         32       38
D367V3, multiclass
            clus
vv           IFRD1 MUTATED IFRD1 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IFRD1 MUTATED     1   3   4   1
  IFRD1 WILD-TYPE  21  89 169  96
D367V4, multiclass
    clus
vv   IFRD1 MUTATED IFRD1 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             4             169
  T4             1              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
  IFRD1 MUTATED     4   5   0   0
  IFRD1 WILD-TYPE 114  99  77  77
D367V5, multiclass
    clus
vv   IFRD1 MUTATED IFRD1 WILD-TYPE
  N0             4             114
  N1             5              99
  N2             0              77
  N3             0              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"
D367V6, binary
                 cls
clus                0   1
  IFRD1 MUTATED     8   0
  IFRD1 WILD-TYPE 338  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFRD1 MUTATED      8    0
  IFRD1 WILD-TYPE  338   29
   clus
vv  IFRD1 MUTATED IFRD1 WILD-TYPE
  0             8             338
  1             0              29
[1] 2 2
[1] FALSE
D367V7, binary
                 cls
clus                0   1
  IFRD1 MUTATED     5   5
  IFRD1 WILD-TYPE 140 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFRD1 MUTATED      5    5
  IFRD1 WILD-TYPE  140  243
        clus
vv       IFRD1 MUTATED IFRD1 WILD-TYPE
  FEMALE             5             140
  MALE               5             243
[1] 2 2
[1] FALSE
D367V8, binary
                 cls
clus                0   1
  IFRD1 MUTATED     9   0
  IFRD1 WILD-TYPE 283  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFRD1 MUTATED      9    0
  IFRD1 WILD-TYPE  283   59
     clus
vv    IFRD1 MUTATED IFRD1 WILD-TYPE
  NO              9             283
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IFRD1 MUTATED                                          0
  IFRD1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IFRD1 MUTATED                                       1
  IFRD1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IFRD1 MUTATED                                                        9
  IFRD1 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IFRD1 MUTATED                                                   0
  IFRD1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IFRD1 MUTATED                                                                   0
  IFRD1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IFRD1 MUTATED                                                    0
  IFRD1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IFRD1 MUTATED                                                  0
  IFRD1 WILD-TYPE                                               61
D367V9, multiclass
                                                                   clus
vv                                                                  IFRD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  IFRD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IFRD1 MUTATED     6   0   0   3
  IFRD1 WILD-TYPE 305  14  15  21
D367V10, multiclass
    clus
vv   IFRD1 MUTATED IFRD1 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IFRD1 MUTATED       1                         1
  IFRD1 WILD-TYPE    86                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IFRD1 MUTATED                                           0     8
  IFRD1 WILD-TYPE                                         1   235
D367V12, multiclass
                                           clus
vv                                          IFRD1 MUTATED IFRD1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V13, binary
                 cls
clus                0   1
  IFRD1 MUTATED     0  10
  IFRD1 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFRD1 MUTATED      0   10
  IFRD1 WILD-TYPE    4  300
                        clus
vv                       IFRD1 MUTATED IFRD1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(368) Variable = IGFBP1 MUTATION ANALYSIS
D368V1, survival
                  sevent
clus2                0   1
  IGFBP1 MUTATED     7   4
  IGFBP1 WILD-TYPE 223 135
  IGFBP1 MUTATED IGFBP1 WILD-TYPE 
              11              358 
  IGFBP1 MUTATED IGFBP1 WILD-TYPE 
               4              135 
$`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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-5719 
        9.01        18.97         7.07        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-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-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 

  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            14.12 
[1] "0.3 - 36.0 (19.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D368V2, 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       2       15       37       27        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGFBP1 MUTATED           0          0          1          0        2
  IGFBP1 WILD-TYPE         3         70         52         32       36
D368V3, multiclass
            clus
vv           IGFBP1 MUTATED IGFBP1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                3               27
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IGFBP1 MUTATED     0   4   4   3
  IGFBP1 WILD-TYPE  22  88 169  94
D368V4, multiclass
    clus
vv   IGFBP1 MUTATED IGFBP1 WILD-TYPE
  T1              0               22
  T2              4               88
  T3              4              169
  T4              3               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
  IGFBP1 MUTATED     7   2   1   1
  IGFBP1 WILD-TYPE 111 102  76  76
D368V5, multiclass
    clus
vv   IGFBP1 MUTATED IGFBP1 WILD-TYPE
  N0              7              111
  N1              2              102
  N2              1               76
  N3              1               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"
D368V6, binary
                  cls
clus                 0   1
  IGFBP1 MUTATED    10   1
  IGFBP1 WILD-TYPE 336  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP1 MUTATED     10    1
  IGFBP1 WILD-TYPE  336   28
   clus
vv  IGFBP1 MUTATED IGFBP1 WILD-TYPE
  0             10              336
  1              1               28
[1] 2 2
[1] FALSE
D368V7, binary
                  cls
clus                 0   1
  IGFBP1 MUTATED     6   5
  IGFBP1 WILD-TYPE 139 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP1 MUTATED      6    5
  IGFBP1 WILD-TYPE  139  243
        clus
vv       IGFBP1 MUTATED IGFBP1 WILD-TYPE
  FEMALE              6              139
  MALE                5              243
[1] 2 2
[1] FALSE
D368V8, binary
                  cls
clus                 0   1
  IGFBP1 MUTATED    11   0
  IGFBP1 WILD-TYPE 281  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP1 MUTATED     11    0
  IGFBP1 WILD-TYPE  281   59
     clus
vv    IGFBP1 MUTATED IGFBP1 WILD-TYPE
  NO              11              281
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IGFBP1 MUTATED                                          0
  IGFBP1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IGFBP1 MUTATED                                       3
  IGFBP1 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IGFBP1 MUTATED                                                        5
  IGFBP1 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IGFBP1 MUTATED                                                   0
  IGFBP1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IGFBP1 MUTATED                                                                   2
  IGFBP1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IGFBP1 MUTATED                                                    0
  IGFBP1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IGFBP1 MUTATED                                                  1
  IGFBP1 WILD-TYPE                                               60
D368V9, multiclass
                                                                   clus
vv                                                                  IGFBP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  IGFBP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IGFBP1 MUTATED    10   0   0   0
  IGFBP1 WILD-TYPE 301  14  15  24
D368V10, multiclass
    clus
vv   IGFBP1 MUTATED IGFBP1 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  IGFBP1 MUTATED       3                         0
  IGFBP1 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IGFBP1 MUTATED                                           0     6
  IGFBP1 WILD-TYPE                                         1   237
D368V12, multiclass
                                           clus
vv                                          IGFBP1 MUTATED IGFBP1 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V13, binary
                  cls
clus                 0   1
  IGFBP1 MUTATED     0   9
  IGFBP1 WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP1 MUTATED      0    9
  IGFBP1 WILD-TYPE    4  301
                        clus
vv                       IGFBP1 MUTATED IGFBP1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(369) Variable = SH3KBP1 MUTATION ANALYSIS
D369V1, survival
                   sevent
clus2                 0   1
  SH3KBP1 MUTATED    10   4
  SH3KBP1 WILD-TYPE 220 135
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
               14               355 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
                4               135 
$`SH3KBP1 MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-7704 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8487 
        6.61         6.97        35.24        32.25         4.31         1.12 
TCGA-BR-8680 TCGA-CG-4477 TCGA-CG-5721 TCGA-D7-A4YV TCGA-HU-A4GQ TCGA-HU-A4GU 
       31.96        30.97         6.02         5.92         0.10         6.58 
TCGA-HU-A4GX TCGA-R5-A7ZI 
       20.25        74.53 

$`SH3KBP1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         9.44         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-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-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-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-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-A4GT TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        8.98         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-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 

  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
              0.1               0.0 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
            74.53            122.30 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
             6.79             14.43 
[1] "0.1 - 74.5 (6.8)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D369V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SH3KBP1 MUTATED         0        0        2        1         1         3
  SH3KBP1 WILD-TYPE       2       15       38       29        36        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SH3KBP1 MUTATED           0          2          0          2        3
  SH3KBP1 WILD-TYPE         3         68         53         30       35
D369V3, multiclass
            clus
vv           SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                3                49
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               2                30
  STAGE IV                 3                35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SH3KBP1 MUTATED     0   2   6   6
  SH3KBP1 WILD-TYPE  22  90 167  91
D369V4, multiclass
    clus
vv   SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  T1               0                22
  T2               2                90
  T3               6               167
  T4               6                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
  SH3KBP1 MUTATED     5   7   3   0
  SH3KBP1 WILD-TYPE 113  97  74  77
D369V5, multiclass
    clus
vv   SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  N0               5               113
  N1               7                97
  N2               3                74
  N3               0                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"
D369V6, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED    12   2
  SH3KBP1 WILD-TYPE 334  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED     12    2
  SH3KBP1 WILD-TYPE  334   27
   clus
vv  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  0              12               334
  1               2                27
[1] 2 2
[1] FALSE
D369V7, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED    10   5
  SH3KBP1 WILD-TYPE 135 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED     10    5
  SH3KBP1 WILD-TYPE  135  243
        clus
vv       SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  FEMALE              10               135
  MALE                 5               243
[1] 2 2
[1] FALSE
D369V8, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED    13   1
  SH3KBP1 WILD-TYPE 279  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED     13    1
  SH3KBP1 WILD-TYPE  279   58
     clus
vv    SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  NO               13               279
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SH3KBP1 MUTATED                                          0
  SH3KBP1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SH3KBP1 MUTATED                                       3
  SH3KBP1 WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SH3KBP1 MUTATED                                                        6
  SH3KBP1 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SH3KBP1 MUTATED                                                   0
  SH3KBP1 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SH3KBP1 MUTATED                                                                   3
  SH3KBP1 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SH3KBP1 MUTATED                                                    0
  SH3KBP1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SH3KBP1 MUTATED                                                  3
  SH3KBP1 WILD-TYPE                                               58
D369V9, multiclass
                                                                   clus
vv                                                                  SH3KBP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  SH3KBP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SH3KBP1 MUTATED    12   0   0   3
  SH3KBP1 WILD-TYPE 299  14  15  21
D369V10, multiclass
    clus
vv   SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  R0              12               299
  R1               0                14
  R2               0                15
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SH3KBP1 MUTATED       4                         0
  SH3KBP1 WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SH3KBP1 MUTATED                                           0     9
  SH3KBP1 WILD-TYPE                                         1   234
D369V12, multiclass
                                           clus
vv                                          SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V13, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED     1  12
  SH3KBP1 WILD-TYPE   3 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED      1   12
  SH3KBP1 WILD-TYPE    3  298
                        clus
vv                       SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              12               298
[1] 2 2
[1] FALSE

Clustering(370) Variable = HIST1H1A MUTATION ANALYSIS
D370V1, survival
                    sevent
clus2                  0   1
  HIST1H1A MUTATED     5   3
  HIST1H1A WILD-TYPE 225 136
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 8                361 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 3                136 
$`HIST1H1A MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-8360 TCGA-BR-8591 
       21.99         6.97        30.90        32.78         6.18        28.14 
TCGA-CG-5723 TCGA-D7-6521 
      105.07        18.54 

$`HIST1H1A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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 

  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
              6.18               0.00 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
            105.07             122.30 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
            25.065             14.070 
[1] "6.2 - 105.1 (25.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D370V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HIST1H1A MUTATED         0        0        0        1         2         0
  HIST1H1A WILD-TYPE       2       15       40       29        35        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1A MUTATED           0          1          0          1        1
  HIST1H1A WILD-TYPE         3         69         53         31       37
D370V3, multiclass
            clus
vv           HIST1H1A MUTATED HIST1H1A WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  1                 29
  STAGE IIA                 2                 35
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                0                 53
  STAGE IIIC                1                 31
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H1A MUTATED     0   3   3   2
  HIST1H1A WILD-TYPE  22  89 170  95
D370V4, multiclass
    clus
vv   HIST1H1A MUTATED HIST1H1A WILD-TYPE
  T1                0                 22
  T2                3                 89
  T3                3                170
  T4                2                 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
  HIST1H1A MUTATED     2   4   1   1
  HIST1H1A WILD-TYPE 116 100  76  76
D370V5, multiclass
    clus
vv   HIST1H1A MUTATED HIST1H1A WILD-TYPE
  N0                2                116
  N1                4                100
  N2                1                 76
  N3                1                 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"
D370V6, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     7   1
  HIST1H1A WILD-TYPE 339  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      7    1
  HIST1H1A WILD-TYPE  339   28
   clus
vv  HIST1H1A MUTATED HIST1H1A WILD-TYPE
  0                7                339
  1                1                 28
[1] 2 2
[1] FALSE
D370V7, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     4   5
  HIST1H1A WILD-TYPE 141 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      4    5
  HIST1H1A WILD-TYPE  141  243
        clus
vv       HIST1H1A MUTATED HIST1H1A WILD-TYPE
  FEMALE                4                141
  MALE                  5                243
[1] 2 2
[1] FALSE
D370V8, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     8   0
  HIST1H1A WILD-TYPE 284  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      8    0
  HIST1H1A WILD-TYPE  284   59
     clus
vv    HIST1H1A MUTATED HIST1H1A WILD-TYPE
  NO                 8                284
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HIST1H1A MUTATED                                          0
  HIST1H1A WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HIST1H1A MUTATED                                       1
  HIST1H1A WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HIST1H1A MUTATED                                                        6
  HIST1H1A WILD-TYPE                                                    152
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HIST1H1A MUTATED                                                   0
  HIST1H1A WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HIST1H1A MUTATED                                                                   2
  HIST1H1A WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HIST1H1A MUTATED                                                    0
  HIST1H1A WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HIST1H1A MUTATED                                                  0
  HIST1H1A WILD-TYPE                                               61
D370V9, multiclass
                                                                   clus
vv                                                                  HIST1H1A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 0
                                                                   clus
vv                                                                  HIST1H1A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HIST1H1A MUTATED     5   0   1   3
  HIST1H1A WILD-TYPE 306  14  14  21
D370V10, multiclass
    clus
vv   HIST1H1A MUTATED HIST1H1A WILD-TYPE
  R0                5                306
  R1                0                 14
  R2                1                 14
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  HIST1H1A MUTATED       0                         0
  HIST1H1A WILD-TYPE    87                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HIST1H1A MUTATED                                           0     7
  HIST1H1A WILD-TYPE                                         1   236
D370V12, multiclass
                                           clus
vv                                          HIST1H1A MUTATED HIST1H1A WILD-TYPE
  ASIAN                                                    0                 87
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V13, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     0   7
  HIST1H1A WILD-TYPE   4 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      0    7
  HIST1H1A WILD-TYPE    4  303
                        clus
vv                       HIST1H1A MUTATED HIST1H1A WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                7                303
[1] 2 2
[1] FALSE

Clustering(371) Variable = TUBE1 MUTATION ANALYSIS
D371V1, survival
                 sevent
clus2               0   1
  TUBE1 MUTATED     6   3
  TUBE1 WILD-TYPE 224 136
  TUBE1 MUTATED TUBE1 WILD-TYPE 
              9             360 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
              3             136 
$`TUBE1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8361 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL 
        6.97        30.90        31.10        28.14        31.96        16.14 
TCGA-D7-8572 TCGA-F1-A448 TCGA-IN-A6RN 
       16.80        21.27        19.53 

$`TUBE1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  TUBE1 MUTATED TUBE1 WILD-TYPE 
           6.97            0.00 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
          31.96          122.30 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
         21.270          14.055 
[1] "7.0 - 32.0 (21.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D371V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TUBE1 MUTATED         0        0        0        0         1         1
  TUBE1 WILD-TYPE       2       15       40       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TUBE1 MUTATED           0          1          2          2        1
  TUBE1 WILD-TYPE         3         69         51         30       37
D371V3, multiclass
            clus
vv           TUBE1 MUTATED TUBE1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TUBE1 MUTATED     1   2   3   3
  TUBE1 WILD-TYPE  21  90 170  94
D371V4, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             3             170
  T4             3              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
  TUBE1 MUTATED     0   1   4   3
  TUBE1 WILD-TYPE 118 103  73  74
D371V5, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  N0             0             118
  N1             1             103
  N2             4              73
  N3             3              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"
D371V6, binary
                 cls
clus                0   1
  TUBE1 MUTATED     7   1
  TUBE1 WILD-TYPE 339  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      7    1
  TUBE1 WILD-TYPE  339   28
   clus
vv  TUBE1 MUTATED TUBE1 WILD-TYPE
  0             7             339
  1             1              28
[1] 2 2
[1] FALSE
D371V7, binary
                 cls
clus                0   1
  TUBE1 MUTATED     4   5
  TUBE1 WILD-TYPE 141 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      4    5
  TUBE1 WILD-TYPE  141  243
        clus
vv       TUBE1 MUTATED TUBE1 WILD-TYPE
  FEMALE             4             141
  MALE               5             243
[1] 2 2
[1] FALSE
D371V8, binary
                 cls
clus                0   1
  TUBE1 MUTATED     8   1
  TUBE1 WILD-TYPE 284  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      8    1
  TUBE1 WILD-TYPE  284   58
     clus
vv    TUBE1 MUTATED TUBE1 WILD-TYPE
  NO              8             284
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TUBE1 MUTATED                                          0
  TUBE1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TUBE1 MUTATED                                       0
  TUBE1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TUBE1 MUTATED                                                        7
  TUBE1 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TUBE1 MUTATED                                                   1
  TUBE1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TUBE1 MUTATED                                                                   0
  TUBE1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TUBE1 MUTATED                                                    0
  TUBE1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TUBE1 MUTATED                                                  1
  TUBE1 WILD-TYPE                                               60
D371V9, multiclass
                                                                   clus
vv                                                                  TUBE1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  TUBE1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TUBE1 MUTATED     7   0   0   2
  TUBE1 WILD-TYPE 304  14  15  22
D371V10, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TUBE1 MUTATED       1                         0
  TUBE1 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TUBE1 MUTATED                                           0     8
  TUBE1 WILD-TYPE                                         1   235
D371V12, multiclass
                                           clus
vv                                          TUBE1 MUTATED TUBE1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V13, binary
                 cls
clus                0   1
  TUBE1 MUTATED     1   8
  TUBE1 WILD-TYPE   3 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      1    8
  TUBE1 WILD-TYPE    3  302
                        clus
vv                       TUBE1 MUTATED TUBE1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(372) Variable = IPO11 MUTATION ANALYSIS
D372V1, survival
                 sevent
clus2               0   1
  IPO11 MUTATED     7   3
  IPO11 WILD-TYPE 223 136
  IPO11 MUTATED IPO11 WILD-TYPE 
             10             359 
  IPO11 MUTATED IPO11 WILD-TYPE 
              3             136 
$`IPO11 MUTATED`
TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-8360 TCGA-BR-8589 TCGA-CD-8536 TCGA-CD-A4MI 
       26.70         9.67         6.18        27.12        12.43        11.77 
TCGA-D7-6818 TCGA-F1-6874 TCGA-FP-A4BE TCGA-MX-A5UJ 
       12.36        14.47        11.08        19.73 

$`IPO11 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-D7-6820 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-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 

  IPO11 MUTATED IPO11 WILD-TYPE 
           6.18            0.00 
  IPO11 MUTATED IPO11 WILD-TYPE 
          27.12          122.30 
  IPO11 MUTATED IPO11 WILD-TYPE 
         12.395          14.430 
[1] "6.2 - 27.1 (12.4)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D372V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IPO11 MUTATED         0        0        1        1         2         1
  IPO11 WILD-TYPE       2       15       39       29        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IPO11 MUTATED           0          4          1          0        0
  IPO11 WILD-TYPE         3         66         52         32       38
D372V3, multiclass
            clus
vv           IPO11 MUTATED IPO11 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IPO11 MUTATED     0   2   5   3
  IPO11 WILD-TYPE  22  90 168  94
D372V4, multiclass
    clus
vv   IPO11 MUTATED IPO11 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             5             168
  T4             3              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
  IPO11 MUTATED     6   2   1   1
  IPO11 WILD-TYPE 112 102  76  76
D372V5, multiclass
    clus
vv   IPO11 MUTATED IPO11 WILD-TYPE
  N0             6             112
  N1             2             102
  N2             1              76
  N3             1              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"
D372V6, binary
                 cls
clus                0   1
  IPO11 MUTATED    11   0
  IPO11 WILD-TYPE 335  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED     11    0
  IPO11 WILD-TYPE  335   29
   clus
vv  IPO11 MUTATED IPO11 WILD-TYPE
  0            11             335
  1             0              29
[1] 2 2
[1] FALSE
D372V7, binary
                 cls
clus                0   1
  IPO11 MUTATED     4   7
  IPO11 WILD-TYPE 141 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED      4    7
  IPO11 WILD-TYPE  141  241
        clus
vv       IPO11 MUTATED IPO11 WILD-TYPE
  FEMALE             4             141
  MALE               7             241
[1] 2 2
[1] FALSE
D372V8, binary
                 cls
clus                0   1
  IPO11 MUTATED     8   2
  IPO11 WILD-TYPE 284  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED      8    2
  IPO11 WILD-TYPE  284   57
     clus
vv    IPO11 MUTATED IPO11 WILD-TYPE
  NO              8             284
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IPO11 MUTATED                                          0
  IPO11 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IPO11 MUTATED                                       2
  IPO11 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IPO11 MUTATED                                                        6
  IPO11 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IPO11 MUTATED                                                   0
  IPO11 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IPO11 MUTATED                                                                   2
  IPO11 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IPO11 MUTATED                                                    0
  IPO11 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IPO11 MUTATED                                                  1
  IPO11 WILD-TYPE                                               60
D372V9, multiclass
                                                                   clus
vv                                                                  IPO11 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  IPO11 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IPO11 MUTATED     8   0   0   2
  IPO11 WILD-TYPE 303  14  15  22
D372V10, multiclass
    clus
vv   IPO11 MUTATED IPO11 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IPO11 MUTATED       2                         1
  IPO11 WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IPO11 MUTATED                                           0     8
  IPO11 WILD-TYPE                                         1   235
D372V12, multiclass
                                           clus
vv                                          IPO11 MUTATED IPO11 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V13, binary
                 cls
clus                0   1
  IPO11 MUTATED     0  11
  IPO11 WILD-TYPE   4 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED      0   11
  IPO11 WILD-TYPE    4  299
                        clus
vv                       IPO11 MUTATED IPO11 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(373) Variable = IDH2 MUTATION ANALYSIS
D373V1, survival
                sevent
clus2              0   1
  IDH2 MUTATED     4   0
  IDH2 WILD-TYPE 226 139
  IDH2 MUTATED IDH2 WILD-TYPE 
             4            365 
  IDH2 MUTATED IDH2 WILD-TYPE 
             0            139 
$`IDH2 MUTATED`
TCGA-BR-A4IY TCGA-CG-5723 TCGA-HU-A4G9 TCGA-HU-A4GT 
       12.89       105.07        24.20         6.51 

$`IDH2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  IDH2 MUTATED IDH2 WILD-TYPE 
          6.51           0.00 
  IDH2 MUTATED IDH2 WILD-TYPE 
        105.07         122.30 
  IDH2 MUTATED IDH2 WILD-TYPE 
        18.545         14.270 
[1] "6.5 - 105.1 (18.5)" "0.0 - 122.3 (14.3)"
[1] "hr="     "9300000"
D373V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IDH2 MUTATED         0        1        0        1         1         1
  IDH2 WILD-TYPE       2       14       40       29        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IDH2 MUTATED           0          0          0          0        0
  IDH2 WILD-TYPE         3         70         53         32       38
D373V3, multiclass
            clus
vv           IDH2 MUTATED IDH2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IDH2 MUTATED     1   1   1   1
  IDH2 WILD-TYPE  21  91 172  96
D373V4, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  T1            1             21
  T2            1             91
  T3            1            172
  T4            1             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
  IDH2 MUTATED     3   1   0   0
  IDH2 WILD-TYPE 115 103  77  77
D373V5, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  N0            3            115
  N1            1            103
  N2            0             77
  N3            0             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"
D373V6, binary
                cls
clus               0   1
  IDH2 MUTATED     4   0
  IDH2 WILD-TYPE 342  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      4    0
  IDH2 WILD-TYPE  342   29
   clus
vv  IDH2 MUTATED IDH2 WILD-TYPE
  0            4            342
  1            0             29
[1] 2 2
[1] FALSE
D373V7, binary
                cls
clus               0   1
  IDH2 MUTATED     2   2
  IDH2 WILD-TYPE 143 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      2    2
  IDH2 WILD-TYPE  143  246
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  FEMALE            2            143
  MALE              2            246
[1] 2 2
[1] FALSE
D373V8, binary
                cls
clus               0   1
  IDH2 MUTATED     4   0
  IDH2 WILD-TYPE 288  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      4    0
  IDH2 WILD-TYPE  288   59
     clus
vv    IDH2 MUTATED IDH2 WILD-TYPE
  NO             4            288
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IDH2 MUTATED                                          0
  IDH2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IDH2 MUTATED                                       0
  IDH2 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IDH2 MUTATED                                                        2
  IDH2 WILD-TYPE                                                    156
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IDH2 MUTATED                                                   0
  IDH2 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IDH2 MUTATED                                                                   0
  IDH2 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IDH2 MUTATED                                                    0
  IDH2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IDH2 MUTATED                                                  2
  IDH2 WILD-TYPE                                               59
D373V9, multiclass
                                                                   clus
vv                                                                  IDH2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  IDH2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IDH2 MUTATED     4   0   0   0
  IDH2 WILD-TYPE 307  14  15  24
D373V10, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  R0            4            307
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IDH2 MUTATED       3                         0
  IDH2 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IDH2 MUTATED                                           0     0
  IDH2 WILD-TYPE                                         1   243
D373V12, multiclass
                                           clus
vv                                          IDH2 MUTATED IDH2 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                0            243
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V13, binary
                cls
clus               0   1
  IDH2 MUTATED     0   3
  IDH2 WILD-TYPE   4 307
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      0    3
  IDH2 WILD-TYPE    4  307
                        clus
vv                       IDH2 MUTATED IDH2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            3            307
[1] 2 2
[1] FALSE

Clustering(374) Variable = ZCCHC11 MUTATION ANALYSIS
D374V1, survival
                   sevent
clus2                 0   1
  ZCCHC11 MUTATED    11   4
  ZCCHC11 WILD-TYPE 219 135
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
               15               354 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
                4               135 
$`ZCCHC11 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-8384 
       14.04         3.32        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-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-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-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-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-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-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 

  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
             6.51              0.00 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
            35.84            122.30 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
            19.56             14.07 
[1] "6.5 - 35.8 (19.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D374V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZCCHC11 MUTATED         0        0        2        2         2         2
  ZCCHC11 WILD-TYPE       2       15       38       28        35        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZCCHC11 MUTATED           0          1          1          4        2
  ZCCHC11 WILD-TYPE         3         69         52         28       36
D374V3, multiclass
            clus
vv           ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 2                28
  STAGE IIA                2                35
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               4                28
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZCCHC11 MUTATED     0   4   5   7
  ZCCHC11 WILD-TYPE  22  88 168  90
D374V4, multiclass
    clus
vv   ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  T1               0                22
  T2               4                88
  T3               5               168
  T4               7                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
  ZCCHC11 MUTATED     5   6   2   5
  ZCCHC11 WILD-TYPE 113  98  75  72
D374V5, multiclass
    clus
vv   ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  N0               5               113
  N1               6                98
  N2               2                75
  N3               5                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"
D374V6, binary
                   cls
clus                  0   1
  ZCCHC11 MUTATED    16   1
  ZCCHC11 WILD-TYPE 330  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED     16    1
  ZCCHC11 WILD-TYPE  330   28
   clus
vv  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  0              16               330
  1               1                28
[1] 2 2
[1] FALSE
D374V7, binary
                   cls
clus                  0   1
  ZCCHC11 MUTATED     9   9
  ZCCHC11 WILD-TYPE 136 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED      9    9
  ZCCHC11 WILD-TYPE  136  239
        clus
vv       ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  FEMALE               9               136
  MALE                 9               239
[1] 2 2
[1] FALSE
D374V8, binary
                   cls
clus                  0   1
  ZCCHC11 MUTATED    14   2
  ZCCHC11 WILD-TYPE 278  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED     14    2
  ZCCHC11 WILD-TYPE  278   57
     clus
vv    ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  NO               14               278
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZCCHC11 MUTATED                                          0
  ZCCHC11 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZCCHC11 MUTATED                                       4
  ZCCHC11 WILD-TYPE                                    66
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZCCHC11 MUTATED                                                        8
  ZCCHC11 WILD-TYPE                                                    150
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZCCHC11 MUTATED                                                   1
  ZCCHC11 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZCCHC11 MUTATED                                                                   1
  ZCCHC11 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZCCHC11 MUTATED                                                    0
  ZCCHC11 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZCCHC11 MUTATED                                                  4
  ZCCHC11 WILD-TYPE                                               57
D374V9, multiclass
                                                                   clus
vv                                                                  ZCCHC11 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                4
                                                                   clus
vv                                                                  ZCCHC11 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZCCHC11 MUTATED    11   1   0   4
  ZCCHC11 WILD-TYPE 300  13  15  20
D374V10, multiclass
    clus
vv   ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  R0              11               300
  R1               1                13
  R2               0                15
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ZCCHC11 MUTATED       5                         0
  ZCCHC11 WILD-TYPE    82                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZCCHC11 MUTATED                                           0    11
  ZCCHC11 WILD-TYPE                                         1   232
D374V12, multiclass
                                           clus
vv                                          ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  ASIAN                                                   5                82
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V13, binary
                   cls
clus                  0   1
  ZCCHC11 MUTATED     0  16
  ZCCHC11 WILD-TYPE   4 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED      0   16
  ZCCHC11 WILD-TYPE    4  294
                        clus
vv                       ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              16               294
[1] 2 2
[1] FALSE

Clustering(375) Variable = SYNCRIP MUTATION ANALYSIS
D375V1, survival
                   sevent
clus2                 0   1
  SYNCRIP MUTATED     8   7
  SYNCRIP WILD-TYPE 222 132
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               15               354 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
                7               132 
$`SYNCRIP MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7717 
       21.99        26.70        19.56         6.97        34.68        18.15 
TCGA-BR-8295 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A486 TCGA-CD-A4MG TCGA-CG-5728 
        2.20         1.12        31.96         6.31         6.58        65.10 
TCGA-HF-A5NB TCGA-HU-A4GT TCGA-VQ-A8PE 
       30.51         6.51        22.19 

$`SYNCRIP WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
        9.86        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-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-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-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-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-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-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-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 

  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
             1.12              0.00 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
             65.1             122.3 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
            19.56             14.12 
[1] "1.1 - 65.1 (19.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D375V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SYNCRIP MUTATED         0        0        1        0         5         2
  SYNCRIP WILD-TYPE       2       15       39       30        32        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYNCRIP MUTATED           0          1          1          2        3
  SYNCRIP WILD-TYPE         3         69         52         30       35
D375V3, multiclass
            clus
vv           SYNCRIP MUTATED SYNCRIP WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                5                32
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               2                30
  STAGE IV                 3                35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SYNCRIP MUTATED     0   1   7   7
  SYNCRIP WILD-TYPE  22  91 166  90
D375V4, multiclass
    clus
vv   SYNCRIP MUTATED SYNCRIP WILD-TYPE
  T1               0                22
  T2               1                91
  T3               7               166
  T4               7                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
  SYNCRIP MUTATED     8   3   1   3
  SYNCRIP WILD-TYPE 110 101  76  74
D375V5, multiclass
    clus
vv   SYNCRIP MUTATED SYNCRIP WILD-TYPE
  N0               8               110
  N1               3               101
  N2               1                76
  N3               3                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"
D375V6, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED    12   2
  SYNCRIP WILD-TYPE 334  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED     12    2
  SYNCRIP WILD-TYPE  334   27
   clus
vv  SYNCRIP MUTATED SYNCRIP WILD-TYPE
  0              12               334
  1               2                27
[1] 2 2
[1] FALSE
D375V7, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED     8   7
  SYNCRIP WILD-TYPE 137 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      8    7
  SYNCRIP WILD-TYPE  137  241
        clus
vv       SYNCRIP MUTATED SYNCRIP WILD-TYPE
  FEMALE               8               137
  MALE                 7               241
[1] 2 2
[1] FALSE
D375V8, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED    13   1
  SYNCRIP WILD-TYPE 279  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED     13    1
  SYNCRIP WILD-TYPE  279   58
     clus
vv    SYNCRIP MUTATED SYNCRIP WILD-TYPE
  NO               13               279
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SYNCRIP MUTATED                                          0
  SYNCRIP WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SYNCRIP MUTATED                                       3
  SYNCRIP WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SYNCRIP MUTATED                                                        6
  SYNCRIP WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SYNCRIP MUTATED                                                   1
  SYNCRIP WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SYNCRIP MUTATED                                                                   2
  SYNCRIP WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SYNCRIP MUTATED                                                    0
  SYNCRIP WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SYNCRIP MUTATED                                                  3
  SYNCRIP WILD-TYPE                                               58
D375V9, multiclass
                                                                   clus
vv                                                                  SYNCRIP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  SYNCRIP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SYNCRIP MUTATED     9   1   1   1
  SYNCRIP WILD-TYPE 302  13  14  23
D375V10, multiclass
    clus
vv   SYNCRIP MUTATED SYNCRIP WILD-TYPE
  R0               9               302
  R1               1                13
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SYNCRIP MUTATED       4                         0
  SYNCRIP WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SYNCRIP MUTATED                                           0     8
  SYNCRIP WILD-TYPE                                         1   235
D375V12, multiclass
                                           clus
vv                                          SYNCRIP MUTATED SYNCRIP WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V13, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED     0  11
  SYNCRIP WILD-TYPE   4 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      0   11
  SYNCRIP WILD-TYPE    4  299
                        clus
vv                       SYNCRIP MUTATED SYNCRIP WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              11               299
[1] 2 2
[1] FALSE

Clustering(376) Variable = BAT3 MUTATION ANALYSIS
D376V1, survival
                sevent
clus2              0   1
  BAT3 MUTATED     8   4
  BAT3 WILD-TYPE 222 135
  BAT3 MUTATED BAT3 WILD-TYPE 
            12            357 
  BAT3 MUTATED BAT3 WILD-TYPE 
             4            135 
$`BAT3 MUTATED`
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5726 
       34.68        35.84        14.43        16.14         6.02        28.96 
TCGA-D7-A4YY TCGA-HF-7133 TCGA-HU-A4GQ TCGA-MX-A5UJ TCGA-MX-A666 TCGA-VQ-A8P2 
       13.78        63.06         0.10        19.73        14.04        38.14 

$`BAT3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        77.29        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-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        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 

  BAT3 MUTATED BAT3 WILD-TYPE 
           0.1            0.0 
  BAT3 MUTATED BAT3 WILD-TYPE 
         63.06         122.30 
  BAT3 MUTATED BAT3 WILD-TYPE 
        17.935         14.070 
[1] "0.1 - 63.1 (17.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D376V2, 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       2       14       39       30        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BAT3 MUTATED           1          2          2          2        2
  BAT3 WILD-TYPE         2         68         51         30       36
D376V3, multiclass
            clus
vv           BAT3 MUTATED BAT3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             1              2
  STAGE IIIA            2             68
  STAGE IIIB            2             51
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BAT3 MUTATED     1   3   4   5
  BAT3 WILD-TYPE  21  89 169  92
D376V4, multiclass
    clus
vv   BAT3 MUTATED BAT3 WILD-TYPE
  T1            1             21
  T2            3             89
  T3            4            169
  T4            5             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
  BAT3 MUTATED     3   3   2   4
  BAT3 WILD-TYPE 115 101  75  73
D376V5, multiclass
    clus
vv   BAT3 MUTATED BAT3 WILD-TYPE
  N0            3            115
  N1            3            101
  N2            2             75
  N3            4             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"
D376V6, binary
                cls
clus               0   1
  BAT3 MUTATED    12   0
  BAT3 WILD-TYPE 334  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT3 MUTATED     12    0
  BAT3 WILD-TYPE  334   29
   clus
vv  BAT3 MUTATED BAT3 WILD-TYPE
  0           12            334
  1            0             29
[1] 2 2
[1] FALSE
D376V7, binary
                cls
clus               0   1
  BAT3 MUTATED     5   8
  BAT3 WILD-TYPE 140 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT3 MUTATED      5    8
  BAT3 WILD-TYPE  140  240
        clus
vv       BAT3 MUTATED BAT3 WILD-TYPE
  FEMALE            5            140
  MALE              8            240
[1] 2 2
[1] FALSE
D376V8, binary
                cls
clus               0   1
  BAT3 MUTATED     8   3
  BAT3 WILD-TYPE 284  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT3 MUTATED      8    3
  BAT3 WILD-TYPE  284   56
     clus
vv    BAT3 MUTATED BAT3 WILD-TYPE
  NO             8            284
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BAT3 MUTATED                                          0
  BAT3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BAT3 MUTATED                                       1
  BAT3 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BAT3 MUTATED                                                        5
  BAT3 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BAT3 MUTATED                                                   2
  BAT3 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BAT3 MUTATED                                                                   3
  BAT3 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BAT3 MUTATED                                                    0
  BAT3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BAT3 MUTATED                                                  2
  BAT3 WILD-TYPE                                               59
D376V9, multiclass
                                                                   clus
vv                                                                  BAT3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  BAT3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BAT3 MUTATED    11   1   0   0
  BAT3 WILD-TYPE 300  13  15  24
D376V10, multiclass
    clus
vv   BAT3 MUTATED BAT3 WILD-TYPE
  R0           11            300
  R1            1             13
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BAT3 MUTATED       1                         0
  BAT3 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BAT3 MUTATED                                           0     8
  BAT3 WILD-TYPE                                         1   235
D376V12, multiclass
                                           clus
vv                                          BAT3 MUTATED BAT3 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V13, binary
                cls
clus               0   1
  BAT3 MUTATED     0   8
  BAT3 WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT3 MUTATED      0    8
  BAT3 WILD-TYPE    4  302
                        clus
vv                       BAT3 MUTATED BAT3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(377) Variable = PRPF40B MUTATION ANALYSIS
D377V1, survival
                   sevent
clus2                 0   1
  PRPF40B MUTATED    10   5
  PRPF40B WILD-TYPE 220 134
  PRPF40B MUTATED PRPF40B WILD-TYPE 
               15               354 
  PRPF40B MUTATED PRPF40B WILD-TYPE 
                5               134 
$`PRPF40B MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8680 
       26.70        30.90         9.34        34.68        30.90        31.96 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4306 TCGA-D7-6815 TCGA-F1-6874 TCGA-FP-A4BE 
       11.77        12.62         1.02        15.98        14.47        11.08 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-VQ-A8P2 
       29.98         0.10        38.14 

$`PRPF40B WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        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-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-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 

  PRPF40B MUTATED PRPF40B WILD-TYPE 
              0.1               0.0 
  PRPF40B MUTATED PRPF40B WILD-TYPE 
            38.14            122.30 
  PRPF40B MUTATED PRPF40B WILD-TYPE 
            15.98             14.12 
[1] "0.1 - 38.1 (16.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D377V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRPF40B MUTATED         0        1        2        0         3         2
  PRPF40B WILD-TYPE       2       14       38       30        34        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRPF40B MUTATED           0          3          0          1        2
  PRPF40B WILD-TYPE         3         67         53         31       36
D377V3, multiclass
            clus
vv           PRPF40B MUTATED PRPF40B WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                3                34
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               3                67
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PRPF40B MUTATED     2   5   5   4
  PRPF40B WILD-TYPE  20  87 168  93
D377V4, multiclass
    clus
vv   PRPF40B MUTATED PRPF40B WILD-TYPE
  T1               2                20
  T2               5                87
  T3               5               168
  T4               4                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
  PRPF40B MUTATED     6   4   5   0
  PRPF40B WILD-TYPE 112 100  72  77
D377V5, multiclass
    clus
vv   PRPF40B MUTATED PRPF40B WILD-TYPE
  N0               6               112
  N1               4               100
  N2               5                72
  N3               0                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"
D377V6, binary
                   cls
clus                  0   1
  PRPF40B MUTATED    15   2
  PRPF40B WILD-TYPE 331  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRPF40B MUTATED     15    2
  PRPF40B WILD-TYPE  331   27
   clus
vv  PRPF40B MUTATED PRPF40B WILD-TYPE
  0              15               331
  1               2                27
[1] 2 2
[1] FALSE
D377V7, binary
                   cls
clus                  0   1
  PRPF40B MUTATED     5  12
  PRPF40B WILD-TYPE 140 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRPF40B MUTATED      5   12
  PRPF40B WILD-TYPE  140  236
        clus
vv       PRPF40B MUTATED PRPF40B WILD-TYPE
  FEMALE               5               140
  MALE                12               236
[1] 2 2
[1] FALSE
D377V8, binary
                   cls
clus                  0   1
  PRPF40B MUTATED    12   3
  PRPF40B WILD-TYPE 280  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRPF40B MUTATED     12    3
  PRPF40B WILD-TYPE  280   56
     clus
vv    PRPF40B MUTATED PRPF40B WILD-TYPE
  NO               12               280
  YES               3                56
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PRPF40B MUTATED                                          0
  PRPF40B WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PRPF40B MUTATED                                       1
  PRPF40B WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRPF40B MUTATED                                                       10
  PRPF40B WILD-TYPE                                                    148
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PRPF40B MUTATED                                                   1
  PRPF40B WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRPF40B MUTATED                                                                   1
  PRPF40B WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PRPF40B MUTATED                                                    0
  PRPF40B WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PRPF40B MUTATED                                                  4
  PRPF40B WILD-TYPE                                               57
D377V9, multiclass
                                                                   clus
vv                                                                  PRPF40B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                4
                                                                   clus
vv                                                                  PRPF40B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PRPF40B MUTATED    11   0   1   3
  PRPF40B WILD-TYPE 300  14  14  21
D377V10, multiclass
    clus
vv   PRPF40B MUTATED PRPF40B WILD-TYPE
  R0              11               300
  R1               0                14
  R2               1                14
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PRPF40B MUTATED       6                         1
  PRPF40B WILD-TYPE    81                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRPF40B MUTATED                                           0     9
  PRPF40B WILD-TYPE                                         1   234
D377V12, multiclass
                                           clus
vv                                          PRPF40B MUTATED PRPF40B WILD-TYPE
  ASIAN                                                   6                81
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V13, binary
                   cls
clus                  0   1
  PRPF40B MUTATED     0  15
  PRPF40B WILD-TYPE   4 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRPF40B MUTATED      0   15
  PRPF40B WILD-TYPE    4  295
                        clus
vv                       PRPF40B MUTATED PRPF40B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              15               295
[1] 2 2
[1] FALSE

Clustering(378) Variable = OXNAD1 MUTATION ANALYSIS
D378V1, survival
                  sevent
clus2                0   1
  OXNAD1 MUTATED     4   2
  OXNAD1 WILD-TYPE 226 137
  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
               6              363 
  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
               2              137 
$`OXNAD1 MUTATED`
TCGA-BR-8080 TCGA-BR-8487 TCGA-BR-A4PE TCGA-CD-A4MG TCGA-HU-A4G8 TCGA-VQ-A8P2 
        9.60         1.12        20.42         6.58        22.68        38.14 

$`OXNAD1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
            1.12             0.00 
  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
           38.14           122.30 
  OXNAD1 MUTATED OXNAD1 WILD-TYPE 
           15.01            14.27 
[1] "1.1 - 38.1 (15.0)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D378V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OXNAD1 MUTATED         0        0        1        0         2         1
  OXNAD1 WILD-TYPE       2       15       39       30        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OXNAD1 MUTATED           0          1          0          1        0
  OXNAD1 WILD-TYPE         3         69         53         31       38
D378V3, multiclass
            clus
vv           OXNAD1 MUTATED OXNAD1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OXNAD1 MUTATED     0   1   3   2
  OXNAD1 WILD-TYPE  22  91 170  95
D378V4, multiclass
    clus
vv   OXNAD1 MUTATED OXNAD1 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              3              170
  T4              2               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
  OXNAD1 MUTATED     3   2   0   1
  OXNAD1 WILD-TYPE 115 102  77  76
D378V5, multiclass
    clus
vv   OXNAD1 MUTATED OXNAD1 WILD-TYPE
  N0              3              115
  N1              2              102
  N2              0               77
  N3              1               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"
D378V6, binary
                  cls
clus                 0   1
  OXNAD1 MUTATED     6   0
  OXNAD1 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OXNAD1 MUTATED      6    0
  OXNAD1 WILD-TYPE  340   29
   clus
vv  OXNAD1 MUTATED OXNAD1 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D378V7, binary
                  cls
clus                 0   1
  OXNAD1 MUTATED     4   2
  OXNAD1 WILD-TYPE 141 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OXNAD1 MUTATED      4    2
  OXNAD1 WILD-TYPE  141  246
        clus
vv       OXNAD1 MUTATED OXNAD1 WILD-TYPE
  FEMALE              4              141
  MALE                2              246
[1] 2 2
[1] FALSE
D378V8, binary
                  cls
clus                 0   1
  OXNAD1 MUTATED     5   1
  OXNAD1 WILD-TYPE 287  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OXNAD1 MUTATED      5    1
  OXNAD1 WILD-TYPE  287   58
     clus
vv    OXNAD1 MUTATED OXNAD1 WILD-TYPE
  NO               5              287
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OXNAD1 MUTATED                                          0
  OXNAD1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OXNAD1 MUTATED                                       2
  OXNAD1 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OXNAD1 MUTATED                                                        2
  OXNAD1 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OXNAD1 MUTATED                                                   2
  OXNAD1 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OXNAD1 MUTATED                                                                   0
  OXNAD1 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OXNAD1 MUTATED                                                    0
  OXNAD1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OXNAD1 MUTATED                                                  0
  OXNAD1 WILD-TYPE                                               61
D378V9, multiclass
                                                                   clus
vv                                                                  OXNAD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  OXNAD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OXNAD1 MUTATED     4   0   0   0
  OXNAD1 WILD-TYPE 307  14  15  24
D378V10, multiclass
    clus
vv   OXNAD1 MUTATED OXNAD1 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  OXNAD1 MUTATED       2                         0
  OXNAD1 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OXNAD1 MUTATED                                           0     4
  OXNAD1 WILD-TYPE                                         1   239
D378V12, multiclass
                                           clus
vv                                          OXNAD1 MUTATED OXNAD1 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V13, binary
                  cls
clus                 0   1
  OXNAD1 MUTATED     0   5
  OXNAD1 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OXNAD1 MUTATED      0    5
  OXNAD1 WILD-TYPE    4  305
                        clus
vv                       OXNAD1 MUTATED OXNAD1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(379) Variable = YLPM1 MUTATION ANALYSIS
D379V1, survival
                 sevent
clus2               0   1
  YLPM1 MUTATED    16   4
  YLPM1 WILD-TYPE 214 135
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             20             349 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
              4             135 
$`YLPM1 MUTATED`
TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8078 
        9.47         6.97         9.34        34.68        44.94        29.59 
TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8382 TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-5721 
       32.25         6.18        25.05        31.96        15.95         6.02 
TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6822 TCGA-HF-A5NB TCGA-HU-A4GT TCGA-HU-A4GX 
      105.07        21.07        12.33        30.51         6.51        20.25 
TCGA-R5-A7ZI TCGA-VQ-A8P2 
       74.53        38.14 

$`YLPM1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        26.70        11.70        19.56        11.01 
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-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-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-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-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-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-D7-8570 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-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         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-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 

  YLPM1 MUTATED YLPM1 WILD-TYPE 
           6.02            0.00 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
         105.07          122.30 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
          23.06           14.07 
[1] "6.0 - 105.1 (23.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.6"
D379V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  YLPM1 MUTATED         1        0        1        2         4         3
  YLPM1 WILD-TYPE       1       15       39       28        33        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  YLPM1 MUTATED           0          4          0          3        4
  YLPM1 WILD-TYPE         3         66         53         29       34
D379V3, multiclass
            clus
vv           YLPM1 MUTATED YLPM1 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              4              33
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  YLPM1 MUTATED     2   4   5  12
  YLPM1 WILD-TYPE  20  88 168  85
D379V4, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  T1             2              20
  T2             4              88
  T3             5             168
  T4            12              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
  YLPM1 MUTATED     8   8   4   2
  YLPM1 WILD-TYPE 110  96  73  75
D379V5, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  N0             8             110
  N1             8              96
  N2             4              73
  N3             2              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"
D379V6, binary
                 cls
clus                0   1
  YLPM1 MUTATED    20   2
  YLPM1 WILD-TYPE 326  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     20    2
  YLPM1 WILD-TYPE  326   27
   clus
vv  YLPM1 MUTATED YLPM1 WILD-TYPE
  0            20             326
  1             2              27
[1] 2 2
[1] FALSE
D379V7, binary
                 cls
clus                0   1
  YLPM1 MUTATED    12  12
  YLPM1 WILD-TYPE 133 236
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     12   12
  YLPM1 WILD-TYPE  133  236
        clus
vv       YLPM1 MUTATED YLPM1 WILD-TYPE
  FEMALE            12             133
  MALE              12             236
[1] 2 2
[1] FALSE
D379V8, binary
                 cls
clus                0   1
  YLPM1 MUTATED    20   2
  YLPM1 WILD-TYPE 272  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     20    2
  YLPM1 WILD-TYPE  272   57
     clus
vv    YLPM1 MUTATED YLPM1 WILD-TYPE
  NO             20             272
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  YLPM1 MUTATED                                          0
  YLPM1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  YLPM1 MUTATED                                       2
  YLPM1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  YLPM1 MUTATED                                                       12
  YLPM1 WILD-TYPE                                                    146
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  YLPM1 MUTATED                                                   2
  YLPM1 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  YLPM1 MUTATED                                                                   5
  YLPM1 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  YLPM1 MUTATED                                                    0
  YLPM1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  YLPM1 MUTATED                                                  3
  YLPM1 WILD-TYPE                                               58
D379V9, multiclass
                                                                   clus
vv                                                                  YLPM1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  YLPM1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  YLPM1 MUTATED    18   1   0   4
  YLPM1 WILD-TYPE 293  13  15  20
D379V10, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  R0            18             293
  R1             1              13
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  YLPM1 MUTATED       3                         1
  YLPM1 WILD-TYPE    84                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  YLPM1 MUTATED                                           0    15
  YLPM1 WILD-TYPE                                         1   228
D379V12, multiclass
                                           clus
vv                                          YLPM1 MUTATED YLPM1 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V13, binary
                 cls
clus                0   1
  YLPM1 MUTATED     1  17
  YLPM1 WILD-TYPE   3 293
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED      1   17
  YLPM1 WILD-TYPE    3  293
                        clus
vv                       YLPM1 MUTATED YLPM1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            17             293
[1] 2 2
[1] FALSE

Clustering(380) Variable = PLEKHA5 MUTATION ANALYSIS
D380V1, survival
                   sevent
clus2                 0   1
  PLEKHA5 MUTATED    12   5
  PLEKHA5 WILD-TYPE 218 134
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
               17               352 
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
                5               134 
$`PLEKHA5 MUTATED`
TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8589 TCGA-BR-8591 
        6.97         9.67         0.26        31.27        27.12        28.14 
TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-5723 TCGA-D7-A6EY TCGA-F1-6874 
       16.14        12.62        15.95       105.07        11.44        14.47 
TCGA-HU-A4GN TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       29.98        23.84        14.07        37.41        38.14 

$`PLEKHA5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-CG-4300 TCGA-CG-4301 
       11.61         6.58        12.20        11.77        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-F1-6875 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-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-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-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 

  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
             0.26              0.00 
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
           105.07            122.30 
  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE 
           16.140            14.055 
[1] "0.3 - 105.1 (16.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D380V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLEKHA5 MUTATED         1        0        4        2         1         1
  PLEKHA5 WILD-TYPE       1       15       36       28        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHA5 MUTATED           0          2          3          2        1
  PLEKHA5 WILD-TYPE         3         68         50         30       37
D380V3, multiclass
            clus
vv           PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 4                36
  STAGE II                 2                28
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               3                50
  STAGE IIIC               2                30
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHA5 MUTATED     2   7   4   4
  PLEKHA5 WILD-TYPE  20  85 169  93
D380V4, multiclass
    clus
vv   PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  T1               2                20
  T2               7                85
  T3               4               169
  T4               4                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
  PLEKHA5 MUTATED     3   9   1   4
  PLEKHA5 WILD-TYPE 115  95  76  73
D380V5, multiclass
    clus
vv   PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  N0               3               115
  N1               9                95
  N2               1                76
  N3               4                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"
D380V6, binary
                   cls
clus                  0   1
  PLEKHA5 MUTATED    16   1
  PLEKHA5 WILD-TYPE 330  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA5 MUTATED     16    1
  PLEKHA5 WILD-TYPE  330   28
   clus
vv  PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  0              16               330
  1               1                28
[1] 2 2
[1] FALSE
D380V7, binary
                   cls
clus                  0   1
  PLEKHA5 MUTATED     6  13
  PLEKHA5 WILD-TYPE 139 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA5 MUTATED      6   13
  PLEKHA5 WILD-TYPE  139  235
        clus
vv       PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  FEMALE               6               139
  MALE                13               235
[1] 2 2
[1] FALSE
D380V8, binary
                   cls
clus                  0   1
  PLEKHA5 MUTATED    17   1
  PLEKHA5 WILD-TYPE 275  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA5 MUTATED     17    1
  PLEKHA5 WILD-TYPE  275   58
     clus
vv    PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  NO               17               275
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PLEKHA5 MUTATED                                          0
  PLEKHA5 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PLEKHA5 MUTATED                                       0
  PLEKHA5 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLEKHA5 MUTATED                                                       12
  PLEKHA5 WILD-TYPE                                                    146
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PLEKHA5 MUTATED                                                   1
  PLEKHA5 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLEKHA5 MUTATED                                                                   1
  PLEKHA5 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PLEKHA5 MUTATED                                                    0
  PLEKHA5 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PLEKHA5 MUTATED                                                  5
  PLEKHA5 WILD-TYPE                                               56
D380V9, multiclass
                                                                   clus
vv                                                                  PLEKHA5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                5
                                                                   clus
vv                                                                  PLEKHA5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PLEKHA5 MUTATED    15   0   0   3
  PLEKHA5 WILD-TYPE 296  14  15  21
D380V10, multiclass
    clus
vv   PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  R0              15               296
  R1               0                14
  R2               0                15
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PLEKHA5 MUTATED       4                         1
  PLEKHA5 WILD-TYPE    83                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLEKHA5 MUTATED                                           0    12
  PLEKHA5 WILD-TYPE                                         1   231
D380V12, multiclass
                                           clus
vv                                          PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V13, binary
                   cls
clus                  0   1
  PLEKHA5 MUTATED     0  15
  PLEKHA5 WILD-TYPE   4 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA5 MUTATED      0   15
  PLEKHA5 WILD-TYPE    4  295
                        clus
vv                       PLEKHA5 MUTATED PLEKHA5 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              15               295
[1] 2 2
[1] FALSE

Clustering(381) Variable = TM7SF4 MUTATION ANALYSIS
D381V1, survival
                  sevent
clus2                0   1
  TM7SF4 MUTATED    13   4
  TM7SF4 WILD-TYPE 217 135
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
              17              352 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               4              135 
$`TM7SF4 MUTATED`
TCGA-B7-A5TI TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-8372 TCGA-BR-A452 TCGA-BR-A4QL 
       19.56         9.21        36.16        31.27         7.53        16.14 
TCGA-CD-5801 TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5723 TCGA-D7-6528 TCGA-F1-6874 
       13.18        12.43        11.77       105.07        15.22        14.47 
TCGA-FP-A9TM TCGA-HU-8602 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A91V 
        6.21        22.32        38.14        37.22        42.64 

$`TM7SF4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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 
           16.14            14.07 
[1] "6.2 - 105.1 (16.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.1"
D381V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TM7SF4 MUTATED         0        1        2        3         0         1
  TM7SF4 WILD-TYPE       2       14       38       27        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TM7SF4 MUTATED           0          6          1          2        1
  TM7SF4 WILD-TYPE         3         64         52         30       37
D381V3, multiclass
            clus
vv           TM7SF4 MUTATED TM7SF4 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                3               27
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              6               64
  STAGE IIIB              1               52
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TM7SF4 MUTATED     3   3   6   7
  TM7SF4 WILD-TYPE  19  89 167  90
D381V4, multiclass
    clus
vv   TM7SF4 MUTATED TM7SF4 WILD-TYPE
  T1              3               19
  T2              3               89
  T3              6              167
  T4              7               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
  TM7SF4 MUTATED     6   7   2   3
  TM7SF4 WILD-TYPE 112  97  75  74
D381V5, multiclass
    clus
vv   TM7SF4 MUTATED TM7SF4 WILD-TYPE
  N0              6              112
  N1              7               97
  N2              2               75
  N3              3               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"
D381V6, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED    19   0
  TM7SF4 WILD-TYPE 327  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED     19    0
  TM7SF4 WILD-TYPE  327   29
   clus
vv  TM7SF4 MUTATED TM7SF4 WILD-TYPE
  0             19              327
  1              0               29
[1] 2 2
[1] FALSE
D381V7, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED     5  14
  TM7SF4 WILD-TYPE 140 234
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      5   14
  TM7SF4 WILD-TYPE  140  234
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  FEMALE              5              140
  MALE               14              234
[1] 2 2
[1] FALSE
D381V8, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED    13   4
  TM7SF4 WILD-TYPE 279  55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED     13    4
  TM7SF4 WILD-TYPE  279   55
     clus
vv    TM7SF4 MUTATED TM7SF4 WILD-TYPE
  NO              13              279
  YES              4               55
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TM7SF4 MUTATED                                          0
  TM7SF4 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TM7SF4 MUTATED                                       2
  TM7SF4 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TM7SF4 MUTATED                                                       10
  TM7SF4 WILD-TYPE                                                    148
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TM7SF4 MUTATED                                                   1
  TM7SF4 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TM7SF4 MUTATED                                                                   1
  TM7SF4 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TM7SF4 MUTATED                                                    1
  TM7SF4 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TM7SF4 MUTATED                                                  4
  TM7SF4 WILD-TYPE                                               57
D381V9, multiclass
                                                                   clus
vv                                                                  TM7SF4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  TM7SF4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TM7SF4 MUTATED    15   0   0   2
  TM7SF4 WILD-TYPE 296  14  15  22
D381V10, multiclass
    clus
vv   TM7SF4 MUTATED TM7SF4 WILD-TYPE
  R0             15              296
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TM7SF4 MUTATED       5                         0
  TM7SF4 WILD-TYPE    82                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TM7SF4 MUTATED                                           0    12
  TM7SF4 WILD-TYPE                                         1   231
D381V12, multiclass
                                           clus
vv                                          TM7SF4 MUTATED TM7SF4 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V13, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED     0  15
  TM7SF4 WILD-TYPE   4 295
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      0   15
  TM7SF4 WILD-TYPE    4  295
                        clus
vv                       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             15              295
[1] 2 2
[1] FALSE

Clustering(382) Variable = CTNNB1 MUTATION ANALYSIS
D382V1, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED    20   4
  CTNNB1 WILD-TYPE 210 135
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              24              345 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               4              135 
$`CTNNB1 MUTATED`
TCGA-CG-5727 TCGA-B7-5816 TCGA-BR-4188 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 
       79.07        26.70         7.43        34.68        32.78        35.84 
TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-A4J5 TCGA-CG-4469 TCGA-CG-5721 TCGA-D7-6524 
       27.12        31.96        28.34         7.07         6.02        17.85 
TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-A4YX TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A747 
       12.33        19.50        36.43        11.31        20.32         8.38 
TCGA-HF-7134 TCGA-HU-8602 TCGA-HU-A4G6 TCGA-HU-A4H5 TCGA-VQ-A8P2 TCGA-VQ-AA69 
       52.21        22.32        24.26        23.80        38.14        28.41 

$`CTNNB1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
        6.61         6.97         4.64        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-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-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-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-D7-6525 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-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       12.36        11.31        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-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F0 
       13.78        14.76        26.43        11.24        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-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-A4G8 
       22.82        21.07         0.76        24.30         5.59        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-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        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 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            6.02             0.00 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           79.07           122.30 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           25.48            14.01 
[1] "6.0 - 79.1 (25.5)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "3.3"
D382V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTNNB1 MUTATED         0        2        3        2         3         4
  CTNNB1 WILD-TYPE       2       13       37       28        34        48
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNNB1 MUTATED           0          5          1          0        3
  CTNNB1 WILD-TYPE         3         65         52         32       35
D382V3, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                2               13
  STAGE IB                3               37
  STAGE II                2               28
  STAGE IIA               3               34
  STAGE IIB               4               48
  STAGE III               0                3
  STAGE IIIA              5               65
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CTNNB1 MUTATED     2   4  10   7
  CTNNB1 WILD-TYPE  20  88 163  90
D382V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1              2               20
  T2              4               88
  T3             10              163
  T4              7               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
  CTNNB1 MUTATED    11   8   4   1
  CTNNB1 WILD-TYPE 107  96  73  76
D382V5, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  N0             11              107
  N1              8               96
  N2              4               73
  N3              1               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"
D382V6, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    23   1
  CTNNB1 WILD-TYPE 323  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     23    1
  CTNNB1 WILD-TYPE  323   28
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             23              323
  1              1               28
[1] 2 2
[1] FALSE
D382V7, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     7  17
  CTNNB1 WILD-TYPE 138 231
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      7   17
  CTNNB1 WILD-TYPE  138  231
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE              7              138
  MALE               17              231
[1] 2 2
[1] FALSE
D382V8, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    21   2
  CTNNB1 WILD-TYPE 271  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     21    2
  CTNNB1 WILD-TYPE  271   57
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO              21              271
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CTNNB1 MUTATED                                          0
  CTNNB1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CTNNB1 MUTATED                                       4
  CTNNB1 WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTNNB1 MUTATED                                                        6
  CTNNB1 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CTNNB1 MUTATED                                                   2
  CTNNB1 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTNNB1 MUTATED                                                                   6
  CTNNB1 WILD-TYPE                                                                62
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CTNNB1 MUTATED                                                    2
  CTNNB1 WILD-TYPE                                                  3
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CTNNB1 MUTATED                                                  4
  CTNNB1 WILD-TYPE                                               57
D382V9, multiclass
                                                                   clus
vv                                                                  CTNNB1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  CTNNB1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED    21   2   0   1
  CTNNB1 WILD-TYPE 290  12  15  23
D382V10, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0             21              290
  R1              2               12
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CTNNB1 MUTATED       5                         0
  CTNNB1 WILD-TYPE    82                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTNNB1 MUTATED                                           0    15
  CTNNB1 WILD-TYPE                                         1   228
D382V12, multiclass
                                           clus
vv                                          CTNNB1 MUTATED CTNNB1 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 15              228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V13, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     0  18
  CTNNB1 WILD-TYPE   4 292
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      0   18
  CTNNB1 WILD-TYPE    4  292
                        clus
vv                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             18              292
[1] 2 2
[1] FALSE

Clustering(383) Variable = SNAPC2 MUTATION ANALYSIS
D383V1, survival
                  sevent
clus2                0   1
  SNAPC2 MUTATED     8   1
  SNAPC2 WILD-TYPE 222 138
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               9              360 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               1              138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  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            14.35 
[1] "0.1 - 36.2 (14.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "3.7"
D383V2, 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       2       14       39       30        36        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNAPC2 MUTATED           0          0          1          2        1
  SNAPC2 WILD-TYPE         3         70         52         30       37
D383V3, multiclass
            clus
vv           SNAPC2 MUTATED SNAPC2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              1               52
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SNAPC2 MUTATED     2   0   3   4
  SNAPC2 WILD-TYPE  20  92 170  93
D383V4, multiclass
    clus
vv   SNAPC2 MUTATED SNAPC2 WILD-TYPE
  T1              2               20
  T2              0               92
  T3              3              170
  T4              4               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
  SNAPC2 MUTATED     3   3   2   1
  SNAPC2 WILD-TYPE 115 101  75  76
D383V5, multiclass
    clus
vv   SNAPC2 MUTATED SNAPC2 WILD-TYPE
  N0              3              115
  N1              3              101
  N2              2               75
  N3              1               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"
D383V6, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     9   0
  SNAPC2 WILD-TYPE 337  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      9    0
  SNAPC2 WILD-TYPE  337   29
   clus
vv  SNAPC2 MUTATED SNAPC2 WILD-TYPE
  0              9              337
  1              0               29
[1] 2 2
[1] FALSE
D383V7, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     3   6
  SNAPC2 WILD-TYPE 142 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      3    6
  SNAPC2 WILD-TYPE  142  242
        clus
vv       SNAPC2 MUTATED SNAPC2 WILD-TYPE
  FEMALE              3              142
  MALE                6              242
[1] 2 2
[1] FALSE
D383V8, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     8   1
  SNAPC2 WILD-TYPE 284  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      8    1
  SNAPC2 WILD-TYPE  284   58
     clus
vv    SNAPC2 MUTATED SNAPC2 WILD-TYPE
  NO               8              284
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SNAPC2 MUTATED                                          0
  SNAPC2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SNAPC2 MUTATED                                       1
  SNAPC2 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SNAPC2 MUTATED                                                        4
  SNAPC2 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SNAPC2 MUTATED                                                   0
  SNAPC2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SNAPC2 MUTATED                                                                   1
  SNAPC2 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SNAPC2 MUTATED                                                    1
  SNAPC2 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SNAPC2 MUTATED                                                  2
  SNAPC2 WILD-TYPE                                               59
D383V9, multiclass
                                                                   clus
vv                                                                  SNAPC2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  SNAPC2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SNAPC2 MUTATED     9   0   0   0
  SNAPC2 WILD-TYPE 302  14  15  24
D383V10, multiclass
    clus
vv   SNAPC2 MUTATED SNAPC2 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SNAPC2 MUTATED       3                         0
  SNAPC2 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SNAPC2 MUTATED                                           0     5
  SNAPC2 WILD-TYPE                                         1   238
D383V12, multiclass
                                           clus
vv                                          SNAPC2 MUTATED SNAPC2 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V13, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     0   8
  SNAPC2 WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      0    8
  SNAPC2 WILD-TYPE    4  302
                        clus
vv                       SNAPC2 MUTATED SNAPC2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(384) Variable = MAP2K7 MUTATION ANALYSIS
D384V1, survival
                  sevent
clus2                0   1
  MAP2K7 MUTATED    15   8
  MAP2K7 WILD-TYPE 215 131
  MAP2K7 MUTATED MAP2K7 WILD-TYPE 
              23              346 
  MAP2K7 MUTATED MAP2K7 WILD-TYPE 
               8              131 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.53        28.34         0.66        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-5719 TCGA-CG-5720 
       18.97         7.07        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        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-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-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-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-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-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-A804 TCGA-R5-A805 TCGA-RD-A7BT 
       18.21         8.52        74.53         4.60         9.24         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-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 

  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            14.35 
[1] "0.8 - 115.7 (12.0)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D384V2, 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       2       12       37       29        34        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP2K7 MUTATED           1          8          1          1        3
  MAP2K7 WILD-TYPE         2         62         52         31       35
D384V3, multiclass
            clus
vv           MAP2K7 MUTATED MAP2K7 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                3               12
  STAGE IB                3               37
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               1               51
  STAGE III               1                2
  STAGE IIIA              8               62
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP2K7 MUTATED     4   5  12   6
  MAP2K7 WILD-TYPE  18  87 161  91
D384V4, multiclass
    clus
vv   MAP2K7 MUTATED MAP2K7 WILD-TYPE
  T1              4               18
  T2              5               87
  T3             12              161
  T4              6               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
  MAP2K7 MUTATED     9   6   6   3
  MAP2K7 WILD-TYPE 109  98  71  74
D384V5, multiclass
    clus
vv   MAP2K7 MUTATED MAP2K7 WILD-TYPE
  N0              9              109
  N1              6               98
  N2              6               71
  N3              3               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"
D384V6, binary
                  cls
clus                 0   1
  MAP2K7 MUTATED    24   2
  MAP2K7 WILD-TYPE 322  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K7 MUTATED     24    2
  MAP2K7 WILD-TYPE  322   27
   clus
vv  MAP2K7 MUTATED MAP2K7 WILD-TYPE
  0             24              322
  1              2               27
[1] 2 2
[1] FALSE
D384V7, binary
                  cls
clus                 0   1
  MAP2K7 MUTATED    10  17
  MAP2K7 WILD-TYPE 135 231
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K7 MUTATED     10   17
  MAP2K7 WILD-TYPE  135  231
        clus
vv       MAP2K7 MUTATED MAP2K7 WILD-TYPE
  FEMALE             10              135
  MALE               17              231
[1] 2 2
[1] FALSE
D384V8, binary
                  cls
clus                 0   1
  MAP2K7 MUTATED    18   6
  MAP2K7 WILD-TYPE 274  53
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K7 MUTATED     18    6
  MAP2K7 WILD-TYPE  274   53
     clus
vv    MAP2K7 MUTATED MAP2K7 WILD-TYPE
  NO              18              274
  YES              6               53
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MAP2K7 MUTATED                                          0
  MAP2K7 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MAP2K7 MUTATED                                       4
  MAP2K7 WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP2K7 MUTATED                                                       10
  MAP2K7 WILD-TYPE                                                    148
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MAP2K7 MUTATED                                                   3
  MAP2K7 WILD-TYPE                                                18
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP2K7 MUTATED                                                                   6
  MAP2K7 WILD-TYPE                                                                62
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MAP2K7 MUTATED                                                    0
  MAP2K7 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MAP2K7 MUTATED                                                  4
  MAP2K7 WILD-TYPE                                               57
D384V9, multiclass
                                                                   clus
vv                                                                  MAP2K7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  MAP2K7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP2K7 MUTATED    20   1   1   3
  MAP2K7 WILD-TYPE 291  13  14  21
D384V10, multiclass
    clus
vv   MAP2K7 MUTATED MAP2K7 WILD-TYPE
  R0             20              291
  R1              1               13
  R2              1               14
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAP2K7 MUTATED       5                         2
  MAP2K7 WILD-TYPE    82                         7
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP2K7 MUTATED                                           0    14
  MAP2K7 WILD-TYPE                                         1   229
D384V12, multiclass
                                           clus
vv                                          MAP2K7 MUTATED MAP2K7 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              2                7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 14              229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V13, binary
                  cls
clus                 0   1
  MAP2K7 MUTATED     0  20
  MAP2K7 WILD-TYPE   4 290
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K7 MUTATED      0   20
  MAP2K7 WILD-TYPE    4  290
                        clus
vv                       MAP2K7 MUTATED MAP2K7 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             20              290
[1] 2 2
[1] FALSE

Clustering(385) Variable = CETN3 MUTATION ANALYSIS
D385V1, survival
                 sevent
clus2               0   1
  CETN3 MUTATED     6   1
  CETN3 WILD-TYPE 224 138
  CETN3 MUTATED CETN3 WILD-TYPE 
              7             362 
  CETN3 MUTATED CETN3 WILD-TYPE 
              1             138 
$`CETN3 MUTATED`
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5728 TCGA-HU-A4GN TCGA-HU-A4GT 
       31.96        16.14         6.02        65.10        29.98         6.51 
TCGA-MX-A5UJ 
       19.73 

$`CETN3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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           14.12 
[1] "6.0 - 65.1 (19.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.3"
D385V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CETN3 MUTATED         0        0        1        0         2         0
  CETN3 WILD-TYPE       2       15       39       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CETN3 MUTATED           0          1          1          0        3
  CETN3 WILD-TYPE         3         69         52         32       35
D385V3, multiclass
            clus
vv           CETN3 MUTATED CETN3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CETN3 MUTATED     1   2   3   3
  CETN3 WILD-TYPE  21  90 170  94
D385V4, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             3             170
  T4             3              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
  CETN3 MUTATED     2   2   3   1
  CETN3 WILD-TYPE 116 102  74  76
D385V5, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  N0             2             116
  N1             2             102
  N2             3              74
  N3             1              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"
D385V6, binary
                 cls
clus                0   1
  CETN3 MUTATED     8   1
  CETN3 WILD-TYPE 338  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      8    1
  CETN3 WILD-TYPE  338   28
   clus
vv  CETN3 MUTATED CETN3 WILD-TYPE
  0             8             338
  1             1              28
[1] 2 2
[1] FALSE
D385V7, binary
                 cls
clus                0   1
  CETN3 MUTATED     6   3
  CETN3 WILD-TYPE 139 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      6    3
  CETN3 WILD-TYPE  139  245
        clus
vv       CETN3 MUTATED CETN3 WILD-TYPE
  FEMALE             6             139
  MALE               3             245
[1] 2 2
[1] FALSE
D385V8, binary
                 cls
clus                0   1
  CETN3 MUTATED     6   0
  CETN3 WILD-TYPE 286  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      6    0
  CETN3 WILD-TYPE  286   59
     clus
vv    CETN3 MUTATED CETN3 WILD-TYPE
  NO              6             286
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CETN3 MUTATED                                          0
  CETN3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CETN3 MUTATED                                       0
  CETN3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CETN3 MUTATED                                                        3
  CETN3 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CETN3 MUTATED                                                   0
  CETN3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CETN3 MUTATED                                                                   2
  CETN3 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CETN3 MUTATED                                                    0
  CETN3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CETN3 MUTATED                                                  4
  CETN3 WILD-TYPE                                               57
D385V9, multiclass
                                                                   clus
vv                                                                  CETN3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  CETN3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CETN3 MUTATED     7   0   0   2
  CETN3 WILD-TYPE 304  14  15  22
D385V10, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CETN3 MUTATED       3                         0
  CETN3 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CETN3 MUTATED                                           0     4
  CETN3 WILD-TYPE                                         1   239
D385V12, multiclass
                                           clus
vv                                          CETN3 MUTATED CETN3 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V13, binary
                 cls
clus                0   1
  CETN3 MUTATED     0   7
  CETN3 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      0    7
  CETN3 WILD-TYPE    4  303
                        clus
vv                       CETN3 MUTATED CETN3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(386) Variable = CUBN MUTATION ANALYSIS
D386V1, survival
                sevent
clus2              0   1
  CUBN MUTATED    32  20
  CUBN WILD-TYPE 198 119
  CUBN MUTATED CUBN WILD-TYPE 
            52            317 
  CUBN MUTATED CUBN WILD-TYPE 
            20            119 
$`CUBN MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 
       21.99         6.97        30.90         9.34         9.67        34.68 
TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-7197 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7901 
       32.78        30.90         9.21        35.84        33.63         3.45 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8485 
        9.60        32.25         2.66         6.18         4.31         9.21 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4QI 
        1.12        27.12        31.96         0.53        28.34        21.44 
TCGA-BR-A4QL TCGA-CD-A486 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4301 
       16.14         6.31        11.61         6.58        11.77         3.02 
TCGA-CG-4306 TCGA-CG-4455 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-6527 
        1.02        12.03         6.02       105.07        65.10        10.26 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-F1-6874 TCGA-FP-7829 TCGA-FP-A4BE TCGA-HF-A5NB 
       16.44        11.31        14.47        19.53        11.08        30.51 
TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-IN-8663 TCGA-IN-A6RR 
       22.68         6.58        20.25        12.95         3.39         6.74 
TCGA-MX-A5UJ TCGA-RD-A7C1 TCGA-VQ-A8P3 TCGA-VQ-A91U 
       19.73        16.67        37.22         1.71 

$`CUBN WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-7703 TCGA-BR-7704 TCGA-BR-7716 
       31.20        44.94        21.90        36.16        35.24        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-8284 
       37.25        14.43        11.44         0.69        29.59         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 
        0.56        29.42        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-8486 TCGA-BR-8588 TCGA-BR-8590 
        3.72         5.39        25.18        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-A4J6 TCGA-BR-A4J7 
       12.89         8.98         0.72        14.17         0.66        32.52 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5798 
       13.51        20.65        20.42         1.15         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-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH 
       12.82        12.43        12.30        11.31        12.43        12.20 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
       12.62        20.02        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-4462 
       54.08         4.01        14.01        29.98        19.07         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-D7-6528 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-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-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-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-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-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-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-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-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-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-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 

  CUBN MUTATED CUBN WILD-TYPE 
          0.53           0.00 
  CUBN MUTATED CUBN WILD-TYPE 
        105.07         122.30 
  CUBN MUTATED CUBN WILD-TYPE 
         11.90          14.66 
[1] "0.5 - 105.1 (11.9)" "0.0 - 122.3 (14.7)"
[1] "hr=" "1.1"
D386V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CUBN MUTATED         0        0        5        4         9         7
  CUBN WILD-TYPE       2       15       35       26        28        45
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CUBN MUTATED           0          9          5          4        7
  CUBN WILD-TYPE         3         61         48         28       31
D386V3, multiclass
            clus
vv           CUBN MUTATED CUBN WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              5             35
  STAGE II              4             26
  STAGE IIA             9             28
  STAGE IIB             7             45
  STAGE III             0              3
  STAGE IIIA            9             61
  STAGE IIIB            5             48
  STAGE IIIC            4             28
  STAGE IV              7             31
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CUBN MUTATED     1  11  27  15
  CUBN WILD-TYPE  21  81 146  82
D386V4, multiclass
    clus
vv   CUBN MUTATED CUBN WILD-TYPE
  T1            1             21
  T2           11             81
  T3           27            146
  T4           15             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
  CUBN MUTATED    16  20   9   7
  CUBN WILD-TYPE 102  84  68  70
D386V5, multiclass
    clus
vv   CUBN MUTATED CUBN WILD-TYPE
  N0           16            102
  N1           20             84
  N2            9             68
  N3            7             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"
D386V6, binary
                cls
clus               0   1
  CUBN MUTATED    51   5
  CUBN WILD-TYPE 295  24
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED     51    5
  CUBN WILD-TYPE  295   24
   clus
vv  CUBN MUTATED CUBN WILD-TYPE
  0           51            295
  1            5             24
[1] 2 2
[1] FALSE
D386V7, binary
                cls
clus               0   1
  CUBN MUTATED    27  31
  CUBN WILD-TYPE 118 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED     27   31
  CUBN WILD-TYPE  118  217
        clus
vv       CUBN MUTATED CUBN WILD-TYPE
  FEMALE           27            118
  MALE             31            217
[1] 2 2
[1] FALSE
D386V8, binary
                cls
clus               0   1
  CUBN MUTATED    43   5
  CUBN WILD-TYPE 249  54
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED     43    5
  CUBN WILD-TYPE  249   54
     clus
vv    CUBN MUTATED CUBN WILD-TYPE
  NO            43            249
  YES            5             54
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CUBN MUTATED                                          0
  CUBN WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CUBN MUTATED                                       5
  CUBN WILD-TYPE                                    65
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CUBN MUTATED                                                       34
  CUBN WILD-TYPE                                                    124
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CUBN MUTATED                                                   5
  CUBN WILD-TYPE                                                16
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CUBN MUTATED                                                                   7
  CUBN WILD-TYPE                                                                61
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CUBN MUTATED                                                    1
  CUBN WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CUBN MUTATED                                                  6
  CUBN WILD-TYPE                                               55
D386V9, multiclass
                                                                   clus
vv                                                                  CUBN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      34
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            7
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             6
                                                                   clus
vv                                                                  CUBN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       124
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             61
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CUBN MUTATED    39   1   3  10
  CUBN WILD-TYPE 272  13  12  14
D386V10, multiclass
    clus
vv   CUBN MUTATED CUBN WILD-TYPE
  R0           39            272
  R1            1             13
  R2            3             12
  RX           10             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CUBN MUTATED      12                         1
  CUBN WILD-TYPE    75                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CUBN MUTATED                                           0    37
  CUBN WILD-TYPE                                         1   206
D386V12, multiclass
                                           clus
vv                                          CUBN MUTATED CUBN WILD-TYPE
  ASIAN                                               12             75
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               37            206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V13, binary
                cls
clus               0   1
  CUBN MUTATED     0  48
  CUBN WILD-TYPE   4 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED      0   48
  CUBN WILD-TYPE    4  262
                        clus
vv                       CUBN MUTATED CUBN WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           48            262
[1] 2 2
[1] FALSE

Clustering(387) Variable = TRMT6 MUTATION ANALYSIS
D387V1, survival
                 sevent
clus2               0   1
  TRMT6 MUTATED     6   1
  TRMT6 WILD-TYPE 224 138
  TRMT6 MUTATED TRMT6 WILD-TYPE 
              7             362 
  TRMT6 MUTATED TRMT6 WILD-TYPE 
              1             138 
$`TRMT6 MUTATED`
TCGA-BR-7716 TCGA-BR-8589 TCGA-CD-8536 TCGA-CG-4306 TCGA-CG-5721 TCGA-HF-A5NB 
       39.78        27.12        12.43         1.02         6.02        30.51 
TCGA-HU-A4GT 
        6.51 

$`TRMT6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-D7-6526 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-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 

  TRMT6 MUTATED TRMT6 WILD-TYPE 
           1.02            0.00 
  TRMT6 MUTATED TRMT6 WILD-TYPE 
          39.78          122.30 
  TRMT6 MUTATED TRMT6 WILD-TYPE 
          12.43           14.35 
[1] "1.0 - 39.8 (12.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.6"
D387V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRMT6 MUTATED         0        0        0        1         1         1
  TRMT6 WILD-TYPE       2       15       40       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRMT6 MUTATED           0          0          1          1        2
  TRMT6 WILD-TYPE         3         70         52         31       36
D387V3, multiclass
            clus
vv           TRMT6 MUTATED TRMT6 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRMT6 MUTATED     0   0   4   3
  TRMT6 WILD-TYPE  22  92 169  94
D387V4, multiclass
    clus
vv   TRMT6 MUTATED TRMT6 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             4             169
  T4             3              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
  TRMT6 MUTATED     2   3   1   1
  TRMT6 WILD-TYPE 116 101  76  76
D387V5, multiclass
    clus
vv   TRMT6 MUTATED TRMT6 WILD-TYPE
  N0             2             116
  N1             3             101
  N2             1              76
  N3             1              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"
D387V6, binary
                 cls
clus                0   1
  TRMT6 MUTATED     6   1
  TRMT6 WILD-TYPE 340  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT6 MUTATED      6    1
  TRMT6 WILD-TYPE  340   28
   clus
vv  TRMT6 MUTATED TRMT6 WILD-TYPE
  0             6             340
  1             1              28
[1] 2 2
[1] FALSE
D387V7, binary
                 cls
clus                0   1
  TRMT6 MUTATED     3   4
  TRMT6 WILD-TYPE 142 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT6 MUTATED      3    4
  TRMT6 WILD-TYPE  142  244
        clus
vv       TRMT6 MUTATED TRMT6 WILD-TYPE
  FEMALE             3             142
  MALE               4             244
[1] 2 2
[1] FALSE
D387V8, binary
                 cls
clus                0   1
  TRMT6 MUTATED     5   1
  TRMT6 WILD-TYPE 287  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT6 MUTATED      5    1
  TRMT6 WILD-TYPE  287   58
     clus
vv    TRMT6 MUTATED TRMT6 WILD-TYPE
  NO              5             287
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TRMT6 MUTATED                                          0
  TRMT6 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TRMT6 MUTATED                                       0
  TRMT6 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRMT6 MUTATED                                                        4
  TRMT6 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TRMT6 MUTATED                                                   1
  TRMT6 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRMT6 MUTATED                                                                   1
  TRMT6 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TRMT6 MUTATED                                                    0
  TRMT6 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TRMT6 MUTATED                                                  1
  TRMT6 WILD-TYPE                                               60
D387V9, multiclass
                                                                   clus
vv                                                                  TRMT6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  TRMT6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRMT6 MUTATED     5   1   1   0
  TRMT6 WILD-TYPE 306  13  14  24
D387V10, multiclass
    clus
vv   TRMT6 MUTATED TRMT6 WILD-TYPE
  R0             5             306
  R1             1              13
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TRMT6 MUTATED       2                         0
  TRMT6 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRMT6 MUTATED                                           0     2
  TRMT6 WILD-TYPE                                         1   241
D387V12, multiclass
                                           clus
vv                                          TRMT6 MUTATED TRMT6 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V13, binary
                 cls
clus                0   1
  TRMT6 MUTATED     0   4
  TRMT6 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT6 MUTATED      0    4
  TRMT6 WILD-TYPE    4  306
                        clus
vv                       TRMT6 MUTATED TRMT6 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(388) Variable = ATM MUTATION ANALYSIS
D388V1, survival
               sevent
clus2             0   1
  ATM MUTATED    27   6
  ATM WILD-TYPE 203 133
  ATM MUTATED ATM WILD-TYPE 
           33           336 
  ATM MUTATED ATM WILD-TYPE 
            6           133 
$`ATM MUTATED`
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-7717 
        9.67        34.68        32.78        30.90        35.84        18.15 
TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8591 
       32.25        31.10         0.26         4.31         1.12        28.14 
TCGA-BR-8680 TCGA-BR-A4CQ TCGA-BR-A4J7 TCGA-CD-5798 TCGA-CD-8534 TCGA-CD-A4MI 
       31.96        34.98        32.52        13.41        12.07        11.77 
TCGA-CG-4301 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-8573 TCGA-D7-8575 
        3.02         6.02       105.07        65.10        19.50        18.21 
TCGA-D7-8579 TCGA-HF-A5NB TCGA-HU-8249 TCGA-HU-A4GT TCGA-HU-A4GX TCGA-R5-A7ZI 
       20.91        30.51        28.96         6.51        20.25        74.53 
TCGA-RD-A8MV TCGA-VQ-A8P2 TCGA-VQ-AA6K 
      122.30        38.14        12.43 

$`ATM WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44        16.14         5.13        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-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-A4MJ 
       11.31        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02        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-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-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU 
       16.80        17.19        14.66        21.14        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-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-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-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-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-ZA-A8F6 
       32.94        54.12        26.04        16.14        27.55        17.26 

  ATM MUTATED ATM WILD-TYPE 
         0.26          0.00 
  ATM MUTATED ATM WILD-TYPE 
       122.30        116.38 
  ATM MUTATED ATM WILD-TYPE 
       28.140        14.025 
[1] "0.3 - 122.3 (28.1)" "0.0 - 116.4 (14.0)"
[1] "hr=" "3.1"
D388V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATM MUTATED         0        0        4        3         6         4
  ATM WILD-TYPE       2       15       36       27        31        48
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATM MUTATED           0          7          1          5        5
  ATM WILD-TYPE         3         63         52         27       33
D388V3, multiclass
            clus
vv           ATM MUTATED ATM WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             4            36
  STAGE II             3            27
  STAGE IIA            6            31
  STAGE IIB            4            48
  STAGE III            0             3
  STAGE IIIA           7            63
  STAGE IIIB           1            52
  STAGE IIIC           5            27
  STAGE IV             5            33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ATM MUTATED     1   6  13  16
  ATM WILD-TYPE  21  86 160  81
D388V4, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T1           1            21
  T2           6            86
  T3          13           160
  T4          16            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"
               vv
clus             N0  N1  N2  N3
  ATM MUTATED    15   8   8   3
  ATM WILD-TYPE 103  96  69  74
D388V5, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  N0          15           103
  N1           8            96
  N2           8            69
  N3           3            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"
D388V6, binary
               cls
clus              0   1
  ATM MUTATED    35   3
  ATM WILD-TYPE 311  26
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     35    3
  ATM WILD-TYPE  311   26
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0          35           311
  1           3            26
[1] 2 2
[1] FALSE
D388V7, binary
               cls
clus              0   1
  ATM MUTATED    19  19
  ATM WILD-TYPE 126 229
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     19   19
  ATM WILD-TYPE  126  229
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE          19           126
  MALE            19           229
[1] 2 2
[1] FALSE
D388V8, binary
               cls
clus              0   1
  ATM MUTATED    27   5
  ATM WILD-TYPE 265  54
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     27    5
  ATM WILD-TYPE  265   54
     clus
vv    ATM MUTATED ATM WILD-TYPE
  NO           27           265
  YES           5            54
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ATM MUTATED                                          1
  ATM WILD-TYPE                                        7
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ATM MUTATED                                       3
  ATM WILD-TYPE                                    67
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATM MUTATED                                                       20
  ATM WILD-TYPE                                                    138
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ATM MUTATED                                                   4
  ATM WILD-TYPE                                                17
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATM MUTATED                                                                   5
  ATM WILD-TYPE                                                                63
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ATM MUTATED                                                    0
  ATM WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ATM MUTATED                                                  5
  ATM WILD-TYPE                                               56
D388V9, multiclass
                                                                   clus
vv                                                                  ATM MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                     20
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            5
                                                                   clus
vv                                                                  ATM WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      138
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  ATM MUTATED    29   2   1   4
  ATM WILD-TYPE 282  12  14  20
D388V10, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  R0          29           282
  R1           2            12
  R2           1            14
  RX           4            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  ATM MUTATED       8                         0
  ATM WILD-TYPE    79                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATM MUTATED                                           0    25
  ATM WILD-TYPE                                         1   218
D388V12, multiclass
                                           clus
vv                                          ATM MUTATED ATM WILD-TYPE
  ASIAN                                               8            79
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              25           218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V13, binary
               cls
clus              0   1
  ATM MUTATED     1  30
  ATM WILD-TYPE   3 280
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      1   30
  ATM WILD-TYPE    3  280
                        clus
vv                       ATM MUTATED ATM WILD-TYPE
  HISPANIC OR LATINO               1             3
  NOT HISPANIC OR LATINO          30           280
[1] 2 2
[1] FALSE

Clustering(389) Variable = PMEPA1 MUTATION ANALYSIS
D389V1, survival
                  sevent
clus2                0   1
  PMEPA1 MUTATED     4   1
  PMEPA1 WILD-TYPE 226 138
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
               5              364 
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
               1              138 
$`PMEPA1 MUTATED`
TCGA-BR-6852 TCGA-BR-8363 TCGA-HU-8602 TCGA-HU-A4GT TCGA-VQ-A8P2 
       44.94         0.26        22.32         6.51        38.14 

$`PMEPA1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
            0.26             0.00 
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
           44.94           122.30 
  PMEPA1 MUTATED PMEPA1 WILD-TYPE 
           22.32            14.22 
[1] "0.3 - 44.9 (22.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.1"
D389V2, 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       2       15       39       30        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PMEPA1 MUTATED           0          1          0          0        0
  PMEPA1 WILD-TYPE         3         69         53         32       38
D389V3, multiclass
            clus
vv           PMEPA1 MUTATED PMEPA1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PMEPA1 MUTATED     0   1   2   2
  PMEPA1 WILD-TYPE  22  91 171  95
D389V4, multiclass
    clus
vv   PMEPA1 MUTATED PMEPA1 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              2              171
  T4              2               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
  PMEPA1 MUTATED     4   1   0   0
  PMEPA1 WILD-TYPE 114 103  77  77
D389V5, multiclass
    clus
vv   PMEPA1 MUTATED PMEPA1 WILD-TYPE
  N0              4              114
  N1              1              103
  N2              0               77
  N3              0               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"
D389V6, binary
                  cls
clus                 0   1
  PMEPA1 MUTATED     6   0
  PMEPA1 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PMEPA1 MUTATED      6    0
  PMEPA1 WILD-TYPE  340   29
   clus
vv  PMEPA1 MUTATED PMEPA1 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D389V7, binary
                  cls
clus                 0   1
  PMEPA1 MUTATED     5   1
  PMEPA1 WILD-TYPE 140 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PMEPA1 MUTATED      5    1
  PMEPA1 WILD-TYPE  140  247
        clus
vv       PMEPA1 MUTATED PMEPA1 WILD-TYPE
  FEMALE              5              140
  MALE                1              247
[1] 2 2
[1] FALSE
D389V8, binary
                  cls
clus                 0   1
  PMEPA1 MUTATED     4   1
  PMEPA1 WILD-TYPE 288  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PMEPA1 MUTATED      4    1
  PMEPA1 WILD-TYPE  288   58
     clus
vv    PMEPA1 MUTATED PMEPA1 WILD-TYPE
  NO               4              288
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PMEPA1 MUTATED                                          0
  PMEPA1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PMEPA1 MUTATED                                       1
  PMEPA1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PMEPA1 MUTATED                                                        3
  PMEPA1 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PMEPA1 MUTATED                                                   1
  PMEPA1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PMEPA1 MUTATED                                                                   0
  PMEPA1 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PMEPA1 MUTATED                                                    0
  PMEPA1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PMEPA1 MUTATED                                                  1
  PMEPA1 WILD-TYPE                                               60
D389V9, multiclass
                                                                   clus
vv                                                                  PMEPA1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  PMEPA1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PMEPA1 MUTATED     5   0   0   1
  PMEPA1 WILD-TYPE 306  14  15  23
D389V10, multiclass
    clus
vv   PMEPA1 MUTATED PMEPA1 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PMEPA1 MUTATED       2                         0
  PMEPA1 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PMEPA1 MUTATED                                           0     4
  PMEPA1 WILD-TYPE                                         1   239
D389V12, multiclass
                                           clus
vv                                          PMEPA1 MUTATED PMEPA1 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V13, binary
                  cls
clus                 0   1
  PMEPA1 MUTATED     0   5
  PMEPA1 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PMEPA1 MUTATED      0    5
  PMEPA1 WILD-TYPE    4  305
                        clus
vv                       PMEPA1 MUTATED PMEPA1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(390) Variable = POP1 MUTATION ANALYSIS
D390V1, survival
                sevent
clus2              0   1
  POP1 MUTATED    11   5
  POP1 WILD-TYPE 219 134
  POP1 MUTATED POP1 WILD-TYPE 
            16            353 
  POP1 MUTATED POP1 WILD-TYPE 
             5            134 
$`POP1 MUTATED`
TCGA-CG-4460 TCGA-BR-4191 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-8059 TCGA-BR-8081 
       21.99        18.35        44.94         9.21        14.43        32.25 
TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5721 TCGA-FP-A4BE 
       31.10        31.27        31.96         6.58         6.02        11.08 
TCGA-HU-A4GN TCGA-IN-7808 TCGA-SW-A7EA TCGA-VQ-A8P2 
       29.98         3.45        19.04        38.14 

$`POP1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-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-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-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 

  POP1 MUTATED POP1 WILD-TYPE 
          3.45           0.00 
  POP1 MUTATED POP1 WILD-TYPE 
         44.94         122.30 
  POP1 MUTATED POP1 WILD-TYPE 
        20.515         14.070 
[1] "3.5 - 44.9 (20.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D390V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  POP1 MUTATED         0        0        2        1         4         1
  POP1 WILD-TYPE       2       15       38       29        33        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POP1 MUTATED           1          1          0          2        3
  POP1 WILD-TYPE         2         69         53         30       35
D390V3, multiclass
            clus
vv           POP1 MUTATED POP1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             4             33
  STAGE IIB             1             51
  STAGE III             1              2
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  POP1 MUTATED     0   3   6   8
  POP1 WILD-TYPE  22  89 167  89
D390V4, multiclass
    clus
vv   POP1 MUTATED POP1 WILD-TYPE
  T1            0             22
  T2            3             89
  T3            6            167
  T4            8             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
  POP1 MUTATED     7   6   2   2
  POP1 WILD-TYPE 111  98  75  75
D390V5, multiclass
    clus
vv   POP1 MUTATED POP1 WILD-TYPE
  N0            7            111
  N1            6             98
  N2            2             75
  N3            2             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"
D390V6, binary
                cls
clus               0   1
  POP1 MUTATED    15   3
  POP1 WILD-TYPE 331  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP1 MUTATED     15    3
  POP1 WILD-TYPE  331   26
   clus
vv  POP1 MUTATED POP1 WILD-TYPE
  0           15            331
  1            3             26
[1] 2 2
[1] FALSE
D390V7, binary
                cls
clus               0   1
  POP1 MUTATED     6  13
  POP1 WILD-TYPE 139 235
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP1 MUTATED      6   13
  POP1 WILD-TYPE  139  235
        clus
vv       POP1 MUTATED POP1 WILD-TYPE
  FEMALE            6            139
  MALE             13            235
[1] 2 2
[1] FALSE
D390V8, binary
                cls
clus               0   1
  POP1 MUTATED    14   2
  POP1 WILD-TYPE 278  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP1 MUTATED     14    2
  POP1 WILD-TYPE  278   57
     clus
vv    POP1 MUTATED POP1 WILD-TYPE
  NO            14            278
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  POP1 MUTATED                                          0
  POP1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  POP1 MUTATED                                       3
  POP1 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  POP1 MUTATED                                                        9
  POP1 WILD-TYPE                                                    149
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  POP1 MUTATED                                                   1
  POP1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  POP1 MUTATED                                                                   4
  POP1 WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  POP1 MUTATED                                                    0
  POP1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  POP1 MUTATED                                                  2
  POP1 WILD-TYPE                                               59
D390V9, multiclass
                                                                   clus
vv                                                                  POP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  POP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  POP1 MUTATED    13   0   1   3
  POP1 WILD-TYPE 298  14  14  21
D390V10, multiclass
    clus
vv   POP1 MUTATED POP1 WILD-TYPE
  R0           13            298
  R1            0             14
  R2            1             14
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  POP1 MUTATED       3                         1
  POP1 WILD-TYPE    84                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  POP1 MUTATED                                           0    12
  POP1 WILD-TYPE                                         1   231
D390V12, multiclass
                                           clus
vv                                          POP1 MUTATED POP1 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               12            231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V13, binary
                cls
clus               0   1
  POP1 MUTATED     0  15
  POP1 WILD-TYPE   4 295
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP1 MUTATED      0   15
  POP1 WILD-TYPE    4  295
                        clus
vv                       POP1 MUTATED POP1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           15            295
[1] 2 2
[1] FALSE

Clustering(391) Variable = EPHA2 MUTATION ANALYSIS
D391V1, survival
                 sevent
clus2               0   1
  EPHA2 MUTATED    20   5
  EPHA2 WILD-TYPE 210 134
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             25             344 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              5             134 
$`EPHA2 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-A4GJ 
       24.26        22.68         3.25        22.75        25.81        21.37 
TCGA-HU-A4GP TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        8.98         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-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-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 

  EPHA2 MUTATED EPHA2 WILD-TYPE 
            0.1             0.0 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          77.29          122.30 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
         19.730          14.055 
[1] "0.1 - 77.3 (19.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.3"
D391V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPHA2 MUTATED         1        3        1        1         8         2
  EPHA2 WILD-TYPE       1       12       39       29        29        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPHA2 MUTATED           0          3          2          3        2
  EPHA2 WILD-TYPE         3         67         51         29       36
D391V3, multiclass
            clus
vv           EPHA2 MUTATED EPHA2 WILD-TYPE
  STAGE I                1               1
  STAGE IA               3              12
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              8              29
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHA2 MUTATED     5   4  10   8
  EPHA2 WILD-TYPE  17  88 163  89
D391V4, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  T1             5              17
  T2             4              88
  T3            10             163
  T4             8              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
  EPHA2 MUTATED    11   9   3   3
  EPHA2 WILD-TYPE 107  95  74  74
D391V5, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  N0            11             107
  N1             9              95
  N2             3              74
  N3             3              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"
D391V6, binary
                 cls
clus                0   1
  EPHA2 MUTATED    25   1
  EPHA2 WILD-TYPE 321  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED     25    1
  EPHA2 WILD-TYPE  321   28
   clus
vv  EPHA2 MUTATED EPHA2 WILD-TYPE
  0            25             321
  1             1              28
[1] 2 2
[1] FALSE
D391V7, binary
                 cls
clus                0   1
  EPHA2 MUTATED    12  15
  EPHA2 WILD-TYPE 133 233
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED     12   15
  EPHA2 WILD-TYPE  133  233
        clus
vv       EPHA2 MUTATED EPHA2 WILD-TYPE
  FEMALE            12             133
  MALE              15             233
[1] 2 2
[1] FALSE
D391V8, binary
                 cls
clus                0   1
  EPHA2 MUTATED    21   4
  EPHA2 WILD-TYPE 271  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED     21    4
  EPHA2 WILD-TYPE  271   55
     clus
vv    EPHA2 MUTATED EPHA2 WILD-TYPE
  NO             21             271
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EPHA2 MUTATED                                          0
  EPHA2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EPHA2 MUTATED                                       4
  EPHA2 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPHA2 MUTATED                                                       10
  EPHA2 WILD-TYPE                                                    148
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EPHA2 MUTATED                                                   3
  EPHA2 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPHA2 MUTATED                                                                   2
  EPHA2 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EPHA2 MUTATED                                                    0
  EPHA2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EPHA2 MUTATED                                                  8
  EPHA2 WILD-TYPE                                               53
D391V9, multiclass
                                                                   clus
vv                                                                  EPHA2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              8
                                                                   clus
vv                                                                  EPHA2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               53
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EPHA2 MUTATED    24   0   0   2
  EPHA2 WILD-TYPE 287  14  15  22
D391V10, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  R0            24             287
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EPHA2 MUTATED       9                         2
  EPHA2 WILD-TYPE    78                         7
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPHA2 MUTATED                                           0    13
  EPHA2 WILD-TYPE                                         1   230
D391V12, multiclass
                                           clus
vv                                          EPHA2 MUTATED EPHA2 WILD-TYPE
  ASIAN                                                 9              78
  BLACK OR AFRICAN AMERICAN                             2               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V13, binary
                 cls
clus                0   1
  EPHA2 MUTATED     2  21
  EPHA2 WILD-TYPE   2 289
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      2   21
  EPHA2 WILD-TYPE    2  289
                        clus
vv                       EPHA2 MUTATED EPHA2 WILD-TYPE
  HISPANIC OR LATINO                 2               2
  NOT HISPANIC OR LATINO            21             289
[1] 2 2
[1] FALSE

Clustering(392) Variable = MPRIP MUTATION ANALYSIS
D392V1, survival
                 sevent
clus2               0   1
  MPRIP MUTATED     9   5
  MPRIP WILD-TYPE 221 134
  MPRIP MUTATED MPRIP WILD-TYPE 
             14             355 
  MPRIP MUTATED MPRIP WILD-TYPE 
              5             134 
$`MPRIP MUTATED`
TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8590 
        6.97        32.78        44.94         6.18         4.31         9.34 
TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4465 TCGA-HF-A5NB TCGA-HU-8602 
       28.14        16.14         6.58         9.01        30.51        22.32 
TCGA-HU-A4H8 TCGA-VQ-A8P2 
       14.07        38.14 

$`MPRIP WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-8487 
        3.72         5.39        25.18         9.21        20.22         1.12 
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-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-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-F1-6874 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-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 

  MPRIP MUTATED MPRIP WILD-TYPE 
           4.31            0.00 
  MPRIP MUTATED MPRIP WILD-TYPE 
          44.94          122.30 
  MPRIP MUTATED MPRIP WILD-TYPE 
         15.105          14.270 
[1] "4.3 - 44.9 (15.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D392V2, 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       2       15       38       30        33        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MPRIP MUTATED           0          3          1          3        1
  MPRIP WILD-TYPE         3         67         52         29       37
D392V3, multiclass
            clus
vv           MPRIP MUTATED MPRIP WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              4              33
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             3              29
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MPRIP MUTATED     2   1   7   7
  MPRIP WILD-TYPE  20  91 166  90
D392V4, multiclass
    clus
vv   MPRIP MUTATED MPRIP WILD-TYPE
  T1             2              20
  T2             1              91
  T3             7             166
  T4             7              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
  MPRIP MUTATED     7   3   1   4
  MPRIP WILD-TYPE 111 101  76  73
D392V5, multiclass
    clus
vv   MPRIP MUTATED MPRIP WILD-TYPE
  N0             7             111
  N1             3             101
  N2             1              76
  N3             4              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"
D392V6, binary
                 cls
clus                0   1
  MPRIP MUTATED    14   1
  MPRIP WILD-TYPE 332  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPRIP MUTATED     14    1
  MPRIP WILD-TYPE  332   28
   clus
vv  MPRIP MUTATED MPRIP WILD-TYPE
  0            14             332
  1             1              28
[1] 2 2
[1] FALSE
D392V7, binary
                 cls
clus                0   1
  MPRIP MUTATED    10   7
  MPRIP WILD-TYPE 135 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPRIP MUTATED     10    7
  MPRIP WILD-TYPE  135  241
        clus
vv       MPRIP MUTATED MPRIP WILD-TYPE
  FEMALE            10             135
  MALE               7             241
[1] 2 2
[1] FALSE
D392V8, binary
                 cls
clus                0   1
  MPRIP MUTATED    11   2
  MPRIP WILD-TYPE 281  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPRIP MUTATED     11    2
  MPRIP WILD-TYPE  281   57
     clus
vv    MPRIP MUTATED MPRIP WILD-TYPE
  NO             11             281
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MPRIP MUTATED                                          0
  MPRIP WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MPRIP MUTATED                                       3
  MPRIP WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MPRIP MUTATED                                                       10
  MPRIP WILD-TYPE                                                    148
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MPRIP MUTATED                                                   2
  MPRIP WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MPRIP MUTATED                                                                   1
  MPRIP WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MPRIP MUTATED                                                    0
  MPRIP WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MPRIP MUTATED                                                  1
  MPRIP WILD-TYPE                                               60
D392V9, multiclass
                                                                   clus
vv                                                                  MPRIP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  MPRIP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MPRIP MUTATED    10   1   1   4
  MPRIP WILD-TYPE 301  13  14  20
D392V10, multiclass
    clus
vv   MPRIP MUTATED MPRIP WILD-TYPE
  R0            10             301
  R1             1              13
  R2             1              14
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MPRIP MUTATED       3                         0
  MPRIP WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MPRIP MUTATED                                           0    12
  MPRIP WILD-TYPE                                         1   231
D392V12, multiclass
                                           clus
vv                                          MPRIP MUTATED MPRIP WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V13, binary
                 cls
clus                0   1
  MPRIP MUTATED     0  14
  MPRIP WILD-TYPE   4 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPRIP MUTATED      0   14
  MPRIP WILD-TYPE    4  296
                        clus
vv                       MPRIP MUTATED MPRIP WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(393) Variable = LARP1B MUTATION ANALYSIS
D393V1, survival
                  sevent
clus2                0   1
  LARP1B MUTATED     5   7
  LARP1B WILD-TYPE 225 132
  LARP1B MUTATED LARP1B WILD-TYPE 
              12              357 
  LARP1B MUTATED LARP1B WILD-TYPE 
               7              132 
$`LARP1B MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-8363 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5733 
        6.97         6.61         0.26         6.58        11.77        21.07 
TCGA-HF-7132 TCGA-HU-8238 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4H5 TCGA-VQ-A8P2 
       77.29         1.51        22.68         0.10        23.80        38.14 

$`LARP1B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-7133 TCGA-HF-7134 
        0.56        11.08         5.52         6.21        63.06        52.21 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       30.51        26.47         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-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 

  LARP1B MUTATED LARP1B WILD-TYPE 
             0.1              0.0 
  LARP1B MUTATED LARP1B WILD-TYPE 
           77.29           122.30 
  LARP1B MUTATED LARP1B WILD-TYPE 
            9.37            14.43 
[1] "0.1 - 77.3 (9.4)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.8"
D393V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LARP1B MUTATED         0        0        2        1         1         1
  LARP1B WILD-TYPE       2       15       38       29        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LARP1B MUTATED           1          4          0          1        0
  LARP1B WILD-TYPE         2         66         53         31       38
D393V3, multiclass
            clus
vv           LARP1B MUTATED LARP1B WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               1                2
  STAGE IIIA              4               66
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LARP1B MUTATED     0   5   5   2
  LARP1B WILD-TYPE  22  87 168  95
D393V4, multiclass
    clus
vv   LARP1B MUTATED LARP1B WILD-TYPE
  T1              0               22
  T2              5               87
  T3              5              168
  T4              2               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
  LARP1B MUTATED     3   6   3   0
  LARP1B WILD-TYPE 115  98  74  77
D393V5, multiclass
    clus
vv   LARP1B MUTATED LARP1B WILD-TYPE
  N0              3              115
  N1              6               98
  N2              3               74
  N3              0               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"
D393V6, binary
                  cls
clus                 0   1
  LARP1B MUTATED    11   0
  LARP1B WILD-TYPE 335  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP1B MUTATED     11    0
  LARP1B WILD-TYPE  335   29
   clus
vv  LARP1B MUTATED LARP1B WILD-TYPE
  0             11              335
  1              0               29
[1] 2 2
[1] FALSE
D393V7, binary
                  cls
clus                 0   1
  LARP1B MUTATED     4   8
  LARP1B WILD-TYPE 141 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP1B MUTATED      4    8
  LARP1B WILD-TYPE  141  240
        clus
vv       LARP1B MUTATED LARP1B WILD-TYPE
  FEMALE              4              141
  MALE                8              240
[1] 2 2
[1] FALSE
D393V8, binary
                  cls
clus                 0   1
  LARP1B MUTATED    10   2
  LARP1B WILD-TYPE 282  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP1B MUTATED     10    2
  LARP1B WILD-TYPE  282   57
     clus
vv    LARP1B MUTATED LARP1B WILD-TYPE
  NO              10              282
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LARP1B MUTATED                                          0
  LARP1B WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LARP1B MUTATED                                       2
  LARP1B WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LARP1B MUTATED                                                        4
  LARP1B WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LARP1B MUTATED                                                   2
  LARP1B WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LARP1B MUTATED                                                                   1
  LARP1B WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LARP1B MUTATED                                                    1
  LARP1B WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LARP1B MUTATED                                                  2
  LARP1B WILD-TYPE                                               59
D393V9, multiclass
                                                                   clus
vv                                                                  LARP1B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  LARP1B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LARP1B MUTATED     7   0   0   2
  LARP1B WILD-TYPE 304  14  15  22
D393V10, multiclass
    clus
vv   LARP1B MUTATED LARP1B WILD-TYPE
  R0              7              304
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  LARP1B MUTATED       6                         0
  LARP1B WILD-TYPE    81                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LARP1B MUTATED                                           0     4
  LARP1B WILD-TYPE                                         1   239
D393V12, multiclass
                                           clus
vv                                          LARP1B MUTATED LARP1B WILD-TYPE
  ASIAN                                                  6               81
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V13, binary
                  cls
clus                 0   1
  LARP1B MUTATED     0   9
  LARP1B WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP1B MUTATED      0    9
  LARP1B WILD-TYPE    4  301
                        clus
vv                       LARP1B MUTATED LARP1B WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(394) Variable = EIF5A2 MUTATION ANALYSIS
D394V1, survival
                  sevent
clus2                0   1
  EIF5A2 MUTATED     2   1
  EIF5A2 WILD-TYPE 228 138
  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
               3              366 
  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
               1              138 
$`EIF5A2 MUTATED`
TCGA-CG-5726 TCGA-HU-8602 TCGA-MX-A5UJ 
       28.96        22.32        19.73 

$`EIF5A2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
           19.73             0.00 
  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
           28.96           122.30 
  EIF5A2 MUTATED EIF5A2 WILD-TYPE 
           22.32            14.12 
[1] "19.7 - 29.0 (22.3)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D394V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EIF5A2 MUTATED         1        1        0        0         0         2
  EIF5A2 WILD-TYPE       1       14       40       30        37        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF5A2 MUTATED           0          1          0          0        0
  EIF5A2 WILD-TYPE         3         69         53         32       38
D394V3, multiclass
            clus
vv           EIF5A2 MUTATED EIF5A2 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EIF5A2 MUTATED     2   0   1   2
  EIF5A2 WILD-TYPE  20  92 172  95
D394V4, multiclass
    clus
vv   EIF5A2 MUTATED EIF5A2 WILD-TYPE
  T1              2               20
  T2              0               92
  T3              1              172
  T4              2               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
  EIF5A2 MUTATED     3   1   1   0
  EIF5A2 WILD-TYPE 115 103  76  77
D394V5, multiclass
    clus
vv   EIF5A2 MUTATED EIF5A2 WILD-TYPE
  N0              3              115
  N1              1              103
  N2              1               76
  N3              0               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"
D394V6, binary
                  cls
clus                 0   1
  EIF5A2 MUTATED     4   0
  EIF5A2 WILD-TYPE 342  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF5A2 MUTATED      4    0
  EIF5A2 WILD-TYPE  342   29
   clus
vv  EIF5A2 MUTATED EIF5A2 WILD-TYPE
  0              4              342
  1              0               29
[1] 2 2
[1] FALSE
D394V7, binary
                  cls
clus                 0   1
  EIF5A2 MUTATED     2   3
  EIF5A2 WILD-TYPE 143 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF5A2 MUTATED      2    3
  EIF5A2 WILD-TYPE  143  245
        clus
vv       EIF5A2 MUTATED EIF5A2 WILD-TYPE
  FEMALE              2              143
  MALE                3              245
[1] 2 2
[1] FALSE
D394V8, binary
                  cls
clus                 0   1
  EIF5A2 MUTATED     4   0
  EIF5A2 WILD-TYPE 288  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF5A2 MUTATED      4    0
  EIF5A2 WILD-TYPE  288   59
     clus
vv    EIF5A2 MUTATED EIF5A2 WILD-TYPE
  NO               4              288
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EIF5A2 MUTATED                                          0
  EIF5A2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EIF5A2 MUTATED                                       1
  EIF5A2 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EIF5A2 MUTATED                                                        1
  EIF5A2 WILD-TYPE                                                    157
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EIF5A2 MUTATED                                                   0
  EIF5A2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EIF5A2 MUTATED                                                                   2
  EIF5A2 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EIF5A2 MUTATED                                                    0
  EIF5A2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EIF5A2 MUTATED                                                  1
  EIF5A2 WILD-TYPE                                               60
D394V9, multiclass
                                                                   clus
vv                                                                  EIF5A2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  EIF5A2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EIF5A2 MUTATED     5   0   0   0
  EIF5A2 WILD-TYPE 306  14  15  24
D394V10, multiclass
    clus
vv   EIF5A2 MUTATED EIF5A2 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D394V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  EIF5A2 MUTATED       1                         1
  EIF5A2 WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EIF5A2 MUTATED                                           0     2
  EIF5A2 WILD-TYPE                                         1   241
D394V12, multiclass
                                           clus
vv                                          EIF5A2 MUTATED EIF5A2 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D394V13, binary
                  cls
clus                 0   1
  EIF5A2 MUTATED     0   4
  EIF5A2 WILD-TYPE   4 306
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF5A2 MUTATED      0    4
  EIF5A2 WILD-TYPE    4  306
                        clus
vv                       EIF5A2 MUTATED EIF5A2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              306
[1] 2 2
[1] FALSE

Clustering(395) Variable = RING1 MUTATION ANALYSIS
D395V1, survival
                 sevent
clus2               0   1
  RING1 MUTATED     6   0
  RING1 WILD-TYPE 224 139
  RING1 MUTATED RING1 WILD-TYPE 
              6             363 
  RING1 MUTATED RING1 WILD-TYPE 
              0             139 
$`RING1 MUTATED`
TCGA-B7-A5TI TCGA-BR-6452 TCGA-CD-5802 TCGA-CG-5721 TCGA-D7-A4YY TCGA-HU-A4H3 
       19.56        34.68        13.35         6.02        13.78        29.00 

$`RING1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  RING1 MUTATED RING1 WILD-TYPE 
           6.02            0.00 
  RING1 MUTATED RING1 WILD-TYPE 
          34.68          122.30 
  RING1 MUTATED RING1 WILD-TYPE 
          16.67           14.27 
[1] "6.0 - 34.7 (16.7)"  "0.0 - 122.3 (14.3)"
[1] "hr="     "9200000"
D395V2, 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       2       15       40       29        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RING1 MUTATED           0          0          1          2        2
  RING1 WILD-TYPE         3         70         52         30       36
D395V3, multiclass
            clus
vv           RING1 MUTATED RING1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RING1 MUTATED     0   0   3   4
  RING1 WILD-TYPE  22  92 170  93
D395V4, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             3             170
  T4             4              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
  RING1 MUTATED     2   1   1   3
  RING1 WILD-TYPE 116 103  76  74
D395V5, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  N0             2             116
  N1             1             103
  N2             1              76
  N3             3              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"
D395V6, binary
                 cls
clus                0   1
  RING1 MUTATED     8   0
  RING1 WILD-TYPE 338  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      8    0
  RING1 WILD-TYPE  338   29
   clus
vv  RING1 MUTATED RING1 WILD-TYPE
  0             8             338
  1             0              29
[1] 2 2
[1] FALSE
D395V7, binary
                 cls
clus                0   1
  RING1 MUTATED     4   4
  RING1 WILD-TYPE 141 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      4    4
  RING1 WILD-TYPE  141  244
        clus
vv       RING1 MUTATED RING1 WILD-TYPE
  FEMALE             4             141
  MALE               4             244
[1] 2 2
[1] FALSE
D395V8, binary
                 cls
clus                0   1
  RING1 MUTATED     3   2
  RING1 WILD-TYPE 289  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      3    2
  RING1 WILD-TYPE  289   57
     clus
vv    RING1 MUTATED RING1 WILD-TYPE
  NO              3             289
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RING1 MUTATED                                          0
  RING1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RING1 MUTATED                                       2
  RING1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RING1 MUTATED                                                        5
  RING1 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RING1 MUTATED                                                   0
  RING1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RING1 MUTATED                                                                   1
  RING1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RING1 MUTATED                                                    0
  RING1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RING1 MUTATED                                                  0
  RING1 WILD-TYPE                                               61
D395V9, multiclass
                                                                   clus
vv                                                                  RING1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  RING1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RING1 MUTATED     4   0   0   2
  RING1 WILD-TYPE 307  14  15  22
D395V10, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D395V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RING1 MUTATED       2                         0
  RING1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RING1 MUTATED                                           0     5
  RING1 WILD-TYPE                                         1   238
D395V12, multiclass
                                           clus
vv                                          RING1 MUTATED RING1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D395V13, binary
                 cls
clus                0   1
  RING1 MUTATED     0   7
  RING1 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      0    7
  RING1 WILD-TYPE    4  303
                        clus
vv                       RING1 MUTATED RING1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(396) Variable = FAM83E MUTATION ANALYSIS
D396V1, survival
                  sevent
clus2                0   1
  FAM83E MUTATED     8   3
  FAM83E WILD-TYPE 222 136
  FAM83E MUTATED FAM83E WILD-TYPE 
              11              358 
  FAM83E MUTATED FAM83E WILD-TYPE 
               3              136 
$`FAM83E MUTATED`
TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5721 
       44.94         6.18         1.12        16.14         6.58         6.02 
TCGA-D7-A6EY TCGA-FP-A4BE TCGA-HU-A4GU TCGA-HU-A4GX TCGA-MX-A5UJ 
       11.44        11.08         6.58        20.25        19.73 

$`FAM83E WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  FAM83E MUTATED FAM83E WILD-TYPE 
            1.12             0.00 
  FAM83E MUTATED FAM83E WILD-TYPE 
           44.94           122.30 
  FAM83E MUTATED FAM83E WILD-TYPE 
           11.08            14.45 
[1] "1.1 - 44.9 (11.1)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1"  
D396V2, 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       2       15       39       30        32        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM83E MUTATED           0          1          2          1        1
  FAM83E WILD-TYPE         3         69         51         31       37
D396V3, multiclass
            clus
vv           FAM83E MUTATED FAM83E WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               5               32
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              2               51
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM83E MUTATED     1   1   9   2
  FAM83E WILD-TYPE  21  91 164  95
D396V4, multiclass
    clus
vv   FAM83E MUTATED FAM83E WILD-TYPE
  T1              1               21
  T2              1               91
  T3              9              164
  T4              2               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
  FAM83E MUTATED     6   2   2   2
  FAM83E WILD-TYPE 112 102  75  75
D396V5, multiclass
    clus
vv   FAM83E MUTATED FAM83E WILD-TYPE
  N0              6              112
  N1              2              102
  N2              2               75
  N3              2               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"
D396V6, binary
                  cls
clus                 0   1
  FAM83E MUTATED    13   0
  FAM83E WILD-TYPE 333  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83E MUTATED     13    0
  FAM83E WILD-TYPE  333   29
   clus
vv  FAM83E MUTATED FAM83E WILD-TYPE
  0             13              333
  1              0               29
[1] 2 2
[1] FALSE
D396V7, binary
                  cls
clus                 0   1
  FAM83E MUTATED     7   6
  FAM83E WILD-TYPE 138 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83E MUTATED      7    6
  FAM83E WILD-TYPE  138  242
        clus
vv       FAM83E MUTATED FAM83E WILD-TYPE
  FEMALE              7              138
  MALE                6              242
[1] 2 2
[1] FALSE
D396V8, binary
                  cls
clus                 0   1
  FAM83E MUTATED    10   1
  FAM83E WILD-TYPE 282  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83E MUTATED     10    1
  FAM83E WILD-TYPE  282   58
     clus
vv    FAM83E MUTATED FAM83E WILD-TYPE
  NO              10              282
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM83E MUTATED                                          0
  FAM83E WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM83E MUTATED                                       3
  FAM83E WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM83E MUTATED                                                        5
  FAM83E WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM83E MUTATED                                                   0
  FAM83E WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM83E MUTATED                                                                   3
  FAM83E WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM83E MUTATED                                                    0
  FAM83E WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM83E MUTATED                                                  2
  FAM83E WILD-TYPE                                               59
D396V9, multiclass
                                                                   clus
vv                                                                  FAM83E MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  FAM83E WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAM83E MUTATED    11   0   0   1
  FAM83E WILD-TYPE 300  14  15  23
D396V10, multiclass
    clus
vv   FAM83E MUTATED FAM83E WILD-TYPE
  R0             11              300
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D396V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAM83E MUTATED       3                         1
  FAM83E WILD-TYPE    84                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM83E MUTATED                                           0     7
  FAM83E WILD-TYPE                                         1   236
D396V12, multiclass
                                           clus
vv                                          FAM83E MUTATED FAM83E WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D396V13, binary
                  cls
clus                 0   1
  FAM83E MUTATED     0  11
  FAM83E WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM83E MUTATED      0   11
  FAM83E WILD-TYPE    4  299
                        clus
vv                       FAM83E MUTATED FAM83E WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(397) Variable = CLDN6 MUTATION ANALYSIS
D397V1, survival
                 sevent
clus2               0   1
  CLDN6 MUTATED     5   3
  CLDN6 WILD-TYPE 225 136
  CLDN6 MUTATED CLDN6 WILD-TYPE 
              8             361 
  CLDN6 MUTATED CLDN6 WILD-TYPE 
              3             136 
$`CLDN6 MUTATED`
TCGA-CG-4460 TCGA-BR-7707 TCGA-BR-8368 TCGA-BR-8680 TCGA-BR-A4QL TCGA-D7-A4YV 
       21.99        35.84         4.31        31.96        16.14         5.92 
TCGA-HU-A4GT TCGA-MX-A5UJ 
        6.51        19.73 

$`CLDN6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  CLDN6 MUTATED CLDN6 WILD-TYPE 
           4.31            0.00 
  CLDN6 MUTATED CLDN6 WILD-TYPE 
          35.84          122.30 
  CLDN6 MUTATED CLDN6 WILD-TYPE 
         17.935          14.170 
[1] "4.3 - 35.8 (17.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1"  
D397V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CLDN6 MUTATED         0        0        2        0         1         1
  CLDN6 WILD-TYPE       2       15       38       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLDN6 MUTATED           0          2          1          0        2
  CLDN6 WILD-TYPE         3         68         52         32       36
D397V3, multiclass
            clus
vv           CLDN6 MUTATED CLDN6 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CLDN6 MUTATED     0   2   4   3
  CLDN6 WILD-TYPE  22  90 169  94
D397V4, multiclass
    clus
vv   CLDN6 MUTATED CLDN6 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             4             169
  T4             3              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
  CLDN6 MUTATED     4   2   2   1
  CLDN6 WILD-TYPE 114 102  75  76
D397V5, multiclass
    clus
vv   CLDN6 MUTATED CLDN6 WILD-TYPE
  N0             4             114
  N1             2             102
  N2             2              75
  N3             1              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"
D397V6, binary
                 cls
clus                0   1
  CLDN6 MUTATED     7   2
  CLDN6 WILD-TYPE 339  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN6 MUTATED      7    2
  CLDN6 WILD-TYPE  339   27
   clus
vv  CLDN6 MUTATED CLDN6 WILD-TYPE
  0             7             339
  1             2              27
[1] 2 2
[1] FALSE
D397V7, binary
                 cls
clus                0   1
  CLDN6 MUTATED     8   1
  CLDN6 WILD-TYPE 137 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN6 MUTATED      8    1
  CLDN6 WILD-TYPE  137  247
        clus
vv       CLDN6 MUTATED CLDN6 WILD-TYPE
  FEMALE             8             137
  MALE               1             247
[1] 2 2
[1] FALSE
D397V8, binary
                 cls
clus                0   1
  CLDN6 MUTATED     8   0
  CLDN6 WILD-TYPE 284  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN6 MUTATED      8    0
  CLDN6 WILD-TYPE  284   59
     clus
vv    CLDN6 MUTATED CLDN6 WILD-TYPE
  NO              8             284
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CLDN6 MUTATED                                          0
  CLDN6 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CLDN6 MUTATED                                       0
  CLDN6 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CLDN6 MUTATED                                                        4
  CLDN6 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CLDN6 MUTATED                                                   0
  CLDN6 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CLDN6 MUTATED                                                                   1
  CLDN6 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CLDN6 MUTATED                                                    0
  CLDN6 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CLDN6 MUTATED                                                  4
  CLDN6 WILD-TYPE                                               57
D397V9, multiclass
                                                                   clus
vv                                                                  CLDN6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  CLDN6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CLDN6 MUTATED     7   0   1   1
  CLDN6 WILD-TYPE 304  14  14  23
D397V10, multiclass
    clus
vv   CLDN6 MUTATED CLDN6 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D397V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CLDN6 MUTATED       2                         0
  CLDN6 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CLDN6 MUTATED                                           0     6
  CLDN6 WILD-TYPE                                         1   237
D397V12, multiclass
                                           clus
vv                                          CLDN6 MUTATED CLDN6 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D397V13, binary
                 cls
clus                0   1
  CLDN6 MUTATED     0   8
  CLDN6 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN6 MUTATED      0    8
  CLDN6 WILD-TYPE    4  302
                        clus
vv                       CLDN6 MUTATED CLDN6 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(398) Variable = SULF1 MUTATION ANALYSIS
D398V1, survival
                 sevent
clus2               0   1
  SULF1 MUTATED    20   2
  SULF1 WILD-TYPE 210 137
  SULF1 MUTATED SULF1 WILD-TYPE 
             22             347 
  SULF1 MUTATED SULF1 WILD-TYPE 
              2             137 
$`SULF1 MUTATED`
TCGA-CG-5727 TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-6453 TCGA-BR-6802 TCGA-BR-7703 
       79.07        26.70         9.67        15.95        30.90        36.16 
TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4J8 TCGA-CD-5802 
       37.25        29.59         1.12        28.14        13.51        13.35 
TCGA-CD-8534 TCGA-CG-5721 TCGA-D7-5578 TCGA-D7-A6EY TCGA-F1-6874 TCGA-HU-A4G8 
       12.07         6.02        12.66        11.44        14.47        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GX TCGA-HU-A4H3 
       24.20         3.25        20.25        29.00 

$`SULF1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        40.21        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-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-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-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-5803 
        5.13        13.41        13.02        13.15        13.18        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-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-D7-5579 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-F1-6875 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-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.30         5.59        24.26        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-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 

  SULF1 MUTATED SULF1 WILD-TYPE 
           1.12            0.00 
  SULF1 MUTATED SULF1 WILD-TYPE 
          79.07          122.30 
  SULF1 MUTATED SULF1 WILD-TYPE 
          18.10           14.07 
[1] "1.1 - 79.1 (18.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "5.2"
D398V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SULF1 MUTATED         0        2        1        3         2         3
  SULF1 WILD-TYPE       2       13       39       27        35        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SULF1 MUTATED           0          2          4          3        2
  SULF1 WILD-TYPE         3         68         49         29       36
D398V3, multiclass
            clus
vv           SULF1 MUTATED SULF1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               1              39
  STAGE II               3              27
  STAGE IIA              2              35
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             4              49
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SULF1 MUTATED     2   2   9   9
  SULF1 WILD-TYPE  20  90 164  88
D398V4, multiclass
    clus
vv   SULF1 MUTATED SULF1 WILD-TYPE
  T1             2              20
  T2             2              90
  T3             9             164
  T4             9              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
  SULF1 MUTATED     9   3   6   4
  SULF1 WILD-TYPE 109 101  71  73
D398V5, multiclass
    clus
vv   SULF1 MUTATED SULF1 WILD-TYPE
  N0             9             109
  N1             3             101
  N2             6              71
  N3             4              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"
D398V6, binary
                 cls
clus                0   1
  SULF1 MUTATED    24   0
  SULF1 WILD-TYPE 322  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF1 MUTATED     24    0
  SULF1 WILD-TYPE  322   29
   clus
vv  SULF1 MUTATED SULF1 WILD-TYPE
  0            24             322
  1             0              29
[1] 2 2
[1] FALSE
D398V7, binary
                 cls
clus                0   1
  SULF1 MUTATED    13  11
  SULF1 WILD-TYPE 132 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF1 MUTATED     13   11
  SULF1 WILD-TYPE  132  237
        clus
vv       SULF1 MUTATED SULF1 WILD-TYPE
  FEMALE            13             132
  MALE              11             237
[1] 2 2
[1] FALSE
D398V8, binary
                 cls
clus                0   1
  SULF1 MUTATED    20   1
  SULF1 WILD-TYPE 272  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF1 MUTATED     20    1
  SULF1 WILD-TYPE  272   58
     clus
vv    SULF1 MUTATED SULF1 WILD-TYPE
  NO             20             272
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SULF1 MUTATED                                          0
  SULF1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SULF1 MUTATED                                       6
  SULF1 WILD-TYPE                                    64
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SULF1 MUTATED                                                       11
  SULF1 WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SULF1 MUTATED                                                   0
  SULF1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SULF1 MUTATED                                                                   3
  SULF1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SULF1 MUTATED                                                    1
  SULF1 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SULF1 MUTATED                                                  3
  SULF1 WILD-TYPE                                               58
D398V9, multiclass
                                                                   clus
vv                                                                  SULF1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  SULF1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SULF1 MUTATED    19   0   0   3
  SULF1 WILD-TYPE 292  14  15  21
D398V10, multiclass
    clus
vv   SULF1 MUTATED SULF1 WILD-TYPE
  R0            19             292
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D398V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SULF1 MUTATED       7                         0
  SULF1 WILD-TYPE    80                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SULF1 MUTATED                                           0    15
  SULF1 WILD-TYPE                                         1   228
D398V12, multiclass
                                           clus
vv                                          SULF1 MUTATED SULF1 WILD-TYPE
  ASIAN                                                 7              80
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D398V13, binary
                 cls
clus                0   1
  SULF1 MUTATED     0  22
  SULF1 WILD-TYPE   4 288
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF1 MUTATED      0   22
  SULF1 WILD-TYPE    4  288
                        clus
vv                       SULF1 MUTATED SULF1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            22             288
[1] 2 2
[1] FALSE

Clustering(399) Variable = PCGF3 MUTATION ANALYSIS
D399V1, survival
                 sevent
clus2               0   1
  PCGF3 MUTATED     3   3
  PCGF3 WILD-TYPE 227 136
  PCGF3 MUTATED PCGF3 WILD-TYPE 
              6             363 
  PCGF3 MUTATED PCGF3 WILD-TYPE 
              3             136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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          14.270 
[1] "6.6 - 36.2 (15.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D399V2, 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       1       14       39       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCGF3 MUTATED           0          0          2          1        0
  PCGF3 WILD-TYPE         3         70         51         31       38
D399V3, multiclass
            clus
vv           PCGF3 MUTATED PCGF3 WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PCGF3 MUTATED     3   0   3   1
  PCGF3 WILD-TYPE  19  92 170  96
D399V4, multiclass
    clus
vv   PCGF3 MUTATED PCGF3 WILD-TYPE
  T1             3              19
  T2             0              92
  T3             3             170
  T4             1              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
  PCGF3 MUTATED     2   2   0   3
  PCGF3 WILD-TYPE 116 102  77  74
D399V5, multiclass
    clus
vv   PCGF3 MUTATED PCGF3 WILD-TYPE
  N0             2             116
  N1             2             102
  N2             0              77
  N3             3              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"
D399V6, binary
                 cls
clus                0   1
  PCGF3 MUTATED     6   0
  PCGF3 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCGF3 MUTATED      6    0
  PCGF3 WILD-TYPE  340   29
   clus
vv  PCGF3 MUTATED PCGF3 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D399V7, binary
                 cls
clus                0   1
  PCGF3 MUTATED     2   5
  PCGF3 WILD-TYPE 143 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCGF3 MUTATED      2    5
  PCGF3 WILD-TYPE  143  243
        clus
vv       PCGF3 MUTATED PCGF3 WILD-TYPE
  FEMALE             2             143
  MALE               5             243
[1] 2 2
[1] FALSE
D399V8, binary
                 cls
clus                0   1
  PCGF3 MUTATED     6   1
  PCGF3 WILD-TYPE 286  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCGF3 MUTATED      6    1
  PCGF3 WILD-TYPE  286   58
     clus
vv    PCGF3 MUTATED PCGF3 WILD-TYPE
  NO              6             286
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PCGF3 MUTATED                                          0
  PCGF3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PCGF3 MUTATED                                       1
  PCGF3 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PCGF3 MUTATED                                                        4
  PCGF3 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PCGF3 MUTATED                                                   0
  PCGF3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PCGF3 MUTATED                                                                   0
  PCGF3 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PCGF3 MUTATED                                                    1
  PCGF3 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PCGF3 MUTATED                                                  1
  PCGF3 WILD-TYPE                                               60
D399V9, multiclass
                                                                   clus
vv                                                                  PCGF3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  PCGF3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PCGF3 MUTATED     6   0   0   0
  PCGF3 WILD-TYPE 305  14  15  24
D399V10, multiclass
    clus
vv   PCGF3 MUTATED PCGF3 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D399V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PCGF3 MUTATED       2                         1
  PCGF3 WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PCGF3 MUTATED                                           0     4
  PCGF3 WILD-TYPE                                         1   239
D399V12, multiclass
                                           clus
vv                                          PCGF3 MUTATED PCGF3 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D399V13, binary
                 cls
clus                0   1
  PCGF3 MUTATED     0   7
  PCGF3 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCGF3 MUTATED      0    7
  PCGF3 WILD-TYPE    4  303
                        clus
vv                       PCGF3 MUTATED PCGF3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(400) Variable = SF3B2 MUTATION ANALYSIS
D400V1, survival
                 sevent
clus2               0   1
  SF3B2 MUTATED    10   5
  SF3B2 WILD-TYPE 220 134
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             15             354 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
              5             134 
$`SF3B2 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6565 TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-8588 
       26.70         6.97         9.17         6.18         1.12        12.79 
TCGA-BR-8680 TCGA-CG-4477 TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A4YY TCGA-HJ-7597 
       31.96        30.97         6.02        28.96        13.78        26.47 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GQ 
       22.68        29.98         0.10 

$`SF3B2 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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 

  SF3B2 MUTATED SF3B2 WILD-TYPE 
            0.1             0.0 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
          31.96          122.30 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
          13.78           14.35 
[1] "0.1 - 32.0 (13.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D400V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SF3B2 MUTATED         0        1        2        0         3         4
  SF3B2 WILD-TYPE       2       14       38       30        34        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SF3B2 MUTATED           0          1          1          1        2
  SF3B2 WILD-TYPE         3         69         52         31       36
D400V3, multiclass
            clus
vv           SF3B2 MUTATED SF3B2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SF3B2 MUTATED     1   3   5   6
  SF3B2 WILD-TYPE  21  89 168  91
D400V4, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             5             168
  T4             6              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
  SF3B2 MUTATED     8   4   2   1
  SF3B2 WILD-TYPE 110 100  75  76
D400V5, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  N0             8             110
  N1             4             100
  N2             2              75
  N3             1              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"
D400V6, binary
                 cls
clus                0   1
  SF3B2 MUTATED    13   1
  SF3B2 WILD-TYPE 333  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED     13    1
  SF3B2 WILD-TYPE  333   28
   clus
vv  SF3B2 MUTATED SF3B2 WILD-TYPE
  0            13             333
  1             1              28
[1] 2 2
[1] FALSE
D400V7, binary
                 cls
clus                0   1
  SF3B2 MUTATED     7   9
  SF3B2 WILD-TYPE 138 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED      7    9
  SF3B2 WILD-TYPE  138  239
        clus
vv       SF3B2 MUTATED SF3B2 WILD-TYPE
  FEMALE             7             138
  MALE               9             239
[1] 2 2
[1] FALSE
D400V8, binary
                 cls
clus                0   1
  SF3B2 MUTATED    12   2
  SF3B2 WILD-TYPE 280  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED     12    2
  SF3B2 WILD-TYPE  280   57
     clus
vv    SF3B2 MUTATED SF3B2 WILD-TYPE
  NO             12             280
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SF3B2 MUTATED                                          1
  SF3B2 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SF3B2 MUTATED                                       2
  SF3B2 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SF3B2 MUTATED                                                        6
  SF3B2 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SF3B2 MUTATED                                                   0
  SF3B2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SF3B2 MUTATED                                                                   4
  SF3B2 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SF3B2 MUTATED                                                    0
  SF3B2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SF3B2 MUTATED                                                  3
  SF3B2 WILD-TYPE                                               58
D400V9, multiclass
                                                                   clus
vv                                                                  SF3B2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  SF3B2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SF3B2 MUTATED    13   0   0   2
  SF3B2 WILD-TYPE 298  14  15  22
D400V10, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  R0            13             298
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D400V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SF3B2 MUTATED       4                         0
  SF3B2 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SF3B2 MUTATED                                           0     9
  SF3B2 WILD-TYPE                                         1   234
D400V12, multiclass
                                           clus
vv                                          SF3B2 MUTATED SF3B2 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D400V13, binary
                 cls
clus                0   1
  SF3B2 MUTATED     0  13
  SF3B2 WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED      0   13
  SF3B2 WILD-TYPE    4  297
                        clus
vv                       SF3B2 MUTATED SF3B2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(401) Variable = C19ORF70 MUTATION ANALYSIS
D401V1, survival
                    sevent
clus2                  0   1
  C19ORF70 MUTATED     3   2
  C19ORF70 WILD-TYPE 227 137
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
                 5                364 
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
                 2                137 
$`C19ORF70 MUTATED`
TCGA-BR-4257 TCGA-BR-8360 TCGA-BR-8361 TCGA-CD-A4MG TCGA-HU-A4G8 
        9.67         6.18        31.10         6.58        22.68 

$`C19ORF70 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
              6.18               0.00 
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
              31.1              122.3 
  C19ORF70 MUTATED C19ORF70 WILD-TYPE 
              9.67              14.35 
[1] "6.2 - 31.1 (9.7)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D401V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C19ORF70 MUTATED         0        0        0        0         2         2
  C19ORF70 WILD-TYPE       2       15       40       30        35        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C19ORF70 MUTATED           0          0          0          1        0
  C19ORF70 WILD-TYPE         3         70         53         31       38
D401V3, multiclass
            clus
vv           C19ORF70 MUTATED C19ORF70 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 2                 35
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                0                 53
  STAGE IIIC                1                 31
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C19ORF70 MUTATED     0   0   3   2
  C19ORF70 WILD-TYPE  22  92 170  95
D401V4, multiclass
    clus
vv   C19ORF70 MUTATED C19ORF70 WILD-TYPE
  T1                0                 22
  T2                0                 92
  T3                3                170
  T4                2                 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
  C19ORF70 MUTATED     3   1   1   0
  C19ORF70 WILD-TYPE 115 103  76  77
D401V5, multiclass
    clus
vv   C19ORF70 MUTATED C19ORF70 WILD-TYPE
  N0                3                115
  N1                1                103
  N2                1                 76
  N3                0                 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"
D401V6, binary
                    cls
clus                   0   1
  C19ORF70 MUTATED     6   0
  C19ORF70 WILD-TYPE 340  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF70 MUTATED      6    0
  C19ORF70 WILD-TYPE  340   29
   clus
vv  C19ORF70 MUTATED C19ORF70 WILD-TYPE
  0                6                340
  1                0                 29
[1] 2 2
[1] FALSE
D401V7, binary
                    cls
clus                   0   1
  C19ORF70 MUTATED     3   3
  C19ORF70 WILD-TYPE 142 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF70 MUTATED      3    3
  C19ORF70 WILD-TYPE  142  245
        clus
vv       C19ORF70 MUTATED C19ORF70 WILD-TYPE
  FEMALE                3                142
  MALE                  3                245
[1] 2 2
[1] FALSE
D401V8, binary
                    cls
clus                   0   1
  C19ORF70 MUTATED     6   0
  C19ORF70 WILD-TYPE 286  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF70 MUTATED      6    0
  C19ORF70 WILD-TYPE  286   59
     clus
vv    C19ORF70 MUTATED C19ORF70 WILD-TYPE
  NO                 6                286
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C19ORF70 MUTATED                                          0
  C19ORF70 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C19ORF70 MUTATED                                       2
  C19ORF70 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C19ORF70 MUTATED                                                        2
  C19ORF70 WILD-TYPE                                                    156
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C19ORF70 MUTATED                                                   0
  C19ORF70 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C19ORF70 MUTATED                                                                   2
  C19ORF70 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C19ORF70 MUTATED                                                    0
  C19ORF70 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C19ORF70 MUTATED                                                  0
  C19ORF70 WILD-TYPE                                               61
D401V9, multiclass
                                                                   clus
vv                                                                  C19ORF70 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 0
                                                                   clus
vv                                                                  C19ORF70 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C19ORF70 MUTATED     3   0   0   1
  C19ORF70 WILD-TYPE 308  14  15  23
D401V10, multiclass
    clus
vv   C19ORF70 MUTATED C19ORF70 WILD-TYPE
  R0                3                308
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D401V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C19ORF70 MUTATED       2                         0
  C19ORF70 WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C19ORF70 MUTATED                                           0     4
  C19ORF70 WILD-TYPE                                         1   239
D401V12, multiclass
                                           clus
vv                                          C19ORF70 MUTATED C19ORF70 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D401V13, binary
                    cls
clus                   0   1
  C19ORF70 MUTATED     0   6
  C19ORF70 WILD-TYPE   4 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF70 MUTATED      0    6
  C19ORF70 WILD-TYPE    4  304
                        clus
vv                       C19ORF70 MUTATED C19ORF70 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                6                304
[1] 2 2
[1] FALSE

Clustering(402) Variable = RNASEH2B MUTATION ANALYSIS
D402V1, survival
                    sevent
clus2                  0   1
  RNASEH2B MUTATED     3   0
  RNASEH2B WILD-TYPE 227 139
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 3                366 
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 0                139 
$`RNASEH2B MUTATED`
TCGA-B7-A5TI TCGA-BR-8369 TCGA-HF-A5NB 
       19.56        14.04        30.51 

$`RNASEH2B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  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              14.22 
[1] "14.0 - 30.5 (19.6)" "0.0 - 122.3 (14.2)"
[1] "hr="   "9e+06"
D402V2, 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       2       15       40       30        37        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNASEH2B MUTATED           0          0          1          2        0
  RNASEH2B WILD-TYPE         3         70         52         30       38
D402V3, multiclass
            clus
vv           RNASEH2B MUTATED RNASEH2B WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 0                 37
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                1                 52
  STAGE IIIC                2                 30
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  RNASEH2B MUTATED     0   0   1   3
  RNASEH2B WILD-TYPE  22  92 172  94
D402V4, multiclass
    clus
vv   RNASEH2B MUTATED RNASEH2B WILD-TYPE
  T1                0                 22
  T2                0                 92
  T3                1                172
  T4                3                 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
  RNASEH2B MUTATED     1   0   0   3
  RNASEH2B WILD-TYPE 117 104  77  74
D402V5, multiclass
    clus
vv   RNASEH2B MUTATED RNASEH2B WILD-TYPE
  N0                1                117
  N1                0                104
  N2                0                 77
  N3                3                 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"
D402V6, binary
                    cls
clus                   0   1
  RNASEH2B MUTATED     4   0
  RNASEH2B WILD-TYPE 342  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      4    0
  RNASEH2B WILD-TYPE  342   29
   clus
vv  RNASEH2B MUTATED RNASEH2B WILD-TYPE
  0                4                342
  1                0                 29
[1] 2 2
[1] FALSE
D402V7, binary
                    cls
clus                   0   1
  RNASEH2B MUTATED     2   2
  RNASEH2B WILD-TYPE 143 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      2    2
  RNASEH2B WILD-TYPE  143  246
        clus
vv       RNASEH2B MUTATED RNASEH2B WILD-TYPE
  FEMALE                2                143
  MALE                  2                246
[1] 2 2
[1] FALSE
D402V8, binary
                    cls
clus                   0   1
  RNASEH2B MUTATED     3   1
  RNASEH2B WILD-TYPE 289  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      3    1
  RNASEH2B WILD-TYPE  289   58
     clus
vv    RNASEH2B MUTATED RNASEH2B WILD-TYPE
  NO                 3                289
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RNASEH2B MUTATED                                          0
  RNASEH2B WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RNASEH2B MUTATED                                       1
  RNASEH2B WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RNASEH2B MUTATED                                                        1
  RNASEH2B WILD-TYPE                                                    157
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RNASEH2B MUTATED                                                   1
  RNASEH2B WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RNASEH2B MUTATED                                                                   1
  RNASEH2B WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RNASEH2B MUTATED                                                    0
  RNASEH2B WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RNASEH2B MUTATED                                                  0
  RNASEH2B WILD-TYPE                                               61
D402V9, multiclass
                                                                   clus
vv                                                                  RNASEH2B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 0
                                                                   clus
vv                                                                  RNASEH2B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  RNASEH2B MUTATED     2   1   0   0
  RNASEH2B WILD-TYPE 309  13  15  24
D402V10, multiclass
    clus
vv   RNASEH2B MUTATED RNASEH2B WILD-TYPE
  R0                2                309
  R1                1                 13
  R2                0                 15
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D402V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  RNASEH2B MUTATED       0                         0
  RNASEH2B WILD-TYPE    87                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RNASEH2B MUTATED                                           0     3
  RNASEH2B WILD-TYPE                                         1   240
D402V12, multiclass
                                           clus
vv                                          RNASEH2B MUTATED RNASEH2B WILD-TYPE
  ASIAN                                                    0                 87
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D402V13, binary
                    cls
clus                   0   1
  RNASEH2B MUTATED     0   3
  RNASEH2B WILD-TYPE   4 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      0    3
  RNASEH2B WILD-TYPE    4  307
                        clus
vv                       RNASEH2B MUTATED RNASEH2B WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                3                307
[1] 2 2
[1] FALSE

Clustering(403) Variable = GPR161 MUTATION ANALYSIS
D403V1, survival
                  sevent
clus2                0   1
  GPR161 MUTATED     7   4
  GPR161 WILD-TYPE 223 135
  GPR161 MUTATED GPR161 WILD-TYPE 
              11              358 
  GPR161 MUTATED GPR161 WILD-TYPE 
               4              135 
$`GPR161 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18        13.35        11.21        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-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-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-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-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 

  GPR161 MUTATED GPR161 WILD-TYPE 
            6.97             0.00 
  GPR161 MUTATED GPR161 WILD-TYPE 
            65.1            122.3 
  GPR161 MUTATED GPR161 WILD-TYPE 
           14.07            14.35 
[1] "7.0 - 65.1 (14.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D403V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR161 MUTATED         0        1        2        1         0         1
  GPR161 WILD-TYPE       2       14       38       29        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR161 MUTATED           0          3          0          0        0
  GPR161 WILD-TYPE         3         67         53         32       38
D403V3, multiclass
            clus
vv           GPR161 MUTATED GPR161 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR161 MUTATED     2   2   6   1
  GPR161 WILD-TYPE  20  90 167  96
D403V4, multiclass
    clus
vv   GPR161 MUTATED GPR161 WILD-TYPE
  T1              2               20
  T2              2               90
  T3              6              167
  T4              1               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
  GPR161 MUTATED     3   5   1   0
  GPR161 WILD-TYPE 115  99  76  77
D403V5, multiclass
    clus
vv   GPR161 MUTATED GPR161 WILD-TYPE
  N0              3              115
  N1              5               99
  N2              1               76
  N3              0               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"
D403V6, binary
                  cls
clus                 0   1
  GPR161 MUTATED     9   0
  GPR161 WILD-TYPE 337  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      9    0
  GPR161 WILD-TYPE  337   29
   clus
vv  GPR161 MUTATED GPR161 WILD-TYPE
  0              9              337
  1              0               29
[1] 2 2
[1] FALSE
D403V7, binary
                  cls
clus                 0   1
  GPR161 MUTATED     5   7
  GPR161 WILD-TYPE 140 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      5    7
  GPR161 WILD-TYPE  140  241
        clus
vv       GPR161 MUTATED GPR161 WILD-TYPE
  FEMALE              5              140
  MALE                7              241
[1] 2 2
[1] FALSE
D403V8, binary
                  cls
clus                 0   1
  GPR161 MUTATED     7   2
  GPR161 WILD-TYPE 285  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      7    2
  GPR161 WILD-TYPE  285   57
     clus
vv    GPR161 MUTATED GPR161 WILD-TYPE
  NO               7              285
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GPR161 MUTATED                                          0
  GPR161 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GPR161 MUTATED                                       0
  GPR161 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR161 MUTATED                                                        7
  GPR161 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GPR161 MUTATED                                                   1
  GPR161 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR161 MUTATED                                                                   2
  GPR161 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GPR161 MUTATED                                                    0
  GPR161 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GPR161 MUTATED                                                  2
  GPR161 WILD-TYPE                                               59
D403V9, multiclass
                                                                   clus
vv                                                                  GPR161 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  GPR161 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR161 MUTATED     7   1   0   4
  GPR161 WILD-TYPE 304  13  15  20
D403V10, multiclass
    clus
vv   GPR161 MUTATED GPR161 WILD-TYPE
  R0              7              304
  R1              1               13
  R2              0               15
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D403V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GPR161 MUTATED       3                         0
  GPR161 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR161 MUTATED                                           0     7
  GPR161 WILD-TYPE                                         1   236
D403V12, multiclass
                                           clus
vv                                          GPR161 MUTATED GPR161 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D403V13, binary
                  cls
clus                 0   1
  GPR161 MUTATED     0   9
  GPR161 WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR161 MUTATED      0    9
  GPR161 WILD-TYPE    4  301
                        clus
vv                       GPR161 MUTATED GPR161 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(404) Variable = RRS1 MUTATION ANALYSIS
D404V1, survival
                sevent
clus2              0   1
  RRS1 MUTATED     4   1
  RRS1 WILD-TYPE 226 138
  RRS1 MUTATED RRS1 WILD-TYPE 
             5            364 
  RRS1 MUTATED RRS1 WILD-TYPE 
             1            138 
$`RRS1 MUTATED`
TCGA-CG-4460 TCGA-BR-7707 TCGA-BR-8487 TCGA-D7-5578 TCGA-D7-A4YT 
       21.99        35.84         1.12        12.66        14.27 

$`RRS1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-D7-5579 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-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-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 

  RRS1 MUTATED RRS1 WILD-TYPE 
          1.12           0.00 
  RRS1 MUTATED RRS1 WILD-TYPE 
         35.84         122.30 
  RRS1 MUTATED RRS1 WILD-TYPE 
         14.27          14.30 
[1] "1.1 - 35.8 (14.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.9"
D404V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RRS1 MUTATED         0        0        1        0         1         1
  RRS1 WILD-TYPE       2       15       39       30        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RRS1 MUTATED           0          3          0          0        1
  RRS1 WILD-TYPE         3         67         53         32       37
D404V3, multiclass
            clus
vv           RRS1 MUTATED RRS1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RRS1 MUTATED     0   2   2   3
  RRS1 WILD-TYPE  22  90 171  94
D404V4, multiclass
    clus
vv   RRS1 MUTATED RRS1 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            2            171
  T4            3             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
  RRS1 MUTATED     4   1   1   1
  RRS1 WILD-TYPE 114 103  76  76
D404V5, multiclass
    clus
vv   RRS1 MUTATED RRS1 WILD-TYPE
  N0            4            114
  N1            1            103
  N2            1             76
  N3            1             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"
D404V6, binary
                cls
clus               0   1
  RRS1 MUTATED     6   1
  RRS1 WILD-TYPE 340  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      6    1
  RRS1 WILD-TYPE  340   28
   clus
vv  RRS1 MUTATED RRS1 WILD-TYPE
  0            6            340
  1            1             28
[1] 2 2
[1] FALSE
D404V7, binary
                cls
clus               0   1
  RRS1 MUTATED     4   3
  RRS1 WILD-TYPE 141 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      4    3
  RRS1 WILD-TYPE  141  245
        clus
vv       RRS1 MUTATED RRS1 WILD-TYPE
  FEMALE            4            141
  MALE              3            245
[1] 2 2
[1] FALSE
D404V8, binary
                cls
clus               0   1
  RRS1 MUTATED     6   0
  RRS1 WILD-TYPE 286  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      6    0
  RRS1 WILD-TYPE  286   59
     clus
vv    RRS1 MUTATED RRS1 WILD-TYPE
  NO             6            286
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RRS1 MUTATED                                          0
  RRS1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RRS1 MUTATED                                       0
  RRS1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RRS1 MUTATED                                                        3
  RRS1 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RRS1 MUTATED                                                   0
  RRS1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RRS1 MUTATED                                                                   2
  RRS1 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RRS1 MUTATED                                                    0
  RRS1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RRS1 MUTATED                                                  2
  RRS1 WILD-TYPE                                               59
D404V9, multiclass
                                                                   clus
vv                                                                  RRS1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  RRS1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RRS1 MUTATED     5   0   1   1
  RRS1 WILD-TYPE 306  14  14  23
D404V10, multiclass
    clus
vv   RRS1 MUTATED RRS1 WILD-TYPE
  R0            5            306
  R1            0             14
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D404V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RRS1 MUTATED       0                         0
  RRS1 WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RRS1 MUTATED                                           0     6
  RRS1 WILD-TYPE                                         1   237
D404V12, multiclass
                                           clus
vv                                          RRS1 MUTATED RRS1 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D404V13, binary
                cls
clus               0   1
  RRS1 MUTATED     0   6
  RRS1 WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      0    6
  RRS1 WILD-TYPE    4  304
                        clus
vv                       RRS1 MUTATED RRS1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(405) Variable = ZCRB1 MUTATION ANALYSIS
D405V1, survival
                 sevent
clus2               0   1
  ZCRB1 MUTATED     5   0
  ZCRB1 WILD-TYPE 225 139
  ZCRB1 MUTATED ZCRB1 WILD-TYPE 
              5             364 
  ZCRB1 MUTATED ZCRB1 WILD-TYPE 
              0             139 
$`ZCRB1 MUTATED`
TCGA-BR-8591 TCGA-HF-A5NB TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-VQ-A8P2 
       28.14        30.51        24.20        29.98        38.14 

$`ZCRB1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  ZCRB1 MUTATED ZCRB1 WILD-TYPE 
           24.2             0.0 
  ZCRB1 MUTATED ZCRB1 WILD-TYPE 
          38.14          122.30 
  ZCRB1 MUTATED ZCRB1 WILD-TYPE 
          29.98           14.07 
[1] "24.2 - 38.1 (30.0)" "0.0 - 122.3 (14.1)"
[1] "hr="     "9300000"
D405V2, 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       2       14       40       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZCRB1 MUTATED           0          2          0          2        0
  ZCRB1 WILD-TYPE         3         68         53         30       38
D405V3, multiclass
            clus
vv           ZCRB1 MUTATED ZCRB1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZCRB1 MUTATED     1   1   0   4
  ZCRB1 WILD-TYPE  21  91 173  93
D405V4, multiclass
    clus
vv   ZCRB1 MUTATED ZCRB1 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             0             173
  T4             4              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
  ZCRB1 MUTATED     2   2   0   2
  ZCRB1 WILD-TYPE 116 102  77  75
D405V5, multiclass
    clus
vv   ZCRB1 MUTATED ZCRB1 WILD-TYPE
  N0             2             116
  N1             2             102
  N2             0              77
  N3             2              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"
D405V6, binary
                 cls
clus                0   1
  ZCRB1 MUTATED     6   0
  ZCRB1 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZCRB1 MUTATED      6    0
  ZCRB1 WILD-TYPE  340   29
   clus
vv  ZCRB1 MUTATED ZCRB1 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D405V7, binary
                 cls
clus                0   1
  ZCRB1 MUTATED     3   3
  ZCRB1 WILD-TYPE 142 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZCRB1 MUTATED      3    3
  ZCRB1 WILD-TYPE  142  245
        clus
vv       ZCRB1 MUTATED ZCRB1 WILD-TYPE
  FEMALE             3             142
  MALE               3             245
[1] 2 2
[1] FALSE
D405V8, binary
                 cls
clus                0   1
  ZCRB1 MUTATED     3   2
  ZCRB1 WILD-TYPE 289  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZCRB1 MUTATED      3    2
  ZCRB1 WILD-TYPE  289   57
     clus
vv    ZCRB1 MUTATED ZCRB1 WILD-TYPE
  NO              3             289
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZCRB1 MUTATED                                          0
  ZCRB1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZCRB1 MUTATED                                       0
  ZCRB1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZCRB1 MUTATED                                                        2
  ZCRB1 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZCRB1 MUTATED                                                   2
  ZCRB1 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZCRB1 MUTATED                                                                   0
  ZCRB1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZCRB1 MUTATED                                                    0
  ZCRB1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZCRB1 MUTATED                                                  2
  ZCRB1 WILD-TYPE                                               59
D405V9, multiclass
                                                                   clus
vv                                                                  ZCRB1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  ZCRB1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZCRB1 MUTATED     4   1   0   1
  ZCRB1 WILD-TYPE 307  13  15  23
D405V10, multiclass
    clus
vv   ZCRB1 MUTATED ZCRB1 WILD-TYPE
  R0             4             307
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D405V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZCRB1 MUTATED       2                         0
  ZCRB1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZCRB1 MUTATED                                           0     3
  ZCRB1 WILD-TYPE                                         1   240
D405V12, multiclass
                                           clus
vv                                          ZCRB1 MUTATED ZCRB1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D405V13, binary
                 cls
clus                0   1
  ZCRB1 MUTATED     0   4
  ZCRB1 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZCRB1 MUTATED      0    4
  ZCRB1 WILD-TYPE    4  306
                        clus
vv                       ZCRB1 MUTATED ZCRB1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(406) Variable = LINGO4 MUTATION ANALYSIS
D406V1, survival
                  sevent
clus2                0   1
  LINGO4 MUTATED     5   4
  LINGO4 WILD-TYPE 225 135
  LINGO4 MUTATED LINGO4 WILD-TYPE 
               9              360 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
               4              135 
$`LINGO4 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8081 TCGA-CD-A489 TCGA-D7-A4YV 
        6.97        34.68        35.84        32.25        11.31         5.92 
TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4GT 
       11.08        26.47         6.51 

$`LINGO4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  LINGO4 MUTATED LINGO4 WILD-TYPE 
            5.92             0.00 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
           35.84           122.30 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
           11.31            14.35 
[1] "5.9 - 35.8 (11.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D406V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LINGO4 MUTATED         0        0        2        0         5         2
  LINGO4 WILD-TYPE       2       15       38       30        32        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LINGO4 MUTATED           0          1          0          0        1
  LINGO4 WILD-TYPE         3         69         53         32       37
D406V3, multiclass
            clus
vv           LINGO4 MUTATED LINGO4 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               5               32
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LINGO4 MUTATED     0   2   7   2
  LINGO4 WILD-TYPE  22  90 166  95
D406V4, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              7              166
  T4              2               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
  LINGO4 MUTATED     8   2   1   0
  LINGO4 WILD-TYPE 110 102  76  77
D406V5, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  N0              8              110
  N1              2              102
  N2              1               76
  N3              0               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"
D406V6, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     9   0
  LINGO4 WILD-TYPE 337  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      9    0
  LINGO4 WILD-TYPE  337   29
   clus
vv  LINGO4 MUTATED LINGO4 WILD-TYPE
  0              9              337
  1              0               29
[1] 2 2
[1] FALSE
D406V7, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     7   4
  LINGO4 WILD-TYPE 138 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      7    4
  LINGO4 WILD-TYPE  138  244
        clus
vv       LINGO4 MUTATED LINGO4 WILD-TYPE
  FEMALE              7              138
  MALE                4              244
[1] 2 2
[1] FALSE
D406V8, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     8   1
  LINGO4 WILD-TYPE 284  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      8    1
  LINGO4 WILD-TYPE  284   58
     clus
vv    LINGO4 MUTATED LINGO4 WILD-TYPE
  NO               8              284
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LINGO4 MUTATED                                          1
  LINGO4 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LINGO4 MUTATED                                       1
  LINGO4 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LINGO4 MUTATED                                                        7
  LINGO4 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LINGO4 MUTATED                                                   0
  LINGO4 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LINGO4 MUTATED                                                                   0
  LINGO4 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LINGO4 MUTATED                                                    0
  LINGO4 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LINGO4 MUTATED                                                  2
  LINGO4 WILD-TYPE                                               59
D406V9, multiclass
                                                                   clus
vv                                                                  LINGO4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  LINGO4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LINGO4 MUTATED     8   0   0   2
  LINGO4 WILD-TYPE 303  14  15  22
D406V10, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D406V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  LINGO4 MUTATED       2                         1
  LINGO4 WILD-TYPE    85                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LINGO4 MUTATED                                           0     8
  LINGO4 WILD-TYPE                                         1   235
D406V12, multiclass
                                           clus
vv                                          LINGO4 MUTATED LINGO4 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D406V13, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     0  11
  LINGO4 WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      0   11
  LINGO4 WILD-TYPE    4  299
                        clus
vv                       LINGO4 MUTATED LINGO4 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(407) Variable = MAP9 MUTATION ANALYSIS
D407V1, survival
                sevent
clus2              0   1
  MAP9 MUTATED     6   5
  MAP9 WILD-TYPE 224 134
  MAP9 MUTATED MAP9 WILD-TYPE 
            11            358 
  MAP9 MUTATED MAP9 WILD-TYPE 
             5            134 
$`MAP9 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8680 
        6.97        30.90        25.05        28.14         7.53        31.96 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-FP-A4BE TCGA-HJ-7597 TCGA-VQ-AA68 
        6.58        12.62        11.08        26.47        43.66 

$`MAP9 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8592 
       20.22         1.12        12.79        27.12         9.34         6.28 
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-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-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-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-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 

  MAP9 MUTATED MAP9 WILD-TYPE 
          6.58           0.00 
  MAP9 MUTATED MAP9 WILD-TYPE 
         43.66         122.30 
  MAP9 MUTATED MAP9 WILD-TYPE 
         25.05          14.22 
[1] "6.6 - 43.7 (25.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1"  
D407V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP9 MUTATED         1        0        3        0         2         0
  MAP9 WILD-TYPE       1       15       37       30        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP9 MUTATED           0          1          1          3        1
  MAP9 WILD-TYPE         3         69         52         29       37
D407V3, multiclass
            clus
vv           MAP9 MUTATED MAP9 WILD-TYPE
  STAGE I               1              1
  STAGE IA              0             15
  STAGE IB              3             37
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            3             29
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MAP9 MUTATED     1   4   4   4
  MAP9 WILD-TYPE  21  88 169  93
D407V4, multiclass
    clus
vv   MAP9 MUTATED MAP9 WILD-TYPE
  T1            1             21
  T2            4             88
  T3            4            169
  T4            4             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
  MAP9 MUTATED     5   2   1   4
  MAP9 WILD-TYPE 113 102  76  73
D407V5, multiclass
    clus
vv   MAP9 MUTATED MAP9 WILD-TYPE
  N0            5            113
  N1            2            102
  N2            1             76
  N3            4             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"
D407V6, binary
                cls
clus               0   1
  MAP9 MUTATED     9   1
  MAP9 WILD-TYPE 337  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED      9    1
  MAP9 WILD-TYPE  337   28
   clus
vv  MAP9 MUTATED MAP9 WILD-TYPE
  0            9            337
  1            1             28
[1] 2 2
[1] FALSE
D407V7, binary
                cls
clus               0   1
  MAP9 MUTATED     5   8
  MAP9 WILD-TYPE 140 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED      5    8
  MAP9 WILD-TYPE  140  240
        clus
vv       MAP9 MUTATED MAP9 WILD-TYPE
  FEMALE            5            140
  MALE              8            240
[1] 2 2
[1] FALSE
D407V8, binary
                cls
clus               0   1
  MAP9 MUTATED    11   2
  MAP9 WILD-TYPE 281  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED     11    2
  MAP9 WILD-TYPE  281   57
     clus
vv    MAP9 MUTATED MAP9 WILD-TYPE
  NO            11            281
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MAP9 MUTATED                                          1
  MAP9 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MAP9 MUTATED                                       1
  MAP9 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP9 MUTATED                                                        8
  MAP9 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MAP9 MUTATED                                                   0
  MAP9 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP9 MUTATED                                                                   1
  MAP9 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MAP9 MUTATED                                                    0
  MAP9 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MAP9 MUTATED                                                  2
  MAP9 WILD-TYPE                                               59
D407V9, multiclass
                                                                   clus
vv                                                                  MAP9 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  MAP9 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MAP9 MUTATED     9   0   0   2
  MAP9 WILD-TYPE 302  14  15  22
D407V10, multiclass
    clus
vv   MAP9 MUTATED MAP9 WILD-TYPE
  R0            9            302
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D407V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MAP9 MUTATED       3                         2
  MAP9 WILD-TYPE    84                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP9 MUTATED                                           0     8
  MAP9 WILD-TYPE                                         1   235
D407V12, multiclass
                                           clus
vv                                          MAP9 MUTATED MAP9 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D407V13, binary
                cls
clus               0   1
  MAP9 MUTATED     0  12
  MAP9 WILD-TYPE   4 298
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED      0   12
  MAP9 WILD-TYPE    4  298
                        clus
vv                       MAP9 MUTATED MAP9 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           12            298
[1] 2 2
[1] FALSE

Clustering(408) Variable = CCDC27 MUTATION ANALYSIS
D408V1, survival
                  sevent
clus2                0   1
  CCDC27 MUTATED     4   3
  CCDC27 WILD-TYPE 226 136
  CCDC27 MUTATED CCDC27 WILD-TYPE 
               7              362 
  CCDC27 MUTATED CCDC27 WILD-TYPE 
               3              136 
$`CCDC27 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7717 TCGA-BR-8081 TCGA-BR-8590 TCGA-CG-5721 
       30.90        34.68        18.15        32.25         9.34         6.02 
TCGA-CG-5728 
       65.10 

$`CCDC27 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  CCDC27 MUTATED CCDC27 WILD-TYPE 
            6.02             0.00 
  CCDC27 MUTATED CCDC27 WILD-TYPE 
            65.1            122.3 
  CCDC27 MUTATED CCDC27 WILD-TYPE 
           30.90            14.12 
[1] "6.0 - 65.1 (30.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D408V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC27 MUTATED         1        0        1        0         1         1
  CCDC27 WILD-TYPE       1       15       39       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC27 MUTATED           0          0          0          1        2
  CCDC27 WILD-TYPE         3         70         53         31       36
D408V3, multiclass
            clus
vv           CCDC27 MUTATED CCDC27 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC27 MUTATED     1   2   1   4
  CCDC27 WILD-TYPE  21  90 172  93
D408V4, multiclass
    clus
vv   CCDC27 MUTATED CCDC27 WILD-TYPE
  T1              1               21
  T2              2               90
  T3              1              172
  T4              4               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
  CCDC27 MUTATED     3   3   1   0
  CCDC27 WILD-TYPE 115 101  76  77
D408V5, multiclass
    clus
vv   CCDC27 MUTATED CCDC27 WILD-TYPE
  N0              3              115
  N1              3              101
  N2              1               76
  N3              0               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"
D408V6, binary
                  cls
clus                 0   1
  CCDC27 MUTATED     7   0
  CCDC27 WILD-TYPE 339  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC27 MUTATED      7    0
  CCDC27 WILD-TYPE  339   29
   clus
vv  CCDC27 MUTATED CCDC27 WILD-TYPE
  0              7              339
  1              0               29
[1] 2 2
[1] FALSE
D408V7, binary
                  cls
clus                 0   1
  CCDC27 MUTATED     4   4
  CCDC27 WILD-TYPE 141 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC27 MUTATED      4    4
  CCDC27 WILD-TYPE  141  244
        clus
vv       CCDC27 MUTATED CCDC27 WILD-TYPE
  FEMALE              4              141
  MALE                4              244
[1] 2 2
[1] FALSE
D408V8, binary
                  cls
clus                 0   1
  CCDC27 MUTATED     7   0
  CCDC27 WILD-TYPE 285  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC27 MUTATED      7    0
  CCDC27 WILD-TYPE  285   59
     clus
vv    CCDC27 MUTATED CCDC27 WILD-TYPE
  NO               7              285
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CCDC27 MUTATED                                          0
  CCDC27 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CCDC27 MUTATED                                       0
  CCDC27 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC27 MUTATED                                                        6
  CCDC27 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CCDC27 MUTATED                                                   0
  CCDC27 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC27 MUTATED                                                                   2
  CCDC27 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CCDC27 MUTATED                                                    0
  CCDC27 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CCDC27 MUTATED                                                  0
  CCDC27 WILD-TYPE                                               61
D408V9, multiclass
                                                                   clus
vv                                                                  CCDC27 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  CCDC27 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CCDC27 MUTATED     7   0   0   1
  CCDC27 WILD-TYPE 304  14  15  23
D408V10, multiclass
    clus
vv   CCDC27 MUTATED CCDC27 WILD-TYPE
  R0              7              304
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D408V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CCDC27 MUTATED       0                         1
  CCDC27 WILD-TYPE    87                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC27 MUTATED                                           0     5
  CCDC27 WILD-TYPE                                         1   238
D408V12, multiclass
                                           clus
vv                                          CCDC27 MUTATED CCDC27 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D408V13, binary
                  cls
clus                 0   1
  CCDC27 MUTATED     0   6
  CCDC27 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC27 MUTATED      0    6
  CCDC27 WILD-TYPE    4  304
                        clus
vv                       CCDC27 MUTATED CCDC27 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(409) Variable = DDX60 MUTATION ANALYSIS
D409V1, survival
                 sevent
clus2               0   1
  DDX60 MUTATED    11   3
  DDX60 WILD-TYPE 219 136
  DDX60 MUTATED DDX60 WILD-TYPE 
             14             355 
  DDX60 MUTATED DDX60 WILD-TYPE 
              3             136 
$`DDX60 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8591 TCGA-BR-8680 TCGA-CG-5721 
       26.70        30.90        34.68        28.14        31.96         6.02 
TCGA-CG-5728 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-VQ-A8DZ 
       65.10        30.51        26.47        24.20        29.98        13.02 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       38.14        37.22 

$`DDX60 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8PE 
       48.79         5.46        13.25        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 

  DDX60 MUTATED DDX60 WILD-TYPE 
           6.02            0.00 
  DDX60 MUTATED DDX60 WILD-TYPE 
           65.1           122.3 
  DDX60 MUTATED DDX60 WILD-TYPE 
         30.245          14.040 
[1] "6.0 - 65.1 (30.2)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "3"  
D409V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX60 MUTATED         0        1        2        0         2         1
  DDX60 WILD-TYPE       2       14       38       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDX60 MUTATED           0          2          0          2        3
  DDX60 WILD-TYPE         3         68         53         30       35
D409V3, multiclass
            clus
vv           DDX60 MUTATED DDX60 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX60 MUTATED     1   4   1   8
  DDX60 WILD-TYPE  21  88 172  89
D409V4, multiclass
    clus
vv   DDX60 MUTATED DDX60 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             1             172
  T4             8              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
  DDX60 MUTATED     5   4   1   3
  DDX60 WILD-TYPE 113 100  76  74
D409V5, multiclass
    clus
vv   DDX60 MUTATED DDX60 WILD-TYPE
  N0             5             113
  N1             4             100
  N2             1              76
  N3             3              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"
D409V6, binary
                 cls
clus                0   1
  DDX60 MUTATED    12   2
  DDX60 WILD-TYPE 334  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX60 MUTATED     12    2
  DDX60 WILD-TYPE  334   27
   clus
vv  DDX60 MUTATED DDX60 WILD-TYPE
  0            12             334
  1             2              27
[1] 2 2
[1] FALSE
D409V7, binary
                 cls
clus                0   1
  DDX60 MUTATED     8   7
  DDX60 WILD-TYPE 137 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX60 MUTATED      8    7
  DDX60 WILD-TYPE  137  241
        clus
vv       DDX60 MUTATED DDX60 WILD-TYPE
  FEMALE             8             137
  MALE               7             241
[1] 2 2
[1] FALSE
D409V8, binary
                 cls
clus                0   1
  DDX60 MUTATED    10   3
  DDX60 WILD-TYPE 282  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX60 MUTATED     10    3
  DDX60 WILD-TYPE  282   56
     clus
vv    DDX60 MUTATED DDX60 WILD-TYPE
  NO             10             282
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DDX60 MUTATED                                          2
  DDX60 WILD-TYPE                                        6
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DDX60 MUTATED                                       1
  DDX60 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DDX60 MUTATED                                                        4
  DDX60 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DDX60 MUTATED                                                   2
  DDX60 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DDX60 MUTATED                                                                   2
  DDX60 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DDX60 MUTATED                                                    0
  DDX60 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DDX60 MUTATED                                                  4
  DDX60 WILD-TYPE                                               57
D409V9, multiclass
                                                                   clus
vv                                                                  DDX60 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  DDX60 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DDX60 MUTATED    11   1   1   2
  DDX60 WILD-TYPE 300  13  14  22
D409V10, multiclass
    clus
vv   DDX60 MUTATED DDX60 WILD-TYPE
  R0            11             300
  R1             1              13
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D409V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DDX60 MUTATED       3                         1
  DDX60 WILD-TYPE    84                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDX60 MUTATED                                           0     8
  DDX60 WILD-TYPE                                         1   235
D409V12, multiclass
                                           clus
vv                                          DDX60 MUTATED DDX60 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D409V13, binary
                 cls
clus                0   1
  DDX60 MUTATED     0   9
  DDX60 WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX60 MUTATED      0    9
  DDX60 WILD-TYPE    4  301
                        clus
vv                       DDX60 MUTATED DDX60 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(410) Variable = ACTL6A MUTATION ANALYSIS
D410V1, survival
                  sevent
clus2                0   1
  ACTL6A MUTATED     5   3
  ACTL6A WILD-TYPE 225 136
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               8              361 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               3              136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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           14.070 
[1] "0.1 - 77.3 (29.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D410V2, 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       2       13       40       29        36        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACTL6A MUTATED           0          0          1          1        0
  ACTL6A WILD-TYPE         3         70         52         31       38
D410V3, multiclass
            clus
vv           ACTL6A MUTATED ACTL6A WILD-TYPE
  STAGE I                 0                2
  STAGE IA                2               13
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ACTL6A MUTATED     2   1   2   3
  ACTL6A WILD-TYPE  20  91 171  94
D410V4, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  T1              2               20
  T2              1               91
  T3              2              171
  T4              3               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
  ACTL6A MUTATED     5   1   1   1
  ACTL6A WILD-TYPE 113 103  76  76
D410V5, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  N0              5              113
  N1              1              103
  N2              1               76
  N3              1               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"
D410V6, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     8   0
  ACTL6A WILD-TYPE 338  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      8    0
  ACTL6A WILD-TYPE  338   29
   clus
vv  ACTL6A MUTATED ACTL6A WILD-TYPE
  0              8              338
  1              0               29
[1] 2 2
[1] FALSE
D410V7, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     3   5
  ACTL6A WILD-TYPE 142 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      3    5
  ACTL6A WILD-TYPE  142  243
        clus
vv       ACTL6A MUTATED ACTL6A WILD-TYPE
  FEMALE              3              142
  MALE                5              243
[1] 2 2
[1] FALSE
D410V8, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     6   1
  ACTL6A WILD-TYPE 286  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      6    1
  ACTL6A WILD-TYPE  286   58
     clus
vv    ACTL6A MUTATED ACTL6A WILD-TYPE
  NO               6              286
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ACTL6A MUTATED                                          0
  ACTL6A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ACTL6A MUTATED                                       0
  ACTL6A WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ACTL6A MUTATED                                                        4
  ACTL6A WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ACTL6A MUTATED                                                   1
  ACTL6A WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ACTL6A MUTATED                                                                   1
  ACTL6A WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ACTL6A MUTATED                                                    1
  ACTL6A WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ACTL6A MUTATED                                                  1
  ACTL6A WILD-TYPE                                               60
D410V9, multiclass
                                                                   clus
vv                                                                  ACTL6A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ACTL6A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ACTL6A MUTATED     8   0   0   0
  ACTL6A WILD-TYPE 303  14  15  24
D410V10, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D410V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ACTL6A MUTATED       2                         0
  ACTL6A WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ACTL6A MUTATED                                           0     4
  ACTL6A WILD-TYPE                                         1   239
D410V12, multiclass
                                           clus
vv                                          ACTL6A MUTATED ACTL6A WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D410V13, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     0   6
  ACTL6A WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      0    6
  ACTL6A WILD-TYPE    4  304
                        clus
vv                       ACTL6A MUTATED ACTL6A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(411) Variable = PFKP MUTATION ANALYSIS
D411V1, survival
                sevent
clus2              0   1
  PFKP MUTATED    10   4
  PFKP WILD-TYPE 220 135
  PFKP MUTATED PFKP WILD-TYPE 
            14            355 
  PFKP MUTATED PFKP WILD-TYPE 
             4            135 
$`PFKP MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7723 TCGA-BR-8078 
        6.97        30.90        34.68        32.78        28.73        29.59 
TCGA-BR-8081 TCGA-BR-8591 TCGA-CG-5726 TCGA-HU-A4G2 TCGA-HU-A4GU TCGA-HU-A4H6 
       32.25        28.14        28.96        24.30         6.58        21.17 
TCGA-HU-A4H8 TCGA-VQ-A8P2 
       14.07        38.14 

$`PFKP WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76         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-A4HB TCGA-HU-A4HD 
       12.95        29.00        23.84        23.80        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 

  PFKP MUTATED PFKP WILD-TYPE 
          6.58           0.00 
  PFKP MUTATED PFKP WILD-TYPE 
         38.14         122.30 
  PFKP MUTATED PFKP WILD-TYPE 
        28.845         14.040 
[1] "6.6 - 38.1 (28.8)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "2"  
D411V2, 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       2       14       39       30        35        47
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PFKP MUTATED           0          4          1          1        0
  PFKP WILD-TYPE         3         66         52         31       38
D411V3, multiclass
            clus
vv           PFKP MUTATED PFKP WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             5             47
  STAGE III             0              3
  STAGE IIIA            4             66
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PFKP MUTATED     3   1   7   6
  PFKP WILD-TYPE  19  91 166  91
D411V4, multiclass
    clus
vv   PFKP MUTATED PFKP WILD-TYPE
  T1            3             19
  T2            1             91
  T3            7            166
  T4            6             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
  PFKP MUTATED     7   5   1   2
  PFKP WILD-TYPE 111  99  76  75
D411V5, multiclass
    clus
vv   PFKP MUTATED PFKP WILD-TYPE
  N0            7            111
  N1            5             99
  N2            1             76
  N3            2             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"
D411V6, binary
                cls
clus               0   1
  PFKP MUTATED    17   0
  PFKP WILD-TYPE 329  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFKP MUTATED     17    0
  PFKP WILD-TYPE  329   29
   clus
vv  PFKP MUTATED PFKP WILD-TYPE
  0           17            329
  1            0             29
[1] 2 2
[1] FALSE
D411V7, binary
                cls
clus               0   1
  PFKP MUTATED     9   9
  PFKP WILD-TYPE 136 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFKP MUTATED      9    9
  PFKP WILD-TYPE  136  239
        clus
vv       PFKP MUTATED PFKP WILD-TYPE
  FEMALE            9            136
  MALE              9            239
[1] 2 2
[1] FALSE
D411V8, binary
                cls
clus               0   1
  PFKP MUTATED    13   1
  PFKP WILD-TYPE 279  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFKP MUTATED     13    1
  PFKP WILD-TYPE  279   58
     clus
vv    PFKP MUTATED PFKP WILD-TYPE
  NO            13            279
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PFKP MUTATED                                          0
  PFKP WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PFKP MUTATED                                       2
  PFKP WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PFKP MUTATED                                                       11
  PFKP WILD-TYPE                                                    147
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PFKP MUTATED                                                   1
  PFKP WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PFKP MUTATED                                                                   2
  PFKP WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PFKP MUTATED                                                    0
  PFKP WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PFKP MUTATED                                                  2
  PFKP WILD-TYPE                                               59
D411V9, multiclass
                                                                   clus
vv                                                                  PFKP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  PFKP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PFKP MUTATED    13   0   0   5
  PFKP WILD-TYPE 298  14  15  19
D411V10, multiclass
    clus
vv   PFKP MUTATED PFKP WILD-TYPE
  R0           13            298
  R1            0             14
  R2            0             15
  RX            5             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D411V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PFKP MUTATED       4                         0
  PFKP WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PFKP MUTATED                                           0    13
  PFKP WILD-TYPE                                         1   230
D411V12, multiclass
                                           clus
vv                                          PFKP MUTATED PFKP WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D411V13, binary
                cls
clus               0   1
  PFKP MUTATED     0  16
  PFKP WILD-TYPE   4 294
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFKP MUTATED      0   16
  PFKP WILD-TYPE    4  294
                        clus
vv                       PFKP MUTATED PFKP WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           16            294
[1] 2 2
[1] FALSE

Clustering(412) Variable = OR2J3 MUTATION ANALYSIS
D412V1, survival
                 sevent
clus2               0   1
  OR2J3 MUTATED     5   3
  OR2J3 WILD-TYPE 225 136
  OR2J3 MUTATED OR2J3 WILD-TYPE 
              8             361 
  OR2J3 MUTATED OR2J3 WILD-TYPE 
              3             136 
$`OR2J3 MUTATED`
TCGA-CG-4460 TCGA-BR-4187 TCGA-BR-6452 TCGA-CD-8536 TCGA-D7-6822 TCGA-D7-A4Z0 
       21.99         4.64        34.68        12.43        12.33        14.76 
TCGA-IN-A6RL TCGA-VQ-AA68 
       13.35        43.66 

$`OR2J3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         6.97         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-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-D7-8570 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-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-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-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        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-AA69 TCGA-VQ-AA6A 
       42.64        66.81        11.24        18.41        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 

  OR2J3 MUTATED OR2J3 WILD-TYPE 
           4.64            0.00 
  OR2J3 MUTATED OR2J3 WILD-TYPE 
          43.66          122.30 
  OR2J3 MUTATED OR2J3 WILD-TYPE 
         14.055          14.270 
[1] "4.6 - 43.7 (14.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D412V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR2J3 MUTATED         1        0        1        1         1         1
  OR2J3 WILD-TYPE       1       15       39       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR2J3 MUTATED           0          1          0          1        1
  OR2J3 WILD-TYPE         3         69         53         31       37
D412V3, multiclass
            clus
vv           OR2J3 MUTATED OR2J3 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR2J3 MUTATED     1   3   2   2
  OR2J3 WILD-TYPE  21  89 171  95
D412V4, multiclass
    clus
vv   OR2J3 MUTATED OR2J3 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             2             171
  T4             2              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
  OR2J3 MUTATED     3   3   1   1
  OR2J3 WILD-TYPE 115 101  76  76
D412V5, multiclass
    clus
vv   OR2J3 MUTATED OR2J3 WILD-TYPE
  N0             3             115
  N1             3             101
  N2             1              76
  N3             1              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"
D412V6, binary
                 cls
clus                0   1
  OR2J3 MUTATED     7   1
  OR2J3 WILD-TYPE 339  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2J3 MUTATED      7    1
  OR2J3 WILD-TYPE  339   28
   clus
vv  OR2J3 MUTATED OR2J3 WILD-TYPE
  0             7             339
  1             1              28
[1] 2 2
[1] FALSE
D412V7, binary
                 cls
clus                0   1
  OR2J3 MUTATED     4   5
  OR2J3 WILD-TYPE 141 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2J3 MUTATED      4    5
  OR2J3 WILD-TYPE  141  243
        clus
vv       OR2J3 MUTATED OR2J3 WILD-TYPE
  FEMALE             4             141
  MALE               5             243
[1] 2 2
[1] FALSE
D412V8, binary
                 cls
clus                0   1
  OR2J3 MUTATED     7   2
  OR2J3 WILD-TYPE 285  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2J3 MUTATED      7    2
  OR2J3 WILD-TYPE  285   57
     clus
vv    OR2J3 MUTATED OR2J3 WILD-TYPE
  NO              7             285
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OR2J3 MUTATED                                          0
  OR2J3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OR2J3 MUTATED                                       0
  OR2J3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OR2J3 MUTATED                                                        5
  OR2J3 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OR2J3 MUTATED                                                   1
  OR2J3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OR2J3 MUTATED                                                                   1
  OR2J3 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OR2J3 MUTATED                                                    0
  OR2J3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OR2J3 MUTATED                                                  2
  OR2J3 WILD-TYPE                                               59
D412V9, multiclass
                                                                   clus
vv                                                                  OR2J3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  OR2J3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR2J3 MUTATED     7   0   1   1
  OR2J3 WILD-TYPE 304  14  14  23
D412V10, multiclass
    clus
vv   OR2J3 MUTATED OR2J3 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D412V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OR2J3 MUTATED       1                         1
  OR2J3 WILD-TYPE    86                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OR2J3 MUTATED                                           0     6
  OR2J3 WILD-TYPE                                         1   237
D412V12, multiclass
                                           clus
vv                                          OR2J3 MUTATED OR2J3 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D412V13, binary
                 cls
clus                0   1
  OR2J3 MUTATED     0   7
  OR2J3 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2J3 MUTATED      0    7
  OR2J3 WILD-TYPE    4  303
                        clus
vv                       OR2J3 MUTATED OR2J3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(413) Variable = C20ORF160 MUTATION ANALYSIS
D413V1, survival
                     sevent
clus2                   0   1
  C20ORF160 MUTATED     6   1
  C20ORF160 WILD-TYPE 224 138
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
                  7                 362 
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
                  1                 138 
$`C20ORF160 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8361 TCGA-D7-8572 TCGA-HJ-7597 
       34.68        44.94        29.59        31.10        16.80        26.47 
TCGA-HU-A4G8 
       22.68 

$`C20ORF160 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-8573 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-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 

  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
               16.8                 0.0 
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
              44.94              122.30 
  C20ORF160 MUTATED C20ORF160 WILD-TYPE 
             29.590              14.055 
[1] "16.8 - 44.9 (29.6)" "0.0 - 122.3 (14.1)"
[1] "hr=" "4.4"
D413V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C20ORF160 MUTATED         0        0        1        0         2         3
  C20ORF160 WILD-TYPE       2       15       39       30        35        49
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF160 MUTATED           0          0          0          1        0
  C20ORF160 WILD-TYPE         3         70         53         31       38
D413V3, multiclass
            clus
vv           C20ORF160 MUTATED C20ORF160 WILD-TYPE
  STAGE I                    0                   2
  STAGE IA                   0                  15
  STAGE IB                   1                  39
  STAGE II                   0                  30
  STAGE IIA                  2                  35
  STAGE IIB                  3                  49
  STAGE III                  0                   3
  STAGE IIIA                 0                  70
  STAGE IIIB                 0                  53
  STAGE IIIC                 1                  31
  STAGE IV                   0                  38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C20ORF160 MUTATED     0   2   3   2
  C20ORF160 WILD-TYPE  22  90 170  95
D413V4, multiclass
    clus
vv   C20ORF160 MUTATED C20ORF160 WILD-TYPE
  T1                 0                  22
  T2                 2                  90
  T3                 3                 170
  T4                 2                  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
  C20ORF160 MUTATED     4   1   2   0
  C20ORF160 WILD-TYPE 114 103  75  77
D413V5, multiclass
    clus
vv   C20ORF160 MUTATED C20ORF160 WILD-TYPE
  N0                 4                 114
  N1                 1                 103
  N2                 2                  75
  N3                 0                  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"
D413V6, binary
                     cls
clus                    0   1
  C20ORF160 MUTATED     6   0
  C20ORF160 WILD-TYPE 340  29
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF160 MUTATED      6    0
  C20ORF160 WILD-TYPE  340   29
   clus
vv  C20ORF160 MUTATED C20ORF160 WILD-TYPE
  0                 6                 340
  1                 0                  29
[1] 2 2
[1] FALSE
D413V7, binary
                     cls
clus                    0   1
  C20ORF160 MUTATED     6   1
  C20ORF160 WILD-TYPE 139 247
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF160 MUTATED      6    1
  C20ORF160 WILD-TYPE  139  247
        clus
vv       C20ORF160 MUTATED C20ORF160 WILD-TYPE
  FEMALE                 6                 139
  MALE                   1                 247
[1] 2 2
[1] FALSE
D413V8, binary
                     cls
clus                    0   1
  C20ORF160 MUTATED     7   0
  C20ORF160 WILD-TYPE 285  59
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF160 MUTATED      7    0
  C20ORF160 WILD-TYPE  285   59
     clus
vv    C20ORF160 MUTATED C20ORF160 WILD-TYPE
  NO                  7                 285
  YES                 0                  59
[1] 2 2
[1] FALSE
                     vv
clus                  STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C20ORF160 MUTATED                                          1
  C20ORF160 WILD-TYPE                                        7
                     vv
clus                  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C20ORF160 MUTATED                                       1
  C20ORF160 WILD-TYPE                                    69
                     vv
clus                  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C20ORF160 MUTATED                                                        5
  C20ORF160 WILD-TYPE                                                    153
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C20ORF160 MUTATED                                                   0
  C20ORF160 WILD-TYPE                                                21
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C20ORF160 MUTATED                                                                   0
  C20ORF160 WILD-TYPE                                                                68
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C20ORF160 MUTATED                                                    0
  C20ORF160 WILD-TYPE                                                  5
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C20ORF160 MUTATED                                                  0
  C20ORF160 WILD-TYPE                                               61
D413V9, multiclass
                                                                   clus
vv                                                                  C20ORF160 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  0
                                                                   clus
vv                                                                  C20ORF160 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                            7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                              69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                  21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                  5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                   61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  C20ORF160 MUTATED     6   0   0   0
  C20ORF160 WILD-TYPE 305  14  15  24
D413V10, multiclass
    clus
vv   C20ORF160 MUTATED C20ORF160 WILD-TYPE
  R0                 6                 305
  R1                 0                  14
  R2                 0                  15
  RX                 0                  24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D413V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN
  C20ORF160 MUTATED       1                         0
  C20ORF160 WILD-TYPE    86                         9
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C20ORF160 MUTATED                                           0     6
  C20ORF160 WILD-TYPE                                         1   237
D413V12, multiclass
                                           clus
vv                                          C20ORF160 MUTATED
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                     6
                                           clus
vv                                          C20ORF160 WILD-TYPE
  ASIAN                                                      86
  BLACK OR AFRICAN AMERICAN                                   9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   1
  WHITE                                                     237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D413V13, binary
                     cls
clus                    0   1
  C20ORF160 MUTATED     0   7
  C20ORF160 WILD-TYPE   4 303
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF160 MUTATED      0    7
  C20ORF160 WILD-TYPE    4  303
                        clus
vv                       C20ORF160 MUTATED C20ORF160 WILD-TYPE
  HISPANIC OR LATINO                     0                   4
  NOT HISPANIC OR LATINO                 7                 303
[1] 2 2
[1] FALSE

Clustering(414) Variable = SGK3 MUTATION ANALYSIS
D414V1, survival
                sevent
clus2              0   1
  SGK3 MUTATED     3   1
  SGK3 WILD-TYPE 227 138
  SGK3 MUTATED SGK3 WILD-TYPE 
             4            365 
  SGK3 MUTATED SGK3 WILD-TYPE 
             1            138 
$`SGK3 MUTATED`
TCGA-BR-4184 TCGA-BR-8372 TCGA-BR-8591 TCGA-HU-A4GU 
        6.97        31.27        28.14         6.58 

$`SGK3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  SGK3 MUTATED SGK3 WILD-TYPE 
          6.58           0.00 
  SGK3 MUTATED SGK3 WILD-TYPE 
         31.27         122.30 
  SGK3 MUTATED SGK3 WILD-TYPE 
        17.555         14.270 
[1] "6.6 - 31.3 (17.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D414V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SGK3 MUTATED         0        0        0        0         0         2
  SGK3 WILD-TYPE       2       15       40       30        37        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SGK3 MUTATED           0          2          0          2        0
  SGK3 WILD-TYPE         3         68         53         30       38
D414V3, multiclass
            clus
vv           SGK3 MUTATED SGK3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SGK3 MUTATED     0   0   2   4
  SGK3 WILD-TYPE  22  92 171  93
D414V4, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  T1            0             22
  T2            0             92
  T3            2            171
  T4            4             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
  SGK3 MUTATED     2   2   0   2
  SGK3 WILD-TYPE 116 102  77  75
D414V5, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  N0            2            116
  N1            2            102
  N2            0             77
  N3            2             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"
D414V6, binary
                cls
clus               0   1
  SGK3 MUTATED     6   0
  SGK3 WILD-TYPE 340  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      6    0
  SGK3 WILD-TYPE  340   29
   clus
vv  SGK3 MUTATED SGK3 WILD-TYPE
  0            6            340
  1            0             29
[1] 2 2
[1] FALSE
D414V7, binary
                cls
clus               0   1
  SGK3 MUTATED     2   5
  SGK3 WILD-TYPE 143 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      2    5
  SGK3 WILD-TYPE  143  243
        clus
vv       SGK3 MUTATED SGK3 WILD-TYPE
  FEMALE            2            143
  MALE              5            243
[1] 2 2
[1] FALSE
D414V8, binary
                cls
clus               0   1
  SGK3 MUTATED     5   0
  SGK3 WILD-TYPE 287  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      5    0
  SGK3 WILD-TYPE  287   59
     clus
vv    SGK3 MUTATED SGK3 WILD-TYPE
  NO             5            287
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SGK3 MUTATED                                          0
  SGK3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SGK3 MUTATED                                       1
  SGK3 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SGK3 MUTATED                                                        5
  SGK3 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SGK3 MUTATED                                                   0
  SGK3 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SGK3 MUTATED                                                                   1
  SGK3 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SGK3 MUTATED                                                    0
  SGK3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SGK3 MUTATED                                                  0
  SGK3 WILD-TYPE                                               61
D414V9, multiclass
                                                                   clus
vv                                                                  SGK3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  SGK3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SGK3 MUTATED     4   0   0   3
  SGK3 WILD-TYPE 307  14  15  21
D414V10, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  R0            4            307
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D414V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SGK3 MUTATED       1                         0
  SGK3 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SGK3 MUTATED                                           0     6
  SGK3 WILD-TYPE                                         1   237
D414V12, multiclass
                                           clus
vv                                          SGK3 MUTATED SGK3 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D414V13, binary
                cls
clus               0   1
  SGK3 MUTATED     0   7
  SGK3 WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      0    7
  SGK3 WILD-TYPE    4  303
                        clus
vv                       SGK3 MUTATED SGK3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(415) Variable = SMTN MUTATION ANALYSIS
D415V1, survival
                sevent
clus2              0   1
  SMTN MUTATED    13   5
  SMTN WILD-TYPE 217 134
  SMTN MUTATED SMTN WILD-TYPE 
            18            351 
  SMTN MUTATED SMTN WILD-TYPE 
             5            134 
$`SMTN MUTATED`
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7715 
        9.44         6.97         9.34        44.94        35.84        33.63 
TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4J2 TCGA-CD-A4MG 
        0.26         4.31         1.12        31.96        14.17         6.58 
TCGA-D7-A6EY TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-VQ-A8P2 TCGA-VQ-A92D 
       11.44         6.51        20.25        29.00        38.14        66.81 

$`SMTN WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         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-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-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-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-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-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-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-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-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 

  SMTN MUTATED SMTN WILD-TYPE 
          0.26           0.00 
  SMTN MUTATED SMTN WILD-TYPE 
         66.81         122.30 
  SMTN MUTATED SMTN WILD-TYPE 
        12.805         14.430 
[1] "0.3 - 66.8 (12.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.4"
D415V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMTN MUTATED         1        0        4        0         5         2
  SMTN WILD-TYPE       1       15       36       30        32        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMTN MUTATED           0          2          1          2        2
  SMTN WILD-TYPE         3         68         52         30       36
D415V3, multiclass
            clus
vv           SMTN MUTATED SMTN WILD-TYPE
  STAGE I               1              1
  STAGE IA              0             15
  STAGE IB              4             36
  STAGE II              0             30
  STAGE IIA             5             32
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SMTN MUTATED     1   4   7   7
  SMTN WILD-TYPE  21  88 166  90
D415V4, multiclass
    clus
vv   SMTN MUTATED SMTN WILD-TYPE
  T1            1             21
  T2            4             88
  T3            7            166
  T4            7             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
  SMTN MUTATED    10   4   3   2
  SMTN WILD-TYPE 108 100  74  75
D415V5, multiclass
    clus
vv   SMTN MUTATED SMTN WILD-TYPE
  N0           10            108
  N1            4            100
  N2            3             74
  N3            2             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"
D415V6, binary
                cls
clus               0   1
  SMTN MUTATED    17   1
  SMTN WILD-TYPE 329  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED     17    1
  SMTN WILD-TYPE  329   28
   clus
vv  SMTN MUTATED SMTN WILD-TYPE
  0           17            329
  1            1             28
[1] 2 2
[1] FALSE
D415V7, binary
                cls
clus               0   1
  SMTN MUTATED    10  10
  SMTN WILD-TYPE 135 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED     10   10
  SMTN WILD-TYPE  135  238
        clus
vv       SMTN MUTATED SMTN WILD-TYPE
  FEMALE           10            135
  MALE             10            238
[1] 2 2
[1] FALSE
D415V8, binary
                cls
clus               0   1
  SMTN MUTATED    17   1
  SMTN WILD-TYPE 275  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED     17    1
  SMTN WILD-TYPE  275   58
     clus
vv    SMTN MUTATED SMTN WILD-TYPE
  NO            17            275
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SMTN MUTATED                                          0
  SMTN WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SMTN MUTATED                                       4
  SMTN WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMTN MUTATED                                                       11
  SMTN WILD-TYPE                                                    147
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SMTN MUTATED                                                   1
  SMTN WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMTN MUTATED                                                                   0
  SMTN WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SMTN MUTATED                                                    0
  SMTN WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SMTN MUTATED                                                  4
  SMTN WILD-TYPE                                               57
D415V9, multiclass
                                                                   clus
vv                                                                  SMTN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  SMTN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SMTN MUTATED    15   0   0   3
  SMTN WILD-TYPE 296  14  15  21
D415V10, multiclass
    clus
vv   SMTN MUTATED SMTN WILD-TYPE
  R0           15            296
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D415V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SMTN MUTATED       6                         1
  SMTN WILD-TYPE    81                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMTN MUTATED                                           0    13
  SMTN WILD-TYPE                                         1   230
D415V12, multiclass
                                           clus
vv                                          SMTN MUTATED SMTN WILD-TYPE
  ASIAN                                                6             81
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D415V13, binary
                cls
clus               0   1
  SMTN MUTATED     0  18
  SMTN WILD-TYPE   4 292
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED      0   18
  SMTN WILD-TYPE    4  292
                        clus
vv                       SMTN MUTATED SMTN WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           18            292
[1] 2 2
[1] FALSE

Clustering(416) Variable = SLC9A11 MUTATION ANALYSIS
D416V1, survival
                   sevent
clus2                 0   1
  SLC9A11 MUTATED    13   9
  SLC9A11 WILD-TYPE 217 130
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               22               347 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
                9               130 
$`SLC9A11 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-7715 
       21.99        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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-8291 TCGA-BR-8295 
       32.25         8.05         0.56        29.42        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-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       21.44         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-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-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-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       15.02        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-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-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-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-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 

  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
             2.66              0.00 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
            34.68            122.30 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
           19.725            14.040 
[1] "2.7 - 34.7 (19.7)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.1"
D416V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC9A11 MUTATED         1        1        1        1         3         2
  SLC9A11 WILD-TYPE       1       14       39       29        34        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A11 MUTATED           0          4          1          2        5
  SLC9A11 WILD-TYPE         3         66         52         30       33
D416V3, multiclass
            clus
vv           SLC9A11 MUTATED SLC9A11 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                3                34
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               4                66
  STAGE IIIB               1                52
  STAGE IIIC               2                30
  STAGE IV                 5                33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC9A11 MUTATED     2   5   5  10
  SLC9A11 WILD-TYPE  20  87 168  87
D416V4, multiclass
    clus
vv   SLC9A11 MUTATED SLC9A11 WILD-TYPE
  T1               2                20
  T2               5                87
  T3               5               168
  T4              10                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
  SLC9A11 MUTATED     8   8   3   3
  SLC9A11 WILD-TYPE 110  96  74  74
D416V5, multiclass
    clus
vv   SLC9A11 MUTATED SLC9A11 WILD-TYPE
  N0               8               110
  N1               8                96
  N2               3                74
  N3               3                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"
D416V6, binary
                   cls
clus                  0   1
  SLC9A11 MUTATED    20   4
  SLC9A11 WILD-TYPE 326  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED     20    4
  SLC9A11 WILD-TYPE  326   25
   clus
vv  SLC9A11 MUTATED SLC9A11 WILD-TYPE
  0              20               326
  1               4                25
[1] 2 2
[1] FALSE
D416V7, binary
                   cls
clus                  0   1
  SLC9A11 MUTATED    13  11
  SLC9A11 WILD-TYPE 132 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED     13   11
  SLC9A11 WILD-TYPE  132  237
        clus
vv       SLC9A11 MUTATED SLC9A11 WILD-TYPE
  FEMALE              13               132
  MALE                11               237
[1] 2 2
[1] FALSE
D416V8, binary
                   cls
clus                  0   1
  SLC9A11 MUTATED    19   1
  SLC9A11 WILD-TYPE 273  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED     19    1
  SLC9A11 WILD-TYPE  273   58
     clus
vv    SLC9A11 MUTATED SLC9A11 WILD-TYPE
  NO               19               273
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC9A11 MUTATED                                          0
  SLC9A11 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC9A11 MUTATED                                       3
  SLC9A11 WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC9A11 MUTATED                                                       12
  SLC9A11 WILD-TYPE                                                    146
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC9A11 MUTATED                                                   0
  SLC9A11 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC9A11 MUTATED                                                                   5
  SLC9A11 WILD-TYPE                                                                63
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC9A11 MUTATED                                                    0
  SLC9A11 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC9A11 MUTATED                                                  4
  SLC9A11 WILD-TYPE                                               57
D416V9, multiclass
                                                                   clus
vv                                                                  SLC9A11 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                4
                                                                   clus
vv                                                                  SLC9A11 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC9A11 MUTATED    18   0   2   4
  SLC9A11 WILD-TYPE 293  14  13  20
D416V10, multiclass
    clus
vv   SLC9A11 MUTATED SLC9A11 WILD-TYPE
  R0              18               293
  R1               0                14
  R2               2                13
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC9A11 MUTATED       6                         0
  SLC9A11 WILD-TYPE    81                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC9A11 MUTATED                                           0    13
  SLC9A11 WILD-TYPE                                         1   230
D416V12, multiclass
                                           clus
vv                                          SLC9A11 MUTATED SLC9A11 WILD-TYPE
  ASIAN                                                   6                81
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V13, binary
                   cls
clus                  0   1
  SLC9A11 MUTATED     0  18
  SLC9A11 WILD-TYPE   4 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED      0   18
  SLC9A11 WILD-TYPE    4  292
                        clus
vv                       SLC9A11 MUTATED SLC9A11 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              18               292
[1] 2 2
[1] FALSE

Clustering(417) Variable = JHDM1D MUTATION ANALYSIS
D417V1, survival
                  sevent
clus2                0   1
  JHDM1D MUTATED     6   3
  JHDM1D WILD-TYPE 224 136
  JHDM1D MUTATED JHDM1D WILD-TYPE 
               9              360 
  JHDM1D MUTATED JHDM1D WILD-TYPE 
               3              136 
$`JHDM1D MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8368 TCGA-CD-8535 TCGA-CD-A4MG TCGA-CG-4305 
        6.97        34.68         4.31        12.82         6.58        15.95 
TCGA-D7-A4YV TCGA-F1-6874 TCGA-VQ-A8P2 
        5.92        14.47        38.14 

$`JHDM1D WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  JHDM1D MUTATED JHDM1D WILD-TYPE 
            4.31             0.00 
  JHDM1D MUTATED JHDM1D WILD-TYPE 
           38.14           122.30 
  JHDM1D MUTATED JHDM1D WILD-TYPE 
           12.82            14.35 
[1] "4.3 - 38.1 (12.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D417V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  JHDM1D MUTATED         0        0        3        1         2         1
  JHDM1D WILD-TYPE       2       15       37       29        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  JHDM1D MUTATED           0          3          0          0        0
  JHDM1D WILD-TYPE         3         67         53         32       38
D417V3, multiclass
            clus
vv           JHDM1D MUTATED JHDM1D WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  JHDM1D MUTATED     0   4   5   1
  JHDM1D WILD-TYPE  22  88 168  96
D417V4, multiclass
    clus
vv   JHDM1D MUTATED JHDM1D WILD-TYPE
  T1              0               22
  T2              4               88
  T3              5              168
  T4              1               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
  JHDM1D MUTATED     5   5   0   0
  JHDM1D WILD-TYPE 113  99  77  77
D417V5, multiclass
    clus
vv   JHDM1D MUTATED JHDM1D WILD-TYPE
  N0              5              113
  N1              5               99
  N2              0               77
  N3              0               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"
D417V6, binary
                  cls
clus                 0   1
  JHDM1D MUTATED     9   0
  JHDM1D WILD-TYPE 337  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JHDM1D MUTATED      9    0
  JHDM1D WILD-TYPE  337   29
   clus
vv  JHDM1D MUTATED JHDM1D WILD-TYPE
  0              9              337
  1              0               29
[1] 2 2
[1] FALSE
D417V7, binary
                  cls
clus                 0   1
  JHDM1D MUTATED     3   7
  JHDM1D WILD-TYPE 142 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JHDM1D MUTATED      3    7
  JHDM1D WILD-TYPE  142  241
        clus
vv       JHDM1D MUTATED JHDM1D WILD-TYPE
  FEMALE              3              142
  MALE                7              241
[1] 2 2
[1] FALSE
D417V8, binary
                  cls
clus                 0   1
  JHDM1D MUTATED     8   1
  JHDM1D WILD-TYPE 284  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JHDM1D MUTATED      8    1
  JHDM1D WILD-TYPE  284   58
     clus
vv    JHDM1D MUTATED JHDM1D WILD-TYPE
  NO               8              284
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  JHDM1D MUTATED                                          0
  JHDM1D WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  JHDM1D MUTATED                                       1
  JHDM1D WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  JHDM1D MUTATED                                                        5
  JHDM1D WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  JHDM1D MUTATED                                                   1
  JHDM1D WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  JHDM1D MUTATED                                                                   2
  JHDM1D WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  JHDM1D MUTATED                                                    0
  JHDM1D WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  JHDM1D MUTATED                                                  1
  JHDM1D WILD-TYPE                                               60
D417V9, multiclass
                                                                   clus
vv                                                                  JHDM1D MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  JHDM1D WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  JHDM1D MUTATED     8   0   0   1
  JHDM1D WILD-TYPE 303  14  15  23
D417V10, multiclass
    clus
vv   JHDM1D MUTATED JHDM1D WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D417V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  JHDM1D MUTATED       2                         0
  JHDM1D WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  JHDM1D MUTATED                                           0     6
  JHDM1D WILD-TYPE                                         1   237
D417V12, multiclass
                                           clus
vv                                          JHDM1D MUTATED JHDM1D WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D417V13, binary
                  cls
clus                 0   1
  JHDM1D MUTATED     0   7
  JHDM1D WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JHDM1D MUTATED      0    7
  JHDM1D WILD-TYPE    4  303
                        clus
vv                       JHDM1D MUTATED JHDM1D WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(418) Variable = GLT8D1 MUTATION ANALYSIS
D418V1, survival
                  sevent
clus2                0   1
  GLT8D1 MUTATED     4   2
  GLT8D1 WILD-TYPE 226 137
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               6              363 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               2              137 
$`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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
            26.7              0.0 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
           38.14           122.30 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
           30.44            14.07 
[1] "26.7 - 38.1 (30.4)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.1"
D418V2, 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       2       13       40       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLT8D1 MUTATED           0          1          0          0        0
  GLT8D1 WILD-TYPE         3         69         53         32       38
D418V3, multiclass
            clus
vv           GLT8D1 MUTATED GLT8D1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                2               13
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GLT8D1 MUTATED     3   2   0   2
  GLT8D1 WILD-TYPE  19  90 173  95
D418V4, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  T1              3               19
  T2              2               90
  T3              0              173
  T4              2               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
  GLT8D1 MUTATED     3   2   0   0
  GLT8D1 WILD-TYPE 115 102  77  77
D418V5, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  N0              3              115
  N1              2              102
  N2              0               77
  N3              0               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"
D418V6, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     7   0
  GLT8D1 WILD-TYPE 339  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      7    0
  GLT8D1 WILD-TYPE  339   29
   clus
vv  GLT8D1 MUTATED GLT8D1 WILD-TYPE
  0              7              339
  1              0               29
[1] 2 2
[1] FALSE
D418V7, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     3   4
  GLT8D1 WILD-TYPE 142 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      3    4
  GLT8D1 WILD-TYPE  142  244
        clus
vv       GLT8D1 MUTATED GLT8D1 WILD-TYPE
  FEMALE              3              142
  MALE                4              244
[1] 2 2
[1] FALSE
D418V8, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     4   1
  GLT8D1 WILD-TYPE 288  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      4    1
  GLT8D1 WILD-TYPE  288   58
     clus
vv    GLT8D1 MUTATED GLT8D1 WILD-TYPE
  NO               4              288
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GLT8D1 MUTATED                                          0
  GLT8D1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GLT8D1 MUTATED                                       1
  GLT8D1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GLT8D1 MUTATED                                                        2
  GLT8D1 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GLT8D1 MUTATED                                                   1
  GLT8D1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GLT8D1 MUTATED                                                                   1
  GLT8D1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GLT8D1 MUTATED                                                    1
  GLT8D1 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GLT8D1 MUTATED                                                  1
  GLT8D1 WILD-TYPE                                               60
D418V9, multiclass
                                                                   clus
vv                                                                  GLT8D1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  GLT8D1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GLT8D1 MUTATED     5   0   0   2
  GLT8D1 WILD-TYPE 306  14  15  22
D418V10, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D418V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GLT8D1 MUTATED       1                         0
  GLT8D1 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GLT8D1 MUTATED                                           0     5
  GLT8D1 WILD-TYPE                                         1   238
D418V12, multiclass
                                           clus
vv                                          GLT8D1 MUTATED GLT8D1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D418V13, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     0   5
  GLT8D1 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      0    5
  GLT8D1 WILD-TYPE    4  305
                        clus
vv                       GLT8D1 MUTATED GLT8D1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(419) Variable = DAPK1 MUTATION ANALYSIS
D419V1, survival
                 sevent
clus2               0   1
  DAPK1 MUTATED    14   5
  DAPK1 WILD-TYPE 216 134
  DAPK1 MUTATED DAPK1 WILD-TYPE 
             19             350 
  DAPK1 MUTATED DAPK1 WILD-TYPE 
              5             134 
$`DAPK1 MUTATED`
TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-5802 
       25.05        28.14        31.96        20.42        16.14        13.35 
TCGA-CG-4305 TCGA-D7-A6EY TCGA-FP-7829 TCGA-FP-A4BE TCGA-HU-A4G9 TCGA-HU-A4GP 
       15.95        11.44        19.53        11.08        24.20         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-R5-A7ZI 
        0.10         6.58        20.25        14.07        19.73        74.53 
TCGA-VQ-A91U 
        1.71 

$`DAPK1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-A4PF TCGA-BR-A4QI 
        0.66        32.52        13.51        20.65         1.15        21.44 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.18        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-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-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-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-A4GT 
       22.75        25.81        11.77        21.37        29.98         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-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-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-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 

  DAPK1 MUTATED DAPK1 WILD-TYPE 
            0.1             0.0 
  DAPK1 MUTATED DAPK1 WILD-TYPE 
          74.53          122.30 
  DAPK1 MUTATED DAPK1 WILD-TYPE 
          16.14           14.12 
[1] "0.1 - 74.5 (16.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D419V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DAPK1 MUTATED         0        1        2        2         2         2
  DAPK1 WILD-TYPE       2       14       38       28        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DAPK1 MUTATED           0          3          2          4        2
  DAPK1 WILD-TYPE         3         67         51         28       36
D419V3, multiclass
            clus
vv           DAPK1 MUTATED DAPK1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               2              28
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             4              28
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DAPK1 MUTATED     3   3   8   7
  DAPK1 WILD-TYPE  19  89 165  90
D419V4, multiclass
    clus
vv   DAPK1 MUTATED DAPK1 WILD-TYPE
  T1             3              19
  T2             3              89
  T3             8             165
  T4             7              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
  DAPK1 MUTATED     5   8   4   4
  DAPK1 WILD-TYPE 113  96  73  73
D419V5, multiclass
    clus
vv   DAPK1 MUTATED DAPK1 WILD-TYPE
  N0             5             113
  N1             8              96
  N2             4              73
  N3             4              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"
D419V6, binary
                 cls
clus                0   1
  DAPK1 MUTATED    20   2
  DAPK1 WILD-TYPE 326  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAPK1 MUTATED     20    2
  DAPK1 WILD-TYPE  326   27
   clus
vv  DAPK1 MUTATED DAPK1 WILD-TYPE
  0            20             326
  1             2              27
[1] 2 2
[1] FALSE
D419V7, binary
                 cls
clus                0   1
  DAPK1 MUTATED    12  10
  DAPK1 WILD-TYPE 133 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAPK1 MUTATED     12   10
  DAPK1 WILD-TYPE  133  238
        clus
vv       DAPK1 MUTATED DAPK1 WILD-TYPE
  FEMALE            12             133
  MALE              10             238
[1] 2 2
[1] FALSE
D419V8, binary
                 cls
clus                0   1
  DAPK1 MUTATED    16   3
  DAPK1 WILD-TYPE 276  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAPK1 MUTATED     16    3
  DAPK1 WILD-TYPE  276   56
     clus
vv    DAPK1 MUTATED DAPK1 WILD-TYPE
  NO             16             276
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DAPK1 MUTATED                                          0
  DAPK1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DAPK1 MUTATED                                       4
  DAPK1 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DAPK1 MUTATED                                                       10
  DAPK1 WILD-TYPE                                                    148
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DAPK1 MUTATED                                                   1
  DAPK1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DAPK1 MUTATED                                                                   1
  DAPK1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DAPK1 MUTATED                                                    0
  DAPK1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DAPK1 MUTATED                                                  6
  DAPK1 WILD-TYPE                                               55
D419V9, multiclass
                                                                   clus
vv                                                                  DAPK1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              6
                                                                   clus
vv                                                                  DAPK1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DAPK1 MUTATED    18   0   0   3
  DAPK1 WILD-TYPE 293  14  15  21
D419V10, multiclass
    clus
vv   DAPK1 MUTATED DAPK1 WILD-TYPE
  R0            18             293
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D419V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DAPK1 MUTATED       9                         1
  DAPK1 WILD-TYPE    78                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DAPK1 MUTATED                                           0    11
  DAPK1 WILD-TYPE                                         1   232
D419V12, multiclass
                                           clus
vv                                          DAPK1 MUTATED DAPK1 WILD-TYPE
  ASIAN                                                 9              78
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D419V13, binary
                 cls
clus                0   1
  DAPK1 MUTATED     1  19
  DAPK1 WILD-TYPE   3 291
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAPK1 MUTATED      1   19
  DAPK1 WILD-TYPE    3  291
                        clus
vv                       DAPK1 MUTATED DAPK1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            19             291
[1] 2 2
[1] FALSE

Clustering(420) Variable = EDNRB MUTATION ANALYSIS
D420V1, survival
                 sevent
clus2               0   1
  EDNRB MUTATED    14  11
  EDNRB WILD-TYPE 216 128
  EDNRB MUTATED EDNRB WILD-TYPE 
             25             344 
  EDNRB MUTATED EDNRB WILD-TYPE 
             11             128 
$`EDNRB MUTATED`
TCGA-CG-4460 TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4280 
       21.99        11.01         6.97        18.35         4.08         6.61 
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8372 TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-8524 
       34.68        32.78        31.27        16.14        13.15        12.76 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4466 TCGA-CG-5721 TCGA-CG-5724 TCGA-D7-6527 
       12.43         6.58        18.97         6.02        12.03        10.26 
TCGA-D7-A4Z0 TCGA-HF-7134 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H8 
       14.76        52.21         0.10         6.58        23.84        14.07 
TCGA-VQ-A8PK 
       17.85 

$`EDNRB WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        26.70        11.70        19.56         9.47         9.44 
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4256 
        6.61         4.64         7.43        30.90         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-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-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-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 
       21.44         5.13        13.41        13.02        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-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-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-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99         0.99       105.07        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-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-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-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-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-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 

  EDNRB MUTATED EDNRB WILD-TYPE 
            0.1             0.0 
  EDNRB MUTATED EDNRB WILD-TYPE 
          52.21          122.30 
  EDNRB MUTATED EDNRB WILD-TYPE 
          13.15           14.45 
[1] "0.1 - 52.2 (13.2)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.3"
D420V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EDNRB MUTATED         0        1        3        4         3         4
  EDNRB WILD-TYPE       2       14       37       26        34        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EDNRB MUTATED           1          3          2          2        3
  EDNRB WILD-TYPE         2         67         51         30       35
D420V3, multiclass
            clus
vv           EDNRB MUTATED EDNRB WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               4              26
  STAGE IIA              3              34
  STAGE IIB              4              48
  STAGE III              1               2
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EDNRB MUTATED     3   6  12   6
  EDNRB WILD-TYPE  19  86 161  91
D420V4, multiclass
    clus
vv   EDNRB MUTATED EDNRB WILD-TYPE
  T1             3              19
  T2             6              86
  T3            12             161
  T4             6              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
  EDNRB MUTATED    10   9   3   4
  EDNRB WILD-TYPE 108  95  74  73
D420V5, multiclass
    clus
vv   EDNRB MUTATED EDNRB WILD-TYPE
  N0            10             108
  N1             9              95
  N2             3              74
  N3             4              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"
D420V6, binary
                 cls
clus                0   1
  EDNRB MUTATED    25   2
  EDNRB WILD-TYPE 321  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EDNRB MUTATED     25    2
  EDNRB WILD-TYPE  321   27
   clus
vv  EDNRB MUTATED EDNRB WILD-TYPE
  0            25             321
  1             2              27
[1] 2 2
[1] FALSE
D420V7, binary
                 cls
clus                0   1
  EDNRB MUTATED    13  15
  EDNRB WILD-TYPE 132 233
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EDNRB MUTATED     13   15
  EDNRB WILD-TYPE  132  233
        clus
vv       EDNRB MUTATED EDNRB WILD-TYPE
  FEMALE            13             132
  MALE              15             233
[1] 2 2
[1] FALSE
D420V8, binary
                 cls
clus                0   1
  EDNRB MUTATED    23   2
  EDNRB WILD-TYPE 269  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EDNRB MUTATED     23    2
  EDNRB WILD-TYPE  269   57
     clus
vv    EDNRB MUTATED EDNRB WILD-TYPE
  NO             23             269
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EDNRB MUTATED                                          0
  EDNRB WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EDNRB MUTATED                                       3
  EDNRB WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EDNRB MUTATED                                                       11
  EDNRB WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EDNRB MUTATED                                                   1
  EDNRB WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EDNRB MUTATED                                                                   8
  EDNRB WILD-TYPE                                                                60
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EDNRB MUTATED                                                    2
  EDNRB WILD-TYPE                                                  3
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EDNRB MUTATED                                                  3
  EDNRB WILD-TYPE                                               58
D420V9, multiclass
                                                                   clus
vv                                                                  EDNRB MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             8
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  EDNRB WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              60
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EDNRB MUTATED    18   0   2   6
  EDNRB WILD-TYPE 293  14  13  18
D420V10, multiclass
    clus
vv   EDNRB MUTATED EDNRB WILD-TYPE
  R0            18             293
  R1             0              14
  R2             2              13
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D420V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EDNRB MUTATED       8                         0
  EDNRB WILD-TYPE    79                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EDNRB MUTATED                                           0    14
  EDNRB WILD-TYPE                                         1   229
D420V12, multiclass
                                           clus
vv                                          EDNRB MUTATED EDNRB WILD-TYPE
  ASIAN                                                 8              79
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D420V13, binary
                 cls
clus                0   1
  EDNRB MUTATED     0  21
  EDNRB WILD-TYPE   4 289
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EDNRB MUTATED      0   21
  EDNRB WILD-TYPE    4  289
                        clus
vv                       EDNRB MUTATED EDNRB WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            21             289
[1] 2 2
[1] FALSE

Clustering(421) Variable = C16ORF70 MUTATION ANALYSIS
D421V1, survival
                    sevent
clus2                  0   1
  C16ORF70 MUTATED     4   1
  C16ORF70 WILD-TYPE 226 138
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
                 5                364 
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
                 1                138 
$`C16ORF70 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8591 TCGA-F1-A448 TCGA-HU-A4H8 
        6.97        34.68        28.14        21.27        14.07 

$`C16ORF70 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
              6.97               0.00 
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
             34.68             122.30 
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
             21.27              14.22 
[1] "7.0 - 34.7 (21.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.3"
D421V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C16ORF70 MUTATED         0        0        1        0         1         0
  C16ORF70 WILD-TYPE       2       15       39       30        36        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C16ORF70 MUTATED           0          1          1          1        0
  C16ORF70 WILD-TYPE         3         69         52         31       38
D421V3, multiclass
            clus
vv           C16ORF70 MUTATED C16ORF70 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                1                 52
  STAGE IIIC                1                 31
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C16ORF70 MUTATED     1   0   3   1
  C16ORF70 WILD-TYPE  21  92 170  96
D421V4, multiclass
    clus
vv   C16ORF70 MUTATED C16ORF70 WILD-TYPE
  T1                1                 21
  T2                0                 92
  T3                3                170
  T4                1                 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
  C16ORF70 MUTATED     1   2   0   2
  C16ORF70 WILD-TYPE 117 102  77  75
D421V5, multiclass
    clus
vv   C16ORF70 MUTATED C16ORF70 WILD-TYPE
  N0                1                117
  N1                2                102
  N2                0                 77
  N3                2                 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"
D421V6, binary
                    cls
clus                   0   1
  C16ORF70 MUTATED     5   0
  C16ORF70 WILD-TYPE 341  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF70 MUTATED      5    0
  C16ORF70 WILD-TYPE  341   29
   clus
vv  C16ORF70 MUTATED C16ORF70 WILD-TYPE
  0                5                341
  1                0                 29
[1] 2 2
[1] FALSE
D421V7, binary
                    cls
clus                   0   1
  C16ORF70 MUTATED     2   4
  C16ORF70 WILD-TYPE 143 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF70 MUTATED      2    4
  C16ORF70 WILD-TYPE  143  244
        clus
vv       C16ORF70 MUTATED C16ORF70 WILD-TYPE
  FEMALE                2                143
  MALE                  4                244
[1] 2 2
[1] FALSE
D421V8, binary
                    cls
clus                   0   1
  C16ORF70 MUTATED     4   1
  C16ORF70 WILD-TYPE 288  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF70 MUTATED      4    1
  C16ORF70 WILD-TYPE  288   58
     clus
vv    C16ORF70 MUTATED C16ORF70 WILD-TYPE
  NO                 4                288
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C16ORF70 MUTATED                                          0
  C16ORF70 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C16ORF70 MUTATED                                       0
  C16ORF70 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C16ORF70 MUTATED                                                        4
  C16ORF70 WILD-TYPE                                                    154
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C16ORF70 MUTATED                                                   1
  C16ORF70 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C16ORF70 MUTATED                                                                   0
  C16ORF70 WILD-TYPE                                                                68
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C16ORF70 MUTATED                                                    0
  C16ORF70 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C16ORF70 MUTATED                                                  1
  C16ORF70 WILD-TYPE                                               60
D421V9, multiclass
                                                                   clus
vv                                                                  C16ORF70 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  C16ORF70 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C16ORF70 MUTATED     4   0   0   2
  C16ORF70 WILD-TYPE 307  14  15  22
D421V10, multiclass
    clus
vv   C16ORF70 MUTATED C16ORF70 WILD-TYPE
  R0                4                307
  R1                0                 14
  R2                0                 15
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D421V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C16ORF70 MUTATED       1                         0
  C16ORF70 WILD-TYPE    86                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C16ORF70 MUTATED                                           0     5
  C16ORF70 WILD-TYPE                                         1   238
D421V12, multiclass
                                           clus
vv                                          C16ORF70 MUTATED C16ORF70 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D421V13, binary
                    cls
clus                   0   1
  C16ORF70 MUTATED     1   5
  C16ORF70 WILD-TYPE   3 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF70 MUTATED      1    5
  C16ORF70 WILD-TYPE    3  305
                        clus
vv                       C16ORF70 MUTATED C16ORF70 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO                5                305
[1] 2 2
[1] FALSE

Clustering(422) Variable = SLC10A6 MUTATION ANALYSIS
D422V1, survival
                   sevent
clus2                 0   1
  SLC10A6 MUTATED     6   1
  SLC10A6 WILD-TYPE 224 138
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
                7               362 
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
                1               138 
$`SLC10A6 MUTATED`
TCGA-BR-7707 TCGA-BR-8368 TCGA-BR-8680 TCGA-CD-8536 TCGA-CD-A4MG TCGA-FP-A4BE 
       35.84         4.31        31.96        12.43         6.58        11.08 
TCGA-SW-A7EB 
        5.79 

$`SLC10A6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
        8.94        35.61        19.04         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 

  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
             4.31              0.00 
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
            35.84            122.30 
  SLC10A6 MUTATED SLC10A6 WILD-TYPE 
            11.08             14.45 
[1] "4.3 - 35.8 (11.1)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "2.2"
D422V2, 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       2       15       38       29        35        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC10A6 MUTATED           0          1          0          0        1
  SLC10A6 WILD-TYPE         3         69         53         32       37
D422V3, multiclass
            clus
vv           SLC10A6 MUTATED SLC10A6 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 1                29
  STAGE IIA                2                35
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC10A6 MUTATED     1   2   4   1
  SLC10A6 WILD-TYPE  21  90 169  96
D422V4, multiclass
    clus
vv   SLC10A6 MUTATED SLC10A6 WILD-TYPE
  T1               1                21
  T2               2                90
  T3               4               169
  T4               1                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
  SLC10A6 MUTATED     5   0   2   0
  SLC10A6 WILD-TYPE 113 104  75  77
D422V5, multiclass
    clus
vv   SLC10A6 MUTATED SLC10A6 WILD-TYPE
  N0               5               113
  N1               0               104
  N2               2                75
  N3               0                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"
D422V6, binary
                   cls
clus                  0   1
  SLC10A6 MUTATED     7   1
  SLC10A6 WILD-TYPE 339  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC10A6 MUTATED      7    1
  SLC10A6 WILD-TYPE  339   28
   clus
vv  SLC10A6 MUTATED SLC10A6 WILD-TYPE
  0               7               339
  1               1                28
[1] 2 2
[1] FALSE
D422V7, binary
                   cls
clus                  0   1
  SLC10A6 MUTATED     3   5
  SLC10A6 WILD-TYPE 142 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC10A6 MUTATED      3    5
  SLC10A6 WILD-TYPE  142  243
        clus
vv       SLC10A6 MUTATED SLC10A6 WILD-TYPE
  FEMALE               3               142
  MALE                 5               243
[1] 2 2
[1] FALSE
D422V8, binary
                   cls
clus                  0   1
  SLC10A6 MUTATED     6   1
  SLC10A6 WILD-TYPE 286  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC10A6 MUTATED      6    1
  SLC10A6 WILD-TYPE  286   58
     clus
vv    SLC10A6 MUTATED SLC10A6 WILD-TYPE
  NO                6               286
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC10A6 MUTATED                                          0
  SLC10A6 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC10A6 MUTATED                                       1
  SLC10A6 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC10A6 MUTATED                                                        5
  SLC10A6 WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC10A6 MUTATED                                                   1
  SLC10A6 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC10A6 MUTATED                                                                   0
  SLC10A6 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC10A6 MUTATED                                                    0
  SLC10A6 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC10A6 MUTATED                                                  1
  SLC10A6 WILD-TYPE                                               60
D422V9, multiclass
                                                                   clus
vv                                                                  SLC10A6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  SLC10A6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC10A6 MUTATED     6   0   0   1
  SLC10A6 WILD-TYPE 305  14  15  23
D422V10, multiclass
    clus
vv   SLC10A6 MUTATED SLC10A6 WILD-TYPE
  R0               6               305
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D422V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC10A6 MUTATED       3                         1
  SLC10A6 WILD-TYPE    84                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC10A6 MUTATED                                           0     4
  SLC10A6 WILD-TYPE                                         1   239
D422V12, multiclass
                                           clus
vv                                          SLC10A6 MUTATED SLC10A6 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D422V13, binary
                   cls
clus                  0   1
  SLC10A6 MUTATED     0   8
  SLC10A6 WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC10A6 MUTATED      0    8
  SLC10A6 WILD-TYPE    4  302
                        clus
vv                       SLC10A6 MUTATED SLC10A6 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(423) Variable = CCDC80 MUTATION ANALYSIS
D423V1, survival
                  sevent
clus2                0   1
  CCDC80 MUTATED    12   6
  CCDC80 WILD-TYPE 218 133
  CCDC80 MUTATED CCDC80 WILD-TYPE 
              18              351 
  CCDC80 MUTATED CCDC80 WILD-TYPE 
               6              133 
$`CCDC80 MUTATED`
TCGA-BR-4184 TCGA-BR-4255 TCGA-BR-6802 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8680 
        6.97         4.08        30.90        29.59         1.12        31.96 
TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-5721 TCGA-D7-A4YV TCGA-FP-A4BE 
        6.58        15.95         8.05         6.02         5.92        11.08 
TCGA-HJ-7597 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       26.47        24.20        29.98         0.10         6.51         6.58 

$`CCDC80 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         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-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-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-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-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-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-A4GP TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       21.37         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-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 

  CCDC80 MUTATED CCDC80 WILD-TYPE 
             0.1              0.0 
  CCDC80 MUTATED CCDC80 WILD-TYPE 
           31.96           122.30 
  CCDC80 MUTATED CCDC80 WILD-TYPE 
            7.51            14.47 
[1] "0.1 - 32.0 (7.5)"   "0.0 - 122.3 (14.5)"
[1] "hr=" "1.1"
D423V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC80 MUTATED         1        1        1        2         5         3
  CCDC80 WILD-TYPE       1       14       39       28        32        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC80 MUTATED           0          3          0          1        2
  CCDC80 WILD-TYPE         3         67         53         31       36
D423V3, multiclass
            clus
vv           CCDC80 MUTATED CCDC80 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               5               32
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC80 MUTATED     2   4   9   4
  CCDC80 WILD-TYPE  20  88 164  93
D423V4, multiclass
    clus
vv   CCDC80 MUTATED CCDC80 WILD-TYPE
  T1              2               20
  T2              4               88
  T3              9              164
  T4              4               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
  CCDC80 MUTATED     7   9   3   0
  CCDC80 WILD-TYPE 111  95  74  77
D423V5, multiclass
    clus
vv   CCDC80 MUTATED CCDC80 WILD-TYPE
  N0              7              111
  N1              9               95
  N2              3               74
  N3              0               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"
D423V6, binary
                  cls
clus                 0   1
  CCDC80 MUTATED    15   1
  CCDC80 WILD-TYPE 331  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC80 MUTATED     15    1
  CCDC80 WILD-TYPE  331   28
   clus
vv  CCDC80 MUTATED CCDC80 WILD-TYPE
  0             15              331
  1              1               28
[1] 2 2
[1] FALSE
D423V7, binary
                  cls
clus                 0   1
  CCDC80 MUTATED     7  12
  CCDC80 WILD-TYPE 138 236
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC80 MUTATED      7   12
  CCDC80 WILD-TYPE  138  236
        clus
vv       CCDC80 MUTATED CCDC80 WILD-TYPE
  FEMALE              7              138
  MALE               12              236
[1] 2 2
[1] FALSE
D423V8, binary
                  cls
clus                 0   1
  CCDC80 MUTATED    18   1
  CCDC80 WILD-TYPE 274  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC80 MUTATED     18    1
  CCDC80 WILD-TYPE  274   58
     clus
vv    CCDC80 MUTATED CCDC80 WILD-TYPE
  NO              18              274
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CCDC80 MUTATED                                          1
  CCDC80 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CCDC80 MUTATED                                       2
  CCDC80 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC80 MUTATED                                                        8
  CCDC80 WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CCDC80 MUTATED                                                   0
  CCDC80 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC80 MUTATED                                                                   2
  CCDC80 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CCDC80 MUTATED                                                    0
  CCDC80 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CCDC80 MUTATED                                                  6
  CCDC80 WILD-TYPE                                               55
D423V9, multiclass
                                                                   clus
vv                                                                  CCDC80 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               6
                                                                   clus
vv                                                                  CCDC80 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CCDC80 MUTATED    16   0   0   2
  CCDC80 WILD-TYPE 295  14  15  22
D423V10, multiclass
    clus
vv   CCDC80 MUTATED CCDC80 WILD-TYPE
  R0             16              295
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CCDC80 MUTATED       7                         2
  CCDC80 WILD-TYPE    80                         7
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC80 MUTATED                                           0     7
  CCDC80 WILD-TYPE                                         1   236
D423V12, multiclass
                                           clus
vv                                          CCDC80 MUTATED CCDC80 WILD-TYPE
  ASIAN                                                  7               80
  BLACK OR AFRICAN AMERICAN                              2                7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V13, binary
                  cls
clus                 0   1
  CCDC80 MUTATED     0  16
  CCDC80 WILD-TYPE   4 294
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC80 MUTATED      0   16
  CCDC80 WILD-TYPE    4  294
                        clus
vv                       CCDC80 MUTATED CCDC80 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             16              294
[1] 2 2
[1] FALSE

Clustering(424) Variable = DNAJC1 MUTATION ANALYSIS
D424V1, survival
                  sevent
clus2                0   1
  DNAJC1 MUTATED     8   2
  DNAJC1 WILD-TYPE 222 137
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
              10              359 
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
               2              137 
$`DNAJC1 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MI 
       34.68        44.94         1.12        28.14        31.96        11.77 
TCGA-CG-5721 TCGA-F1-6874 TCGA-HU-A4G8 TCGA-HU-A4GQ 
        6.02        14.47        22.68         0.10 

$`DNAJC1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-F1-6875 
        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-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 

  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
             0.1              0.0 
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
           44.94           122.30 
  DNAJC1 MUTATED DNAJC1 WILD-TYPE 
          18.575           14.170 
[1] "0.1 - 44.9 (18.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2"  
D424V2, 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       2       15       39       30        34        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC1 MUTATED           0          2          0          2        2
  DNAJC1 WILD-TYPE         3         68         53         30       36
D424V3, multiclass
            clus
vv           DNAJC1 MUTATED DNAJC1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DNAJC1 MUTATED     0   1   5   5
  DNAJC1 WILD-TYPE  22  91 168  92
D424V4, multiclass
    clus
vv   DNAJC1 MUTATED DNAJC1 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              5              168
  T4              5               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
  DNAJC1 MUTATED     5   3   2   1
  DNAJC1 WILD-TYPE 113 101  75  76
D424V5, multiclass
    clus
vv   DNAJC1 MUTATED DNAJC1 WILD-TYPE
  N0              5              113
  N1              3              101
  N2              2               75
  N3              1               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"
D424V6, binary
                  cls
clus                 0   1
  DNAJC1 MUTATED    10   1
  DNAJC1 WILD-TYPE 336  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC1 MUTATED     10    1
  DNAJC1 WILD-TYPE  336   28
   clus
vv  DNAJC1 MUTATED DNAJC1 WILD-TYPE
  0             10              336
  1              1               28
[1] 2 2
[1] FALSE
D424V7, binary
                  cls
clus                 0   1
  DNAJC1 MUTATED     5   6
  DNAJC1 WILD-TYPE 140 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC1 MUTATED      5    6
  DNAJC1 WILD-TYPE  140  242
        clus
vv       DNAJC1 MUTATED DNAJC1 WILD-TYPE
  FEMALE              5              140
  MALE                6              242
[1] 2 2
[1] FALSE
D424V8, binary
                  cls
clus                 0   1
  DNAJC1 MUTATED    10   0
  DNAJC1 WILD-TYPE 282  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC1 MUTATED     10    0
  DNAJC1 WILD-TYPE  282   59
     clus
vv    DNAJC1 MUTATED DNAJC1 WILD-TYPE
  NO              10              282
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DNAJC1 MUTATED                                          0
  DNAJC1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DNAJC1 MUTATED                                       1
  DNAJC1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DNAJC1 MUTATED                                                        6
  DNAJC1 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DNAJC1 MUTATED                                                   0
  DNAJC1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DNAJC1 MUTATED                                                                   2
  DNAJC1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DNAJC1 MUTATED                                                    0
  DNAJC1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DNAJC1 MUTATED                                                  2
  DNAJC1 WILD-TYPE                                               59
D424V9, multiclass
                                                                   clus
vv                                                                  DNAJC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  DNAJC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DNAJC1 MUTATED     8   0   0   1
  DNAJC1 WILD-TYPE 303  14  15  23
D424V10, multiclass
    clus
vv   DNAJC1 MUTATED DNAJC1 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D424V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DNAJC1 MUTATED       4                         0
  DNAJC1 WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DNAJC1 MUTATED                                           0     6
  DNAJC1 WILD-TYPE                                         1   237
D424V12, multiclass
                                           clus
vv                                          DNAJC1 MUTATED DNAJC1 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D424V13, binary
                  cls
clus                 0   1
  DNAJC1 MUTATED     0  10
  DNAJC1 WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC1 MUTATED      0   10
  DNAJC1 WILD-TYPE    4  300
                        clus
vv                       DNAJC1 MUTATED DNAJC1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(425) Variable = CADPS2 MUTATION ANALYSIS
D425V1, survival
                  sevent
clus2                0   1
  CADPS2 MUTATED     8   2
  CADPS2 WILD-TYPE 222 137
  CADPS2 MUTATED CADPS2 WILD-TYPE 
              10              359 
  CADPS2 MUTATED CADPS2 WILD-TYPE 
               2              137 
$`CADPS2 MUTATED`
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8361 TCGA-CD-A4MG 
       34.68        15.95        35.84        29.59        31.10         6.58 
TCGA-F1-6874 TCGA-FP-A4BE TCGA-HU-A4GQ TCGA-HU-A4H2 
       14.47        11.08         0.10        12.95 

$`CADPS2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-F1-6875 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-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-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-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 

  CADPS2 MUTATED CADPS2 WILD-TYPE 
             0.1              0.0 
  CADPS2 MUTATED CADPS2 WILD-TYPE 
           35.84           122.30 
  CADPS2 MUTATED CADPS2 WILD-TYPE 
           15.21            14.17 
[1] "0.1 - 35.8 (15.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2"  
D425V2, 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       2       15       38       30        33        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CADPS2 MUTATED           0          0          1          2        0
  CADPS2 WILD-TYPE         3         70         52         30       38
D425V3, multiclass
            clus
vv           CADPS2 MUTATED CADPS2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               4               33
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              1               52
  STAGE IIIC              2               30
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CADPS2 MUTATED     0   3   4   3
  CADPS2 WILD-TYPE  22  89 169  94
D425V4, multiclass
    clus
vv   CADPS2 MUTATED CADPS2 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              4              169
  T4              3               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
  CADPS2 MUTATED     6   1   2   1
  CADPS2 WILD-TYPE 112 103  75  76
D425V5, multiclass
    clus
vv   CADPS2 MUTATED CADPS2 WILD-TYPE
  N0              6              112
  N1              1              103
  N2              2               75
  N3              1               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"
D425V6, binary
                  cls
clus                 0   1
  CADPS2 MUTATED    10   0
  CADPS2 WILD-TYPE 336  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CADPS2 MUTATED     10    0
  CADPS2 WILD-TYPE  336   29
   clus
vv  CADPS2 MUTATED CADPS2 WILD-TYPE
  0             10              336
  1              0               29
[1] 2 2
[1] FALSE
D425V7, binary
                  cls
clus                 0   1
  CADPS2 MUTATED     5   5
  CADPS2 WILD-TYPE 140 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CADPS2 MUTATED      5    5
  CADPS2 WILD-TYPE  140  243
        clus
vv       CADPS2 MUTATED CADPS2 WILD-TYPE
  FEMALE              5              140
  MALE                5              243
[1] 2 2
[1] FALSE
D425V8, binary
                  cls
clus                 0   1
  CADPS2 MUTATED     9   1
  CADPS2 WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CADPS2 MUTATED      9    1
  CADPS2 WILD-TYPE  283   58
     clus
vv    CADPS2 MUTATED CADPS2 WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CADPS2 MUTATED                                          0
  CADPS2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CADPS2 MUTATED                                       1
  CADPS2 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CADPS2 MUTATED                                                        6
  CADPS2 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CADPS2 MUTATED                                                   0
  CADPS2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CADPS2 MUTATED                                                                   1
  CADPS2 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CADPS2 MUTATED                                                    0
  CADPS2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CADPS2 MUTATED                                                  2
  CADPS2 WILD-TYPE                                               59
D425V9, multiclass
                                                                   clus
vv                                                                  CADPS2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  CADPS2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CADPS2 MUTATED     9   0   0   0
  CADPS2 WILD-TYPE 302  14  15  24
D425V10, multiclass
    clus
vv   CADPS2 MUTATED CADPS2 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D425V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CADPS2 MUTATED       3                         1
  CADPS2 WILD-TYPE    84                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CADPS2 MUTATED                                           0     6
  CADPS2 WILD-TYPE                                         1   237
D425V12, multiclass
                                           clus
vv                                          CADPS2 MUTATED CADPS2 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D425V13, binary
                  cls
clus                 0   1
  CADPS2 MUTATED     0  10
  CADPS2 WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CADPS2 MUTATED      0   10
  CADPS2 WILD-TYPE    4  300
                        clus
vv                       CADPS2 MUTATED CADPS2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(426) Variable = ART5 MUTATION ANALYSIS
D426V1, survival
                sevent
clus2              0   1
  ART5 MUTATED     3   2
  ART5 WILD-TYPE 227 137
  ART5 MUTATED ART5 WILD-TYPE 
             5            364 
  ART5 MUTATED ART5 WILD-TYPE 
             2            137 
$`ART5 MUTATED`
TCGA-BR-4201 TCGA-BR-8591 TCGA-D7-6822 TCGA-D7-A4YV TCGA-HF-7132 
       30.90        28.14        12.33         5.92        77.29 

$`ART5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-D7-8570 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-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 

  ART5 MUTATED ART5 WILD-TYPE 
          5.92           0.00 
  ART5 MUTATED ART5 WILD-TYPE 
         77.29         122.30 
  ART5 MUTATED ART5 WILD-TYPE 
         28.14          14.22 
[1] "5.9 - 77.3 (28.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D426V2, 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       2       15       39       29        37        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ART5 MUTATED           0          0          0          1        0
  ART5 WILD-TYPE         3         70         53         31       38
D426V3, multiclass
            clus
vv           ART5 MUTATED ART5 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             0             37
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ART5 MUTATED     0   3   1   1
  ART5 WILD-TYPE  22  89 172  96
D426V4, multiclass
    clus
vv   ART5 MUTATED ART5 WILD-TYPE
  T1            0             22
  T2            3             89
  T3            1            172
  T4            1             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
  ART5 MUTATED     1   2   0   1
  ART5 WILD-TYPE 117 102  77  76
D426V5, multiclass
    clus
vv   ART5 MUTATED ART5 WILD-TYPE
  N0            1            117
  N1            2            102
  N2            0             77
  N3            1             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"
D426V6, binary
                cls
clus               0   1
  ART5 MUTATED     5   0
  ART5 WILD-TYPE 341  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      5    0
  ART5 WILD-TYPE  341   29
   clus
vv  ART5 MUTATED ART5 WILD-TYPE
  0            5            341
  1            0             29
[1] 2 2
[1] FALSE
D426V7, binary
                cls
clus               0   1
  ART5 MUTATED     2   3
  ART5 WILD-TYPE 143 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      2    3
  ART5 WILD-TYPE  143  245
        clus
vv       ART5 MUTATED ART5 WILD-TYPE
  FEMALE            2            143
  MALE              3            245
[1] 2 2
[1] FALSE
D426V8, binary
                cls
clus               0   1
  ART5 MUTATED     4   1
  ART5 WILD-TYPE 288  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      4    1
  ART5 WILD-TYPE  288   58
     clus
vv    ART5 MUTATED ART5 WILD-TYPE
  NO             4            288
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ART5 MUTATED                                          0
  ART5 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ART5 MUTATED                                       0
  ART5 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ART5 MUTATED                                                        2
  ART5 WILD-TYPE                                                    156
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ART5 MUTATED                                                   1
  ART5 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ART5 MUTATED                                                                   0
  ART5 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ART5 MUTATED                                                    0
  ART5 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ART5 MUTATED                                                  2
  ART5 WILD-TYPE                                               59
D426V9, multiclass
                                                                   clus
vv                                                                  ART5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  ART5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ART5 MUTATED     4   0   0   1
  ART5 WILD-TYPE 307  14  15  23
D426V10, multiclass
    clus
vv   ART5 MUTATED ART5 WILD-TYPE
  R0            4            307
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D426V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ART5 MUTATED       0                         0
  ART5 WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ART5 MUTATED                                           0     4
  ART5 WILD-TYPE                                         1   239
D426V12, multiclass
                                           clus
vv                                          ART5 MUTATED ART5 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D426V13, binary
                cls
clus               0   1
  ART5 MUTATED     0   4
  ART5 WILD-TYPE   4 306
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      0    4
  ART5 WILD-TYPE    4  306
                        clus
vv                       ART5 MUTATED ART5 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            4            306
[1] 2 2
[1] FALSE

Clustering(427) Variable = PLAGL2 MUTATION ANALYSIS
D427V1, survival
                  sevent
clus2                0   1
  PLAGL2 MUTATED     5   2
  PLAGL2 WILD-TYPE 225 137
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               7              362 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               2              137 
$`PLAGL2 MUTATED`
TCGA-BR-6566 TCGA-BR-7715 TCGA-BR-8059 TCGA-CG-5721 TCGA-FP-A4BE TCGA-HU-8602 
       32.78        33.63        14.43         6.02        11.08        22.32 
TCGA-HU-A4GQ 
        0.10 

$`PLAGL2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
             0.1              0.0 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
           33.63           122.30 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
           14.43            14.22 
[1] "0.1 - 33.6 (14.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D427V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLAGL2 MUTATED         0        0        0        0         3         1
  PLAGL2 WILD-TYPE       2       15       40       30        34        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLAGL2 MUTATED           1          0          0          1        1
  PLAGL2 WILD-TYPE         2         70         53         31       37
D427V3, multiclass
            clus
vv           PLAGL2 MUTATED PLAGL2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               1               51
  STAGE III               1                2
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PLAGL2 MUTATED     0   0   3   4
  PLAGL2 WILD-TYPE  22  92 170  93
D427V4, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  T1              0               22
  T2              0               92
  T3              3              170
  T4              4               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
  PLAGL2 MUTATED     4   2   1   0
  PLAGL2 WILD-TYPE 114 102  76  77
D427V5, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  N0              4              114
  N1              2              102
  N2              1               76
  N3              0               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"
D427V6, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     7   0
  PLAGL2 WILD-TYPE 339  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      7    0
  PLAGL2 WILD-TYPE  339   29
   clus
vv  PLAGL2 MUTATED PLAGL2 WILD-TYPE
  0              7              339
  1              0               29
[1] 2 2
[1] FALSE
D427V7, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     2   5
  PLAGL2 WILD-TYPE 143 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      2    5
  PLAGL2 WILD-TYPE  143  243
        clus
vv       PLAGL2 MUTATED PLAGL2 WILD-TYPE
  FEMALE              2              143
  MALE                5              243
[1] 2 2
[1] FALSE
D427V8, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     6   1
  PLAGL2 WILD-TYPE 286  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      6    1
  PLAGL2 WILD-TYPE  286   58
     clus
vv    PLAGL2 MUTATED PLAGL2 WILD-TYPE
  NO               6              286
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PLAGL2 MUTATED                                          0
  PLAGL2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PLAGL2 MUTATED                                       1
  PLAGL2 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLAGL2 MUTATED                                                        3
  PLAGL2 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PLAGL2 MUTATED                                                   0
  PLAGL2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLAGL2 MUTATED                                                                   2
  PLAGL2 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PLAGL2 MUTATED                                                    0
  PLAGL2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PLAGL2 MUTATED                                                  1
  PLAGL2 WILD-TYPE                                               60
D427V9, multiclass
                                                                   clus
vv                                                                  PLAGL2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  PLAGL2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PLAGL2 MUTATED     7   0   0   0
  PLAGL2 WILD-TYPE 304  14  15  24
D427V10, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  R0              7              304
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D427V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PLAGL2 MUTATED       2                         1
  PLAGL2 WILD-TYPE    85                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLAGL2 MUTATED                                           0     3
  PLAGL2 WILD-TYPE                                         1   240
D427V12, multiclass
                                           clus
vv                                          PLAGL2 MUTATED PLAGL2 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D427V13, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     0   6
  PLAGL2 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      0    6
  PLAGL2 WILD-TYPE    4  304
                        clus
vv                       PLAGL2 MUTATED PLAGL2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(428) Variable = C16ORF63 MUTATION ANALYSIS
D428V1, survival
                    sevent
clus2                  0   1
  C16ORF63 MUTATED     5   2
  C16ORF63 WILD-TYPE 225 137
  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
                 7                362 
  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
                 2                137 
$`C16ORF63 MUTATED`
TCGA-BR-6452 TCGA-BR-8382 TCGA-CD-A48A TCGA-D7-A6EY TCGA-F1-6874 TCGA-HU-8602 
       34.68        25.05        12.43        11.44        14.47        22.32 
TCGA-HU-A4H3 
       29.00 

$`C16ORF63 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-A48C TCGA-CD-A4MG 
       12.43         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-D7-8573 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-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 

  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
             11.44               0.00 
  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
             34.68             122.30 
  C16ORF63 MUTATED C16ORF63 WILD-TYPE 
             22.32              14.12 
[1] "11.4 - 34.7 (22.3)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D428V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C16ORF63 MUTATED         0        0        1        0         2         1
  C16ORF63 WILD-TYPE       2       15       39       30        35        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C16ORF63 MUTATED           0          0          1          2        0
  C16ORF63 WILD-TYPE         3         70         52         30       38
D428V3, multiclass
            clus
vv           C16ORF63 MUTATED C16ORF63 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 2                 35
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                1                 52
  STAGE IIIC                2                 30
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C16ORF63 MUTATED     0   1   3   3
  C16ORF63 WILD-TYPE  22  91 170  94
D428V4, multiclass
    clus
vv   C16ORF63 MUTATED C16ORF63 WILD-TYPE
  T1                0                 22
  T2                1                 91
  T3                3                170
  T4                3                 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
  C16ORF63 MUTATED     4   1   0   3
  C16ORF63 WILD-TYPE 114 103  77  74
D428V5, multiclass
    clus
vv   C16ORF63 MUTATED C16ORF63 WILD-TYPE
  N0                4                114
  N1                1                103
  N2                0                 77
  N3                3                 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"
D428V6, binary
                    cls
clus                   0   1
  C16ORF63 MUTATED     8   0
  C16ORF63 WILD-TYPE 338  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF63 MUTATED      8    0
  C16ORF63 WILD-TYPE  338   29
   clus
vv  C16ORF63 MUTATED C16ORF63 WILD-TYPE
  0                8                338
  1                0                 29
[1] 2 2
[1] FALSE
D428V7, binary
                    cls
clus                   0   1
  C16ORF63 MUTATED     6   2
  C16ORF63 WILD-TYPE 139 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF63 MUTATED      6    2
  C16ORF63 WILD-TYPE  139  246
        clus
vv       C16ORF63 MUTATED C16ORF63 WILD-TYPE
  FEMALE                6                139
  MALE                  2                246
[1] 2 2
[1] FALSE
D428V8, binary
                    cls
clus                   0   1
  C16ORF63 MUTATED     5   1
  C16ORF63 WILD-TYPE 287  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF63 MUTATED      5    1
  C16ORF63 WILD-TYPE  287   58
     clus
vv    C16ORF63 MUTATED C16ORF63 WILD-TYPE
  NO                 5                287
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C16ORF63 MUTATED                                          0
  C16ORF63 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C16ORF63 MUTATED                                       2
  C16ORF63 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C16ORF63 MUTATED                                                        4
  C16ORF63 WILD-TYPE                                                    154
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C16ORF63 MUTATED                                                   0
  C16ORF63 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C16ORF63 MUTATED                                                                   1
  C16ORF63 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C16ORF63 MUTATED                                                    0
  C16ORF63 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C16ORF63 MUTATED                                                  1
  C16ORF63 WILD-TYPE                                               60
D428V9, multiclass
                                                                   clus
vv                                                                  C16ORF63 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  C16ORF63 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C16ORF63 MUTATED     6   0   0   1
  C16ORF63 WILD-TYPE 305  14  15  23
D428V10, multiclass
    clus
vv   C16ORF63 MUTATED C16ORF63 WILD-TYPE
  R0                6                305
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D428V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C16ORF63 MUTATED       3                         0
  C16ORF63 WILD-TYPE    84                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C16ORF63 MUTATED                                           0     5
  C16ORF63 WILD-TYPE                                         1   238
D428V12, multiclass
                                           clus
vv                                          C16ORF63 MUTATED C16ORF63 WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D428V13, binary
                    cls
clus                   0   1
  C16ORF63 MUTATED     0   8
  C16ORF63 WILD-TYPE   4 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF63 MUTATED      0    8
  C16ORF63 WILD-TYPE    4  302
                        clus
vv                       C16ORF63 MUTATED C16ORF63 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                8                302
[1] 2 2
[1] FALSE

Clustering(429) Variable = GCDH MUTATION ANALYSIS
D429V1, survival
                sevent
clus2              0   1
  GCDH MUTATED     4   2
  GCDH WILD-TYPE 226 137
  GCDH MUTATED GCDH WILD-TYPE 
             6            363 
  GCDH MUTATED GCDH WILD-TYPE 
             2            137 
$`GCDH MUTATED`
TCGA-BR-6452 TCGA-BR-8361 TCGA-CG-5723 TCGA-D7-A6EY TCGA-HJ-7597 TCGA-VQ-A8P2 
       34.68        31.10       105.07        11.44        26.47        38.14 

$`GCDH WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-F1-6874 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 

  GCDH MUTATED GCDH WILD-TYPE 
         11.44           0.00 
  GCDH MUTATED GCDH WILD-TYPE 
        105.07         122.30 
  GCDH MUTATED GCDH WILD-TYPE 
         32.89          14.07 
[1] "11.4 - 105.1 (32.9)" "0.0 - 122.3 (14.1)" 
[1] "hr=" "2.1"
D429V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GCDH MUTATED         0        0        2        1         1         0
  GCDH WILD-TYPE       2       15       38       29        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GCDH MUTATED           0          1          1          1        0
  GCDH WILD-TYPE         3         69         52         31       38
D429V3, multiclass
            clus
vv           GCDH MUTATED GCDH WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GCDH MUTATED     0   3   2   2
  GCDH WILD-TYPE  22  89 171  95
D429V4, multiclass
    clus
vv   GCDH MUTATED GCDH WILD-TYPE
  T1            0             22
  T2            3             89
  T3            2            171
  T4            2             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
  GCDH MUTATED     3   2   1   1
  GCDH WILD-TYPE 115 102  76  76
D429V5, multiclass
    clus
vv   GCDH MUTATED GCDH WILD-TYPE
  N0            3            115
  N1            2            102
  N2            1             76
  N3            1             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"
D429V6, binary
                cls
clus               0   1
  GCDH MUTATED     6   0
  GCDH WILD-TYPE 340  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      6    0
  GCDH WILD-TYPE  340   29
   clus
vv  GCDH MUTATED GCDH WILD-TYPE
  0            6            340
  1            0             29
[1] 2 2
[1] FALSE
D429V7, binary
                cls
clus               0   1
  GCDH MUTATED     4   3
  GCDH WILD-TYPE 141 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      4    3
  GCDH WILD-TYPE  141  245
        clus
vv       GCDH MUTATED GCDH WILD-TYPE
  FEMALE            4            141
  MALE              3            245
[1] 2 2
[1] FALSE
D429V8, binary
                cls
clus               0   1
  GCDH MUTATED     5   1
  GCDH WILD-TYPE 287  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      5    1
  GCDH WILD-TYPE  287   58
     clus
vv    GCDH MUTATED GCDH WILD-TYPE
  NO             5            287
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GCDH MUTATED                                          1
  GCDH WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GCDH MUTATED                                       0
  GCDH WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GCDH MUTATED                                                        3
  GCDH WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GCDH MUTATED                                                   1
  GCDH WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GCDH MUTATED                                                                   1
  GCDH WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GCDH MUTATED                                                    0
  GCDH WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GCDH MUTATED                                                  1
  GCDH WILD-TYPE                                               60
D429V9, multiclass
                                                                   clus
vv                                                                  GCDH MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  GCDH WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GCDH MUTATED     7   0   0   0
  GCDH WILD-TYPE 304  14  15  24
D429V10, multiclass
    clus
vv   GCDH MUTATED GCDH WILD-TYPE
  R0            7            304
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D429V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GCDH MUTATED       0                         0
  GCDH WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GCDH MUTATED                                           0     5
  GCDH WILD-TYPE                                         1   238
D429V12, multiclass
                                           clus
vv                                          GCDH MUTATED GCDH WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D429V13, binary
                cls
clus               0   1
  GCDH MUTATED     0   4
  GCDH WILD-TYPE   4 306
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCDH MUTATED      0    4
  GCDH WILD-TYPE    4  306
                        clus
vv                       GCDH MUTATED GCDH WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            4            306
[1] 2 2
[1] FALSE

Clustering(430) Variable = FBXO34 MUTATION ANALYSIS
D430V1, survival
                  sevent
clus2                0   1
  FBXO34 MUTATED     5   3
  FBXO34 WILD-TYPE 225 136
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               8              361 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               3              136 
$`FBXO34 MUTATED`
TCGA-B7-5816 TCGA-BR-8078 TCGA-BR-8487 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5723 
       26.70        29.59         1.12         6.97         0.99       105.07 
TCGA-D7-6525 TCGA-HU-A4GN 
       13.35        29.98 

$`FBXO34 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-5718 TCGA-CG-5719 TCGA-CG-5721 
       18.97         7.07        30.97        36.00         1.02         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-D7-6526 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-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 

  FBXO34 MUTATED FBXO34 WILD-TYPE 
            0.99             0.00 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
          105.07           122.30 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
          20.025           14.270 
[1] "1.0 - 105.1 (20.0)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D430V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXO34 MUTATED         1        0        1        2         2         2
  FBXO34 WILD-TYPE       1       15       39       28        35        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO34 MUTATED           0          1          0          0        0
  FBXO34 WILD-TYPE         3         69         53         32       38
D430V3, multiclass
            clus
vv           FBXO34 MUTATED FBXO34 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               2               35
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO34 MUTATED     1   5   1   2
  FBXO34 WILD-TYPE  21  87 172  95
D430V4, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  T1              1               21
  T2              5               87
  T3              1              172
  T4              2               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
  FBXO34 MUTATED     4   4   1   0
  FBXO34 WILD-TYPE 114 100  76  77
D430V5, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  N0              4              114
  N1              4              100
  N2              1               76
  N3              0               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"
D430V6, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     8   0
  FBXO34 WILD-TYPE 338  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      8    0
  FBXO34 WILD-TYPE  338   29
   clus
vv  FBXO34 MUTATED FBXO34 WILD-TYPE
  0              8              338
  1              0               29
[1] 2 2
[1] FALSE
D430V7, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     3   6
  FBXO34 WILD-TYPE 142 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      3    6
  FBXO34 WILD-TYPE  142  242
        clus
vv       FBXO34 MUTATED FBXO34 WILD-TYPE
  FEMALE              3              142
  MALE                6              242
[1] 2 2
[1] FALSE
D430V8, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     8   0
  FBXO34 WILD-TYPE 284  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      8    0
  FBXO34 WILD-TYPE  284   59
     clus
vv    FBXO34 MUTATED FBXO34 WILD-TYPE
  NO               8              284
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FBXO34 MUTATED                                          0
  FBXO34 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FBXO34 MUTATED                                       2
  FBXO34 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBXO34 MUTATED                                                        6
  FBXO34 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FBXO34 MUTATED                                                   0
  FBXO34 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBXO34 MUTATED                                                                   0
  FBXO34 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FBXO34 MUTATED                                                    0
  FBXO34 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FBXO34 MUTATED                                                  1
  FBXO34 WILD-TYPE                                               60
D430V9, multiclass
                                                                   clus
vv                                                                  FBXO34 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  FBXO34 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FBXO34 MUTATED     9   0   0   0
  FBXO34 WILD-TYPE 302  14  15  24
D430V10, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D430V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FBXO34 MUTATED       1                         1
  FBXO34 WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXO34 MUTATED                                           0     4
  FBXO34 WILD-TYPE                                         1   239
D430V12, multiclass
                                           clus
vv                                          FBXO34 MUTATED FBXO34 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D430V13, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     0   6
  FBXO34 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      0    6
  FBXO34 WILD-TYPE    4  304
                        clus
vv                       FBXO34 MUTATED FBXO34 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(431) Variable = SERPINA1 MUTATION ANALYSIS
D431V1, survival
                    sevent
clus2                  0   1
  SERPINA1 MUTATED     2   3
  SERPINA1 WILD-TYPE 228 136
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
                 5                364 
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
                 3                136 
$`SERPINA1 MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-8683 TCGA-CD-8536 TCGA-MX-A5UJ 
        6.97         9.34         9.86        12.43        19.73 

$`SERPINA1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
              6.97               0.00 
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
             19.73             122.30 
  SERPINA1 MUTATED SERPINA1 WILD-TYPE 
              9.86              14.45 
[1] "7.0 - 19.7 (9.9)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "2.4"
D431V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPINA1 MUTATED         0        0        0        1         0         0
  SERPINA1 WILD-TYPE       2       15       40       29        37        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINA1 MUTATED           0          3          1          0        1
  SERPINA1 WILD-TYPE         3         67         52         32       37
D431V3, multiclass
            clus
vv           SERPINA1 MUTATED SERPINA1 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  1                 29
  STAGE IIA                 0                 37
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                3                 67
  STAGE IIIB                1                 52
  STAGE IIIC                0                 32
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SERPINA1 MUTATED     0   0   3   3
  SERPINA1 WILD-TYPE  22  92 170  94
D431V4, multiclass
    clus
vv   SERPINA1 MUTATED SERPINA1 WILD-TYPE
  T1                0                 22
  T2                0                 92
  T3                3                170
  T4                3                 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
  SERPINA1 MUTATED     2   2   3   0
  SERPINA1 WILD-TYPE 116 102  74  77
D431V5, multiclass
    clus
vv   SERPINA1 MUTATED SERPINA1 WILD-TYPE
  N0                2                116
  N1                2                102
  N2                3                 74
  N3                0                 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"
D431V6, binary
                    cls
clus                   0   1
  SERPINA1 MUTATED     5   1
  SERPINA1 WILD-TYPE 341  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA1 MUTATED      5    1
  SERPINA1 WILD-TYPE  341   28
   clus
vv  SERPINA1 MUTATED SERPINA1 WILD-TYPE
  0                5                341
  1                1                 28
[1] 2 2
[1] FALSE
D431V7, binary
                    cls
clus                   0   1
  SERPINA1 MUTATED     3   4
  SERPINA1 WILD-TYPE 142 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA1 MUTATED      3    4
  SERPINA1 WILD-TYPE  142  244
        clus
vv       SERPINA1 MUTATED SERPINA1 WILD-TYPE
  FEMALE                3                142
  MALE                  4                244
[1] 2 2
[1] FALSE
D431V8, binary
                    cls
clus                   0   1
  SERPINA1 MUTATED     5   0
  SERPINA1 WILD-TYPE 287  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA1 MUTATED      5    0
  SERPINA1 WILD-TYPE  287   59
     clus
vv    SERPINA1 MUTATED SERPINA1 WILD-TYPE
  NO                 5                287
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SERPINA1 MUTATED                                          0
  SERPINA1 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SERPINA1 MUTATED                                       1
  SERPINA1 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SERPINA1 MUTATED                                                        4
  SERPINA1 WILD-TYPE                                                    154
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SERPINA1 MUTATED                                                   0
  SERPINA1 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SERPINA1 MUTATED                                                                   0
  SERPINA1 WILD-TYPE                                                                68
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SERPINA1 MUTATED                                                    0
  SERPINA1 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SERPINA1 MUTATED                                                  2
  SERPINA1 WILD-TYPE                                               59
D431V9, multiclass
                                                                   clus
vv                                                                  SERPINA1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  SERPINA1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SERPINA1 MUTATED     3   0   1   3
  SERPINA1 WILD-TYPE 308  14  14  21
D431V10, multiclass
    clus
vv   SERPINA1 MUTATED SERPINA1 WILD-TYPE
  R0                3                308
  R1                0                 14
  R2                1                 14
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D431V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SERPINA1 MUTATED       2                         0
  SERPINA1 WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SERPINA1 MUTATED                                           0     4
  SERPINA1 WILD-TYPE                                         1   239
D431V12, multiclass
                                           clus
vv                                          SERPINA1 MUTATED SERPINA1 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D431V13, binary
                    cls
clus                   0   1
  SERPINA1 MUTATED     0   6
  SERPINA1 WILD-TYPE   4 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA1 MUTATED      0    6
  SERPINA1 WILD-TYPE    4  304
                        clus
vv                       SERPINA1 MUTATED SERPINA1 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                6                304
[1] 2 2
[1] FALSE

Clustering(432) Variable = KIAA1632 MUTATION ANALYSIS
D432V1, survival
                    sevent
clus2                  0   1
  KIAA1632 MUTATED    14   9
  KIAA1632 WILD-TYPE 216 130
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                23                346 
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                 9                130 
$`KIAA1632 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-5719 
        9.01        18.97         7.07        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-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-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-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-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU 
       22.75        25.81        21.37        29.98         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-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 

  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              14.35 
[1] "0.1 - 74.5 (14.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D432V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1632 MUTATED         0        1        2        1         3         4
  KIAA1632 WILD-TYPE       2       14       38       29        34        48
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1632 MUTATED           0          3          3          3        4
  KIAA1632 WILD-TYPE         3         67         50         29       34
D432V3, multiclass
            clus
vv           KIAA1632 MUTATED KIAA1632 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  2                 38
  STAGE II                  1                 29
  STAGE IIA                 3                 34
  STAGE IIB                 4                 48
  STAGE III                 0                  3
  STAGE IIIA                3                 67
  STAGE IIIB                3                 50
  STAGE IIIC                3                 29
  STAGE IV                  4                 34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1632 MUTATED     3   3  10   9
  KIAA1632 WILD-TYPE  19  89 163  88
D432V4, multiclass
    clus
vv   KIAA1632 MUTATED KIAA1632 WILD-TYPE
  T1                3                 19
  T2                3                 89
  T3               10                163
  T4                9                 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
  KIAA1632 MUTATED     6  10   4   5
  KIAA1632 WILD-TYPE 112  94  73  72
D432V5, multiclass
    clus
vv   KIAA1632 MUTATED KIAA1632 WILD-TYPE
  N0                6                112
  N1               10                 94
  N2                4                 73
  N3                5                 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"
D432V6, binary
                    cls
clus                   0   1
  KIAA1632 MUTATED    24   3
  KIAA1632 WILD-TYPE 322  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1632 MUTATED     24    3
  KIAA1632 WILD-TYPE  322   26
   clus
vv  KIAA1632 MUTATED KIAA1632 WILD-TYPE
  0               24                322
  1                3                 26
[1] 2 2
[1] FALSE
D432V7, binary
                    cls
clus                   0   1
  KIAA1632 MUTATED    15  12
  KIAA1632 WILD-TYPE 130 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1632 MUTATED     15   12
  KIAA1632 WILD-TYPE  130  236
        clus
vv       KIAA1632 MUTATED KIAA1632 WILD-TYPE
  FEMALE               15                130
  MALE                 12                236
[1] 2 2
[1] FALSE
D432V8, binary
                    cls
clus                   0   1
  KIAA1632 MUTATED    22   1
  KIAA1632 WILD-TYPE 270  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1632 MUTATED     22    1
  KIAA1632 WILD-TYPE  270   58
     clus
vv    KIAA1632 MUTATED KIAA1632 WILD-TYPE
  NO                22                270
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA1632 MUTATED                                          0
  KIAA1632 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA1632 MUTATED                                       4
  KIAA1632 WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1632 MUTATED                                                        8
  KIAA1632 WILD-TYPE                                                    150
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA1632 MUTATED                                                   1
  KIAA1632 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1632 MUTATED                                                                   5
  KIAA1632 WILD-TYPE                                                                63
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA1632 MUTATED                                                    0
  KIAA1632 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA1632 MUTATED                                                  9
  KIAA1632 WILD-TYPE                                               52
D432V9, multiclass
                                                                   clus
vv                                                                  KIAA1632 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 9
                                                                   clus
vv                                                                  KIAA1632 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  52
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1632 MUTATED    21   0   1   3
  KIAA1632 WILD-TYPE 290  14  14  21
D432V10, multiclass
    clus
vv   KIAA1632 MUTATED KIAA1632 WILD-TYPE
  R0               21                290
  R1                0                 14
  R2                1                 14
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D432V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1632 MUTATED       8                         0
  KIAA1632 WILD-TYPE    79                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1632 MUTATED                                           0    15
  KIAA1632 WILD-TYPE                                         1   228
D432V12, multiclass
                                           clus
vv                                          KIAA1632 MUTATED KIAA1632 WILD-TYPE
  ASIAN                                                    8                 79
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   15                228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D432V13, binary
                    cls
clus                   0   1
  KIAA1632 MUTATED     1  21
  KIAA1632 WILD-TYPE   3 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1632 MUTATED      1   21
  KIAA1632 WILD-TYPE    3  289
                        clus
vv                       KIAA1632 MUTATED KIAA1632 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               21                289
[1] 2 2
[1] FALSE

Clustering(433) Variable = CCDC138 MUTATION ANALYSIS
D433V1, survival
                   sevent
clus2                 0   1
  CCDC138 MUTATED     8   1
  CCDC138 WILD-TYPE 222 138
  CCDC138 MUTATED CCDC138 WILD-TYPE 
                9               360 
  CCDC138 MUTATED CCDC138 WILD-TYPE 
                1               138 
$`CCDC138 MUTATED`
TCGA-FP-A8CX TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG 
        0.23        34.68        44.94        28.14        31.96         6.58 
TCGA-CG-4436 TCGA-CG-5721 TCGA-HU-A4H5 
        7.99         6.02        23.80 

$`CCDC138 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       47.05        21.99        22.98        79.07        16.24        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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 

  CCDC138 MUTATED CCDC138 WILD-TYPE 
             0.23              0.00 
  CCDC138 MUTATED CCDC138 WILD-TYPE 
            44.94            122.30 
  CCDC138 MUTATED CCDC138 WILD-TYPE 
            23.80             14.22 
[1] "0.2 - 44.9 (23.8)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3.7"
D433V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC138 MUTATED         0        0        2        0         3         0
  CCDC138 WILD-TYPE       2       15       38       30        34        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC138 MUTATED           0          0          0          2        2
  CCDC138 WILD-TYPE         3         70         53         30       36
D433V3, multiclass
            clus
vv           CCDC138 MUTATED CCDC138 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                3                34
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               2                30
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC138 MUTATED     0   2   3   4
  CCDC138 WILD-TYPE  22  90 170  93
D433V4, multiclass
    clus
vv   CCDC138 MUTATED CCDC138 WILD-TYPE
  T1               0                22
  T2               2                90
  T3               3               170
  T4               4                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
  CCDC138 MUTATED     5   1   1   2
  CCDC138 WILD-TYPE 113 103  76  75
D433V5, multiclass
    clus
vv   CCDC138 MUTATED CCDC138 WILD-TYPE
  N0               5               113
  N1               1               103
  N2               1                76
  N3               2                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"
D433V6, binary
                   cls
clus                  0   1
  CCDC138 MUTATED     8   1
  CCDC138 WILD-TYPE 338  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC138 MUTATED      8    1
  CCDC138 WILD-TYPE  338   28
   clus
vv  CCDC138 MUTATED CCDC138 WILD-TYPE
  0               8               338
  1               1                28
[1] 2 2
[1] FALSE
D433V7, binary
                   cls
clus                  0   1
  CCDC138 MUTATED     3   7
  CCDC138 WILD-TYPE 142 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC138 MUTATED      3    7
  CCDC138 WILD-TYPE  142  241
        clus
vv       CCDC138 MUTATED CCDC138 WILD-TYPE
  FEMALE               3               142
  MALE                 7               241
[1] 2 2
[1] FALSE
D433V8, binary
                   cls
clus                  0   1
  CCDC138 MUTATED     8   0
  CCDC138 WILD-TYPE 284  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC138 MUTATED      8    0
  CCDC138 WILD-TYPE  284   59
     clus
vv    CCDC138 MUTATED CCDC138 WILD-TYPE
  NO                8               284
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CCDC138 MUTATED                                          1
  CCDC138 WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CCDC138 MUTATED                                       1
  CCDC138 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC138 MUTATED                                                        4
  CCDC138 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CCDC138 MUTATED                                                   0
  CCDC138 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC138 MUTATED                                                                   2
  CCDC138 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CCDC138 MUTATED                                                    1
  CCDC138 WILD-TYPE                                                  4
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CCDC138 MUTATED                                                  1
  CCDC138 WILD-TYPE                                               60
D433V9, multiclass
                                                                   clus
vv                                                                  CCDC138 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  CCDC138 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC138 MUTATED     8   0   0   1
  CCDC138 WILD-TYPE 303  14  15  23
D433V10, multiclass
    clus
vv   CCDC138 MUTATED CCDC138 WILD-TYPE
  R0               8               303
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D433V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CCDC138 MUTATED       3                         0
  CCDC138 WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC138 MUTATED                                           0     5
  CCDC138 WILD-TYPE                                         1   238
D433V12, multiclass
                                           clus
vv                                          CCDC138 MUTATED CCDC138 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D433V13, binary
                   cls
clus                  0   1
  CCDC138 MUTATED     0   8
  CCDC138 WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC138 MUTATED      0    8
  CCDC138 WILD-TYPE    4  302
                        clus
vv                       CCDC138 MUTATED CCDC138 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(434) Variable = ALDH3A1 MUTATION ANALYSIS
D434V1, survival
                   sevent
clus2                 0   1
  ALDH3A1 MUTATED     5   4
  ALDH3A1 WILD-TYPE 225 135
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
                9               360 
  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE 
                4               135 
$`ALDH3A1 MUTATED`
TCGA-BR-4257 TCGA-BR-8361 TCGA-BR-8372 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5723 
        9.67        31.10        31.27         6.58         1.02       105.07 
TCGA-F1-A448 TCGA-HJ-7597 TCGA-VQ-A8P2 
       21.27        26.47        38.14 

$`ALDH3A1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  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             14.12 
[1] "1.0 - 105.1 (26.5)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D434V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ALDH3A1 MUTATED         0        0        1        1         1         1
  ALDH3A1 WILD-TYPE       2       15       39       29        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ALDH3A1 MUTATED           0          1          1          2        1
  ALDH3A1 WILD-TYPE         3         69         52         30       37
D434V3, multiclass
            clus
vv           ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               2                30
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ALDH3A1 MUTATED     0   2   3   4
  ALDH3A1 WILD-TYPE  22  90 170  93
D434V4, multiclass
    clus
vv   ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  T1               0                22
  T2               2                90
  T3               3               170
  T4               4                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
  ALDH3A1 MUTATED     3   3   2   2
  ALDH3A1 WILD-TYPE 115 101  75  75
D434V5, multiclass
    clus
vv   ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  N0               3               115
  N1               3               101
  N2               2                75
  N3               2                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"
D434V6, binary
                   cls
clus                  0   1
  ALDH3A1 MUTATED    10   1
  ALDH3A1 WILD-TYPE 336  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH3A1 MUTATED     10    1
  ALDH3A1 WILD-TYPE  336   28
   clus
vv  ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  0              10               336
  1               1                28
[1] 2 2
[1] FALSE
D434V7, binary
                   cls
clus                  0   1
  ALDH3A1 MUTATED     5   7
  ALDH3A1 WILD-TYPE 140 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH3A1 MUTATED      5    7
  ALDH3A1 WILD-TYPE  140  241
        clus
vv       ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  FEMALE               5               140
  MALE                 7               241
[1] 2 2
[1] FALSE
D434V8, binary
                   cls
clus                  0   1
  ALDH3A1 MUTATED     7   2
  ALDH3A1 WILD-TYPE 285  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH3A1 MUTATED      7    2
  ALDH3A1 WILD-TYPE  285   57
     clus
vv    ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  NO                7               285
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ALDH3A1 MUTATED                                          1
  ALDH3A1 WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ALDH3A1 MUTATED                                       1
  ALDH3A1 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ALDH3A1 MUTATED                                                        7
  ALDH3A1 WILD-TYPE                                                    151
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ALDH3A1 MUTATED                                                   2
  ALDH3A1 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ALDH3A1 MUTATED                                                                   1
  ALDH3A1 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ALDH3A1 MUTATED                                                    0
  ALDH3A1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ALDH3A1 MUTATED                                                  0
  ALDH3A1 WILD-TYPE                                               61
D434V9, multiclass
                                                                   clus
vv                                                                  ALDH3A1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  ALDH3A1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ALDH3A1 MUTATED     7   0   1   3
  ALDH3A1 WILD-TYPE 304  14  14  21
D434V10, multiclass
    clus
vv   ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  R0               7               304
  R1               0                14
  R2               1                14
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D434V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ALDH3A1 MUTATED       1                         0
  ALDH3A1 WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ALDH3A1 MUTATED                                           0     9
  ALDH3A1 WILD-TYPE                                         1   234
D434V12, multiclass
                                           clus
vv                                          ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D434V13, binary
                   cls
clus                  0   1
  ALDH3A1 MUTATED     1   8
  ALDH3A1 WILD-TYPE   3 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH3A1 MUTATED      1    8
  ALDH3A1 WILD-TYPE    3  302
                        clus
vv                       ALDH3A1 MUTATED ALDH3A1 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(435) Variable = PAMR1 MUTATION ANALYSIS
D435V1, survival
                 sevent
clus2               0   1
  PAMR1 MUTATED     6   5
  PAMR1 WILD-TYPE 224 134
  PAMR1 MUTATED PAMR1 WILD-TYPE 
             11             358 
  PAMR1 MUTATED PAMR1 WILD-TYPE 
              5             134 
$`PAMR1 MUTATED`
TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7704 TCGA-BR-8372 TCGA-CD-5801 
       30.90         6.61        34.68        35.24        31.27        13.18 
TCGA-CD-A4MI TCGA-CG-4306 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-IN-A7NR 
       11.77         1.02         6.51         6.58         6.51 

$`PAMR1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       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           14.45 
[1] "1.0 - 35.2 (11.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.4"
D435V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAMR1 MUTATED         0        0        0        1         2         1
  PAMR1 WILD-TYPE       2       15       40       29        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAMR1 MUTATED           1          2          0          1        2
  PAMR1 WILD-TYPE         2         68         53         31       36
D435V3, multiclass
            clus
vv           PAMR1 MUTATED PAMR1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PAMR1 MUTATED     1   3   8   1
  PAMR1 WILD-TYPE  21  89 165  96
D435V4, multiclass
    clus
vv   PAMR1 MUTATED PAMR1 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             8             165
  T4             1              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
  PAMR1 MUTATED     3   5   1   2
  PAMR1 WILD-TYPE 115  99  76  75
D435V5, multiclass
    clus
vv   PAMR1 MUTATED PAMR1 WILD-TYPE
  N0             3             115
  N1             5              99
  N2             1              76
  N3             2              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"
D435V6, binary
                 cls
clus                0   1
  PAMR1 MUTATED    13   2
  PAMR1 WILD-TYPE 333  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED     13    2
  PAMR1 WILD-TYPE  333   27
   clus
vv  PAMR1 MUTATED PAMR1 WILD-TYPE
  0            13             333
  1             2              27
[1] 2 2
[1] FALSE
D435V7, binary
                 cls
clus                0   1
  PAMR1 MUTATED     9   6
  PAMR1 WILD-TYPE 136 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED      9    6
  PAMR1 WILD-TYPE  136  242
        clus
vv       PAMR1 MUTATED PAMR1 WILD-TYPE
  FEMALE             9             136
  MALE               6             242
[1] 2 2
[1] FALSE
D435V8, binary
                 cls
clus                0   1
  PAMR1 MUTATED    10   0
  PAMR1 WILD-TYPE 282  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED     10    0
  PAMR1 WILD-TYPE  282   59
     clus
vv    PAMR1 MUTATED PAMR1 WILD-TYPE
  NO             10             282
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PAMR1 MUTATED                                          0
  PAMR1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PAMR1 MUTATED                                       1
  PAMR1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAMR1 MUTATED                                                       11
  PAMR1 WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PAMR1 MUTATED                                                   0
  PAMR1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAMR1 MUTATED                                                                   1
  PAMR1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PAMR1 MUTATED                                                    0
  PAMR1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PAMR1 MUTATED                                                  2
  PAMR1 WILD-TYPE                                               59
D435V9, multiclass
                                                                   clus
vv                                                                  PAMR1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  PAMR1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PAMR1 MUTATED     7   0   1   6
  PAMR1 WILD-TYPE 304  14  14  18
D435V10, multiclass
    clus
vv   PAMR1 MUTATED PAMR1 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             1              14
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D435V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PAMR1 MUTATED       4                         0
  PAMR1 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAMR1 MUTATED                                           0    10
  PAMR1 WILD-TYPE                                         1   233
D435V12, multiclass
                                           clus
vv                                          PAMR1 MUTATED PAMR1 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D435V13, binary
                 cls
clus                0   1
  PAMR1 MUTATED     0  14
  PAMR1 WILD-TYPE   4 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED      0   14
  PAMR1 WILD-TYPE    4  296
                        clus
vv                       PAMR1 MUTATED PAMR1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(436) Variable = ZNF776 MUTATION ANALYSIS
D436V1, survival
                  sevent
clus2                0   1
  ZNF776 MUTATED     5   2
  ZNF776 WILD-TYPE 225 137
  ZNF776 MUTATED ZNF776 WILD-TYPE 
               7              362 
  ZNF776 MUTATED ZNF776 WILD-TYPE 
               2              137 
$`ZNF776 MUTATED`
TCGA-BR-4256 TCGA-BR-6452 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-A6EY TCGA-SW-A7EA 
        9.34        34.68       105.07        65.10        11.44        19.04 
TCGA-VQ-A8P2 
       38.14 

$`ZNF776 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-F1-6874 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-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 

  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            14.12 
[1] "9.3 - 105.1 (34.7)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.2"
D436V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF776 MUTATED         0        0        2        1         1         0
  ZNF776 WILD-TYPE       2       15       38       29        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF776 MUTATED           0          1          1          0        0
  ZNF776 WILD-TYPE         3         69         52         32       38
D436V3, multiclass
            clus
vv           ZNF776 MUTATED ZNF776 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF776 MUTATED     0   3   3   1
  ZNF776 WILD-TYPE  22  89 170  96
D436V4, multiclass
    clus
vv   ZNF776 MUTATED ZNF776 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              3              170
  T4              1               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
  ZNF776 MUTATED     3   3   0   1
  ZNF776 WILD-TYPE 115 101  77  76
D436V5, multiclass
    clus
vv   ZNF776 MUTATED ZNF776 WILD-TYPE
  N0              3              115
  N1              3              101
  N2              0               77
  N3              1               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"
D436V6, binary
                  cls
clus                 0   1
  ZNF776 MUTATED     7   0
  ZNF776 WILD-TYPE 339  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF776 MUTATED      7    0
  ZNF776 WILD-TYPE  339   29
   clus
vv  ZNF776 MUTATED ZNF776 WILD-TYPE
  0              7              339
  1              0               29
[1] 2 2
[1] FALSE
D436V7, binary
                  cls
clus                 0   1
  ZNF776 MUTATED     5   3
  ZNF776 WILD-TYPE 140 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF776 MUTATED      5    3
  ZNF776 WILD-TYPE  140  245
        clus
vv       ZNF776 MUTATED ZNF776 WILD-TYPE
  FEMALE              5              140
  MALE                3              245
[1] 2 2
[1] FALSE
D436V8, binary
                  cls
clus                 0   1
  ZNF776 MUTATED     5   1
  ZNF776 WILD-TYPE 287  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF776 MUTATED      5    1
  ZNF776 WILD-TYPE  287   58
     clus
vv    ZNF776 MUTATED ZNF776 WILD-TYPE
  NO               5              287
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF776 MUTATED                                          0
  ZNF776 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF776 MUTATED                                       1
  ZNF776 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF776 MUTATED                                                        4
  ZNF776 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF776 MUTATED                                                   1
  ZNF776 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF776 MUTATED                                                                   1
  ZNF776 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF776 MUTATED                                                    0
  ZNF776 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF776 MUTATED                                                  1
  ZNF776 WILD-TYPE                                               60
D436V9, multiclass
                                                                   clus
vv                                                                  ZNF776 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ZNF776 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF776 MUTATED     6   0   0   2
  ZNF776 WILD-TYPE 305  14  15  22
D436V10, multiclass
    clus
vv   ZNF776 MUTATED ZNF776 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D436V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF776 MUTATED       0                         0
  ZNF776 WILD-TYPE    87                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF776 MUTATED                                           0     6
  ZNF776 WILD-TYPE                                         1   237
D436V12, multiclass
                                           clus
vv                                          ZNF776 MUTATED ZNF776 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D436V13, binary
                  cls
clus                 0   1
  ZNF776 MUTATED     0   5
  ZNF776 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF776 MUTATED      0    5
  ZNF776 WILD-TYPE    4  305
                        clus
vv                       ZNF776 MUTATED ZNF776 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(437) Variable = SH2B1 MUTATION ANALYSIS
D437V1, survival
                 sevent
clus2               0   1
  SH2B1 MUTATED     6   3
  SH2B1 WILD-TYPE 224 136
  SH2B1 MUTATED SH2B1 WILD-TYPE 
              9             360 
  SH2B1 MUTATED SH2B1 WILD-TYPE 
              3             136 
$`SH2B1 MUTATED`
TCGA-BR-6852 TCGA-BR-8487 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-5723 TCGA-CG-5733 
       44.94         1.12        12.43         6.58       105.07        21.07 
TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HF-A5NB 
        5.92        11.08        30.51 

$`SH2B1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  SH2B1 MUTATED SH2B1 WILD-TYPE 
           1.12            0.00 
  SH2B1 MUTATED SH2B1 WILD-TYPE 
         105.07          122.30 
  SH2B1 MUTATED SH2B1 WILD-TYPE 
          12.43           14.35 
[1] "1.1 - 105.1 (12.4)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D437V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SH2B1 MUTATED         0        0        1        2         4         1
  SH2B1 WILD-TYPE       2       15       39       28        33        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SH2B1 MUTATED           0          1          0          1        0
  SH2B1 WILD-TYPE         3         69         53         31       38
D437V3, multiclass
            clus
vv           SH2B1 MUTATED SH2B1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              4              33
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SH2B1 MUTATED     1   3   6   1
  SH2B1 WILD-TYPE  21  89 167  96
D437V4, multiclass
    clus
vv   SH2B1 MUTATED SH2B1 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             6             167
  T4             1              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
  SH2B1 MUTATED     6   2   1   1
  SH2B1 WILD-TYPE 112 102  76  76
D437V5, multiclass
    clus
vv   SH2B1 MUTATED SH2B1 WILD-TYPE
  N0             6             112
  N1             2             102
  N2             1              76
  N3             1              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"
D437V6, binary
                 cls
clus                0   1
  SH2B1 MUTATED    11   0
  SH2B1 WILD-TYPE 335  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SH2B1 MUTATED     11    0
  SH2B1 WILD-TYPE  335   29
   clus
vv  SH2B1 MUTATED SH2B1 WILD-TYPE
  0            11             335
  1             0              29
[1] 2 2
[1] FALSE
D437V7, binary
                 cls
clus                0   1
  SH2B1 MUTATED     6   5
  SH2B1 WILD-TYPE 139 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SH2B1 MUTATED      6    5
  SH2B1 WILD-TYPE  139  243
        clus
vv       SH2B1 MUTATED SH2B1 WILD-TYPE
  FEMALE             6             139
  MALE               5             243
[1] 2 2
[1] FALSE
D437V8, binary
                 cls
clus                0   1
  SH2B1 MUTATED     7   2
  SH2B1 WILD-TYPE 285  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SH2B1 MUTATED      7    2
  SH2B1 WILD-TYPE  285   57
     clus
vv    SH2B1 MUTATED SH2B1 WILD-TYPE
  NO              7             285
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SH2B1 MUTATED                                          0
  SH2B1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SH2B1 MUTATED                                       1
  SH2B1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SH2B1 MUTATED                                                        6
  SH2B1 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SH2B1 MUTATED                                                   1
  SH2B1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SH2B1 MUTATED                                                                   2
  SH2B1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SH2B1 MUTATED                                                    0
  SH2B1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SH2B1 MUTATED                                                  1
  SH2B1 WILD-TYPE                                               60
D437V9, multiclass
                                                                   clus
vv                                                                  SH2B1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  SH2B1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SH2B1 MUTATED     8   1   0   1
  SH2B1 WILD-TYPE 303  13  15  23
D437V10, multiclass
    clus
vv   SH2B1 MUTATED SH2B1 WILD-TYPE
  R0             8             303
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D437V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SH2B1 MUTATED       2                         1
  SH2B1 WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SH2B1 MUTATED                                           0     4
  SH2B1 WILD-TYPE                                         1   239
D437V12, multiclass
                                           clus
vv                                          SH2B1 MUTATED SH2B1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D437V13, binary
                 cls
clus                0   1
  SH2B1 MUTATED     0   7
  SH2B1 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SH2B1 MUTATED      0    7
  SH2B1 WILD-TYPE    4  303
                        clus
vv                       SH2B1 MUTATED SH2B1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(438) Variable = GPR82 MUTATION ANALYSIS
D438V1, survival
                 sevent
clus2               0   1
  GPR82 MUTATED     7   2
  GPR82 WILD-TYPE 223 137
  GPR82 MUTATED GPR82 WILD-TYPE 
              9             360 
  GPR82 MUTATED GPR82 WILD-TYPE 
              2             137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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           14.22 
[1] "6.6 - 77.3 (25.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.4"
D438V2, 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       2       14       38       29        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR82 MUTATED           0          0          0          1        1
  GPR82 WILD-TYPE         3         70         53         31       37
D438V3, multiclass
            clus
vv           GPR82 MUTATED GPR82 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPR82 MUTATED     1   3   3   2
  GPR82 WILD-TYPE  21  89 170  95
D438V4, multiclass
    clus
vv   GPR82 MUTATED GPR82 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             3             170
  T4             2              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
  GPR82 MUTATED     5   2   1   1
  GPR82 WILD-TYPE 113 102  76  76
D438V5, multiclass
    clus
vv   GPR82 MUTATED GPR82 WILD-TYPE
  N0             5             113
  N1             2             102
  N2             1              76
  N3             1              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"
D438V6, binary
                 cls
clus                0   1
  GPR82 MUTATED     8   1
  GPR82 WILD-TYPE 338  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR82 MUTATED      8    1
  GPR82 WILD-TYPE  338   28
   clus
vv  GPR82 MUTATED GPR82 WILD-TYPE
  0             8             338
  1             1              28
[1] 2 2
[1] FALSE
D438V7, binary
                 cls
clus                0   1
  GPR82 MUTATED     3   6
  GPR82 WILD-TYPE 142 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR82 MUTATED      3    6
  GPR82 WILD-TYPE  142  242
        clus
vv       GPR82 MUTATED GPR82 WILD-TYPE
  FEMALE             3             142
  MALE               6             242
[1] 2 2
[1] FALSE
D438V8, binary
                 cls
clus                0   1
  GPR82 MUTATED     7   1
  GPR82 WILD-TYPE 285  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR82 MUTATED      7    1
  GPR82 WILD-TYPE  285   58
     clus
vv    GPR82 MUTATED GPR82 WILD-TYPE
  NO              7             285
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GPR82 MUTATED                                          0
  GPR82 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GPR82 MUTATED                                       2
  GPR82 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR82 MUTATED                                                        3
  GPR82 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GPR82 MUTATED                                                   1
  GPR82 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR82 MUTATED                                                                   1
  GPR82 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GPR82 MUTATED                                                    0
  GPR82 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GPR82 MUTATED                                                  2
  GPR82 WILD-TYPE                                               59
D438V9, multiclass
                                                                   clus
vv                                                                  GPR82 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  GPR82 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GPR82 MUTATED     7   0   0   0
  GPR82 WILD-TYPE 304  14  15  24
D438V10, multiclass
    clus
vv   GPR82 MUTATED GPR82 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D438V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GPR82 MUTATED       5                         0
  GPR82 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR82 MUTATED                                           0     2
  GPR82 WILD-TYPE                                         1   241
D438V12, multiclass
                                           clus
vv                                          GPR82 MUTATED GPR82 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D438V13, binary
                 cls
clus                0   1
  GPR82 MUTATED     0   7
  GPR82 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR82 MUTATED      0    7
  GPR82 WILD-TYPE    4  303
                        clus
vv                       GPR82 MUTATED GPR82 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(439) Variable = ANK3 MUTATION ANALYSIS
D439V1, survival
                sevent
clus2              0   1
  ANK3 MUTATED    27  15
  ANK3 WILD-TYPE 203 124
  ANK3 MUTATED ANK3 WILD-TYPE 
            42            327 
  ANK3 MUTATED ANK3 WILD-TYPE 
            15            124 
$`ANK3 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7707 
        6.97        30.90         9.67        30.90        44.94        35.84 
TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 
       32.25         0.26         4.31        25.05         1.12        28.14 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-5801 TCGA-CD-8535 TCGA-CG-4305 TCGA-CG-4306 
       31.96        16.14        13.18        12.82        15.95         1.02 
TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-8572 TCGA-D7-8576 
        9.01         6.02       105.07        28.96        16.80        14.66 
TCGA-D7-A4YY TCGA-D7-A6EY TCGA-FP-7735 TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-8602 
       13.78        11.44         3.48        77.29        30.51        22.32 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-KB-A93J 
       22.68        24.20        11.77        20.25        23.84        36.95 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-VQ-A8DV TCGA-VQ-A8P2 TCGA-VQ-AA6K 
       19.73        45.67        74.53        13.25        38.14        12.43 

$`ANK3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-7196 
       19.89        12.16         8.98        40.21        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-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-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-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-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-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-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-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-D7-8573 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-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-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-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-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-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-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-MX-A5UG TCGA-MX-A666 TCGA-R5-A7ZE 
        2.53         5.56        63.62         3.72        14.04        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-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-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-ZA-A8F6 
       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 
         19.99          14.04 
[1] "0.3 - 105.1 (20.0)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.3"
D439V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANK3 MUTATED         0        3        6        4         2         5
  ANK3 WILD-TYPE       2       12       34       26        35        47
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANK3 MUTATED           0          8          4          5        6
  ANK3 WILD-TYPE         3         62         49         27       32
D439V3, multiclass
            clus
vv           ANK3 MUTATED ANK3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              3             12
  STAGE IB              6             34
  STAGE II              4             26
  STAGE IIA             2             35
  STAGE IIB             5             47
  STAGE III             0              3
  STAGE IIIA            8             62
  STAGE IIIB            4             49
  STAGE IIIC            5             27
  STAGE IV              6             32
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ANK3 MUTATED     3  13  15  13
  ANK3 WILD-TYPE  19  79 158  84
D439V4, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  T1            3             19
  T2           13             79
  T3           15            158
  T4           13             84
[1] 4 2
[1] TRUE
[1] "dimension of 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    14  14   7   9
  ANK3 WILD-TYPE 104  90  70  68
D439V5, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  N0           14            104
  N1           14             90
  N2            7             70
  N3            9             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"
D439V6, binary
                cls
clus               0   1
  ANK3 MUTATED    40   5
  ANK3 WILD-TYPE 306  24
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     40    5
  ANK3 WILD-TYPE  306   24
   clus
vv  ANK3 MUTATED ANK3 WILD-TYPE
  0           40            306
  1            5             24
[1] 2 2
[1] FALSE
D439V7, binary
                cls
clus               0   1
  ANK3 MUTATED    24  23
  ANK3 WILD-TYPE 121 225
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     24   23
  ANK3 WILD-TYPE  121  225
        clus
vv       ANK3 MUTATED ANK3 WILD-TYPE
  FEMALE           24            121
  MALE             23            225
[1] 2 2
[1] FALSE
D439V8, binary
                cls
clus               0   1
  ANK3 MUTATED    33   7
  ANK3 WILD-TYPE 259  52
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     33    7
  ANK3 WILD-TYPE  259   52
     clus
vv    ANK3 MUTATED ANK3 WILD-TYPE
  NO            33            259
  YES            7             52
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ANK3 MUTATED                                          1
  ANK3 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ANK3 MUTATED                                       6
  ANK3 WILD-TYPE                                    64
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANK3 MUTATED                                                       25
  ANK3 WILD-TYPE                                                    133
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ANK3 MUTATED                                                   3
  ANK3 WILD-TYPE                                                18
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANK3 MUTATED                                                                   4
  ANK3 WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ANK3 MUTATED                                                    0
  ANK3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ANK3 MUTATED                                                  8
  ANK3 WILD-TYPE                                               53
D439V9, multiclass
                                                                   clus
vv                                                                  ANK3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      25
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             8
                                                                   clus
vv                                                                  ANK3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       133
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              53
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ANK3 MUTATED    34   3   2   6
  ANK3 WILD-TYPE 277  11  13  18
D439V10, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  R0           34            277
  R1            3             11
  R2            2             13
  RX            6             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D439V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ANK3 MUTATED       9                         1
  ANK3 WILD-TYPE    78                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANK3 MUTATED                                           0    27
  ANK3 WILD-TYPE                                         1   216
D439V12, multiclass
                                           clus
vv                                          ANK3 MUTATED ANK3 WILD-TYPE
  ASIAN                                                9             78
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               27            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D439V13, binary
                cls
clus               0   1
  ANK3 MUTATED     2  31
  ANK3 WILD-TYPE   2 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED      2   31
  ANK3 WILD-TYPE    2  279
                        clus
vv                       ANK3 MUTATED ANK3 WILD-TYPE
  HISPANIC OR LATINO                2              2
  NOT HISPANIC OR LATINO           31            279
[1] 2 2
[1] FALSE

Clustering(440) Variable = MLH1 MUTATION ANALYSIS
D440V1, survival
                sevent
clus2              0   1
  MLH1 MUTATED     6   1
  MLH1 WILD-TYPE 224 138
  MLH1 MUTATED MLH1 WILD-TYPE 
             7            362 
  MLH1 MUTATED MLH1 WILD-TYPE 
             1            138 
$`MLH1 MUTATED`
TCGA-B7-A5TI TCGA-BR-4201 TCGA-BR-6802 TCGA-CG-5723 TCGA-F1-6874 TCGA-FP-A4BE 
       19.56        30.90        30.90       105.07        14.47        11.08 
TCGA-R5-A7ZI 
       74.53 

$`MLH1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-F1-6875 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-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 

  MLH1 MUTATED MLH1 WILD-TYPE 
         11.08           0.00 
  MLH1 MUTATED MLH1 WILD-TYPE 
        105.07         122.30 
  MLH1 MUTATED MLH1 WILD-TYPE 
         30.90          14.07 
[1] "11.1 - 105.1 (30.9)" "0.0 - 122.3 (14.1)" 
[1] "hr=" "4.8"
D440V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLH1 MUTATED         0        0        1        1         1         0
  MLH1 WILD-TYPE       2       15       39       29        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MLH1 MUTATED           0          1          0          1        1
  MLH1 WILD-TYPE         3         69         53         31       37
D440V3, multiclass
            clus
vv           MLH1 MUTATED MLH1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MLH1 MUTATED     0   3   2   2
  MLH1 WILD-TYPE  22  89 171  95
D440V4, multiclass
    clus
vv   MLH1 MUTATED MLH1 WILD-TYPE
  T1            0             22
  T2            3             89
  T3            2            171
  T4            2             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
  MLH1 MUTATED     2   2   1   1
  MLH1 WILD-TYPE 116 102  76  76
D440V5, multiclass
    clus
vv   MLH1 MUTATED MLH1 WILD-TYPE
  N0            2            116
  N1            2            102
  N2            1             76
  N3            1             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"
D440V6, binary
                cls
clus               0   1
  MLH1 MUTATED     7   1
  MLH1 WILD-TYPE 339  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED      7    1
  MLH1 WILD-TYPE  339   28
   clus
vv  MLH1 MUTATED MLH1 WILD-TYPE
  0            7            339
  1            1             28
[1] 2 2
[1] FALSE
D440V7, binary
                cls
clus               0   1
  MLH1 MUTATED     3   5
  MLH1 WILD-TYPE 142 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED      3    5
  MLH1 WILD-TYPE  142  243
        clus
vv       MLH1 MUTATED MLH1 WILD-TYPE
  FEMALE            3            142
  MALE              5            243
[1] 2 2
[1] FALSE
D440V8, binary
                cls
clus               0   1
  MLH1 MUTATED     6   1
  MLH1 WILD-TYPE 286  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED      6    1
  MLH1 WILD-TYPE  286   58
     clus
vv    MLH1 MUTATED MLH1 WILD-TYPE
  NO             6            286
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MLH1 MUTATED                                          0
  MLH1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MLH1 MUTATED                                       2
  MLH1 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MLH1 MUTATED                                                        5
  MLH1 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MLH1 MUTATED                                                   0
  MLH1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MLH1 MUTATED                                                                   1
  MLH1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MLH1 MUTATED                                                    0
  MLH1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MLH1 MUTATED                                                  0
  MLH1 WILD-TYPE                                               61
D440V9, multiclass
                                                                   clus
vv                                                                  MLH1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  MLH1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MLH1 MUTATED     5   0   0   2
  MLH1 WILD-TYPE 306  14  15  22
D440V10, multiclass
    clus
vv   MLH1 MUTATED MLH1 WILD-TYPE
  R0            5            306
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D440V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MLH1 MUTATED       0                         1
  MLH1 WILD-TYPE    87                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MLH1 MUTATED                                           0     6
  MLH1 WILD-TYPE                                         1   237
D440V12, multiclass
                                           clus
vv                                          MLH1 MUTATED MLH1 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D440V13, binary
                cls
clus               0   1
  MLH1 MUTATED     1   6
  MLH1 WILD-TYPE   3 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED      1    6
  MLH1 WILD-TYPE    3  304
                        clus
vv                       MLH1 MUTATED MLH1 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(441) Variable = BCKDHA MUTATION ANALYSIS
D441V1, survival
                  sevent
clus2                0   1
  BCKDHA MUTATED     6   4
  BCKDHA WILD-TYPE 224 135
  BCKDHA MUTATED BCKDHA WILD-TYPE 
              10              359 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
               4              135 
$`BCKDHA MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 TCGA-CD-A487 TCGA-D7-8578 
        6.97        30.90        34.68        32.78        12.30        21.14 
TCGA-D7-A4YV TCGA-F1-6874 TCGA-FP-A4BE TCGA-HJ-7597 
        5.92        14.47        11.08        26.47 

$`BCKDHA WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  BCKDHA MUTATED BCKDHA WILD-TYPE 
            5.92             0.00 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
           34.68           122.30 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
          17.805           14.170 
[1] "5.9 - 34.7 (17.8)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D441V2, 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       2       15       37       30        34        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCKDHA MUTATED           0          1          0          0        0
  BCKDHA WILD-TYPE         3         69         53         32       38
D441V3, multiclass
            clus
vv           BCKDHA MUTATED BCKDHA WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BCKDHA MUTATED     0   4   6   0
  BCKDHA WILD-TYPE  22  88 167  97
D441V4, multiclass
    clus
vv   BCKDHA MUTATED BCKDHA WILD-TYPE
  T1              0               22
  T2              4               88
  T3              6              167
  T4              0               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
  BCKDHA MUTATED     6   3   0   0
  BCKDHA WILD-TYPE 112 101  77  77
D441V5, multiclass
    clus
vv   BCKDHA MUTATED BCKDHA WILD-TYPE
  N0              6              112
  N1              3              101
  N2              0               77
  N3              0               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"
D441V6, binary
                  cls
clus                 0   1
  BCKDHA MUTATED     8   0
  BCKDHA WILD-TYPE 338  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED      8    0
  BCKDHA WILD-TYPE  338   29
   clus
vv  BCKDHA MUTATED BCKDHA WILD-TYPE
  0              8              338
  1              0               29
[1] 2 2
[1] FALSE
D441V7, binary
                  cls
clus                 0   1
  BCKDHA MUTATED     5   5
  BCKDHA WILD-TYPE 140 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED      5    5
  BCKDHA WILD-TYPE  140  243
        clus
vv       BCKDHA MUTATED BCKDHA WILD-TYPE
  FEMALE              5              140
  MALE                5              243
[1] 2 2
[1] FALSE
D441V8, binary
                  cls
clus                 0   1
  BCKDHA MUTATED     9   1
  BCKDHA WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED      9    1
  BCKDHA WILD-TYPE  283   58
     clus
vv    BCKDHA MUTATED BCKDHA WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BCKDHA MUTATED                                          1
  BCKDHA WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BCKDHA MUTATED                                       1
  BCKDHA WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BCKDHA MUTATED                                                        6
  BCKDHA WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BCKDHA MUTATED                                                   0
  BCKDHA WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BCKDHA MUTATED                                                                   1
  BCKDHA WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BCKDHA MUTATED                                                    0
  BCKDHA WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BCKDHA MUTATED                                                  1
  BCKDHA WILD-TYPE                                               60
D441V9, multiclass
                                                                   clus
vv                                                                  BCKDHA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  BCKDHA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BCKDHA MUTATED     8   0   0   2
  BCKDHA WILD-TYPE 303  14  15  22
D441V10, multiclass
    clus
vv   BCKDHA MUTATED BCKDHA WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D441V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  BCKDHA MUTATED       1                         1
  BCKDHA WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BCKDHA MUTATED                                           0     8
  BCKDHA WILD-TYPE                                         1   235
D441V12, multiclass
                                           clus
vv                                          BCKDHA MUTATED BCKDHA WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D441V13, binary
                  cls
clus                 0   1
  BCKDHA MUTATED     0  10
  BCKDHA WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED      0   10
  BCKDHA WILD-TYPE    4  300
                        clus
vv                       BCKDHA MUTATED BCKDHA WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(442) Variable = MMP10 MUTATION ANALYSIS
D442V1, survival
                 sevent
clus2               0   1
  MMP10 MUTATED     5   3
  MMP10 WILD-TYPE 225 136
  MMP10 MUTATED MMP10 WILD-TYPE 
              8             361 
  MMP10 MUTATED MMP10 WILD-TYPE 
              3             136 
$`MMP10 MUTATED`
TCGA-CG-4460 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5733 
       21.99        28.14        31.96        16.14         6.02        21.07 
TCGA-HU-A4G8 TCGA-HU-A4H3 
       22.68        29.00 

$`MMP10 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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 

  MMP10 MUTATED MMP10 WILD-TYPE 
           6.02            0.00 
  MMP10 MUTATED MMP10 WILD-TYPE 
          31.96          122.30 
  MMP10 MUTATED MMP10 WILD-TYPE 
         22.335          14.070 
[1] "6.0 - 32.0 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D442V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MMP10 MUTATED         0        0        0        0         0         2
  MMP10 WILD-TYPE       2       15       40       30        37        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MMP10 MUTATED           0          1          1          2        3
  MMP10 WILD-TYPE         3         69         52         30       35
D442V3, multiclass
            clus
vv           MMP10 MUTATED MMP10 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MMP10 MUTATED     0   1   2   6
  MMP10 WILD-TYPE  22  91 171  91
D442V4, multiclass
    clus
vv   MMP10 MUTATED MMP10 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             2             171
  T4             6              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
  MMP10 MUTATED     1   3   2   3
  MMP10 WILD-TYPE 117 101  75  74
D442V5, multiclass
    clus
vv   MMP10 MUTATED MMP10 WILD-TYPE
  N0             1             117
  N1             3             101
  N2             2              75
  N3             3              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"
D442V6, binary
                 cls
clus                0   1
  MMP10 MUTATED     7   2
  MMP10 WILD-TYPE 339  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP10 MUTATED      7    2
  MMP10 WILD-TYPE  339   27
   clus
vv  MMP10 MUTATED MMP10 WILD-TYPE
  0             7             339
  1             2              27
[1] 2 2
[1] FALSE
D442V7, binary
                 cls
clus                0   1
  MMP10 MUTATED     5   4
  MMP10 WILD-TYPE 140 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP10 MUTATED      5    4
  MMP10 WILD-TYPE  140  244
        clus
vv       MMP10 MUTATED MMP10 WILD-TYPE
  FEMALE             5             140
  MALE               4             244
[1] 2 2
[1] FALSE
D442V8, binary
                 cls
clus                0   1
  MMP10 MUTATED     8   0
  MMP10 WILD-TYPE 284  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP10 MUTATED      8    0
  MMP10 WILD-TYPE  284   59
     clus
vv    MMP10 MUTATED MMP10 WILD-TYPE
  NO              8             284
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MMP10 MUTATED                                          0
  MMP10 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MMP10 MUTATED                                       2
  MMP10 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MMP10 MUTATED                                                        2
  MMP10 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MMP10 MUTATED                                                   0
  MMP10 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MMP10 MUTATED                                                                   4
  MMP10 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MMP10 MUTATED                                                    0
  MMP10 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MMP10 MUTATED                                                  1
  MMP10 WILD-TYPE                                               60
D442V9, multiclass
                                                                   clus
vv                                                                  MMP10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  MMP10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MMP10 MUTATED     7   0   1   0
  MMP10 WILD-TYPE 304  14  14  24
D442V10, multiclass
    clus
vv   MMP10 MUTATED MMP10 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D442V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MMP10 MUTATED       3                         0
  MMP10 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MMP10 MUTATED                                           0     3
  MMP10 WILD-TYPE                                         1   240
D442V12, multiclass
                                           clus
vv                                          MMP10 MUTATED MMP10 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D442V13, binary
                 cls
clus                0   1
  MMP10 MUTATED     0   6
  MMP10 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP10 MUTATED      0    6
  MMP10 WILD-TYPE    4  304
                        clus
vv                       MMP10 MUTATED MMP10 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(443) Variable = HAX1 MUTATION ANALYSIS
D443V1, survival
                sevent
clus2              0   1
  HAX1 MUTATED     4   1
  HAX1 WILD-TYPE 226 138
  HAX1 MUTATED HAX1 WILD-TYPE 
             5            364 
  HAX1 MUTATED HAX1 WILD-TYPE 
             1            138 
$`HAX1 MUTATED`
TCGA-BR-8078 TCGA-CG-5721 TCGA-D7-A6EY TCGA-HF-7132 TCGA-VQ-A8P2 
       29.59         6.02        11.44        77.29        38.14 

$`HAX1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  HAX1 MUTATED HAX1 WILD-TYPE 
          6.02           0.00 
  HAX1 MUTATED HAX1 WILD-TYPE 
         77.29         122.30 
  HAX1 MUTATED HAX1 WILD-TYPE 
         29.59          14.22 
[1] "6.0 - 77.3 (29.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.9"
D443V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HAX1 MUTATED         0        0        0        1         0         1
  HAX1 WILD-TYPE       2       15       40       29        37        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HAX1 MUTATED           0          1          1          0        1
  HAX1 WILD-TYPE         3         69         52         32       37
D443V3, multiclass
            clus
vv           HAX1 MUTATED HAX1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             0             37
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HAX1 MUTATED     0   1   1   3
  HAX1 WILD-TYPE  22  91 172  94
D443V4, multiclass
    clus
vv   HAX1 MUTATED HAX1 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            1            172
  T4            3             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
  HAX1 MUTATED     1   3   0   1
  HAX1 WILD-TYPE 117 101  77  76
D443V5, multiclass
    clus
vv   HAX1 MUTATED HAX1 WILD-TYPE
  N0            1            117
  N1            3            101
  N2            0             77
  N3            1             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"
D443V6, binary
                cls
clus               0   1
  HAX1 MUTATED     5   0
  HAX1 WILD-TYPE 341  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAX1 MUTATED      5    0
  HAX1 WILD-TYPE  341   29
   clus
vv  HAX1 MUTATED HAX1 WILD-TYPE
  0            5            341
  1            0             29
[1] 2 2
[1] FALSE
D443V7, binary
                cls
clus               0   1
  HAX1 MUTATED     2   3
  HAX1 WILD-TYPE 143 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAX1 MUTATED      2    3
  HAX1 WILD-TYPE  143  245
        clus
vv       HAX1 MUTATED HAX1 WILD-TYPE
  FEMALE            2            143
  MALE              3            245
[1] 2 2
[1] FALSE
D443V8, binary
                cls
clus               0   1
  HAX1 MUTATED     3   2
  HAX1 WILD-TYPE 289  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAX1 MUTATED      3    2
  HAX1 WILD-TYPE  289   57
     clus
vv    HAX1 MUTATED HAX1 WILD-TYPE
  NO             3            289
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HAX1 MUTATED                                          0
  HAX1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HAX1 MUTATED                                       0
  HAX1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HAX1 MUTATED                                                        1
  HAX1 WILD-TYPE                                                    157
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HAX1 MUTATED                                                   2
  HAX1 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HAX1 MUTATED                                                                   1
  HAX1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HAX1 MUTATED                                                    0
  HAX1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HAX1 MUTATED                                                  1
  HAX1 WILD-TYPE                                               60
D443V9, multiclass
                                                                   clus
vv                                                                  HAX1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  HAX1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HAX1 MUTATED     5   0   0   0
  HAX1 WILD-TYPE 306  14  15  24
D443V10, multiclass
    clus
vv   HAX1 MUTATED HAX1 WILD-TYPE
  R0            5            306
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D443V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  HAX1 MUTATED       0                         0
  HAX1 WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HAX1 MUTATED                                           0     3
  HAX1 WILD-TYPE                                         1   240
D443V12, multiclass
                                           clus
vv                                          HAX1 MUTATED HAX1 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D443V13, binary
                cls
clus               0   1
  HAX1 MUTATED     0   2
  HAX1 WILD-TYPE   4 308
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAX1 MUTATED      0    2
  HAX1 WILD-TYPE    4  308
                        clus
vv                       HAX1 MUTATED HAX1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            2            308
[1] 2 2
[1] FALSE

Clustering(444) Variable = ULK2 MUTATION ANALYSIS
D444V1, survival
                sevent
clus2              0   1
  ULK2 MUTATED     9   2
  ULK2 WILD-TYPE 221 137
  ULK2 MUTATED ULK2 WILD-TYPE 
            11            358 
  ULK2 MUTATED ULK2 WILD-TYPE 
             2            137 
$`ULK2 MUTATED`
TCGA-BR-6452 TCGA-BR-8591 TCGA-CD-8528 TCGA-CG-4306 TCGA-CG-5728 TCGA-D7-5579 
       34.68        28.14        12.33         1.02        65.10        20.91 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H4 
       11.77        29.98         0.10        20.25        23.84 

$`ULK2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-A4GT TCGA-HU-A4GU TCGA-HU-A4GY 
       25.81        21.37         8.98         6.51         6.58         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 

  ULK2 MUTATED ULK2 WILD-TYPE 
           0.1            0.0 
  ULK2 MUTATED ULK2 WILD-TYPE 
          65.1          122.3 
  ULK2 MUTATED ULK2 WILD-TYPE 
         20.91          14.12 
[1] "0.1 - 65.1 (20.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.5"
D444V2, 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       2       14       39       30        35        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ULK2 MUTATED           0          2          0          3        1
  ULK2 WILD-TYPE         3         68         53         29       37
D444V3, multiclass
            clus
vv           ULK2 MUTATED ULK2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            3             29
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ULK2 MUTATED     1   3   3   4
  ULK2 WILD-TYPE  21  89 170  93
D444V4, multiclass
    clus
vv   ULK2 MUTATED ULK2 WILD-TYPE
  T1            1             21
  T2            3             89
  T3            3            170
  T4            4             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
  ULK2 MUTATED     4   1   5   1
  ULK2 WILD-TYPE 114 103  72  76
D444V5, multiclass
    clus
vv   ULK2 MUTATED ULK2 WILD-TYPE
  N0            4            114
  N1            1            103
  N2            5             72
  N3            1             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"
D444V6, binary
                cls
clus               0   1
  ULK2 MUTATED    10   1
  ULK2 WILD-TYPE 336  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK2 MUTATED     10    1
  ULK2 WILD-TYPE  336   28
   clus
vv  ULK2 MUTATED ULK2 WILD-TYPE
  0           10            336
  1            1             28
[1] 2 2
[1] FALSE
D444V7, binary
                cls
clus               0   1
  ULK2 MUTATED     5   6
  ULK2 WILD-TYPE 140 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK2 MUTATED      5    6
  ULK2 WILD-TYPE  140  242
        clus
vv       ULK2 MUTATED ULK2 WILD-TYPE
  FEMALE            5            140
  MALE              6            242
[1] 2 2
[1] FALSE
D444V8, binary
                cls
clus               0   1
  ULK2 MUTATED     8   1
  ULK2 WILD-TYPE 284  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK2 MUTATED      8    1
  ULK2 WILD-TYPE  284   58
     clus
vv    ULK2 MUTATED ULK2 WILD-TYPE
  NO             8            284
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ULK2 MUTATED                                          0
  ULK2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ULK2 MUTATED                                       1
  ULK2 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ULK2 MUTATED                                                        4
  ULK2 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ULK2 MUTATED                                                   1
  ULK2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ULK2 MUTATED                                                                   1
  ULK2 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ULK2 MUTATED                                                    0
  ULK2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ULK2 MUTATED                                                  4
  ULK2 WILD-TYPE                                               57
D444V9, multiclass
                                                                   clus
vv                                                                  ULK2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  ULK2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ULK2 MUTATED     9   1   1   0
  ULK2 WILD-TYPE 302  13  14  24
D444V10, multiclass
    clus
vv   ULK2 MUTATED ULK2 WILD-TYPE
  R0            9            302
  R1            1             13
  R2            1             14
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D444V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ULK2 MUTATED       6                         0
  ULK2 WILD-TYPE    81                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ULK2 MUTATED                                           0     3
  ULK2 WILD-TYPE                                         1   240
D444V12, multiclass
                                           clus
vv                                          ULK2 MUTATED ULK2 WILD-TYPE
  ASIAN                                                6             81
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D444V13, binary
                cls
clus               0   1
  ULK2 MUTATED     0   9
  ULK2 WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK2 MUTATED      0    9
  ULK2 WILD-TYPE    4  301
                        clus
vv                       ULK2 MUTATED ULK2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(445) Variable = C11ORF70 MUTATION ANALYSIS
D445V1, survival
                    sevent
clus2                  0   1
  C11ORF70 MUTATED     3   1
  C11ORF70 WILD-TYPE 227 138
  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
                 4                365 
  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
                 1                138 
$`C11ORF70 MUTATED`
TCGA-B7-5816 TCGA-CD-A4MG TCGA-HU-A4GU TCGA-SW-A7EA 
       26.70         6.58         6.58        19.04 

$`C11ORF70 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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 

  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
              6.58               0.00 
  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
              26.7              122.3 
  C11ORF70 MUTATED C11ORF70 WILD-TYPE 
             12.81              14.27 
[1] "6.6 - 26.7 (12.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D445V2, 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       2       15       39       30        36        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C11ORF70 MUTATED           0          0          0          0        0
  C11ORF70 WILD-TYPE         3         70         53         32       38
D445V3, multiclass
            clus
vv           C11ORF70 MUTATED C11ORF70 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                0                 53
  STAGE IIIC                0                 32
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C11ORF70 MUTATED     0   1   2   1
  C11ORF70 WILD-TYPE  22  91 171  96
D445V4, multiclass
    clus
vv   C11ORF70 MUTATED C11ORF70 WILD-TYPE
  T1                0                 22
  T2                1                 91
  T3                2                171
  T4                1                 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
  C11ORF70 MUTATED     3   1   0   0
  C11ORF70 WILD-TYPE 115 103  77  77
D445V5, multiclass
    clus
vv   C11ORF70 MUTATED C11ORF70 WILD-TYPE
  N0                3                115
  N1                1                103
  N2                0                 77
  N3                0                 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"
D445V6, binary
                    cls
clus                   0   1
  C11ORF70 MUTATED     4   0
  C11ORF70 WILD-TYPE 342  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF70 MUTATED      4    0
  C11ORF70 WILD-TYPE  342   29
   clus
vv  C11ORF70 MUTATED C11ORF70 WILD-TYPE
  0                4                342
  1                0                 29
[1] 2 2
[1] FALSE
D445V7, binary
                    cls
clus                   0   1
  C11ORF70 MUTATED     2   2
  C11ORF70 WILD-TYPE 143 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF70 MUTATED      2    2
  C11ORF70 WILD-TYPE  143  246
        clus
vv       C11ORF70 MUTATED C11ORF70 WILD-TYPE
  FEMALE                2                143
  MALE                  2                246
[1] 2 2
[1] FALSE
D445V8, binary
                    cls
clus                   0   1
  C11ORF70 MUTATED     4   0
  C11ORF70 WILD-TYPE 288  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF70 MUTATED      4    0
  C11ORF70 WILD-TYPE  288   59
     clus
vv    C11ORF70 MUTATED C11ORF70 WILD-TYPE
  NO                 4                288
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C11ORF70 MUTATED                                          0
  C11ORF70 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C11ORF70 MUTATED                                       4
  C11ORF70 WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C11ORF70 MUTATED                                                        0
  C11ORF70 WILD-TYPE                                                    158
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C11ORF70 MUTATED                                                   0
  C11ORF70 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C11ORF70 MUTATED                                                                   0
  C11ORF70 WILD-TYPE                                                                68
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C11ORF70 MUTATED                                                    0
  C11ORF70 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C11ORF70 MUTATED                                                  0
  C11ORF70 WILD-TYPE                                               61
D445V9, multiclass
                                                                   clus
vv                                                                  C11ORF70 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 0
                                                                   clus
vv                                                                  C11ORF70 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           158
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C11ORF70 MUTATED     3   0   0   0
  C11ORF70 WILD-TYPE 308  14  15  24
D445V10, multiclass
    clus
vv   C11ORF70 MUTATED C11ORF70 WILD-TYPE
  R0                3                308
  R1                0                 14
  R2                0                 15
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D445V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C11ORF70 MUTATED       2                         0
  C11ORF70 WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C11ORF70 MUTATED                                           0     2
  C11ORF70 WILD-TYPE                                         1   241
D445V12, multiclass
                                           clus
vv                                          C11ORF70 MUTATED C11ORF70 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    2                241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D445V13, binary
                    cls
clus                   0   1
  C11ORF70 MUTATED     0   4
  C11ORF70 WILD-TYPE   4 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF70 MUTATED      0    4
  C11ORF70 WILD-TYPE    4  306
                        clus
vv                       C11ORF70 MUTATED C11ORF70 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                4                306
[1] 2 2
[1] FALSE

Clustering(446) Variable = AKAP11 MUTATION ANALYSIS
D446V1, survival
                  sevent
clus2                0   1
  AKAP11 MUTATED    10   3
  AKAP11 WILD-TYPE 220 136
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              13              356 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
               3              136 
$`AKAP11 MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-8678 TCGA-CG-4465 
        6.97         9.34        34.68         4.31        24.79         9.01 
TCGA-CG-5721 TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
        6.02        25.81        29.98         6.51         6.58        20.25 
TCGA-HU-A4H3 
       29.00 

$`AKAP11 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        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-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-A4GH 
       24.26        22.68        24.20         3.25        22.75        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
       21.37         8.98         0.10         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 

  AKAP11 MUTATED AKAP11 WILD-TYPE 
            4.31             0.00 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
           34.68           122.30 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
            9.34            14.35 
[1] "4.3 - 34.7 (9.3)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D446V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AKAP11 MUTATED         0        0        2        0         4         2
  AKAP11 WILD-TYPE       2       15       38       30        33        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKAP11 MUTATED           0          2          0          2        2
  AKAP11 WILD-TYPE         3         68         53         30       36
D446V3, multiclass
            clus
vv           AKAP11 MUTATED AKAP11 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               4               33
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AKAP11 MUTATED     0   3   5   6
  AKAP11 WILD-TYPE  22  89 168  91
D446V4, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              5              168
  T4              6               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
  AKAP11 MUTATED     7   5   1   2
  AKAP11 WILD-TYPE 111  99  76  75
D446V5, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  N0              7              111
  N1              5               99
  N2              1               76
  N3              2               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"
D446V6, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    13   1
  AKAP11 WILD-TYPE 333  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     13    1
  AKAP11 WILD-TYPE  333   28
   clus
vv  AKAP11 MUTATED AKAP11 WILD-TYPE
  0             13              333
  1              1               28
[1] 2 2
[1] FALSE
D446V7, binary
                  cls
clus                 0   1
  AKAP11 MUTATED     7   8
  AKAP11 WILD-TYPE 138 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED      7    8
  AKAP11 WILD-TYPE  138  240
        clus
vv       AKAP11 MUTATED AKAP11 WILD-TYPE
  FEMALE              7              138
  MALE                8              240
[1] 2 2
[1] FALSE
D446V8, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    12   0
  AKAP11 WILD-TYPE 280  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     12    0
  AKAP11 WILD-TYPE  280   59
     clus
vv    AKAP11 MUTATED AKAP11 WILD-TYPE
  NO              12              280
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AKAP11 MUTATED                                          0
  AKAP11 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AKAP11 MUTATED                                       4
  AKAP11 WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AKAP11 MUTATED                                                        6
  AKAP11 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AKAP11 MUTATED                                                   0
  AKAP11 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AKAP11 MUTATED                                                                   2
  AKAP11 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AKAP11 MUTATED                                                    0
  AKAP11 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AKAP11 MUTATED                                                  3
  AKAP11 WILD-TYPE                                               58
D446V9, multiclass
                                                                   clus
vv                                                                  AKAP11 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  AKAP11 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  AKAP11 MUTATED    11   0   1   3
  AKAP11 WILD-TYPE 300  14  14  21
D446V10, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  R0             11              300
  R1              0               14
  R2              1               14
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D446V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  AKAP11 MUTATED       6                         0
  AKAP11 WILD-TYPE    81                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AKAP11 MUTATED                                           0     7
  AKAP11 WILD-TYPE                                         1   236
D446V12, multiclass
                                           clus
vv                                          AKAP11 MUTATED AKAP11 WILD-TYPE
  ASIAN                                                  6               81
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D446V13, binary
                  cls
clus                 0   1
  AKAP11 MUTATED     0  13
  AKAP11 WILD-TYPE   4 297
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED      0   13
  AKAP11 WILD-TYPE    4  297
                        clus
vv                       AKAP11 MUTATED AKAP11 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             13              297
[1] 2 2
[1] FALSE

Clustering(447) Variable = MAN1C1 MUTATION ANALYSIS
D447V1, survival
                  sevent
clus2                0   1
  MAN1C1 MUTATED     3   4
  MAN1C1 WILD-TYPE 227 135
  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
               7              362 
  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
               4              135 
$`MAN1C1 MUTATED`
TCGA-BR-4256 TCGA-BR-8078 TCGA-CD-A4MG TCGA-CG-5726 TCGA-D7-5577 TCGA-FP-A4BE 
        9.34        29.59         6.58        28.96        25.71        11.08 
TCGA-HU-A4G8 
       22.68 

$`MAN1C1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-5578 
       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-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-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 

  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
            6.58             0.00 
  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
           29.59           122.30 
  MAN1C1 MUTATED MAN1C1 WILD-TYPE 
           22.68            14.22 
[1] "6.6 - 29.6 (22.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D447V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAN1C1 MUTATED         1        1        0        0         2         3
  MAN1C1 WILD-TYPE       1       14       40       30        35        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAN1C1 MUTATED           0          2          0          0        0
  MAN1C1 WILD-TYPE         3         68         53         32       38
D447V3, multiclass
            clus
vv           MAN1C1 MUTATED MAN1C1 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAN1C1 MUTATED     2   1   3   3
  MAN1C1 WILD-TYPE  20  91 170  94
D447V4, multiclass
    clus
vv   MAN1C1 MUTATED MAN1C1 WILD-TYPE
  T1              2               20
  T2              1               91
  T3              3              170
  T4              3               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
  MAN1C1 MUTATED     6   3   0   1
  MAN1C1 WILD-TYPE 112 101  77  76
D447V5, multiclass
    clus
vv   MAN1C1 MUTATED MAN1C1 WILD-TYPE
  N0              6              112
  N1              3              101
  N2              0               77
  N3              1               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"
D447V6, binary
                  cls
clus                 0   1
  MAN1C1 MUTATED     9   0
  MAN1C1 WILD-TYPE 337  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1C1 MUTATED      9    0
  MAN1C1 WILD-TYPE  337   29
   clus
vv  MAN1C1 MUTATED MAN1C1 WILD-TYPE
  0              9              337
  1              0               29
[1] 2 2
[1] FALSE
D447V7, binary
                  cls
clus                 0   1
  MAN1C1 MUTATED     4   6
  MAN1C1 WILD-TYPE 141 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1C1 MUTATED      4    6
  MAN1C1 WILD-TYPE  141  242
        clus
vv       MAN1C1 MUTATED MAN1C1 WILD-TYPE
  FEMALE              4              141
  MALE                6              242
[1] 2 2
[1] FALSE
D447V8, binary
                  cls
clus                 0   1
  MAN1C1 MUTATED     7   1
  MAN1C1 WILD-TYPE 285  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1C1 MUTATED      7    1
  MAN1C1 WILD-TYPE  285   58
     clus
vv    MAN1C1 MUTATED MAN1C1 WILD-TYPE
  NO               7              285
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MAN1C1 MUTATED                                          0
  MAN1C1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MAN1C1 MUTATED                                       2
  MAN1C1 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAN1C1 MUTATED                                                        5
  MAN1C1 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MAN1C1 MUTATED                                                   0
  MAN1C1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAN1C1 MUTATED                                                                   2
  MAN1C1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MAN1C1 MUTATED                                                    0
  MAN1C1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MAN1C1 MUTATED                                                  1
  MAN1C1 WILD-TYPE                                               60
D447V9, multiclass
                                                                   clus
vv                                                                  MAN1C1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  MAN1C1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAN1C1 MUTATED     6   0   0   2
  MAN1C1 WILD-TYPE 305  14  15  22
D447V10, multiclass
    clus
vv   MAN1C1 MUTATED MAN1C1 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D447V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAN1C1 MUTATED       2                         2
  MAN1C1 WILD-TYPE    85                         7
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAN1C1 MUTATED                                           0     5
  MAN1C1 WILD-TYPE                                         1   238
D447V12, multiclass
                                           clus
vv                                          MAN1C1 MUTATED MAN1C1 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              2                7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D447V13, binary
                  cls
clus                 0   1
  MAN1C1 MUTATED     0   9
  MAN1C1 WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAN1C1 MUTATED      0    9
  MAN1C1 WILD-TYPE    4  301
                        clus
vv                       MAN1C1 MUTATED MAN1C1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(448) Variable = KCTD3 MUTATION ANALYSIS
D448V1, survival
                 sevent
clus2               0   1
  KCTD3 MUTATED     7   4
  KCTD3 WILD-TYPE 223 135
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             11             358 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              4             135 
$`KCTD3 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8360 TCGA-BR-A4IY TCGA-BR-A4QL 
        6.97        34.68        14.43         6.18        12.89        16.14 
TCGA-HF-7132 TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-IP-7968 TCGA-MX-A5UJ 
       77.29        24.20         0.10         2.53        19.73 

$`KCTD3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  KCTD3 MUTATED KCTD3 WILD-TYPE 
            0.1             0.0 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
          77.29          122.30 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
          14.43           14.22 
[1] "0.1 - 77.3 (14.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1"  
D448V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCTD3 MUTATED         0        1        0        1         2         1
  KCTD3 WILD-TYPE       2       14       40       29        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCTD3 MUTATED           1          3          2          2        0
  KCTD3 WILD-TYPE         2         67         51         30       38
D448V3, multiclass
            clus
vv           KCTD3 MUTATED KCTD3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCTD3 MUTATED     1   1   6   5
  KCTD3 WILD-TYPE  21  91 167  92
D448V4, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             6             167
  T4             5              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
  KCTD3 MUTATED     5   4   3   2
  KCTD3 WILD-TYPE 113 100  74  75
D448V5, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  N0             5             113
  N1             4             100
  N2             3              74
  N3             2              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"
D448V6, binary
                 cls
clus                0   1
  KCTD3 MUTATED    12   0
  KCTD3 WILD-TYPE 334  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED     12    0
  KCTD3 WILD-TYPE  334   29
   clus
vv  KCTD3 MUTATED KCTD3 WILD-TYPE
  0            12             334
  1             0              29
[1] 2 2
[1] FALSE
D448V7, binary
                 cls
clus                0   1
  KCTD3 MUTATED     6   8
  KCTD3 WILD-TYPE 139 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      6    8
  KCTD3 WILD-TYPE  139  240
        clus
vv       KCTD3 MUTATED KCTD3 WILD-TYPE
  FEMALE             6             139
  MALE               8             240
[1] 2 2
[1] FALSE
D448V8, binary
                 cls
clus                0   1
  KCTD3 MUTATED     9   1
  KCTD3 WILD-TYPE 283  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      9    1
  KCTD3 WILD-TYPE  283   58
     clus
vv    KCTD3 MUTATED KCTD3 WILD-TYPE
  NO              9             283
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KCTD3 MUTATED                                          0
  KCTD3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KCTD3 MUTATED                                       1
  KCTD3 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCTD3 MUTATED                                                        7
  KCTD3 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KCTD3 MUTATED                                                   1
  KCTD3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCTD3 MUTATED                                                                   2
  KCTD3 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KCTD3 MUTATED                                                    0
  KCTD3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KCTD3 MUTATED                                                  3
  KCTD3 WILD-TYPE                                               58
D448V9, multiclass
                                                                   clus
vv                                                                  KCTD3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  KCTD3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCTD3 MUTATED    11   0   0   3
  KCTD3 WILD-TYPE 300  14  15  21
D448V10, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D448V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCTD3 MUTATED       3                         0
  KCTD3 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCTD3 MUTATED                                           0     9
  KCTD3 WILD-TYPE                                         1   234
D448V12, multiclass
                                           clus
vv                                          KCTD3 MUTATED KCTD3 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D448V13, binary
                 cls
clus                0   1
  KCTD3 MUTATED     0  12
  KCTD3 WILD-TYPE   4 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      0   12
  KCTD3 WILD-TYPE    4  298
                        clus
vv                       KCTD3 MUTATED KCTD3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(449) Variable = RALGAPB MUTATION ANALYSIS
D449V1, survival
                   sevent
clus2                 0   1
  RALGAPB MUTATED    11   4
  RALGAPB WILD-TYPE 219 135
  RALGAPB MUTATED RALGAPB WILD-TYPE 
               15               354 
  RALGAPB MUTATED RALGAPB WILD-TYPE 
                4               135 
$`RALGAPB MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-8690 
        6.97         9.34        32.25         1.12        31.96        10.68 
TCGA-BR-A4J8 TCGA-CG-5733 TCGA-D7-A4YT TCGA-D7-A4YY TCGA-HU-A4G9 TCGA-HU-A4GQ 
       13.51        21.07        14.27        13.78        24.20         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 
        6.51        20.25        29.00 

$`RALGAPB WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
            13.78             14.45 
[1] "0.1 - 32.2 (13.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.3"
D449V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RALGAPB MUTATED         0        1        0        0         2         1
  RALGAPB WILD-TYPE       2       14       40       30        35        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RALGAPB MUTATED           0          3          3          3        1
  RALGAPB WILD-TYPE         3         67         50         29       37
D449V3, multiclass
            clus
vv           RALGAPB MUTATED RALGAPB WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               3                67
  STAGE IIIB               3                50
  STAGE IIIC               3                29
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RALGAPB MUTATED     2   2   7   5
  RALGAPB WILD-TYPE  20  90 166  92
D449V4, multiclass
    clus
vv   RALGAPB MUTATED RALGAPB WILD-TYPE
  T1               2                20
  T2               2                90
  T3               7               166
  T4               5                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
  RALGAPB MUTATED     4   2   4   5
  RALGAPB WILD-TYPE 114 102  73  72
D449V5, multiclass
    clus
vv   RALGAPB MUTATED RALGAPB WILD-TYPE
  N0               4               114
  N1               2               102
  N2               4                73
  N3               5                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"
D449V6, binary
                   cls
clus                  0   1
  RALGAPB MUTATED    14   1
  RALGAPB WILD-TYPE 332  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED     14    1
  RALGAPB WILD-TYPE  332   28
   clus
vv  RALGAPB MUTATED RALGAPB WILD-TYPE
  0              14               332
  1               1                28
[1] 2 2
[1] FALSE
D449V7, binary
                   cls
clus                  0   1
  RALGAPB MUTATED    10   7
  RALGAPB WILD-TYPE 135 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED     10    7
  RALGAPB WILD-TYPE  135  241
        clus
vv       RALGAPB MUTATED RALGAPB WILD-TYPE
  FEMALE              10               135
  MALE                 7               241
[1] 2 2
[1] FALSE
D449V8, binary
                   cls
clus                  0   1
  RALGAPB MUTATED    13   1
  RALGAPB WILD-TYPE 279  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED     13    1
  RALGAPB WILD-TYPE  279   58
     clus
vv    RALGAPB MUTATED RALGAPB WILD-TYPE
  NO               13               279
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RALGAPB MUTATED                                          0
  RALGAPB WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RALGAPB MUTATED                                       2
  RALGAPB WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RALGAPB MUTATED                                                        9
  RALGAPB WILD-TYPE                                                    149
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RALGAPB MUTATED                                                   0
  RALGAPB WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RALGAPB MUTATED                                                                   1
  RALGAPB WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RALGAPB MUTATED                                                    0
  RALGAPB WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RALGAPB MUTATED                                                  5
  RALGAPB WILD-TYPE                                               56
D449V9, multiclass
                                                                   clus
vv                                                                  RALGAPB MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                5
                                                                   clus
vv                                                                  RALGAPB WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RALGAPB MUTATED    13   0   0   4
  RALGAPB WILD-TYPE 298  14  15  20
D449V10, multiclass
    clus
vv   RALGAPB MUTATED RALGAPB WILD-TYPE
  R0              13               298
  R1               0                14
  R2               0                15
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D449V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  RALGAPB MUTATED       6                         0
  RALGAPB WILD-TYPE    81                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RALGAPB MUTATED                                           0    10
  RALGAPB WILD-TYPE                                         1   233
D449V12, multiclass
                                           clus
vv                                          RALGAPB MUTATED RALGAPB WILD-TYPE
  ASIAN                                                   6                81
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D449V13, binary
                   cls
clus                  0   1
  RALGAPB MUTATED     0  16
  RALGAPB WILD-TYPE   4 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED      0   16
  RALGAPB WILD-TYPE    4  294
                        clus
vv                       RALGAPB MUTATED RALGAPB WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              16               294
[1] 2 2
[1] FALSE

Clustering(450) Variable = CRYGA MUTATION ANALYSIS
D450V1, survival
                 sevent
clus2               0   1
  CRYGA MUTATED     8   3
  CRYGA WILD-TYPE 222 136
  CRYGA MUTATED CRYGA WILD-TYPE 
             11             358 
  CRYGA MUTATED CRYGA WILD-TYPE 
              3             136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  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           14.22 
[1] "0.1 - 74.5 (16.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D450V2, 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       2       15       39       30        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CRYGA MUTATED           0          1          0          2        3
  CRYGA WILD-TYPE         3         69         53         30       35
D450V3, multiclass
            clus
vv           CRYGA MUTATED CRYGA WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CRYGA MUTATED     0   1   4   6
  CRYGA WILD-TYPE  22  91 169  91
D450V4, multiclass
    clus
vv   CRYGA MUTATED CRYGA WILD-TYPE
  T1             0              22
  T2             1              91
  T3             4             169
  T4             6              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
  CRYGA MUTATED     4   4   2   1
  CRYGA WILD-TYPE 114 100  75  76
D450V5, multiclass
    clus
vv   CRYGA MUTATED CRYGA WILD-TYPE
  N0             4             114
  N1             4             100
  N2             2              75
  N3             1              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"
D450V6, binary
                 cls
clus                0   1
  CRYGA MUTATED     9   2
  CRYGA WILD-TYPE 337  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      9    2
  CRYGA WILD-TYPE  337   27
   clus
vv  CRYGA MUTATED CRYGA WILD-TYPE
  0             9             337
  1             2              27
[1] 2 2
[1] FALSE
D450V7, binary
                 cls
clus                0   1
  CRYGA MUTATED     4   7
  CRYGA WILD-TYPE 141 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      4    7
  CRYGA WILD-TYPE  141  241
        clus
vv       CRYGA MUTATED CRYGA WILD-TYPE
  FEMALE             4             141
  MALE               7             241
[1] 2 2
[1] FALSE
D450V8, binary
                 cls
clus                0   1
  CRYGA MUTATED    10   0
  CRYGA WILD-TYPE 282  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED     10    0
  CRYGA WILD-TYPE  282   59
     clus
vv    CRYGA MUTATED CRYGA WILD-TYPE
  NO             10             282
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CRYGA MUTATED                                          0
  CRYGA WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CRYGA MUTATED                                       4
  CRYGA WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CRYGA MUTATED                                                        3
  CRYGA WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CRYGA MUTATED                                                   0
  CRYGA WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CRYGA MUTATED                                                                   2
  CRYGA WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CRYGA MUTATED                                                    0
  CRYGA WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CRYGA MUTATED                                                  2
  CRYGA WILD-TYPE                                               59
D450V9, multiclass
                                                                   clus
vv                                                                  CRYGA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  CRYGA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CRYGA MUTATED    10   0   0   0
  CRYGA WILD-TYPE 301  14  15  24
D450V10, multiclass
    clus
vv   CRYGA MUTATED CRYGA WILD-TYPE
  R0            10             301
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D450V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CRYGA MUTATED       5                         0
  CRYGA WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CRYGA MUTATED                                           0     5
  CRYGA WILD-TYPE                                         1   238
D450V12, multiclass
                                           clus
vv                                          CRYGA MUTATED CRYGA WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D450V13, binary
                 cls
clus                0   1
  CRYGA MUTATED     1   9
  CRYGA WILD-TYPE   3 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      1    9
  CRYGA WILD-TYPE    3  301
                        clus
vv                       CRYGA MUTATED CRYGA WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(451) Variable = CROT MUTATION ANALYSIS
D451V1, survival
                sevent
clus2              0   1
  CROT MUTATED    11   3
  CROT WILD-TYPE 219 136
  CROT MUTATED CROT WILD-TYPE 
            14            355 
  CROT MUTATED CROT WILD-TYPE 
             3            136 
$`CROT MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8589 TCGA-BR-8680 
        6.97        34.68        32.25         4.31        27.12        31.96 
TCGA-CD-8529 TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-A6EZ TCGA-HU-8602 TCGA-HU-A4GU 
       12.30         6.58         6.02        20.32        22.32         6.58 
TCGA-HU-A4H8 TCGA-VQ-A8P2 
       14.07        38.14 

$`CROT WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  CROT MUTATED CROT WILD-TYPE 
          4.31           0.00 
  CROT MUTATED CROT WILD-TYPE 
         38.14         122.30 
  CROT MUTATED CROT WILD-TYPE 
        17.195         14.270 
[1] "4.3 - 38.1 (17.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.9"
D451V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CROT MUTATED         0        0        2        0         2         3
  CROT WILD-TYPE       2       15       38       30        35        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CROT MUTATED           0          3          1          0        3
  CROT WILD-TYPE         3         67         52         32       35
D451V3, multiclass
            clus
vv           CROT MUTATED CROT WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CROT MUTATED     1   1   5   7
  CROT WILD-TYPE  21  91 168  90
D451V4, multiclass
    clus
vv   CROT MUTATED CROT WILD-TYPE
  T1            1             21
  T2            1             91
  T3            5            168
  T4            7             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
  CROT MUTATED     6   7   2   0
  CROT WILD-TYPE 112  97  75  77
D451V5, multiclass
    clus
vv   CROT MUTATED CROT WILD-TYPE
  N0            6            112
  N1            7             97
  N2            2             75
  N3            0             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"
D451V6, binary
                cls
clus               0   1
  CROT MUTATED    12   2
  CROT WILD-TYPE 334  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED     12    2
  CROT WILD-TYPE  334   27
   clus
vv  CROT MUTATED CROT WILD-TYPE
  0           12            334
  1            2             27
[1] 2 2
[1] FALSE
D451V7, binary
                cls
clus               0   1
  CROT MUTATED     5  10
  CROT WILD-TYPE 140 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED      5   10
  CROT WILD-TYPE  140  238
        clus
vv       CROT MUTATED CROT WILD-TYPE
  FEMALE            5            140
  MALE             10            238
[1] 2 2
[1] FALSE
D451V8, binary
                cls
clus               0   1
  CROT MUTATED    12   2
  CROT WILD-TYPE 280  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED     12    2
  CROT WILD-TYPE  280   57
     clus
vv    CROT MUTATED CROT WILD-TYPE
  NO            12            280
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CROT MUTATED                                          0
  CROT WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CROT MUTATED                                       3
  CROT WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CROT MUTATED                                                        6
  CROT WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CROT MUTATED                                                   2
  CROT WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CROT MUTATED                                                                   2
  CROT WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CROT MUTATED                                                    0
  CROT WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CROT MUTATED                                                  2
  CROT WILD-TYPE                                               59
D451V9, multiclass
                                                                   clus
vv                                                                  CROT MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  CROT WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CROT MUTATED    12   0   0   2
  CROT WILD-TYPE 299  14  15  22
D451V10, multiclass
    clus
vv   CROT MUTATED CROT WILD-TYPE
  R0           12            299
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D451V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CROT MUTATED       6                         0
  CROT WILD-TYPE    81                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CROT MUTATED                                           0     8
  CROT WILD-TYPE                                         1   235
D451V12, multiclass
                                           clus
vv                                          CROT MUTATED CROT WILD-TYPE
  ASIAN                                                6             81
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D451V13, binary
                cls
clus               0   1
  CROT MUTATED     0  13
  CROT WILD-TYPE   4 297
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED      0   13
  CROT WILD-TYPE    4  297
                        clus
vv                       CROT MUTATED CROT WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           13            297
[1] 2 2
[1] FALSE

Clustering(452) Variable = MAP7D3 MUTATION ANALYSIS
D452V1, survival
                  sevent
clus2                0   1
  MAP7D3 MUTATED    11   3
  MAP7D3 WILD-TYPE 219 136
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              14              355 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
               3              136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       14.43        11.44         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-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-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-D7-6524 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-A8DV 
       35.61        19.04         5.79         0.92        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 

  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            14.07 
[1] "0.3 - 32.8 (19.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2"  
D452V2, 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       2       15       36       30        36        48
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP7D3 MUTATED           0          2          2          2        2
  MAP7D3 WILD-TYPE         3         68         51         30       36
D452V3, multiclass
            clus
vv           MAP7D3 MUTATED MAP7D3 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                4               36
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               4               48
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              2               51
  STAGE IIIC              2               30
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP7D3 MUTATED     0   4   3  10
  MAP7D3 WILD-TYPE  22  88 170  87
D452V4, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  T1              0               22
  T2              4               88
  T3              3              170
  T4             10               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
  MAP7D3 MUTATED    10   1   4   2
  MAP7D3 WILD-TYPE 108 103  73  75
D452V5, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  N0             10              108
  N1              1              103
  N2              4               73
  N3              2               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"
D452V6, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    17   1
  MAP7D3 WILD-TYPE 329  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     17    1
  MAP7D3 WILD-TYPE  329   28
   clus
vv  MAP7D3 MUTATED MAP7D3 WILD-TYPE
  0             17              329
  1              1               28
[1] 2 2
[1] FALSE
D452V7, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    12   6
  MAP7D3 WILD-TYPE 133 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     12    6
  MAP7D3 WILD-TYPE  133  242
        clus
vv       MAP7D3 MUTATED MAP7D3 WILD-TYPE
  FEMALE             12              133
  MALE                6              242
[1] 2 2
[1] FALSE
D452V8, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    13   0
  MAP7D3 WILD-TYPE 279  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     13    0
  MAP7D3 WILD-TYPE  279   59
     clus
vv    MAP7D3 MUTATED MAP7D3 WILD-TYPE
  NO              13              279
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MAP7D3 MUTATED                                          0
  MAP7D3 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MAP7D3 MUTATED                                       3
  MAP7D3 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP7D3 MUTATED                                                       11
  MAP7D3 WILD-TYPE                                                    147
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MAP7D3 MUTATED                                                   0
  MAP7D3 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP7D3 MUTATED                                                                   2
  MAP7D3 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MAP7D3 MUTATED                                                    0
  MAP7D3 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MAP7D3 MUTATED                                                  2
  MAP7D3 WILD-TYPE                                               59
D452V9, multiclass
                                                                   clus
vv                                                                  MAP7D3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  MAP7D3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP7D3 MUTATED    14   0   0   3
  MAP7D3 WILD-TYPE 297  14  15  21
D452V10, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  R0             14              297
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D452V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAP7D3 MUTATED       4                         0
  MAP7D3 WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP7D3 MUTATED                                           0    13
  MAP7D3 WILD-TYPE                                         1   230
D452V12, multiclass
                                           clus
vv                                          MAP7D3 MUTATED MAP7D3 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D452V13, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED     0  16
  MAP7D3 WILD-TYPE   4 294
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED      0   16
  MAP7D3 WILD-TYPE    4  294
                        clus
vv                       MAP7D3 MUTATED MAP7D3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             16              294
[1] 2 2
[1] FALSE

Clustering(453) Variable = ZFC3H1 MUTATION ANALYSIS
D453V1, survival
                  sevent
clus2                0   1
  ZFC3H1 MUTATED    11   3
  ZFC3H1 WILD-TYPE 219 136
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              14              355 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
               3              136 
$`ZFC3H1 MUTATED`
TCGA-CG-4475 TCGA-BR-4187 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8680 
       22.98         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-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        26.70        11.70        19.56        11.01         9.47 
TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.44         6.61         6.97         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-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-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-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-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-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-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 

  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
            1.02             0.00 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
           38.14           122.30 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
          21.615           14.170 
[1] "1.0 - 38.1 (21.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2"  
D453V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZFC3H1 MUTATED         0        0        1        1         4         1
  ZFC3H1 WILD-TYPE       2       15       39       29        33        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFC3H1 MUTATED           0          3          0          2        3
  ZFC3H1 WILD-TYPE         3         67         53         30       35
D453V3, multiclass
            clus
vv           ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               4               33
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZFC3H1 MUTATED     0   2   6   7
  ZFC3H1 WILD-TYPE  22  90 167  90
D453V4, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              6              167
  T4              7               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
  ZFC3H1 MUTATED     6   5   4   0
  ZFC3H1 WILD-TYPE 112  99  73  77
D453V5, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  N0              6              112
  N1              5               99
  N2              4               73
  N3              0               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"
D453V6, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    14   2
  ZFC3H1 WILD-TYPE 332  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     14    2
  ZFC3H1 WILD-TYPE  332   27
   clus
vv  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  0             14              332
  1              2               27
[1] 2 2
[1] FALSE
D453V7, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED     6  10
  ZFC3H1 WILD-TYPE 139 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED      6   10
  ZFC3H1 WILD-TYPE  139  238
        clus
vv       ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  FEMALE              6              139
  MALE               10              238
[1] 2 2
[1] FALSE
D453V8, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    12   2
  ZFC3H1 WILD-TYPE 280  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     12    2
  ZFC3H1 WILD-TYPE  280   57
     clus
vv    ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  NO              12              280
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZFC3H1 MUTATED                                          0
  ZFC3H1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZFC3H1 MUTATED                                       3
  ZFC3H1 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZFC3H1 MUTATED                                                        8
  ZFC3H1 WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZFC3H1 MUTATED                                                   1
  ZFC3H1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZFC3H1 MUTATED                                                                   1
  ZFC3H1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZFC3H1 MUTATED                                                    0
  ZFC3H1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZFC3H1 MUTATED                                                  2
  ZFC3H1 WILD-TYPE                                               59
D453V9, multiclass
                                                                   clus
vv                                                                  ZFC3H1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  ZFC3H1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZFC3H1 MUTATED    12   0   1   2
  ZFC3H1 WILD-TYPE 299  14  14  22
D453V10, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  R0             12              299
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D453V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZFC3H1 MUTATED       5                         0
  ZFC3H1 WILD-TYPE    82                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZFC3H1 MUTATED                                           0     8
  ZFC3H1 WILD-TYPE                                         1   235
D453V12, multiclass
                                           clus
vv                                          ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D453V13, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED     0  12
  ZFC3H1 WILD-TYPE   4 298
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED      0   12
  ZFC3H1 WILD-TYPE    4  298
                        clus
vv                       ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             12              298
[1] 2 2
[1] FALSE

Clustering(454) Variable = NCOA7 MUTATION ANALYSIS
D454V1, survival
                 sevent
clus2               0   1
  NCOA7 MUTATED    10   4
  NCOA7 WILD-TYPE 220 135
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             14             355 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              4             135 
$`NCOA7 MUTATED`
TCGA-CG-5727 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7704 TCGA-BR-8077 
       79.07         6.97        30.90        34.68        35.24         0.69 
TCGA-BR-8382 TCGA-CG-4305 TCGA-CG-5728 TCGA-D7-A6EY TCGA-HF-A5NB TCGA-HU-A4H4 
       25.05        15.95        65.10        11.44        30.51        23.84 
TCGA-HU-A4H8 TCGA-R5-A7ZI 
       14.07        74.53 

$`NCOA7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-D7-8572 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-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-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-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 

  NCOA7 MUTATED NCOA7 WILD-TYPE 
           0.69            0.00 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
          79.07          122.30 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
          27.78           14.04 
[1] "0.7 - 79.1 (27.8)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "2.1"
D454V2, 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       2       15       38       27        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NCOA7 MUTATED           0          1          2          2        1
  NCOA7 WILD-TYPE         3         69         51         30       37
D454V3, multiclass
            clus
vv           NCOA7 MUTATED NCOA7 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               3              27
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NCOA7 MUTATED     1   4   6   4
  NCOA7 WILD-TYPE  21  88 167  93
D454V4, multiclass
    clus
vv   NCOA7 MUTATED NCOA7 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             6             167
  T4             4              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
  NCOA7 MUTATED     5   6   1   3
  NCOA7 WILD-TYPE 113  98  76  74
D454V5, multiclass
    clus
vv   NCOA7 MUTATED NCOA7 WILD-TYPE
  N0             5             113
  N1             6              98
  N2             1              76
  N3             3              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"
D454V6, binary
                 cls
clus                0   1
  NCOA7 MUTATED    14   1
  NCOA7 WILD-TYPE 332  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     14    1
  NCOA7 WILD-TYPE  332   28
   clus
vv  NCOA7 MUTATED NCOA7 WILD-TYPE
  0            14             332
  1             1              28
[1] 2 2
[1] FALSE
D454V7, binary
                 cls
clus                0   1
  NCOA7 MUTATED    11   5
  NCOA7 WILD-TYPE 134 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     11    5
  NCOA7 WILD-TYPE  134  243
        clus
vv       NCOA7 MUTATED NCOA7 WILD-TYPE
  FEMALE            11             134
  MALE               5             243
[1] 2 2
[1] FALSE
D454V8, binary
                 cls
clus                0   1
  NCOA7 MUTATED    11   1
  NCOA7 WILD-TYPE 281  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     11    1
  NCOA7 WILD-TYPE  281   58
     clus
vv    NCOA7 MUTATED NCOA7 WILD-TYPE
  NO             11             281
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NCOA7 MUTATED                                          0
  NCOA7 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NCOA7 MUTATED                                       1
  NCOA7 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NCOA7 MUTATED                                                        7
  NCOA7 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NCOA7 MUTATED                                                   1
  NCOA7 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NCOA7 MUTATED                                                                   4
  NCOA7 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NCOA7 MUTATED                                                    0
  NCOA7 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NCOA7 MUTATED                                                  3
  NCOA7 WILD-TYPE                                               58
D454V9, multiclass
                                                                   clus
vv                                                                  NCOA7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  NCOA7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NCOA7 MUTATED    12   1   0   3
  NCOA7 WILD-TYPE 299  13  15  21
D454V10, multiclass
    clus
vv   NCOA7 MUTATED NCOA7 WILD-TYPE
  R0            12             299
  R1             1              13
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D454V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NCOA7 MUTATED       2                         0
  NCOA7 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NCOA7 MUTATED                                           0    10
  NCOA7 WILD-TYPE                                         1   233
D454V12, multiclass
                                           clus
vv                                          NCOA7 MUTATED NCOA7 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D454V13, binary
                 cls
clus                0   1
  NCOA7 MUTATED     1  11
  NCOA7 WILD-TYPE   3 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED      1   11
  NCOA7 WILD-TYPE    3  299
                        clus
vv                       NCOA7 MUTATED NCOA7 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(455) Variable = USP13 MUTATION ANALYSIS
D455V1, survival
                 sevent
clus2               0   1
  USP13 MUTATED     6   5
  USP13 WILD-TYPE 224 134
  USP13 MUTATED USP13 WILD-TYPE 
             11             358 
  USP13 MUTATED USP13 WILD-TYPE 
              5             134 
$`USP13 MUTATED`
TCGA-BR-4184 TCGA-BR-8078 TCGA-BR-8382 TCGA-BR-8591 TCGA-CD-5801 TCGA-CD-8527 
        6.97        29.59        25.05        28.14        13.18         7.17 
TCGA-CG-4305 TCGA-CG-4469 TCGA-R5-A7ZI TCGA-VQ-A8P2 TCGA-VQ-AA68 
       15.95         7.07        74.53        38.14        43.66 

$`USP13 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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 

  USP13 MUTATED USP13 WILD-TYPE 
           6.97            0.00 
  USP13 MUTATED USP13 WILD-TYPE 
          74.53          122.30 
  USP13 MUTATED USP13 WILD-TYPE 
          25.05           14.12 
[1] "7.0 - 74.5 (25.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D455V2, 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       2       15       39       28        37        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  USP13 MUTATED           0          3          0          3        2
  USP13 WILD-TYPE         3         67         53         29       36
D455V3, multiclass
            clus
vv           USP13 MUTATED USP13 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              0              37
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP13 MUTATED     0   3   3   6
  USP13 WILD-TYPE  22  89 170  91
D455V4, multiclass
    clus
vv   USP13 MUTATED USP13 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             3             170
  T4             6              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
  USP13 MUTATED     2   6   0   4
  USP13 WILD-TYPE 116  98  77  73
D455V5, multiclass
    clus
vv   USP13 MUTATED USP13 WILD-TYPE
  N0             2             116
  N1             6              98
  N2             0              77
  N3             4              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"
D455V6, binary
                 cls
clus                0   1
  USP13 MUTATED    10   1
  USP13 WILD-TYPE 336  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP13 MUTATED     10    1
  USP13 WILD-TYPE  336   28
   clus
vv  USP13 MUTATED USP13 WILD-TYPE
  0            10             336
  1             1              28
[1] 2 2
[1] FALSE
D455V7, binary
                 cls
clus                0   1
  USP13 MUTATED     5   7
  USP13 WILD-TYPE 140 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP13 MUTATED      5    7
  USP13 WILD-TYPE  140  241
        clus
vv       USP13 MUTATED USP13 WILD-TYPE
  FEMALE             5             140
  MALE               7             241
[1] 2 2
[1] FALSE
D455V8, binary
                 cls
clus                0   1
  USP13 MUTATED     8   2
  USP13 WILD-TYPE 284  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP13 MUTATED      8    2
  USP13 WILD-TYPE  284   57
     clus
vv    USP13 MUTATED USP13 WILD-TYPE
  NO              8             284
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  USP13 MUTATED                                          0
  USP13 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  USP13 MUTATED                                       1
  USP13 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  USP13 MUTATED                                                        6
  USP13 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  USP13 MUTATED                                                   1
  USP13 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  USP13 MUTATED                                                                   3
  USP13 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  USP13 MUTATED                                                    0
  USP13 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  USP13 MUTATED                                                  1
  USP13 WILD-TYPE                                               60
D455V9, multiclass
                                                                   clus
vv                                                                  USP13 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  USP13 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP13 MUTATED    10   1   0   1
  USP13 WILD-TYPE 301  13  15  23
D455V10, multiclass
    clus
vv   USP13 MUTATED USP13 WILD-TYPE
  R0            10             301
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D455V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  USP13 MUTATED       2                         0
  USP13 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP13 MUTATED                                           0     7
  USP13 WILD-TYPE                                         1   236
D455V12, multiclass
                                           clus
vv                                          USP13 MUTATED USP13 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D455V13, binary
                 cls
clus                0   1
  USP13 MUTATED     1   6
  USP13 WILD-TYPE   3 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP13 MUTATED      1    6
  USP13 WILD-TYPE    3  304
                        clus
vv                       USP13 MUTATED USP13 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(456) Variable = ICAM4 MUTATION ANALYSIS
D456V1, survival
                 sevent
clus2               0   1
  ICAM4 MUTATED     4   3
  ICAM4 WILD-TYPE 226 136
  ICAM4 MUTATED ICAM4 WILD-TYPE 
              7             362 
  ICAM4 MUTATED ICAM4 WILD-TYPE 
              3             136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  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           14.22 
[1] "0.1 - 105.1 (19.7)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D456V2, 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       2       15       39       29        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ICAM4 MUTATED           0          1          0          2        2
  ICAM4 WILD-TYPE         3         69         53         30       36
D456V3, multiclass
            clus
vv           ICAM4 MUTATED ICAM4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ICAM4 MUTATED     0   2   3   3
  ICAM4 WILD-TYPE  22  90 170  94
D456V4, multiclass
    clus
vv   ICAM4 MUTATED ICAM4 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             3             170
  T4             3              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
  ICAM4 MUTATED     2   1   3   2
  ICAM4 WILD-TYPE 116 103  74  75
D456V5, multiclass
    clus
vv   ICAM4 MUTATED ICAM4 WILD-TYPE
  N0             2             116
  N1             1             103
  N2             3              74
  N3             2              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"
D456V6, binary
                 cls
clus                0   1
  ICAM4 MUTATED     6   2
  ICAM4 WILD-TYPE 340  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM4 MUTATED      6    2
  ICAM4 WILD-TYPE  340   27
   clus
vv  ICAM4 MUTATED ICAM4 WILD-TYPE
  0             6             340
  1             2              27
[1] 2 2
[1] FALSE
D456V7, binary
                 cls
clus                0   1
  ICAM4 MUTATED     3   5
  ICAM4 WILD-TYPE 142 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM4 MUTATED      3    5
  ICAM4 WILD-TYPE  142  243
        clus
vv       ICAM4 MUTATED ICAM4 WILD-TYPE
  FEMALE             3             142
  MALE               5             243
[1] 2 2
[1] FALSE
D456V8, binary
                 cls
clus                0   1
  ICAM4 MUTATED     5   0
  ICAM4 WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM4 MUTATED      5    0
  ICAM4 WILD-TYPE  287   59
     clus
vv    ICAM4 MUTATED ICAM4 WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ICAM4 MUTATED                                          0
  ICAM4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ICAM4 MUTATED                                       1
  ICAM4 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ICAM4 MUTATED                                                        3
  ICAM4 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ICAM4 MUTATED                                                   0
  ICAM4 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ICAM4 MUTATED                                                                   1
  ICAM4 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ICAM4 MUTATED                                                    0
  ICAM4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ICAM4 MUTATED                                                  3
  ICAM4 WILD-TYPE                                               58
D456V9, multiclass
                                                                   clus
vv                                                                  ICAM4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  ICAM4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ICAM4 MUTATED     6   0   2   0
  ICAM4 WILD-TYPE 305  14  13  24
D456V10, multiclass
    clus
vv   ICAM4 MUTATED ICAM4 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             2              13
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D456V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ICAM4 MUTATED       3                         0
  ICAM4 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ICAM4 MUTATED                                           0     2
  ICAM4 WILD-TYPE                                         1   241
D456V12, multiclass
                                           clus
vv                                          ICAM4 MUTATED ICAM4 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D456V13, binary
                 cls
clus                0   1
  ICAM4 MUTATED     0   5
  ICAM4 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM4 MUTATED      0    5
  ICAM4 WILD-TYPE    4  305
                        clus
vv                       ICAM4 MUTATED ICAM4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(457) Variable = USP15 MUTATION ANALYSIS
D457V1, survival
                 sevent
clus2               0   1
  USP15 MUTATED     6   0
  USP15 WILD-TYPE 224 139
  USP15 MUTATED USP15 WILD-TYPE 
              6             363 
  USP15 MUTATED USP15 WILD-TYPE 
              0             139 
$`USP15 MUTATED`
TCGA-B7-5816 TCGA-BR-8081 TCGA-CG-5721 TCGA-CG-5723 TCGA-HF-A5NB TCGA-HU-A4GT 
       26.70        32.25         6.02       105.07        30.51         6.51 

$`USP15 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  USP15 MUTATED USP15 WILD-TYPE 
           6.02            0.00 
  USP15 MUTATED USP15 WILD-TYPE 
         105.07          122.30 
  USP15 MUTATED USP15 WILD-TYPE 
         28.605          14.170 
[1] "6.0 - 105.1 (28.6)" "0.0 - 122.3 (14.2)"
[1] "hr="     "9400000"
D457V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP15 MUTATED         0        0        1        1         1         2
  USP15 WILD-TYPE       2       15       39       29        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  USP15 MUTATED           0          0          0          1        1
  USP15 WILD-TYPE         3         70         53         31       37
D457V3, multiclass
            clus
vv           USP15 MUTATED USP15 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP15 MUTATED     0   2   1   4
  USP15 WILD-TYPE  22  90 172  93
D457V4, multiclass
    clus
vv   USP15 MUTATED USP15 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             1             172
  T4             4              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
  USP15 MUTATED     4   2   0   1
  USP15 WILD-TYPE 114 102  77  76
D457V5, multiclass
    clus
vv   USP15 MUTATED USP15 WILD-TYPE
  N0             4             114
  N1             2             102
  N2             0              77
  N3             1              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"
D457V6, binary
                 cls
clus                0   1
  USP15 MUTATED     7   0
  USP15 WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP15 MUTATED      7    0
  USP15 WILD-TYPE  339   29
   clus
vv  USP15 MUTATED USP15 WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D457V7, binary
                 cls
clus                0   1
  USP15 MUTATED     4   3
  USP15 WILD-TYPE 141 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP15 MUTATED      4    3
  USP15 WILD-TYPE  141  245
        clus
vv       USP15 MUTATED USP15 WILD-TYPE
  FEMALE             4             141
  MALE               3             245
[1] 2 2
[1] FALSE
D457V8, binary
                 cls
clus                0   1
  USP15 MUTATED     5   1
  USP15 WILD-TYPE 287  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP15 MUTATED      5    1
  USP15 WILD-TYPE  287   58
     clus
vv    USP15 MUTATED USP15 WILD-TYPE
  NO              5             287
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  USP15 MUTATED                                          0
  USP15 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  USP15 MUTATED                                       1
  USP15 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  USP15 MUTATED                                                        2
  USP15 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  USP15 MUTATED                                                   1
  USP15 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  USP15 MUTATED                                                                   2
  USP15 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  USP15 MUTATED                                                    0
  USP15 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  USP15 MUTATED                                                  1
  USP15 WILD-TYPE                                               60
D457V9, multiclass
                                                                   clus
vv                                                                  USP15 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  USP15 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP15 MUTATED     6   1   0   0
  USP15 WILD-TYPE 305  13  15  24
D457V10, multiclass
    clus
vv   USP15 MUTATED USP15 WILD-TYPE
  R0             6             305
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D457V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  USP15 MUTATED       1                         0
  USP15 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP15 MUTATED                                           0     2
  USP15 WILD-TYPE                                         1   241
D457V12, multiclass
                                           clus
vv                                          USP15 MUTATED USP15 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D457V13, binary
                 cls
clus                0   1
  USP15 MUTATED     0   3
  USP15 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP15 MUTATED      0    3
  USP15 WILD-TYPE    4  307
                        clus
vv                       USP15 MUTATED USP15 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(458) Variable = FAM113B MUTATION ANALYSIS
D458V1, survival
                   sevent
clus2                 0   1
  FAM113B MUTATED     8   5
  FAM113B WILD-TYPE 222 134
  FAM113B MUTATED FAM113B WILD-TYPE 
               13               356 
  FAM113B MUTATED FAM113B WILD-TYPE 
                5               134 
$`FAM113B MUTATED`
TCGA-BR-4201 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8680 
       30.90        35.84        14.43        31.10        31.27        31.96 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-A6EY TCGA-F1-6874 TCGA-FP-A4BE 
        6.02       105.07        21.07        11.44        14.47        11.08 
TCGA-IN-A6RL 
       13.35 

$`FAM113B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-F1-6875 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-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        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 

  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             14.07 
[1] "6.0 - 105.1 (21.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D458V2, 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       2       15       38       29        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM113B MUTATED           1          3          1          2        2
  FAM113B WILD-TYPE         2         67         52         30       36
D458V3, multiclass
            clus
vv           FAM113B MUTATED FAM113B WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                1                 2
  STAGE IIIA               3                67
  STAGE IIIB               1                52
  STAGE IIIC               2                30
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM113B MUTATED     0   6   2   7
  FAM113B WILD-TYPE  22  86 171  90
D458V4, multiclass
    clus
vv   FAM113B MUTATED FAM113B WILD-TYPE
  T1               0                22
  T2               6                86
  T3               2               171
  T4               7                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
  FAM113B MUTATED     5   4   3   2
  FAM113B WILD-TYPE 113 100  74  75
D458V5, multiclass
    clus
vv   FAM113B MUTATED FAM113B WILD-TYPE
  N0               5               113
  N1               4               100
  N2               3                74
  N3               2                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"
D458V6, binary
                   cls
clus                  0   1
  FAM113B MUTATED    14   1
  FAM113B WILD-TYPE 332  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113B MUTATED     14    1
  FAM113B WILD-TYPE  332   28
   clus
vv  FAM113B MUTATED FAM113B WILD-TYPE
  0              14               332
  1               1                28
[1] 2 2
[1] FALSE
D458V7, binary
                   cls
clus                  0   1
  FAM113B MUTATED     6   9
  FAM113B WILD-TYPE 139 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113B MUTATED      6    9
  FAM113B WILD-TYPE  139  239
        clus
vv       FAM113B MUTATED FAM113B WILD-TYPE
  FEMALE               6               139
  MALE                 9               239
[1] 2 2
[1] FALSE
D458V8, binary
                   cls
clus                  0   1
  FAM113B MUTATED    13   1
  FAM113B WILD-TYPE 279  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113B MUTATED     13    1
  FAM113B WILD-TYPE  279   58
     clus
vv    FAM113B MUTATED FAM113B WILD-TYPE
  NO               13               279
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM113B MUTATED                                          0
  FAM113B WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM113B MUTATED                                       0
  FAM113B WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM113B MUTATED                                                        8
  FAM113B WILD-TYPE                                                    150
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM113B MUTATED                                                   0
  FAM113B WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM113B MUTATED                                                                   5
  FAM113B WILD-TYPE                                                                63
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM113B MUTATED                                                    0
  FAM113B WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM113B MUTATED                                                  2
  FAM113B WILD-TYPE                                               59
D458V9, multiclass
                                                                   clus
vv                                                                  FAM113B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  FAM113B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM113B MUTATED    13   0   0   2
  FAM113B WILD-TYPE 298  14  15  22
D458V10, multiclass
    clus
vv   FAM113B MUTATED FAM113B WILD-TYPE
  R0              13               298
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D458V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM113B MUTATED       1                         1
  FAM113B WILD-TYPE    86                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM113B MUTATED                                           0    10
  FAM113B WILD-TYPE                                         1   233
D458V12, multiclass
                                           clus
vv                                          FAM113B MUTATED FAM113B WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D458V13, binary
                   cls
clus                  0   1
  FAM113B MUTATED     0  12
  FAM113B WILD-TYPE   4 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113B MUTATED      0   12
  FAM113B WILD-TYPE    4  298
                        clus
vv                       FAM113B MUTATED FAM113B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              12               298
[1] 2 2
[1] FALSE

Clustering(459) Variable = PCCA MUTATION ANALYSIS
D459V1, survival
                sevent
clus2              0   1
  PCCA MUTATED     8   3
  PCCA WILD-TYPE 222 136
  PCCA MUTATED PCCA WILD-TYPE 
            11            358 
  PCCA MUTATED PCCA WILD-TYPE 
             3            136 
$`PCCA MUTATED`
TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8368 TCGA-CG-5721 
        9.44         6.97        34.68        29.59         4.31         6.02 
TCGA-CG-5726 TCGA-CG-5733 TCGA-HU-A4H4 TCGA-SW-A7EA TCGA-VQ-A8P2 
       28.96        21.07        23.84        19.04        38.14 

$`PCCA WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        9.47         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-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-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-D7-6528 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-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 

  PCCA MUTATED PCCA WILD-TYPE 
          4.31           0.00 
  PCCA MUTATED PCCA WILD-TYPE 
         38.14         122.30 
  PCCA MUTATED PCCA WILD-TYPE 
         21.07          14.12 
[1] "4.3 - 38.1 (21.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D459V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCCA MUTATED         0        1        2        0         1         3
  PCCA WILD-TYPE       2       14       38       30        36        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCCA MUTATED           0          4          0          0        1
  PCCA WILD-TYPE         3         66         53         32       37
D459V3, multiclass
            clus
vv           PCCA MUTATED PCCA WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            4             66
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PCCA MUTATED     1   4   2   5
  PCCA WILD-TYPE  21  88 171  92
D459V4, multiclass
    clus
vv   PCCA MUTATED PCCA WILD-TYPE
  T1            1             21
  T2            4             88
  T3            2            171
  T4            5             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
  PCCA MUTATED     6   3   2   0
  PCCA WILD-TYPE 112 101  75  77
D459V5, multiclass
    clus
vv   PCCA MUTATED PCCA WILD-TYPE
  N0            6            112
  N1            3            101
  N2            2             75
  N3            0             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"
D459V6, binary
                cls
clus               0   1
  PCCA MUTATED    11   0
  PCCA WILD-TYPE 335  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCCA MUTATED     11    0
  PCCA WILD-TYPE  335   29
   clus
vv  PCCA MUTATED PCCA WILD-TYPE
  0           11            335
  1            0             29
[1] 2 2
[1] FALSE
D459V7, binary
                cls
clus               0   1
  PCCA MUTATED     7   5
  PCCA WILD-TYPE 138 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCCA MUTATED      7    5
  PCCA WILD-TYPE  138  243
        clus
vv       PCCA MUTATED PCCA WILD-TYPE
  FEMALE            7            138
  MALE              5            243
[1] 2 2
[1] FALSE
D459V8, binary
                cls
clus               0   1
  PCCA MUTATED     9   1
  PCCA WILD-TYPE 283  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCCA MUTATED      9    1
  PCCA WILD-TYPE  283   58
     clus
vv    PCCA MUTATED PCCA WILD-TYPE
  NO             9            283
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PCCA MUTATED                                          0
  PCCA WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PCCA MUTATED                                       1
  PCCA WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PCCA MUTATED                                                        6
  PCCA WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PCCA MUTATED                                                   1
  PCCA WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PCCA MUTATED                                                                   3
  PCCA WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PCCA MUTATED                                                    0
  PCCA WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PCCA MUTATED                                                  1
  PCCA WILD-TYPE                                               60
D459V9, multiclass
                                                                   clus
vv                                                                  PCCA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  PCCA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PCCA MUTATED     9   0   0   2
  PCCA WILD-TYPE 302  14  15  22
D459V10, multiclass
    clus
vv   PCCA MUTATED PCCA WILD-TYPE
  R0            9            302
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D459V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PCCA MUTATED       1                         0
  PCCA WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PCCA MUTATED                                           0     8
  PCCA WILD-TYPE                                         1   235
D459V12, multiclass
                                           clus
vv                                          PCCA MUTATED PCCA WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D459V13, binary
                cls
clus               0   1
  PCCA MUTATED     0   8
  PCCA WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCCA MUTATED      0    8
  PCCA WILD-TYPE    4  302
                        clus
vv                       PCCA MUTATED PCCA WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(460) Variable = P2RX1 MUTATION ANALYSIS
D460V1, survival
                 sevent
clus2               0   1
  P2RX1 MUTATED     4   0
  P2RX1 WILD-TYPE 226 139
  P2RX1 MUTATED P2RX1 WILD-TYPE 
              4             365 
  P2RX1 MUTATED P2RX1 WILD-TYPE 
              0             139 
$`P2RX1 MUTATED`
TCGA-B7-5816 TCGA-CG-5728 TCGA-HU-8602 TCGA-HU-A4G8 
       26.70        65.10        22.32        22.68 

$`P2RX1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  P2RX1 MUTATED P2RX1 WILD-TYPE 
          22.32            0.00 
  P2RX1 MUTATED P2RX1 WILD-TYPE 
           65.1           122.3 
  P2RX1 MUTATED P2RX1 WILD-TYPE 
          24.69           14.07 
[1] "22.3 - 65.1 (24.7)" "0.0 - 122.3 (14.1)"
[1] "hr="     "9200000"
D460V2, 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       2       15       39       30        37        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  P2RX1 MUTATED           0          0          0          0        0
  P2RX1 WILD-TYPE         3         70         53         32       38
D460V3, multiclass
            clus
vv           P2RX1 MUTATED P2RX1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  P2RX1 MUTATED     0   1   1   2
  P2RX1 WILD-TYPE  22  91 172  95
D460V4, multiclass
    clus
vv   P2RX1 MUTATED P2RX1 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             1             172
  T4             2              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
  P2RX1 MUTATED     3   1   0   0
  P2RX1 WILD-TYPE 115 103  77  77
D460V5, multiclass
    clus
vv   P2RX1 MUTATED P2RX1 WILD-TYPE
  N0             3             115
  N1             1             103
  N2             0              77
  N3             0              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"
D460V6, binary
                 cls
clus                0   1
  P2RX1 MUTATED     4   0
  P2RX1 WILD-TYPE 342  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX1 MUTATED      4    0
  P2RX1 WILD-TYPE  342   29
   clus
vv  P2RX1 MUTATED P2RX1 WILD-TYPE
  0             4             342
  1             0              29
[1] 2 2
[1] FALSE
D460V7, binary
                 cls
clus                0   1
  P2RX1 MUTATED     4   0
  P2RX1 WILD-TYPE 141 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX1 MUTATED      4    0
  P2RX1 WILD-TYPE  141  248
        clus
vv       P2RX1 MUTATED P2RX1 WILD-TYPE
  FEMALE             4             141
  MALE               0             248
[1] 2 2
[1] FALSE
D460V8, binary
                 cls
clus                0   1
  P2RX1 MUTATED     3   0
  P2RX1 WILD-TYPE 289  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX1 MUTATED      3    0
  P2RX1 WILD-TYPE  289   59
     clus
vv    P2RX1 MUTATED P2RX1 WILD-TYPE
  NO              3             289
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  P2RX1 MUTATED                                          0
  P2RX1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  P2RX1 MUTATED                                       3
  P2RX1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  P2RX1 MUTATED                                                        0
  P2RX1 WILD-TYPE                                                    158
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  P2RX1 MUTATED                                                   0
  P2RX1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  P2RX1 MUTATED                                                                   1
  P2RX1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  P2RX1 MUTATED                                                    0
  P2RX1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  P2RX1 MUTATED                                                  0
  P2RX1 WILD-TYPE                                               61
D460V9, multiclass
                                                                   clus
vv                                                                  P2RX1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        0
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  P2RX1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        158
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  P2RX1 MUTATED     3   0   0   0
  P2RX1 WILD-TYPE 308  14  15  24
D460V10, multiclass
    clus
vv   P2RX1 MUTATED P2RX1 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D460V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  P2RX1 MUTATED       2                         0
  P2RX1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  P2RX1 MUTATED                                           0     1
  P2RX1 WILD-TYPE                                         1   242
D460V12, multiclass
                                           clus
vv                                          P2RX1 MUTATED P2RX1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 1             242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D460V13, binary
                 cls
clus                0   1
  P2RX1 MUTATED     0   3
  P2RX1 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX1 MUTATED      0    3
  P2RX1 WILD-TYPE    4  307
                        clus
vv                       P2RX1 MUTATED P2RX1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(461) Variable = KIAA0649 MUTATION ANALYSIS
D461V1, survival
                    sevent
clus2                  0   1
  KIAA0649 MUTATED    10   5
  KIAA0649 WILD-TYPE 220 134
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                15                354 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                 5                134 
$`KIAA0649 MUTATED`
TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-6802 TCGA-BR-8080 TCGA-BR-8372 TCGA-BR-8487 
       34.68        19.33        30.90         9.60        31.27         1.12 
TCGA-BR-8591 TCGA-BR-A4QI TCGA-CG-4305 TCGA-CG-5721 TCGA-D7-6818 TCGA-D7-A6EY 
       28.14        21.44        15.95         6.02        12.36        11.44 
TCGA-HU-8602 TCGA-HU-A4G9 TCGA-VQ-A8P2 
       22.32        24.20        38.14 

$`KIAA0649 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-D7-5579 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-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 

  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
              1.12               0.00 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
             38.14             122.30 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
             21.44              14.07 
[1] "1.1 - 38.1 (21.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D461V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0649 MUTATED         1        1        1        1         3         3
  KIAA0649 WILD-TYPE       1       14       39       29        34        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0649 MUTATED           0          3          1          3        1
  KIAA0649 WILD-TYPE         3         67         52         29       37
D461V3, multiclass
            clus
vv           KIAA0649 MUTATED KIAA0649 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  1                 14
  STAGE IB                  1                 39
  STAGE II                  1                 29
  STAGE IIA                 3                 34
  STAGE IIB                 3                 49
  STAGE III                 0                  3
  STAGE IIIA                3                 67
  STAGE IIIB                1                 52
  STAGE IIIC                3                 29
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0649 MUTATED     2   3   6   7
  KIAA0649 WILD-TYPE  20  89 167  90
D461V4, multiclass
    clus
vv   KIAA0649 MUTATED KIAA0649 WILD-TYPE
  T1                2                 20
  T2                3                 89
  T3                6                167
  T4                7                 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
  KIAA0649 MUTATED     7   5   1   5
  KIAA0649 WILD-TYPE 111  99  76  72
D461V5, multiclass
    clus
vv   KIAA0649 MUTATED KIAA0649 WILD-TYPE
  N0                7                111
  N1                5                 99
  N2                1                 76
  N3                5                 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"
D461V6, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED    17   0
  KIAA0649 WILD-TYPE 329  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED     17    0
  KIAA0649 WILD-TYPE  329   29
   clus
vv  KIAA0649 MUTATED KIAA0649 WILD-TYPE
  0               17                329
  1                0                 29
[1] 2 2
[1] FALSE
D461V7, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED     8  10
  KIAA0649 WILD-TYPE 137 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED      8   10
  KIAA0649 WILD-TYPE  137  238
        clus
vv       KIAA0649 MUTATED KIAA0649 WILD-TYPE
  FEMALE                8                137
  MALE                 10                238
[1] 2 2
[1] FALSE
D461V8, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED    15   2
  KIAA0649 WILD-TYPE 277  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED     15    2
  KIAA0649 WILD-TYPE  277   57
     clus
vv    KIAA0649 MUTATED KIAA0649 WILD-TYPE
  NO                15                277
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA0649 MUTATED                                          0
  KIAA0649 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA0649 MUTATED                                       2
  KIAA0649 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0649 MUTATED                                                        9
  KIAA0649 WILD-TYPE                                                    149
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA0649 MUTATED                                                   2
  KIAA0649 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0649 MUTATED                                                                   3
  KIAA0649 WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA0649 MUTATED                                                    0
  KIAA0649 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA0649 MUTATED                                                  2
  KIAA0649 WILD-TYPE                                               59
D461V9, multiclass
                                                                   clus
vv                                                                  KIAA0649 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  KIAA0649 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0649 MUTATED    18   0   0   0
  KIAA0649 WILD-TYPE 293  14  15  24
D461V10, multiclass
    clus
vv   KIAA0649 MUTATED KIAA0649 WILD-TYPE
  R0               18                293
  R1                0                 14
  R2                0                 15
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D461V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0649 MUTATED       2                         1
  KIAA0649 WILD-TYPE    85                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0649 MUTATED                                           0    12
  KIAA0649 WILD-TYPE                                         1   231
D461V12, multiclass
                                           clus
vv                                          KIAA0649 MUTATED KIAA0649 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   12                231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D461V13, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED     0  14
  KIAA0649 WILD-TYPE   4 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED      0   14
  KIAA0649 WILD-TYPE    4  296
                        clus
vv                       KIAA0649 MUTATED KIAA0649 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               14                296
[1] 2 2
[1] FALSE

Clustering(462) Variable = CD79A MUTATION ANALYSIS
D462V1, survival
                 sevent
clus2               0   1
  CD79A MUTATED     5   2
  CD79A WILD-TYPE 225 137
  CD79A MUTATED CD79A WILD-TYPE 
              7             362 
  CD79A MUTATED CD79A WILD-TYPE 
              2             137 
$`CD79A MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 TCGA-CG-4306 TCGA-CG-5721 
        6.97        34.68        35.84         1.12         1.02         6.02 
TCGA-CG-5723 
      105.07 

$`CD79A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  CD79A MUTATED CD79A WILD-TYPE 
           1.02            0.00 
  CD79A MUTATED CD79A WILD-TYPE 
         105.07          122.30 
  CD79A MUTATED CD79A WILD-TYPE 
           6.97           14.35 
[1] "1.0 - 105.1 (7.0)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D462V2, 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       2       15       39       29        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CD79A MUTATED           0          1          0          0        2
  CD79A WILD-TYPE         3         69         53         32       36
D462V3, multiclass
            clus
vv           CD79A MUTATED CD79A WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CD79A MUTATED     0   2   4   1
  CD79A WILD-TYPE  22  90 169  96
D462V4, multiclass
    clus
vv   CD79A MUTATED CD79A WILD-TYPE
  T1             0              22
  T2             2              90
  T3             4             169
  T4             1              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
  CD79A MUTATED     3   3   1   0
  CD79A WILD-TYPE 115 101  76  77
D462V5, multiclass
    clus
vv   CD79A MUTATED CD79A WILD-TYPE
  N0             3             115
  N1             3             101
  N2             1              76
  N3             0              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"
D462V6, binary
                 cls
clus                0   1
  CD79A MUTATED     5   1
  CD79A WILD-TYPE 341  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      5    1
  CD79A WILD-TYPE  341   28
   clus
vv  CD79A MUTATED CD79A WILD-TYPE
  0             5             341
  1             1              28
[1] 2 2
[1] FALSE
D462V7, binary
                 cls
clus                0   1
  CD79A MUTATED     3   4
  CD79A WILD-TYPE 142 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      3    4
  CD79A WILD-TYPE  142  244
        clus
vv       CD79A MUTATED CD79A WILD-TYPE
  FEMALE             3             142
  MALE               4             244
[1] 2 2
[1] FALSE
D462V8, binary
                 cls
clus                0   1
  CD79A MUTATED     6   0
  CD79A WILD-TYPE 286  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      6    0
  CD79A WILD-TYPE  286   59
     clus
vv    CD79A MUTATED CD79A WILD-TYPE
  NO              6             286
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CD79A MUTATED                                          0
  CD79A WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CD79A MUTATED                                       0
  CD79A WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD79A MUTATED                                                        6
  CD79A WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CD79A MUTATED                                                   0
  CD79A WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD79A MUTATED                                                                   1
  CD79A WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CD79A MUTATED                                                    0
  CD79A WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CD79A MUTATED                                                  0
  CD79A WILD-TYPE                                               61
D462V9, multiclass
                                                                   clus
vv                                                                  CD79A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  CD79A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CD79A MUTATED     5   0   1   1
  CD79A WILD-TYPE 306  14  14  23
D462V10, multiclass
    clus
vv   CD79A MUTATED CD79A WILD-TYPE
  R0             5             306
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D462V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CD79A MUTATED       0                         0
  CD79A WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD79A MUTATED                                           0     4
  CD79A WILD-TYPE                                         1   239
D462V12, multiclass
                                           clus
vv                                          CD79A MUTATED CD79A WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D462V13, binary
                 cls
clus                0   1
  CD79A MUTATED     0   4
  CD79A WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      0    4
  CD79A WILD-TYPE    4  306
                        clus
vv                       CD79A MUTATED CD79A WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(463) Variable = C22ORF30 MUTATION ANALYSIS
D463V1, survival
                    sevent
clus2                  0   1
  C22ORF30 MUTATED     5   0
  C22ORF30 WILD-TYPE 225 139
  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
                 5                364 
  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
                 0                139 
$`C22ORF30 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-CG-5723 TCGA-HU-A4G8 TCGA-SW-A7EA 
       26.70        34.68       105.07        22.68        19.04 

$`C22ORF30 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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 
             19.04               0.00 
  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
            105.07             122.30 
  C22ORF30 MUTATED C22ORF30 WILD-TYPE 
             26.70              14.07 
[1] "19.0 - 105.1 (26.7)" "0.0 - 122.3 (14.1)" 
[1] "hr="     "9400000"
D463V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C22ORF30 MUTATED         0        0        1        1         1         2
  C22ORF30 WILD-TYPE       2       15       39       29        36        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C22ORF30 MUTATED           0          1          0          0        0
  C22ORF30 WILD-TYPE         3         69         53         32       38
D463V3, multiclass
            clus
vv           C22ORF30 MUTATED C22ORF30 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  1                 29
  STAGE IIA                 1                 36
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                0                 53
  STAGE IIIC                0                 32
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C22ORF30 MUTATED     0   2   2   2
  C22ORF30 WILD-TYPE  22  90 171  95
D463V4, multiclass
    clus
vv   C22ORF30 MUTATED C22ORF30 WILD-TYPE
  T1                0                 22
  T2                2                 90
  T3                2                171
  T4                2                 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
  C22ORF30 MUTATED     4   2   0   0
  C22ORF30 WILD-TYPE 114 102  77  77
D463V5, multiclass
    clus
vv   C22ORF30 MUTATED C22ORF30 WILD-TYPE
  N0                4                114
  N1                2                102
  N2                0                 77
  N3                0                 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"
D463V6, binary
                    cls
clus                   0   1
  C22ORF30 MUTATED     6   0
  C22ORF30 WILD-TYPE 340  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C22ORF30 MUTATED      6    0
  C22ORF30 WILD-TYPE  340   29
   clus
vv  C22ORF30 MUTATED C22ORF30 WILD-TYPE
  0                6                340
  1                0                 29
[1] 2 2
[1] FALSE
D463V7, binary
                    cls
clus                   0   1
  C22ORF30 MUTATED     5   1
  C22ORF30 WILD-TYPE 140 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C22ORF30 MUTATED      5    1
  C22ORF30 WILD-TYPE  140  247
        clus
vv       C22ORF30 MUTATED C22ORF30 WILD-TYPE
  FEMALE                5                140
  MALE                  1                247
[1] 2 2
[1] FALSE
D463V8, binary
                    cls
clus                   0   1
  C22ORF30 MUTATED     5   0
  C22ORF30 WILD-TYPE 287  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C22ORF30 MUTATED      5    0
  C22ORF30 WILD-TYPE  287   59
     clus
vv    C22ORF30 MUTATED C22ORF30 WILD-TYPE
  NO                 5                287
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C22ORF30 MUTATED                                          0
  C22ORF30 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C22ORF30 MUTATED                                       3
  C22ORF30 WILD-TYPE                                    67
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C22ORF30 MUTATED                                                        3
  C22ORF30 WILD-TYPE                                                    155
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C22ORF30 MUTATED                                                   0
  C22ORF30 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C22ORF30 MUTATED                                                                   0
  C22ORF30 WILD-TYPE                                                                68
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C22ORF30 MUTATED                                                    0
  C22ORF30 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C22ORF30 MUTATED                                                  0
  C22ORF30 WILD-TYPE                                               61
D463V9, multiclass
                                                                   clus
vv                                                                  C22ORF30 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 0
                                                                   clus
vv                                                                  C22ORF30 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C22ORF30 MUTATED     4   0   0   1
  C22ORF30 WILD-TYPE 307  14  15  23
D463V10, multiclass
    clus
vv   C22ORF30 MUTATED C22ORF30 WILD-TYPE
  R0                4                307
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D463V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C22ORF30 MUTATED       1                         0
  C22ORF30 WILD-TYPE    86                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C22ORF30 MUTATED                                           0     4
  C22ORF30 WILD-TYPE                                         1   239
D463V12, multiclass
                                           clus
vv                                          C22ORF30 MUTATED C22ORF30 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D463V13, binary
                    cls
clus                   0   1
  C22ORF30 MUTATED     0   5
  C22ORF30 WILD-TYPE   4 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C22ORF30 MUTATED      0    5
  C22ORF30 WILD-TYPE    4  305
                        clus
vv                       C22ORF30 MUTATED C22ORF30 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                5                305
[1] 2 2
[1] FALSE

Clustering(464) Variable = SRP72 MUTATION ANALYSIS
D464V1, survival
                 sevent
clus2               0   1
  SRP72 MUTATED     6   6
  SRP72 WILD-TYPE 224 133
  SRP72 MUTATED SRP72 WILD-TYPE 
             12             357 
  SRP72 MUTATED SRP72 WILD-TYPE 
              6             133 
$`SRP72 MUTATED`
TCGA-CG-4460 TCGA-BR-4256 TCGA-BR-7707 TCGA-BR-8487 TCGA-BR-8677 TCGA-BR-A4IZ 
       21.99         9.34        35.84         1.12        26.73         8.98 
TCGA-CD-A4MI TCGA-CG-4465 TCGA-HF-7132 TCGA-MX-A5UJ TCGA-SW-A7EA TCGA-VQ-A8PQ 
       11.77         9.01        77.29        19.73        19.04        15.65 

$`SRP72 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        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-A4J1 
       34.98         1.48        27.55        28.57        12.89         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-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-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-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-A91Q 
       38.14        37.22        22.19        17.85         1.87        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 

  SRP72 MUTATED SRP72 WILD-TYPE 
           1.12            0.00 
  SRP72 MUTATED SRP72 WILD-TYPE 
          77.29          122.30 
  SRP72 MUTATED SRP72 WILD-TYPE 
         17.345          14.170 
[1] "1.1 - 77.3 (17.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D464V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SRP72 MUTATED         0        0        2        1         1         1
  SRP72 WILD-TYPE       2       15       38       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SRP72 MUTATED           0          2          2          0        3
  SRP72 WILD-TYPE         3         68         51         32       35
D464V3, multiclass
            clus
vv           SRP72 MUTATED SRP72 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             0              32
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SRP72 MUTATED     0   3   5   5
  SRP72 WILD-TYPE  22  89 168  92
D464V4, multiclass
    clus
vv   SRP72 MUTATED SRP72 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             5             168
  T4             5              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
  SRP72 MUTATED     4   5   2   2
  SRP72 WILD-TYPE 114  99  75  75
D464V5, multiclass
    clus
vv   SRP72 MUTATED SRP72 WILD-TYPE
  N0             4             114
  N1             5              99
  N2             2              75
  N3             2              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"
D464V6, binary
                 cls
clus                0   1
  SRP72 MUTATED    10   3
  SRP72 WILD-TYPE 336  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP72 MUTATED     10    3
  SRP72 WILD-TYPE  336   26
   clus
vv  SRP72 MUTATED SRP72 WILD-TYPE
  0            10             336
  1             3              26
[1] 2 2
[1] FALSE
D464V7, binary
                 cls
clus                0   1
  SRP72 MUTATED    10   4
  SRP72 WILD-TYPE 135 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP72 MUTATED     10    4
  SRP72 WILD-TYPE  135  244
        clus
vv       SRP72 MUTATED SRP72 WILD-TYPE
  FEMALE            10             135
  MALE               4             244
[1] 2 2
[1] FALSE
D464V8, binary
                 cls
clus                0   1
  SRP72 MUTATED    11   1
  SRP72 WILD-TYPE 281  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP72 MUTATED     11    1
  SRP72 WILD-TYPE  281   58
     clus
vv    SRP72 MUTATED SRP72 WILD-TYPE
  NO             11             281
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SRP72 MUTATED                                          0
  SRP72 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SRP72 MUTATED                                       3
  SRP72 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SRP72 MUTATED                                                        6
  SRP72 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SRP72 MUTATED                                                   1
  SRP72 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SRP72 MUTATED                                                                   2
  SRP72 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SRP72 MUTATED                                                    0
  SRP72 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SRP72 MUTATED                                                  2
  SRP72 WILD-TYPE                                               59
D464V9, multiclass
                                                                   clus
vv                                                                  SRP72 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  SRP72 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SRP72 MUTATED     8   0   3   2
  SRP72 WILD-TYPE 303  14  12  22
D464V10, multiclass
    clus
vv   SRP72 MUTATED SRP72 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             3              12
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D464V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SRP72 MUTATED       2                         0
  SRP72 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SRP72 MUTATED                                           0     9
  SRP72 WILD-TYPE                                         1   234
D464V12, multiclass
                                           clus
vv                                          SRP72 MUTATED SRP72 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D464V13, binary
                 cls
clus                0   1
  SRP72 MUTATED     0  10
  SRP72 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP72 MUTATED      0   10
  SRP72 WILD-TYPE    4  300
                        clus
vv                       SRP72 MUTATED SRP72 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(465) Variable = PLAG1 MUTATION ANALYSIS
D465V1, survival
                 sevent
clus2               0   1
  PLAG1 MUTATED     5   5
  PLAG1 WILD-TYPE 225 134
  PLAG1 MUTATED PLAG1 WILD-TYPE 
             10             359 
  PLAG1 MUTATED PLAG1 WILD-TYPE 
              5             134 
$`PLAG1 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8487 TCGA-BR-8592 TCGA-CG-4465 TCGA-CG-5721 
        6.97        34.68         1.12         6.28         9.01         6.02 
TCGA-CG-5726 TCGA-D7-A6EZ TCGA-HU-A4H8 TCGA-KB-A6F7 
       28.96        20.32        14.07        63.62 

$`PLAG1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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 

  PLAG1 MUTATED PLAG1 WILD-TYPE 
           1.12            0.00 
  PLAG1 MUTATED PLAG1 WILD-TYPE 
          63.62          122.30 
  PLAG1 MUTATED PLAG1 WILD-TYPE 
          11.54           14.43 
[1] "1.1 - 63.6 (11.5)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.4"
D465V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLAG1 MUTATED         0        1        2        0         2         0
  PLAG1 WILD-TYPE       2       14       38       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLAG1 MUTATED           0          3          1          0        3
  PLAG1 WILD-TYPE         3         67         52         32       35
D465V3, multiclass
            clus
vv           PLAG1 MUTATED PLAG1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PLAG1 MUTATED     3   0   4   5
  PLAG1 WILD-TYPE  19  92 169  92
D465V4, multiclass
    clus
vv   PLAG1 MUTATED PLAG1 WILD-TYPE
  T1             3              19
  T2             0              92
  T3             4             169
  T4             5              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
  PLAG1 MUTATED     4   5   2   1
  PLAG1 WILD-TYPE 114  99  75  76
D465V5, multiclass
    clus
vv   PLAG1 MUTATED PLAG1 WILD-TYPE
  N0             4             114
  N1             5              99
  N2             2              75
  N3             1              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"
D465V6, binary
                 cls
clus                0   1
  PLAG1 MUTATED    10   1
  PLAG1 WILD-TYPE 336  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAG1 MUTATED     10    1
  PLAG1 WILD-TYPE  336   28
   clus
vv  PLAG1 MUTATED PLAG1 WILD-TYPE
  0            10             336
  1             1              28
[1] 2 2
[1] FALSE
D465V7, binary
                 cls
clus                0   1
  PLAG1 MUTATED     7   5
  PLAG1 WILD-TYPE 138 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAG1 MUTATED      7    5
  PLAG1 WILD-TYPE  138  243
        clus
vv       PLAG1 MUTATED PLAG1 WILD-TYPE
  FEMALE             7             138
  MALE               5             243
[1] 2 2
[1] FALSE
D465V8, binary
                 cls
clus                0   1
  PLAG1 MUTATED     7   1
  PLAG1 WILD-TYPE 285  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAG1 MUTATED      7    1
  PLAG1 WILD-TYPE  285   58
     clus
vv    PLAG1 MUTATED PLAG1 WILD-TYPE
  NO              7             285
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PLAG1 MUTATED                                          0
  PLAG1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PLAG1 MUTATED                                       2
  PLAG1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLAG1 MUTATED                                                        5
  PLAG1 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PLAG1 MUTATED                                                   0
  PLAG1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLAG1 MUTATED                                                                   4
  PLAG1 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PLAG1 MUTATED                                                    0
  PLAG1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PLAG1 MUTATED                                                  1
  PLAG1 WILD-TYPE                                               60
D465V9, multiclass
                                                                   clus
vv                                                                  PLAG1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  PLAG1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PLAG1 MUTATED     8   0   1   3
  PLAG1 WILD-TYPE 303  14  14  21
D465V10, multiclass
    clus
vv   PLAG1 MUTATED PLAG1 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D465V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PLAG1 MUTATED       1                         0
  PLAG1 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLAG1 MUTATED                                           0     7
  PLAG1 WILD-TYPE                                         1   236
D465V12, multiclass
                                           clus
vv                                          PLAG1 MUTATED PLAG1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D465V13, binary
                 cls
clus                0   1
  PLAG1 MUTATED     0   8
  PLAG1 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAG1 MUTATED      0    8
  PLAG1 WILD-TYPE    4  302
                        clus
vv                       PLAG1 MUTATED PLAG1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(466) Variable = HSPA14 MUTATION ANALYSIS
D466V1, survival
                  sevent
clus2                0   1
  HSPA14 MUTATED     3   2
  HSPA14 WILD-TYPE 227 137
  HSPA14 MUTATED HSPA14 WILD-TYPE 
               5              364 
  HSPA14 MUTATED HSPA14 WILD-TYPE 
               2              137 
$`HSPA14 MUTATED`
TCGA-B7-5816 TCGA-CG-5733 TCGA-FP-A4BE TCGA-KB-A93J TCGA-VQ-A8DU 
       26.70        21.07        11.08        36.95         5.46 

$`HSPA14 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  HSPA14 MUTATED HSPA14 WILD-TYPE 
            5.46             0.00 
  HSPA14 MUTATED HSPA14 WILD-TYPE 
           36.95           122.30 
  HSPA14 MUTATED HSPA14 WILD-TYPE 
           21.07            14.22 
[1] "5.5 - 37.0 (21.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D466V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HSPA14 MUTATED         0        0        0        1         1         1
  HSPA14 WILD-TYPE       2       15       40       29        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSPA14 MUTATED           0          2          0          0        0
  HSPA14 WILD-TYPE         3         68         53         32       38
D466V3, multiclass
            clus
vv           HSPA14 MUTATED HSPA14 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HSPA14 MUTATED     0   2   2   1
  HSPA14 WILD-TYPE  22  90 171  96
D466V4, multiclass
    clus
vv   HSPA14 MUTATED HSPA14 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              2              171
  T4              1               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
  HSPA14 MUTATED     2   1   2   0
  HSPA14 WILD-TYPE 116 103  75  77
D466V5, multiclass
    clus
vv   HSPA14 MUTATED HSPA14 WILD-TYPE
  N0              2              116
  N1              1              103
  N2              2               75
  N3              0               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"
D466V6, binary
                  cls
clus                 0   1
  HSPA14 MUTATED     6   0
  HSPA14 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA14 MUTATED      6    0
  HSPA14 WILD-TYPE  340   29
   clus
vv  HSPA14 MUTATED HSPA14 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D466V7, binary
                  cls
clus                 0   1
  HSPA14 MUTATED     3   3
  HSPA14 WILD-TYPE 142 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA14 MUTATED      3    3
  HSPA14 WILD-TYPE  142  245
        clus
vv       HSPA14 MUTATED HSPA14 WILD-TYPE
  FEMALE              3              142
  MALE                3              245
[1] 2 2
[1] FALSE
D466V8, binary
                  cls
clus                 0   1
  HSPA14 MUTATED     3   2
  HSPA14 WILD-TYPE 289  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA14 MUTATED      3    2
  HSPA14 WILD-TYPE  289   57
     clus
vv    HSPA14 MUTATED HSPA14 WILD-TYPE
  NO               3              289
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HSPA14 MUTATED                                          0
  HSPA14 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HSPA14 MUTATED                                       2
  HSPA14 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HSPA14 MUTATED                                                        2
  HSPA14 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HSPA14 MUTATED                                                   0
  HSPA14 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HSPA14 MUTATED                                                                   1
  HSPA14 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HSPA14 MUTATED                                                    0
  HSPA14 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HSPA14 MUTATED                                                  1
  HSPA14 WILD-TYPE                                               60
D466V9, multiclass
                                                                   clus
vv                                                                  HSPA14 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  HSPA14 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HSPA14 MUTATED     5   0   0   1
  HSPA14 WILD-TYPE 306  14  15  23
D466V10, multiclass
    clus
vv   HSPA14 MUTATED HSPA14 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D466V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  HSPA14 MUTATED       0                         1
  HSPA14 WILD-TYPE    87                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HSPA14 MUTATED                                           0     4
  HSPA14 WILD-TYPE                                         1   239
D466V12, multiclass
                                           clus
vv                                          HSPA14 MUTATED HSPA14 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D466V13, binary
                  cls
clus                 0   1
  HSPA14 MUTATED     0   3
  HSPA14 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA14 MUTATED      0    3
  HSPA14 WILD-TYPE    4  307
                        clus
vv                       HSPA14 MUTATED HSPA14 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(467) Variable = CYP7B1 MUTATION ANALYSIS
D467V1, survival
                  sevent
clus2                0   1
  CYP7B1 MUTATED    12   7
  CYP7B1 WILD-TYPE 218 132
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
              19              350 
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
               7              132 
$`CYP7B1 MUTATED`
TCGA-BR-4201 TCGA-BR-7703 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8483 TCGA-BR-8591 
       30.90        36.16        14.43        29.59         5.39        28.14 
TCGA-CD-5798 TCGA-CD-8535 TCGA-CD-A487 TCGA-CG-4465 TCGA-CG-5723 TCGA-CG-5728 
       13.41        12.82        12.30         9.01       105.07        65.10 
TCGA-D7-5579 TCGA-D7-6818 TCGA-D7-A4YU TCGA-D7-A747 TCGA-VQ-A8PE TCGA-VQ-AA6A 
       20.91        12.36        16.44         8.38        22.19        38.93 
TCGA-VQ-AA6I 
       16.14 

$`CYP7B1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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-D7-6518 
       69.04        21.07         7.99        25.71        12.66        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-D7-8570 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-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-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-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       37.41        38.14        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-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J 
       43.66        28.41        32.94        54.12        26.04        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
            5.39             0.00 
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
          105.07           122.30 
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
           16.44            14.07 
[1] "5.4 - 105.1 (16.4)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D467V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CYP7B1 MUTATED         0        1        1        2         0         3
  CYP7B1 WILD-TYPE       2       14       39       28        37        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP7B1 MUTATED           1          4          3          2        1
  CYP7B1 WILD-TYPE         2         66         50         30       37
D467V3, multiclass
            clus
vv           CYP7B1 MUTATED CYP7B1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               0               37
  STAGE IIB               3               49
  STAGE III               1                2
  STAGE IIIA              4               66
  STAGE IIIB              3               50
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CYP7B1 MUTATED     1   4   9   5
  CYP7B1 WILD-TYPE  21  88 164  92
D467V4, multiclass
    clus
vv   CYP7B1 MUTATED CYP7B1 WILD-TYPE
  T1              1               21
  T2              4               88
  T3              9              164
  T4              5               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
  CYP7B1 MUTATED     4   5   2   7
  CYP7B1 WILD-TYPE 114  99  75  70
D467V5, multiclass
    clus
vv   CYP7B1 MUTATED CYP7B1 WILD-TYPE
  N0              4              114
  N1              5               99
  N2              2               75
  N3              7               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"
D467V6, binary
                  cls
clus                 0   1
  CYP7B1 MUTATED    19   1
  CYP7B1 WILD-TYPE 327  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP7B1 MUTATED     19    1
  CYP7B1 WILD-TYPE  327   28
   clus
vv  CYP7B1 MUTATED CYP7B1 WILD-TYPE
  0             19              327
  1              1               28
[1] 2 2
[1] FALSE
D467V7, binary
                  cls
clus                 0   1
  CYP7B1 MUTATED     4  16
  CYP7B1 WILD-TYPE 141 232
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP7B1 MUTATED      4   16
  CYP7B1 WILD-TYPE  141  232
        clus
vv       CYP7B1 MUTATED CYP7B1 WILD-TYPE
  FEMALE              4              141
  MALE               16              232
[1] 2 2
[1] FALSE
D467V8, binary
                  cls
clus                 0   1
  CYP7B1 MUTATED    15   2
  CYP7B1 WILD-TYPE 277  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP7B1 MUTATED     15    2
  CYP7B1 WILD-TYPE  277   57
     clus
vv    CYP7B1 MUTATED CYP7B1 WILD-TYPE
  NO              15              277
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CYP7B1 MUTATED                                          0
  CYP7B1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CYP7B1 MUTATED                                       4
  CYP7B1 WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CYP7B1 MUTATED                                                        6
  CYP7B1 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CYP7B1 MUTATED                                                   2
  CYP7B1 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CYP7B1 MUTATED                                                                   5
  CYP7B1 WILD-TYPE                                                                63
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CYP7B1 MUTATED                                                    1
  CYP7B1 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CYP7B1 MUTATED                                                  2
  CYP7B1 WILD-TYPE                                               59
D467V9, multiclass
                                                                   clus
vv                                                                  CYP7B1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  CYP7B1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CYP7B1 MUTATED    15   1   1   2
  CYP7B1 WILD-TYPE 296  13  14  22
D467V10, multiclass
    clus
vv   CYP7B1 MUTATED CYP7B1 WILD-TYPE
  R0             15              296
  R1              1               13
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D467V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CYP7B1 MUTATED       3                         0
  CYP7B1 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CYP7B1 MUTATED                                           0    14
  CYP7B1 WILD-TYPE                                         1   229
D467V12, multiclass
                                           clus
vv                                          CYP7B1 MUTATED CYP7B1 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 14              229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D467V13, binary
                  cls
clus                 0   1
  CYP7B1 MUTATED     0  14
  CYP7B1 WILD-TYPE   4 296
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP7B1 MUTATED      0   14
  CYP7B1 WILD-TYPE    4  296
                        clus
vv                       CYP7B1 MUTATED CYP7B1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             14              296
[1] 2 2
[1] FALSE

Clustering(468) Variable = SLC7A10 MUTATION ANALYSIS
D468V1, survival
                   sevent
clus2                 0   1
  SLC7A10 MUTATED     4   0
  SLC7A10 WILD-TYPE 226 139
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                4               365 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                0               139 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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            14.430 
[1] "6.0 - 77.3 (11.8)"  "0.0 - 122.3 (14.4)"
[1] "hr="     "9300000"
D468V2, 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       2       15       40       28        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC7A10 MUTATED           0          0          0          1        1
  SLC7A10 WILD-TYPE         3         70         53         31       37
D468V3, multiclass
            clus
vv           SLC7A10 MUTATED SLC7A10 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 2                28
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC7A10 MUTATED     0   1   2   3
  SLC7A10 WILD-TYPE  22  91 171  94
D468V4, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  T1               0                22
  T2               1                91
  T3               2               171
  T4               3                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
  SLC7A10 MUTATED     3   2   0   1
  SLC7A10 WILD-TYPE 115 102  77  76
D468V5, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  N0               3               115
  N1               2               102
  N2               0                77
  N3               1                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"
D468V6, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     6   0
  SLC7A10 WILD-TYPE 340  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      6    0
  SLC7A10 WILD-TYPE  340   29
   clus
vv  SLC7A10 MUTATED SLC7A10 WILD-TYPE
  0               6               340
  1               0                29
[1] 2 2
[1] FALSE
D468V7, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     1   5
  SLC7A10 WILD-TYPE 144 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      1    5
  SLC7A10 WILD-TYPE  144  243
        clus
vv       SLC7A10 MUTATED SLC7A10 WILD-TYPE
  FEMALE               1               144
  MALE                 5               243
[1] 2 2
[1] FALSE
D468V8, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     4   2
  SLC7A10 WILD-TYPE 288  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      4    2
  SLC7A10 WILD-TYPE  288   57
     clus
vv    SLC7A10 MUTATED SLC7A10 WILD-TYPE
  NO                4               288
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC7A10 MUTATED                                          0
  SLC7A10 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC7A10 MUTATED                                       0
  SLC7A10 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC7A10 MUTATED                                                        3
  SLC7A10 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC7A10 MUTATED                                                   1
  SLC7A10 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC7A10 MUTATED                                                                   2
  SLC7A10 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC7A10 MUTATED                                                    0
  SLC7A10 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC7A10 MUTATED                                                  0
  SLC7A10 WILD-TYPE                                               61
D468V9, multiclass
                                                                   clus
vv                                                                  SLC7A10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  SLC7A10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC7A10 MUTATED     6   0   0   0
  SLC7A10 WILD-TYPE 305  14  15  24
D468V10, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  R0               6               305
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D468V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC7A10 MUTATED       1                         1
  SLC7A10 WILD-TYPE    86                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC7A10 MUTATED                                           0     2
  SLC7A10 WILD-TYPE                                         1   241
D468V12, multiclass
                                           clus
vv                                          SLC7A10 MUTATED SLC7A10 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D468V13, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     0   4
  SLC7A10 WILD-TYPE   4 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      0    4
  SLC7A10 WILD-TYPE    4  306
                        clus
vv                       SLC7A10 MUTATED SLC7A10 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4               306
[1] 2 2
[1] FALSE

Clustering(469) Variable = FASTKD1 MUTATION ANALYSIS
D469V1, survival
                   sevent
clus2                 0   1
  FASTKD1 MUTATED     8   4
  FASTKD1 WILD-TYPE 222 135
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
               12               357 
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
                4               135 
$`FASTKD1 MUTATED`
TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8589 TCGA-BR-A4QL TCGA-CD-8527 TCGA-CG-5721 
       32.25         4.31        27.12        16.14         7.17         6.02 
TCGA-CG-5726 TCGA-D7-A4YV TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-VQ-A8P2 
       28.96         5.92         6.51        20.25        29.00        38.14 

$`FASTKD1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-A4GY 
       21.37        29.98         8.98         0.10         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-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 

  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
             4.31              0.00 
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
            38.14            122.30 
  FASTKD1 MUTATED FASTKD1 WILD-TYPE 
           18.195            14.170 
[1] "4.3 - 38.1 (18.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D469V2, 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       2       14       39       29        36        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FASTKD1 MUTATED           0          1          2          2        1
  FASTKD1 WILD-TYPE         3         69         51         30       37
D469V3, multiclass
            clus
vv           FASTKD1 MUTATED FASTKD1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               2                51
  STAGE IIIC               2                30
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FASTKD1 MUTATED     1   2   3   6
  FASTKD1 WILD-TYPE  21  90 170  91
D469V4, multiclass
    clus
vv   FASTKD1 MUTATED FASTKD1 WILD-TYPE
  T1               1                21
  T2               2                90
  T3               3               170
  T4               6                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
  FASTKD1 MUTATED     4   5   1   2
  FASTKD1 WILD-TYPE 114  99  76  75
D469V5, multiclass
    clus
vv   FASTKD1 MUTATED FASTKD1 WILD-TYPE
  N0               4               114
  N1               5                99
  N2               1                76
  N3               2                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"
D469V6, binary
                   cls
clus                  0   1
  FASTKD1 MUTATED    12   0
  FASTKD1 WILD-TYPE 334  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FASTKD1 MUTATED     12    0
  FASTKD1 WILD-TYPE  334   29
   clus
vv  FASTKD1 MUTATED FASTKD1 WILD-TYPE
  0              12               334
  1               0                29
[1] 2 2
[1] FALSE
D469V7, binary
                   cls
clus                  0   1
  FASTKD1 MUTATED     8   4
  FASTKD1 WILD-TYPE 137 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FASTKD1 MUTATED      8    4
  FASTKD1 WILD-TYPE  137  244
        clus
vv       FASTKD1 MUTATED FASTKD1 WILD-TYPE
  FEMALE               8               137
  MALE                 4               244
[1] 2 2
[1] FALSE
D469V8, binary
                   cls
clus                  0   1
  FASTKD1 MUTATED     9   1
  FASTKD1 WILD-TYPE 283  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FASTKD1 MUTATED      9    1
  FASTKD1 WILD-TYPE  283   58
     clus
vv    FASTKD1 MUTATED FASTKD1 WILD-TYPE
  NO                9               283
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FASTKD1 MUTATED                                          0
  FASTKD1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FASTKD1 MUTATED                                       2
  FASTKD1 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FASTKD1 MUTATED                                                        4
  FASTKD1 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FASTKD1 MUTATED                                                   1
  FASTKD1 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FASTKD1 MUTATED                                                                   3
  FASTKD1 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FASTKD1 MUTATED                                                    0
  FASTKD1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FASTKD1 MUTATED                                                  2
  FASTKD1 WILD-TYPE                                               59
D469V9, multiclass
                                                                   clus
vv                                                                  FASTKD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  FASTKD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FASTKD1 MUTATED    12   0   0   0
  FASTKD1 WILD-TYPE 299  14  15  24
D469V10, multiclass
    clus
vv   FASTKD1 MUTATED FASTKD1 WILD-TYPE
  R0              12               299
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D469V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FASTKD1 MUTATED       4                         0
  FASTKD1 WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FASTKD1 MUTATED                                           0     6
  FASTKD1 WILD-TYPE                                         1   237
D469V12, multiclass
                                           clus
vv                                          FASTKD1 MUTATED FASTKD1 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D469V13, binary
                   cls
clus                  0   1
  FASTKD1 MUTATED     0   9
  FASTKD1 WILD-TYPE   4 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FASTKD1 MUTATED      0    9
  FASTKD1 WILD-TYPE    4  301
                        clus
vv                       FASTKD1 MUTATED FASTKD1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               9               301
[1] 2 2
[1] FALSE

Clustering(470) Variable = NEUROD6 MUTATION ANALYSIS
D470V1, survival
                   sevent
clus2                 0   1
  NEUROD6 MUTATED     3   3
  NEUROD6 WILD-TYPE 227 136
  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
                6               363 
  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
                3               136 
$`NEUROD6 MUTATED`
TCGA-BR-4184 TCGA-BR-6566 TCGA-CG-4305 TCGA-CG-4306 TCGA-HU-A4GD TCGA-HU-A4GQ 
        6.97        32.78        15.95         1.02        22.75         0.10 

$`NEUROD6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
              0.1               0.0 
  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
            32.78            122.30 
  NEUROD6 MUTATED NEUROD6 WILD-TYPE 
            11.46             14.27 
[1] "0.1 - 32.8 (11.5)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.7"
D470V2, 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       2       15       40       29        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NEUROD6 MUTATED           0          1          0          1        1
  NEUROD6 WILD-TYPE         3         69         53         31       37
D470V3, multiclass
            clus
vv           NEUROD6 MUTATED NEUROD6 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  NEUROD6 MUTATED     0   1   4   1
  NEUROD6 WILD-TYPE  22  91 169  96
D470V4, multiclass
    clus
vv   NEUROD6 MUTATED NEUROD6 WILD-TYPE
  T1               0                22
  T2               1                91
  T3               4               169
  T4               1                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
  NEUROD6 MUTATED     1   3   2   0
  NEUROD6 WILD-TYPE 117 101  75  77
D470V5, multiclass
    clus
vv   NEUROD6 MUTATED NEUROD6 WILD-TYPE
  N0               1               117
  N1               3               101
  N2               2                75
  N3               0                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"
D470V6, binary
                   cls
clus                  0   1
  NEUROD6 MUTATED     4   1
  NEUROD6 WILD-TYPE 342  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD6 MUTATED      4    1
  NEUROD6 WILD-TYPE  342   28
   clus
vv  NEUROD6 MUTATED NEUROD6 WILD-TYPE
  0               4               342
  1               1                28
[1] 2 2
[1] FALSE
D470V7, binary
                   cls
clus                  0   1
  NEUROD6 MUTATED     1   5
  NEUROD6 WILD-TYPE 144 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD6 MUTATED      1    5
  NEUROD6 WILD-TYPE  144  243
        clus
vv       NEUROD6 MUTATED NEUROD6 WILD-TYPE
  FEMALE               1               144
  MALE                 5               243
[1] 2 2
[1] FALSE
D470V8, binary
                   cls
clus                  0   1
  NEUROD6 MUTATED     5   0
  NEUROD6 WILD-TYPE 287  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD6 MUTATED      5    0
  NEUROD6 WILD-TYPE  287   59
     clus
vv    NEUROD6 MUTATED NEUROD6 WILD-TYPE
  NO                5               287
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NEUROD6 MUTATED                                          0
  NEUROD6 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NEUROD6 MUTATED                                       0
  NEUROD6 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NEUROD6 MUTATED                                                        4
  NEUROD6 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NEUROD6 MUTATED                                                   0
  NEUROD6 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NEUROD6 MUTATED                                                                   0
  NEUROD6 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NEUROD6 MUTATED                                                    0
  NEUROD6 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NEUROD6 MUTATED                                                  2
  NEUROD6 WILD-TYPE                                               59
D470V9, multiclass
                                                                   clus
vv                                                                  NEUROD6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  NEUROD6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  NEUROD6 MUTATED     4   0   1   1
  NEUROD6 WILD-TYPE 307  14  14  23
D470V10, multiclass
    clus
vv   NEUROD6 MUTATED NEUROD6 WILD-TYPE
  R0               4               307
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D470V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  NEUROD6 MUTATED       2                         0
  NEUROD6 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NEUROD6 MUTATED                                           0     2
  NEUROD6 WILD-TYPE                                         1   241
D470V12, multiclass
                                           clus
vv                                          NEUROD6 MUTATED NEUROD6 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D470V13, binary
                   cls
clus                  0   1
  NEUROD6 MUTATED     0   4
  NEUROD6 WILD-TYPE   4 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD6 MUTATED      0    4
  NEUROD6 WILD-TYPE    4  306
                        clus
vv                       NEUROD6 MUTATED NEUROD6 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4               306
[1] 2 2
[1] FALSE

Clustering(471) Variable = KRTAP10-9 MUTATION ANALYSIS
D471V1, survival
                     sevent
clus2                   0   1
  KRTAP10-9 MUTATED     5   2
  KRTAP10-9 WILD-TYPE 225 137
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  7                 362 
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  2                 137 
$`KRTAP10-9 MUTATED`
TCGA-BR-4184 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-5723 
        6.97        28.14        31.96        11.77        15.95       105.07 
TCGA-CG-5730 
        4.01 

$`KRTAP10-9 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  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 
              15.95               14.22 
[1] "4.0 - 105.1 (15.9)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D471V2, 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       1       15       40       28        37        52
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRTAP10-9 MUTATED           0          2          0          1        2
  KRTAP10-9 WILD-TYPE         3         68         53         31       36
D471V3, multiclass
            clus
vv           KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  STAGE I                    1                   1
  STAGE IA                   0                  15
  STAGE IB                   0                  40
  STAGE II                   2                  28
  STAGE IIA                  0                  37
  STAGE IIB                  0                  52
  STAGE III                  0                   3
  STAGE IIIA                 2                  68
  STAGE IIIB                 0                  53
  STAGE IIIC                 1                  31
  STAGE IV                   2                  36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  KRTAP10-9 MUTATED     1   3   2   2
  KRTAP10-9 WILD-TYPE  21  89 171  95
D471V4, multiclass
    clus
vv   KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  T1                 1                  21
  T2                 3                  89
  T3                 2                 171
  T4                 2                  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
  KRTAP10-9 MUTATED     0   6   1   1
  KRTAP10-9 WILD-TYPE 118  98  76  76
D471V5, multiclass
    clus
vv   KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  N0                 0                 118
  N1                 6                  98
  N2                 1                  76
  N3                 1                  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"
D471V6, binary
                     cls
clus                    0   1
  KRTAP10-9 MUTATED     4   2
  KRTAP10-9 WILD-TYPE 342  27
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-9 MUTATED      4    2
  KRTAP10-9 WILD-TYPE  342   27
   clus
vv  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  0                 4                 342
  1                 2                  27
[1] 2 2
[1] FALSE
D471V7, binary
                     cls
clus                    0   1
  KRTAP10-9 MUTATED     1   7
  KRTAP10-9 WILD-TYPE 144 241
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-9 MUTATED      1    7
  KRTAP10-9 WILD-TYPE  144  241
        clus
vv       KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  FEMALE                 1                 144
  MALE                   7                 241
[1] 2 2
[1] FALSE
D471V8, binary
                     cls
clus                    0   1
  KRTAP10-9 MUTATED     7   0
  KRTAP10-9 WILD-TYPE 285  59
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-9 MUTATED      7    0
  KRTAP10-9 WILD-TYPE  285   59
     clus
vv    KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  NO                  7                 285
  YES                 0                  59
[1] 2 2
[1] FALSE
                     vv
clus                  STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KRTAP10-9 MUTATED                                          0
  KRTAP10-9 WILD-TYPE                                        8
                     vv
clus                  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KRTAP10-9 MUTATED                                       0
  KRTAP10-9 WILD-TYPE                                    70
                     vv
clus                  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KRTAP10-9 MUTATED                                                        6
  KRTAP10-9 WILD-TYPE                                                    152
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KRTAP10-9 MUTATED                                                   0
  KRTAP10-9 WILD-TYPE                                                21
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KRTAP10-9 MUTATED                                                                   1
  KRTAP10-9 WILD-TYPE                                                                67
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KRTAP10-9 MUTATED                                                    0
  KRTAP10-9 WILD-TYPE                                                  5
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KRTAP10-9 MUTATED                                                  1
  KRTAP10-9 WILD-TYPE                                               60
D471V9, multiclass
                                                                   clus
vv                                                                  KRTAP10-9 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  1
                                                                   clus
vv                                                                  KRTAP10-9 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                            8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                              70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                  21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                  5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                   60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  KRTAP10-9 MUTATED     5   0   1   1
  KRTAP10-9 WILD-TYPE 306  14  14  23
D471V10, multiclass
    clus
vv   KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  R0                 5                 306
  R1                 0                  14
  R2                 1                  14
  RX                 1                  23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D471V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN
  KRTAP10-9 MUTATED       2                         1
  KRTAP10-9 WILD-TYPE    85                         8
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KRTAP10-9 MUTATED                                           0     2
  KRTAP10-9 WILD-TYPE                                         1   241
D471V12, multiclass
                                           clus
vv                                          KRTAP10-9 MUTATED
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                     2
                                           clus
vv                                          KRTAP10-9 WILD-TYPE
  ASIAN                                                      85
  BLACK OR AFRICAN AMERICAN                                   8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   1
  WHITE                                                     241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D471V13, binary
                     cls
clus                    0   1
  KRTAP10-9 MUTATED     0   5
  KRTAP10-9 WILD-TYPE   4 305
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-9 MUTATED      0    5
  KRTAP10-9 WILD-TYPE    4  305
                        clus
vv                       KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  HISPANIC OR LATINO                     0                   4
  NOT HISPANIC OR LATINO                 5                 305
[1] 2 2
[1] FALSE

Clustering(472) Variable = RBMX MUTATION ANALYSIS
D472V1, survival
                sevent
clus2              0   1
  RBMX MUTATED     5   4
  RBMX WILD-TYPE 225 135
  RBMX MUTATED RBMX WILD-TYPE 
             9            360 
  RBMX MUTATED RBMX WILD-TYPE 
             4            135 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8081 TCGA-BR-8284 
       14.43        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-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-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-F1-6874 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-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 
       63.06        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-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 

  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          14.22 
[1] "6.6 - 105.1 (19.7)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1"  
D472V2, 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       2       13       40       29        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RBMX MUTATED           0          3          0          2        0
  RBMX WILD-TYPE         3         67         53         30       38
D472V3, multiclass
            clus
vv           RBMX MUTATED RBMX WILD-TYPE
  STAGE I               0              2
  STAGE IA              2             13
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RBMX MUTATED     2   1   4   2
  RBMX WILD-TYPE  20  91 169  95
D472V4, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  T1            2             20
  T2            1             91
  T3            4            169
  T4            2             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
  RBMX MUTATED     3   3   1   2
  RBMX WILD-TYPE 115 101  76  75
D472V5, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  N0            3            115
  N1            3            101
  N2            1             76
  N3            2             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"
D472V6, binary
                cls
clus               0   1
  RBMX MUTATED     9   0
  RBMX WILD-TYPE 337  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      9    0
  RBMX WILD-TYPE  337   29
   clus
vv  RBMX MUTATED RBMX WILD-TYPE
  0            9            337
  1            0             29
[1] 2 2
[1] FALSE
D472V7, binary
                cls
clus               0   1
  RBMX MUTATED     5   5
  RBMX WILD-TYPE 140 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      5    5
  RBMX WILD-TYPE  140  243
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  FEMALE            5            140
  MALE              5            243
[1] 2 2
[1] FALSE
D472V8, binary
                cls
clus               0   1
  RBMX MUTATED     8   1
  RBMX WILD-TYPE 284  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      8    1
  RBMX WILD-TYPE  284   58
     clus
vv    RBMX MUTATED RBMX WILD-TYPE
  NO             8            284
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RBMX MUTATED                                          0
  RBMX WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RBMX MUTATED                                       1
  RBMX WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RBMX MUTATED                                                        4
  RBMX WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RBMX MUTATED                                                   2
  RBMX WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RBMX MUTATED                                                                   1
  RBMX WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RBMX MUTATED                                                    0
  RBMX WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RBMX MUTATED                                                  2
  RBMX WILD-TYPE                                               59
D472V9, multiclass
                                                                   clus
vv                                                                  RBMX MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  RBMX WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RBMX MUTATED     5   1   0   2
  RBMX WILD-TYPE 306  13  15  22
D472V10, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  R0            5            306
  R1            1             13
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D472V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RBMX MUTATED       3                         0
  RBMX WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RBMX MUTATED                                           0     4
  RBMX WILD-TYPE                                         1   239
D472V12, multiclass
                                           clus
vv                                          RBMX MUTATED RBMX WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D472V13, binary
                cls
clus               0   1
  RBMX MUTATED     0   7
  RBMX WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      0    7
  RBMX WILD-TYPE    4  303
                        clus
vv                       RBMX MUTATED RBMX WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(473) Variable = C10ORF71 MUTATION ANALYSIS
D473V1, survival
                    sevent
clus2                  0   1
  C10ORF71 MUTATED     6   5
  C10ORF71 WILD-TYPE 224 134
  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
                11                358 
  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
                 5                134 
$`C10ORF71 MUTATED`
TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-8487 TCGA-BR-8682 TCGA-CD-A4MI TCGA-CG-4300 
        6.97        44.94         1.12        32.58        11.77        20.02 
TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-A4YY TCGA-IN-7806 
        9.01         6.02        21.07        13.78        36.36 

$`C10ORF71 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4MG TCGA-CD-A4MH 
       12.30        11.31        12.43        11.61         6.58        12.20 
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-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-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-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-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        33.40         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 

  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
              1.12               0.00 
  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
             44.94             122.30 
  C10ORF71 MUTATED C10ORF71 WILD-TYPE 
             13.78              14.35 
[1] "1.1 - 44.9 (13.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D473V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C10ORF71 MUTATED         1        0        0        0         2         2
  C10ORF71 WILD-TYPE       1       15       40       30        35        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C10ORF71 MUTATED           0          3          2          0        2
  C10ORF71 WILD-TYPE         3         67         51         32       36
D473V3, multiclass
            clus
vv           C10ORF71 MUTATED C10ORF71 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 2                 35
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                3                 67
  STAGE IIIB                2                 51
  STAGE IIIC                0                 32
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C10ORF71 MUTATED     1   1   7   3
  C10ORF71 WILD-TYPE  21  91 166  94
D473V4, multiclass
    clus
vv   C10ORF71 MUTATED C10ORF71 WILD-TYPE
  T1                1                 21
  T2                1                 91
  T3                7                166
  T4                3                 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
  C10ORF71 MUTATED     3   5   2   2
  C10ORF71 WILD-TYPE 115  99  75  75
D473V5, multiclass
    clus
vv   C10ORF71 MUTATED C10ORF71 WILD-TYPE
  N0                3                115
  N1                5                 99
  N2                2                 75
  N3                2                 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"
D473V6, binary
                    cls
clus                   0   1
  C10ORF71 MUTATED     9   1
  C10ORF71 WILD-TYPE 337  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF71 MUTATED      9    1
  C10ORF71 WILD-TYPE  337   28
   clus
vv  C10ORF71 MUTATED C10ORF71 WILD-TYPE
  0                9                337
  1                1                 28
[1] 2 2
[1] FALSE
D473V7, binary
                    cls
clus                   0   1
  C10ORF71 MUTATED     4   8
  C10ORF71 WILD-TYPE 141 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF71 MUTATED      4    8
  C10ORF71 WILD-TYPE  141  240
        clus
vv       C10ORF71 MUTATED C10ORF71 WILD-TYPE
  FEMALE                4                141
  MALE                  8                240
[1] 2 2
[1] FALSE
D473V8, binary
                    cls
clus                   0   1
  C10ORF71 MUTATED     9   1
  C10ORF71 WILD-TYPE 283  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF71 MUTATED      9    1
  C10ORF71 WILD-TYPE  283   58
     clus
vv    C10ORF71 MUTATED C10ORF71 WILD-TYPE
  NO                 9                283
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C10ORF71 MUTATED                                          0
  C10ORF71 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C10ORF71 MUTATED                                       2
  C10ORF71 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C10ORF71 MUTATED                                                        7
  C10ORF71 WILD-TYPE                                                    151
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C10ORF71 MUTATED                                                   1
  C10ORF71 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C10ORF71 MUTATED                                                                   2
  C10ORF71 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C10ORF71 MUTATED                                                    0
  C10ORF71 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C10ORF71 MUTATED                                                  0
  C10ORF71 WILD-TYPE                                               61
D473V9, multiclass
                                                                   clus
vv                                                                  C10ORF71 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 0
                                                                   clus
vv                                                                  C10ORF71 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C10ORF71 MUTATED     9   0   1   1
  C10ORF71 WILD-TYPE 302  14  14  23
D473V10, multiclass
    clus
vv   C10ORF71 MUTATED C10ORF71 WILD-TYPE
  R0                9                302
  R1                0                 14
  R2                1                 14
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D473V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C10ORF71 MUTATED       2                         1
  C10ORF71 WILD-TYPE    85                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C10ORF71 MUTATED                                           0     5
  C10ORF71 WILD-TYPE                                         1   238
D473V12, multiclass
                                           clus
vv                                          C10ORF71 MUTATED C10ORF71 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D473V13, binary
                    cls
clus                   0   1
  C10ORF71 MUTATED     0   8
  C10ORF71 WILD-TYPE   4 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF71 MUTATED      0    8
  C10ORF71 WILD-TYPE    4  302
                        clus
vv                       C10ORF71 MUTATED C10ORF71 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                8                302
[1] 2 2
[1] FALSE

Clustering(474) Variable = MRE11A MUTATION ANALYSIS
D474V1, survival
                  sevent
clus2                0   1
  MRE11A MUTATED     3   3
  MRE11A WILD-TYPE 227 136
  MRE11A MUTATED MRE11A WILD-TYPE 
               6              363 
  MRE11A MUTATED MRE11A WILD-TYPE 
               3              136 
$`MRE11A MUTATED`
TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8363 TCGA-D7-A4YV TCGA-HU-A4GX 
       11.01         6.97        34.68         0.26         5.92        20.25 

$`MRE11A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  MRE11A MUTATED MRE11A WILD-TYPE 
            0.26             0.00 
  MRE11A MUTATED MRE11A WILD-TYPE 
           34.68           122.30 
  MRE11A MUTATED MRE11A WILD-TYPE 
            8.99            14.43 
[1] "0.3 - 34.7 (9.0)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.9"
D474V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MRE11A MUTATED         0        0        2        0         1         2
  MRE11A WILD-TYPE       2       15       38       30        36        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRE11A MUTATED           0          1          0          1        0
  MRE11A WILD-TYPE         3         69         53         31       38
D474V3, multiclass
            clus
vv           MRE11A MUTATED MRE11A WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MRE11A MUTATED     0   2   3   2
  MRE11A WILD-TYPE  22  90 170  95
D474V4, multiclass
    clus
vv   MRE11A MUTATED MRE11A WILD-TYPE
  T1              0               22
  T2              2               90
  T3              3              170
  T4              2               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
  MRE11A MUTATED     3   2   1   0
  MRE11A WILD-TYPE 115 102  76  77
D474V5, multiclass
    clus
vv   MRE11A MUTATED MRE11A WILD-TYPE
  N0              3              115
  N1              2              102
  N2              1               76
  N3              0               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"
D474V6, binary
                  cls
clus                 0   1
  MRE11A MUTATED     6   0
  MRE11A WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED      6    0
  MRE11A WILD-TYPE  340   29
   clus
vv  MRE11A MUTATED MRE11A WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D474V7, binary
                  cls
clus                 0   1
  MRE11A MUTATED     4   3
  MRE11A WILD-TYPE 141 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED      4    3
  MRE11A WILD-TYPE  141  245
        clus
vv       MRE11A MUTATED MRE11A WILD-TYPE
  FEMALE              4              141
  MALE                3              245
[1] 2 2
[1] FALSE
D474V8, binary
                  cls
clus                 0   1
  MRE11A MUTATED     6   0
  MRE11A WILD-TYPE 286  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED      6    0
  MRE11A WILD-TYPE  286   59
     clus
vv    MRE11A MUTATED MRE11A WILD-TYPE
  NO               6              286
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MRE11A MUTATED                                          0
  MRE11A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MRE11A MUTATED                                       1
  MRE11A WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MRE11A MUTATED                                                        3
  MRE11A WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MRE11A MUTATED                                                   0
  MRE11A WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MRE11A MUTATED                                                                   2
  MRE11A WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MRE11A MUTATED                                                    0
  MRE11A WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MRE11A MUTATED                                                  1
  MRE11A WILD-TYPE                                               60
D474V9, multiclass
                                                                   clus
vv                                                                  MRE11A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  MRE11A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MRE11A MUTATED     5   0   0   1
  MRE11A WILD-TYPE 306  14  15  23
D474V10, multiclass
    clus
vv   MRE11A MUTATED MRE11A WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D474V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MRE11A MUTATED       1                         0
  MRE11A WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MRE11A MUTATED                                           0     5
  MRE11A WILD-TYPE                                         1   238
D474V12, multiclass
                                           clus
vv                                          MRE11A MUTATED MRE11A WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D474V13, binary
                  cls
clus                 0   1
  MRE11A MUTATED     0   6
  MRE11A WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED      0    6
  MRE11A WILD-TYPE    4  304
                        clus
vv                       MRE11A MUTATED MRE11A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(475) Variable = MAP2K1 MUTATION ANALYSIS
D475V1, survival
                  sevent
clus2                0   1
  MAP2K1 MUTATED     5   2
  MAP2K1 WILD-TYPE 225 137
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               7              362 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               2              137 
$`MAP2K1 MUTATED`
TCGA-BR-6566 TCGA-BR-8368 TCGA-BR-8683 TCGA-CG-5723 TCGA-D7-5577 TCGA-IN-A6RP 
       32.78         4.31         9.86       105.07        25.71         6.44 
TCGA-VQ-AA6J 
       27.55 

$`MAP2K1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-D7-5578 
       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-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-AA6K TCGA-ZA-A8F6 
       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 
           25.71            14.22 
[1] "4.3 - 105.1 (25.7)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.7"
D475V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP2K1 MUTATED         0        0        1        1         1         0
  MAP2K1 WILD-TYPE       2       15       39       29        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP2K1 MUTATED           0          1          2          1        0
  MAP2K1 WILD-TYPE         3         69         51         31       38
D475V3, multiclass
            clus
vv           MAP2K1 MUTATED MAP2K1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              2               51
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP2K1 MUTATED     1   3   1   2
  MAP2K1 WILD-TYPE  21  89 172  95
D475V4, multiclass
    clus
vv   MAP2K1 MUTATED MAP2K1 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              1              172
  T4              2               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
  MAP2K1 MUTATED     2   1   2   2
  MAP2K1 WILD-TYPE 116 103  75  75
D475V5, multiclass
    clus
vv   MAP2K1 MUTATED MAP2K1 WILD-TYPE
  N0              2              116
  N1              1              103
  N2              2               75
  N3              2               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"
D475V6, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     7   0
  MAP2K1 WILD-TYPE 339  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      7    0
  MAP2K1 WILD-TYPE  339   29
   clus
vv  MAP2K1 MUTATED MAP2K1 WILD-TYPE
  0              7              339
  1              0               29
[1] 2 2
[1] FALSE
D475V7, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     3   4
  MAP2K1 WILD-TYPE 142 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      3    4
  MAP2K1 WILD-TYPE  142  244
        clus
vv       MAP2K1 MUTATED MAP2K1 WILD-TYPE
  FEMALE              3              142
  MALE                4              244
[1] 2 2
[1] FALSE
D475V8, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     6   1
  MAP2K1 WILD-TYPE 286  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      6    1
  MAP2K1 WILD-TYPE  286   58
     clus
vv    MAP2K1 MUTATED MAP2K1 WILD-TYPE
  NO               6              286
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MAP2K1 MUTATED                                          0
  MAP2K1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MAP2K1 MUTATED                                       0
  MAP2K1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP2K1 MUTATED                                                        4
  MAP2K1 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MAP2K1 MUTATED                                                   0
  MAP2K1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP2K1 MUTATED                                                                   1
  MAP2K1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MAP2K1 MUTATED                                                    0
  MAP2K1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MAP2K1 MUTATED                                                  2
  MAP2K1 WILD-TYPE                                               59
D475V9, multiclass
                                                                   clus
vv                                                                  MAP2K1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  MAP2K1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP2K1 MUTATED     7   0   0   0
  MAP2K1 WILD-TYPE 304  14  15  24
D475V10, multiclass
    clus
vv   MAP2K1 MUTATED MAP2K1 WILD-TYPE
  R0              7              304
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D475V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAP2K1 MUTATED       1                         1
  MAP2K1 WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP2K1 MUTATED                                           0     4
  MAP2K1 WILD-TYPE                                         1   239
D475V12, multiclass
                                           clus
vv                                          MAP2K1 MUTATED MAP2K1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D475V13, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     0   5
  MAP2K1 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      0    5
  MAP2K1 WILD-TYPE    4  305
                        clus
vv                       MAP2K1 MUTATED MAP2K1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(476) Variable = C1ORF177 MUTATION ANALYSIS
D476V1, survival
                    sevent
clus2                  0   1
  C1ORF177 MUTATED     8   4
  C1ORF177 WILD-TYPE 222 135
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
                12                357 
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
                 4                135 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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 

  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
              0.26               0.00 
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
             77.29             122.30 
  C1ORF177 MUTATED C1ORF177 WILD-TYPE 
             13.38              14.27 
[1] "0.3 - 77.3 (13.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D476V2, 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       2       15       38       29        33        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF177 MUTATED           0          0          1          0        1
  C1ORF177 WILD-TYPE         3         70         52         32       37
D476V3, multiclass
            clus
vv           C1ORF177 MUTATED C1ORF177 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  2                 38
  STAGE II                  1                 29
  STAGE IIA                 4                 33
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                1                 52
  STAGE IIIC                0                 32
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C1ORF177 MUTATED     0   3   7   1
  C1ORF177 WILD-TYPE  22  89 166  96
D476V4, multiclass
    clus
vv   C1ORF177 MUTATED C1ORF177 WILD-TYPE
  T1                0                 22
  T2                3                 89
  T3                7                166
  T4                1                 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
  C1ORF177 MUTATED     6   5   0   1
  C1ORF177 WILD-TYPE 112  99  77  76
D476V5, multiclass
    clus
vv   C1ORF177 MUTATED C1ORF177 WILD-TYPE
  N0                6                112
  N1                5                 99
  N2                0                 77
  N3                1                 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"
D476V6, binary
                    cls
clus                   0   1
  C1ORF177 MUTATED    11   1
  C1ORF177 WILD-TYPE 335  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF177 MUTATED     11    1
  C1ORF177 WILD-TYPE  335   28
   clus
vv  C1ORF177 MUTATED C1ORF177 WILD-TYPE
  0               11                335
  1                1                 28
[1] 2 2
[1] FALSE
D476V7, binary
                    cls
clus                   0   1
  C1ORF177 MUTATED     8   4
  C1ORF177 WILD-TYPE 137 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF177 MUTATED      8    4
  C1ORF177 WILD-TYPE  137  244
        clus
vv       C1ORF177 MUTATED C1ORF177 WILD-TYPE
  FEMALE                8                137
  MALE                  4                244
[1] 2 2
[1] FALSE
D476V8, binary
                    cls
clus                   0   1
  C1ORF177 MUTATED    11   1
  C1ORF177 WILD-TYPE 281  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF177 MUTATED     11    1
  C1ORF177 WILD-TYPE  281   58
     clus
vv    C1ORF177 MUTATED C1ORF177 WILD-TYPE
  NO                11                281
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C1ORF177 MUTATED                                          0
  C1ORF177 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C1ORF177 MUTATED                                       3
  C1ORF177 WILD-TYPE                                    67
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C1ORF177 MUTATED                                                        6
  C1ORF177 WILD-TYPE                                                    152
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C1ORF177 MUTATED                                                   1
  C1ORF177 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C1ORF177 MUTATED                                                                   0
  C1ORF177 WILD-TYPE                                                                68
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C1ORF177 MUTATED                                                    0
  C1ORF177 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C1ORF177 MUTATED                                                  2
  C1ORF177 WILD-TYPE                                               59
D476V9, multiclass
                                                                   clus
vv                                                                  C1ORF177 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  C1ORF177 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C1ORF177 MUTATED    11   0   0   1
  C1ORF177 WILD-TYPE 300  14  15  23
D476V10, multiclass
    clus
vv   C1ORF177 MUTATED C1ORF177 WILD-TYPE
  R0               11                300
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D476V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C1ORF177 MUTATED       2                         0
  C1ORF177 WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C1ORF177 MUTATED                                           0     9
  C1ORF177 WILD-TYPE                                         1   234
D476V12, multiclass
                                           clus
vv                                          C1ORF177 MUTATED C1ORF177 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    9                234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D476V13, binary
                    cls
clus                   0   1
  C1ORF177 MUTATED     1  10
  C1ORF177 WILD-TYPE   3 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF177 MUTATED      1   10
  C1ORF177 WILD-TYPE    3  300
                        clus
vv                       C1ORF177 MUTATED C1ORF177 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               10                300
[1] 2 2
[1] FALSE

Clustering(477) Variable = IGF2BP3 MUTATION ANALYSIS
D477V1, survival
                   sevent
clus2                 0   1
  IGF2BP3 MUTATED     5   2
  IGF2BP3 WILD-TYPE 225 137
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
                7               362 
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
                2               137 
$`IGF2BP3 MUTATED`
TCGA-BR-8680 TCGA-CG-4437 TCGA-D7-A6EY TCGA-FP-A4BE TCGA-HU-A4GN TCGA-R5-A805 
       31.96         8.05        11.44        11.08        29.98         9.24 
TCGA-VQ-A8P2 
       38.14 

$`IGF2BP3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
             8.05              0.00 
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
            38.14            122.30 
  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE 
            11.44             14.35 
[1] "8.1 - 38.1 (11.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D477V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IGF2BP3 MUTATED         0        0        0        1         2         0
  IGF2BP3 WILD-TYPE       2       15       40       29        35        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGF2BP3 MUTATED           0          1          2          0        1
  IGF2BP3 WILD-TYPE         3         69         51         32       37
D477V3, multiclass
            clus
vv           IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 1                29
  STAGE IIA                2                35
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               2                51
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  IGF2BP3 MUTATED     0   2   3   2
  IGF2BP3 WILD-TYPE  22  90 170  95
D477V4, multiclass
    clus
vv   IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  T1               0                22
  T2               2                90
  T3               3               170
  T4               2                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
  IGF2BP3 MUTATED     1   3   2   1
  IGF2BP3 WILD-TYPE 117 101  75  76
D477V5, multiclass
    clus
vv   IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  N0               1               117
  N1               3               101
  N2               2                75
  N3               1                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"
D477V6, binary
                   cls
clus                  0   1
  IGF2BP3 MUTATED     6   1
  IGF2BP3 WILD-TYPE 340  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IGF2BP3 MUTATED      6    1
  IGF2BP3 WILD-TYPE  340   28
   clus
vv  IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  0               6               340
  1               1                28
[1] 2 2
[1] FALSE
D477V7, binary
                   cls
clus                  0   1
  IGF2BP3 MUTATED     1   6
  IGF2BP3 WILD-TYPE 144 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IGF2BP3 MUTATED      1    6
  IGF2BP3 WILD-TYPE  144  242
        clus
vv       IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  FEMALE               1               144
  MALE                 6               242
[1] 2 2
[1] FALSE
D477V8, binary
                   cls
clus                  0   1
  IGF2BP3 MUTATED     4   2
  IGF2BP3 WILD-TYPE 288  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IGF2BP3 MUTATED      4    2
  IGF2BP3 WILD-TYPE  288   57
     clus
vv    IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  NO                4               288
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IGF2BP3 MUTATED                                          0
  IGF2BP3 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IGF2BP3 MUTATED                                       0
  IGF2BP3 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IGF2BP3 MUTATED                                                        1
  IGF2BP3 WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IGF2BP3 MUTATED                                                   1
  IGF2BP3 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IGF2BP3 MUTATED                                                                   2
  IGF2BP3 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IGF2BP3 MUTATED                                                    0
  IGF2BP3 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IGF2BP3 MUTATED                                                  3
  IGF2BP3 WILD-TYPE                                               58
D477V9, multiclass
                                                                   clus
vv                                                                  IGF2BP3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  IGF2BP3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  IGF2BP3 MUTATED     6   0   0   0
  IGF2BP3 WILD-TYPE 305  14  15  24
D477V10, multiclass
    clus
vv   IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  R0               6               305
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D477V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  IGF2BP3 MUTATED       2                         1
  IGF2BP3 WILD-TYPE    85                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IGF2BP3 MUTATED                                           0     3
  IGF2BP3 WILD-TYPE                                         1   240
D477V12, multiclass
                                           clus
vv                                          IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D477V13, binary
                   cls
clus                  0   1
  IGF2BP3 MUTATED     0   5
  IGF2BP3 WILD-TYPE   4 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IGF2BP3 MUTATED      0    5
  IGF2BP3 WILD-TYPE    4  305
                        clus
vv                       IGF2BP3 MUTATED IGF2BP3 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(478) Variable = AKAP13 MUTATION ANALYSIS
D478V1, survival
                  sevent
clus2                0   1
  AKAP13 MUTATED    17  10
  AKAP13 WILD-TYPE 213 129
  AKAP13 MUTATED AKAP13 WILD-TYPE 
              27              342 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
              10              129 
$`AKAP13 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15         9.86        26.70        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-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-7704 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        35.24        35.84        33.63 
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-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-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-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-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-4437 TCGA-CG-4440 
        3.02        27.02        15.95         7.99         8.05         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-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-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-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-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-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        29.00        23.80        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        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-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-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 

  AKAP13 MUTATED AKAP13 WILD-TYPE 
            0.92             0.00 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
           77.29           122.30 
  AKAP13 MUTATED AKAP13 WILD-TYPE 
           18.15            14.22 
[1] "0.9 - 77.3 (18.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D478V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AKAP13 MUTATED         1        1        1        3         5         4
  AKAP13 WILD-TYPE       1       14       39       27        32        48
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKAP13 MUTATED           0          6          0          1        7
  AKAP13 WILD-TYPE         3         64         53         31       31
D478V3, multiclass
            clus
vv           AKAP13 MUTATED AKAP13 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                3               27
  STAGE IIA               5               32
  STAGE IIB               4               48
  STAGE III               0                3
  STAGE IIIA              6               64
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                7               31
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AKAP13 MUTATED     3   5  14   8
  AKAP13 WILD-TYPE  19  87 159  89
D478V4, multiclass
    clus
vv   AKAP13 MUTATED AKAP13 WILD-TYPE
  T1              3               19
  T2              5               87
  T3             14              159
  T4              8               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
  AKAP13 MUTATED     8   9  10   2
  AKAP13 WILD-TYPE 110  95  67  75
D478V5, multiclass
    clus
vv   AKAP13 MUTATED AKAP13 WILD-TYPE
  N0              8              110
  N1              9               95
  N2             10               67
  N3              2               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"
D478V6, binary
                  cls
clus                 0   1
  AKAP13 MUTATED    29   2
  AKAP13 WILD-TYPE 317  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED     29    2
  AKAP13 WILD-TYPE  317   27
   clus
vv  AKAP13 MUTATED AKAP13 WILD-TYPE
  0             29              317
  1              2               27
[1] 2 2
[1] FALSE
D478V7, binary
                  cls
clus                 0   1
  AKAP13 MUTATED    12  20
  AKAP13 WILD-TYPE 133 228
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED     12   20
  AKAP13 WILD-TYPE  133  228
        clus
vv       AKAP13 MUTATED AKAP13 WILD-TYPE
  FEMALE             12              133
  MALE               20              228
[1] 2 2
[1] FALSE
D478V8, binary
                  cls
clus                 0   1
  AKAP13 MUTATED    21   3
  AKAP13 WILD-TYPE 271  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED     21    3
  AKAP13 WILD-TYPE  271   56
     clus
vv    AKAP13 MUTATED AKAP13 WILD-TYPE
  NO              21              271
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AKAP13 MUTATED                                          0
  AKAP13 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AKAP13 MUTATED                                       2
  AKAP13 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AKAP13 MUTATED                                                       13
  AKAP13 WILD-TYPE                                                    145
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AKAP13 MUTATED                                                   2
  AKAP13 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AKAP13 MUTATED                                                                   9
  AKAP13 WILD-TYPE                                                                59
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AKAP13 MUTATED                                                    1
  AKAP13 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AKAP13 MUTATED                                                  5
  AKAP13 WILD-TYPE                                               56
D478V9, multiclass
                                                                   clus
vv                                                                  AKAP13 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              9
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               5
                                                                   clus
vv                                                                  AKAP13 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               59
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  AKAP13 MUTATED    23   1   1   4
  AKAP13 WILD-TYPE 288  13  14  20
D478V10, multiclass
    clus
vv   AKAP13 MUTATED AKAP13 WILD-TYPE
  R0             23              288
  R1              1               13
  R2              1               14
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D478V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  AKAP13 MUTATED       7                         1
  AKAP13 WILD-TYPE    80                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AKAP13 MUTATED                                           0    17
  AKAP13 WILD-TYPE                                         1   226
D478V12, multiclass
                                           clus
vv                                          AKAP13 MUTATED AKAP13 WILD-TYPE
  ASIAN                                                  7               80
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 17              226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D478V13, binary
                  cls
clus                 0   1
  AKAP13 MUTATED     0  23
  AKAP13 WILD-TYPE   4 287
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP13 MUTATED      0   23
  AKAP13 WILD-TYPE    4  287
                        clus
vv                       AKAP13 MUTATED AKAP13 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             23              287
[1] 2 2
[1] FALSE

Clustering(479) Variable = ABCE1 MUTATION ANALYSIS
D479V1, survival
                 sevent
clus2               0   1
  ABCE1 MUTATED     5   3
  ABCE1 WILD-TYPE 225 136
  ABCE1 MUTATED ABCE1 WILD-TYPE 
              8             361 
  ABCE1 MUTATED ABCE1 WILD-TYPE 
              3             136 
$`ABCE1 MUTATED`
TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6566 TCGA-BR-8081 TCGA-D7-A6EZ TCGA-HU-A4G8 
       30.90         9.34        32.78        32.25        20.32        22.68 
TCGA-HU-A4GX TCGA-IN-A6RI 
       20.25        18.38 

$`ABCE1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  ABCE1 MUTATED ABCE1 WILD-TYPE 
           9.34            0.00 
  ABCE1 MUTATED ABCE1 WILD-TYPE 
          32.78          122.30 
  ABCE1 MUTATED ABCE1 WILD-TYPE 
          21.50           14.07 
[1] "9.3 - 32.8 (21.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D479V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCE1 MUTATED         1        0        1        0         1         3
  ABCE1 WILD-TYPE       1       15       39       30        36        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABCE1 MUTATED           0          1          0          1        0
  ABCE1 WILD-TYPE         3         69         53         31       38
D479V3, multiclass
            clus
vv           ABCE1 MUTATED ABCE1 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCE1 MUTATED     1   2   3   3
  ABCE1 WILD-TYPE  21  90 170  94
D479V4, multiclass
    clus
vv   ABCE1 MUTATED ABCE1 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             3             170
  T4             3              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
  ABCE1 MUTATED     5   2   2   0
  ABCE1 WILD-TYPE 113 102  75  77
D479V5, multiclass
    clus
vv   ABCE1 MUTATED ABCE1 WILD-TYPE
  N0             5             113
  N1             2             102
  N2             2              75
  N3             0              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"
D479V6, binary
                 cls
clus                0   1
  ABCE1 MUTATED    10   0
  ABCE1 WILD-TYPE 336  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCE1 MUTATED     10    0
  ABCE1 WILD-TYPE  336   29
   clus
vv  ABCE1 MUTATED ABCE1 WILD-TYPE
  0            10             336
  1             0              29
[1] 2 2
[1] FALSE
D479V7, binary
                 cls
clus                0   1
  ABCE1 MUTATED     5   5
  ABCE1 WILD-TYPE 140 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCE1 MUTATED      5    5
  ABCE1 WILD-TYPE  140  243
        clus
vv       ABCE1 MUTATED ABCE1 WILD-TYPE
  FEMALE             5             140
  MALE               5             243
[1] 2 2
[1] FALSE
D479V8, binary
                 cls
clus                0   1
  ABCE1 MUTATED     9   0
  ABCE1 WILD-TYPE 283  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCE1 MUTATED      9    0
  ABCE1 WILD-TYPE  283   59
     clus
vv    ABCE1 MUTATED ABCE1 WILD-TYPE
  NO              9             283
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ABCE1 MUTATED                                          0
  ABCE1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ABCE1 MUTATED                                       2
  ABCE1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCE1 MUTATED                                                        5
  ABCE1 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ABCE1 MUTATED                                                   0
  ABCE1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCE1 MUTATED                                                                   3
  ABCE1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ABCE1 MUTATED                                                    0
  ABCE1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ABCE1 MUTATED                                                  0
  ABCE1 WILD-TYPE                                               61
D479V9, multiclass
                                                                   clus
vv                                                                  ABCE1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  ABCE1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCE1 MUTATED     7   0   0   2
  ABCE1 WILD-TYPE 304  14  15  22
D479V10, multiclass
    clus
vv   ABCE1 MUTATED ABCE1 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D479V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCE1 MUTATED       2                         0
  ABCE1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCE1 MUTATED                                           0     7
  ABCE1 WILD-TYPE                                         1   236
D479V12, multiclass
                                           clus
vv                                          ABCE1 MUTATED ABCE1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D479V13, binary
                 cls
clus                0   1
  ABCE1 MUTATED     0   9
  ABCE1 WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCE1 MUTATED      0    9
  ABCE1 WILD-TYPE    4  301
                        clus
vv                       ABCE1 MUTATED ABCE1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(480) Variable = KLHL14 MUTATION ANALYSIS
D480V1, survival
                  sevent
clus2                0   1
  KLHL14 MUTATED    12   4
  KLHL14 WILD-TYPE 218 135
  KLHL14 MUTATED KLHL14 WILD-TYPE 
              16              353 
  KLHL14 MUTATED KLHL14 WILD-TYPE 
               4              135 
$`KLHL14 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8485 TCGA-BR-8487 
       34.68        29.59         0.26         4.31         9.21         1.12 
TCGA-BR-8591 TCGA-BR-A4J8 TCGA-CG-4305 TCGA-CG-5724 TCGA-CG-5733 TCGA-D7-6522 
       28.14        13.51        15.95        12.03        21.07        18.61 
TCGA-D7-A4YV TCGA-D7-A6F0 TCGA-F1-A448 TCGA-HU-8602 
        5.92        22.29        21.27        22.32 

$`KLHL14 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8486 TCGA-BR-8588 
       25.05         3.72         5.39        25.18        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-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-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-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        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-D7-6524 
       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-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-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-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 

  KLHL14 MUTATED KLHL14 WILD-TYPE 
            0.26             0.00 
  KLHL14 MUTATED KLHL14 WILD-TYPE 
           34.68           122.30 
  KLHL14 MUTATED KLHL14 WILD-TYPE 
           17.28            14.17 
[1] "0.3 - 34.7 (17.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.5"
D480V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLHL14 MUTATED         1        0        4        1         2         3
  KLHL14 WILD-TYPE       1       15       36       29        35        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLHL14 MUTATED           0          2          2          2        1
  KLHL14 WILD-TYPE         3         68         51         30       37
D480V3, multiclass
            clus
vv           KLHL14 MUTATED KLHL14 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                4               36
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              2               51
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KLHL14 MUTATED     1   6   6   5
  KLHL14 WILD-TYPE  21  86 167  92
D480V4, multiclass
    clus
vv   KLHL14 MUTATED KLHL14 WILD-TYPE
  T1              1               21
  T2              6               86
  T3              6              167
  T4              5               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
  KLHL14 MUTATED     9   4   1   5
  KLHL14 WILD-TYPE 109 100  76  72
D480V5, multiclass
    clus
vv   KLHL14 MUTATED KLHL14 WILD-TYPE
  N0              9              109
  N1              4              100
  N2              1               76
  N3              5               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"
D480V6, binary
                  cls
clus                 0   1
  KLHL14 MUTATED    17   1
  KLHL14 WILD-TYPE 329  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL14 MUTATED     17    1
  KLHL14 WILD-TYPE  329   28
   clus
vv  KLHL14 MUTATED KLHL14 WILD-TYPE
  0             17              329
  1              1               28
[1] 2 2
[1] FALSE
D480V7, binary
                  cls
clus                 0   1
  KLHL14 MUTATED    13   6
  KLHL14 WILD-TYPE 132 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL14 MUTATED     13    6
  KLHL14 WILD-TYPE  132  242
        clus
vv       KLHL14 MUTATED KLHL14 WILD-TYPE
  FEMALE             13              132
  MALE                6              242
[1] 2 2
[1] FALSE
D480V8, binary
                  cls
clus                 0   1
  KLHL14 MUTATED    16   1
  KLHL14 WILD-TYPE 276  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL14 MUTATED     16    1
  KLHL14 WILD-TYPE  276   58
     clus
vv    KLHL14 MUTATED KLHL14 WILD-TYPE
  NO              16              276
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KLHL14 MUTATED                                          0
  KLHL14 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KLHL14 MUTATED                                       3
  KLHL14 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KLHL14 MUTATED                                                       12
  KLHL14 WILD-TYPE                                                    146
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KLHL14 MUTATED                                                   1
  KLHL14 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KLHL14 MUTATED                                                                   2
  KLHL14 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KLHL14 MUTATED                                                    0
  KLHL14 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KLHL14 MUTATED                                                  1
  KLHL14 WILD-TYPE                                               60
D480V9, multiclass
                                                                   clus
vv                                                                  KLHL14 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  KLHL14 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KLHL14 MUTATED    16   0   1   2
  KLHL14 WILD-TYPE 295  14  14  22
D480V10, multiclass
    clus
vv   KLHL14 MUTATED KLHL14 WILD-TYPE
  R0             16              295
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D480V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KLHL14 MUTATED       1                         1
  KLHL14 WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLHL14 MUTATED                                           0    14
  KLHL14 WILD-TYPE                                         1   229
D480V12, multiclass
                                           clus
vv                                          KLHL14 MUTATED KLHL14 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 14              229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D480V13, binary
                  cls
clus                 0   1
  KLHL14 MUTATED     1  15
  KLHL14 WILD-TYPE   3 295
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL14 MUTATED      1   15
  KLHL14 WILD-TYPE    3  295
                        clus
vv                       KLHL14 MUTATED KLHL14 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             15              295
[1] 2 2
[1] FALSE

Clustering(481) Variable = H2AFY MUTATION ANALYSIS
D481V1, survival
                 sevent
clus2               0   1
  H2AFY MUTATED     5   1
  H2AFY WILD-TYPE 225 138
  H2AFY MUTATED H2AFY WILD-TYPE 
              6             363 
  H2AFY MUTATED H2AFY WILD-TYPE 
              1             138 
$`H2AFY MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8361 TCGA-HU-A4GQ TCGA-HU-A4GX 
       26.70        34.68        29.59        31.10         0.10        20.25 

$`H2AFY WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  H2AFY MUTATED H2AFY WILD-TYPE 
            0.1             0.0 
  H2AFY MUTATED H2AFY WILD-TYPE 
          34.68          122.30 
  H2AFY MUTATED H2AFY WILD-TYPE 
         28.145          14.070 
[1] "0.1 - 34.7 (28.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.2"
D481V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  H2AFY MUTATED         0        0        0        0         1         2
  H2AFY WILD-TYPE       2       15       40       30        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  H2AFY MUTATED           0          1          0          3        0
  H2AFY WILD-TYPE         3         69         53         29       38
D481V3, multiclass
            clus
vv           H2AFY MUTATED H2AFY WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  H2AFY MUTATED     0   0   1   6
  H2AFY WILD-TYPE  22  92 172  91
D481V4, multiclass
    clus
vv   H2AFY MUTATED H2AFY WILD-TYPE
  T1             0              22
  T2             0              92
  T3             1             172
  T4             6              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
  H2AFY MUTATED     4   0   3   0
  H2AFY WILD-TYPE 114 104  74  77
D481V5, multiclass
    clus
vv   H2AFY MUTATED H2AFY WILD-TYPE
  N0             4             114
  N1             0             104
  N2             3              74
  N3             0              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"
D481V6, binary
                 cls
clus                0   1
  H2AFY MUTATED     7   0
  H2AFY WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFY MUTATED      7    0
  H2AFY WILD-TYPE  339   29
   clus
vv  H2AFY MUTATED H2AFY WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D481V7, binary
                 cls
clus                0   1
  H2AFY MUTATED     6   1
  H2AFY WILD-TYPE 139 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFY MUTATED      6    1
  H2AFY WILD-TYPE  139  247
        clus
vv       H2AFY MUTATED H2AFY WILD-TYPE
  FEMALE             6             139
  MALE               1             247
[1] 2 2
[1] FALSE
D481V8, binary
                 cls
clus                0   1
  H2AFY MUTATED     6   0
  H2AFY WILD-TYPE 286  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFY MUTATED      6    0
  H2AFY WILD-TYPE  286   59
     clus
vv    H2AFY MUTATED H2AFY WILD-TYPE
  NO              6             286
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  H2AFY MUTATED                                          0
  H2AFY WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  H2AFY MUTATED                                       2
  H2AFY WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  H2AFY MUTATED                                                        4
  H2AFY WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  H2AFY MUTATED                                                   0
  H2AFY WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  H2AFY MUTATED                                                                   0
  H2AFY WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  H2AFY MUTATED                                                    0
  H2AFY WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  H2AFY MUTATED                                                  1
  H2AFY WILD-TYPE                                               60
D481V9, multiclass
                                                                   clus
vv                                                                  H2AFY MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  H2AFY WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  H2AFY MUTATED     6   0   0   1
  H2AFY WILD-TYPE 305  14  15  23
D481V10, multiclass
    clus
vv   H2AFY MUTATED H2AFY WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D481V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  H2AFY MUTATED       2                         0
  H2AFY WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  H2AFY MUTATED                                           0     5
  H2AFY WILD-TYPE                                         1   238
D481V12, multiclass
                                           clus
vv                                          H2AFY MUTATED H2AFY WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D481V13, binary
                 cls
clus                0   1
  H2AFY MUTATED     0   7
  H2AFY WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFY MUTATED      0    7
  H2AFY WILD-TYPE    4  303
                        clus
vv                       H2AFY MUTATED H2AFY WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(482) Variable = USP35 MUTATION ANALYSIS
D482V1, survival
                 sevent
clus2               0   1
  USP35 MUTATED     6   2
  USP35 WILD-TYPE 224 137
  USP35 MUTATED USP35 WILD-TYPE 
              8             361 
  USP35 MUTATED USP35 WILD-TYPE 
              2             137 
$`USP35 MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8078 TCGA-BR-8361 TCGA-CD-8535 TCGA-CD-A48C 
       34.68        32.78        29.59        31.10        12.82        11.61 
TCGA-HF-A5NB TCGA-HU-A4GQ 
       30.51         0.10 

$`USP35 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  USP35 MUTATED USP35 WILD-TYPE 
            0.1             0.0 
  USP35 MUTATED USP35 WILD-TYPE 
          34.68          122.30 
  USP35 MUTATED USP35 WILD-TYPE 
          30.05           14.17 
[1] "0.1 - 34.7 (30.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2"  
D482V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP35 MUTATED         0        0        0        0         2         2
  USP35 WILD-TYPE       2       15       40       30        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  USP35 MUTATED           0          1          0          3        0
  USP35 WILD-TYPE         3         69         53         29       38
D482V3, multiclass
            clus
vv           USP35 MUTATED USP35 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP35 MUTATED     0   0   4   4
  USP35 WILD-TYPE  22  92 169  93
D482V4, multiclass
    clus
vv   USP35 MUTATED USP35 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             4             169
  T4             4              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
  USP35 MUTATED     3   2   2   1
  USP35 WILD-TYPE 115 102  75  76
D482V5, multiclass
    clus
vv   USP35 MUTATED USP35 WILD-TYPE
  N0             3             115
  N1             2             102
  N2             2              75
  N3             1              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"
D482V6, binary
                 cls
clus                0   1
  USP35 MUTATED     8   0
  USP35 WILD-TYPE 338  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP35 MUTATED      8    0
  USP35 WILD-TYPE  338   29
   clus
vv  USP35 MUTATED USP35 WILD-TYPE
  0             8             338
  1             0              29
[1] 2 2
[1] FALSE
D482V7, binary
                 cls
clus                0   1
  USP35 MUTATED     6   2
  USP35 WILD-TYPE 139 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP35 MUTATED      6    2
  USP35 WILD-TYPE  139  246
        clus
vv       USP35 MUTATED USP35 WILD-TYPE
  FEMALE             6             139
  MALE               2             246
[1] 2 2
[1] FALSE
D482V8, binary
                 cls
clus                0   1
  USP35 MUTATED     7   1
  USP35 WILD-TYPE 285  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP35 MUTATED      7    1
  USP35 WILD-TYPE  285   58
     clus
vv    USP35 MUTATED USP35 WILD-TYPE
  NO              7             285
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  USP35 MUTATED                                          0
  USP35 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  USP35 MUTATED                                       0
  USP35 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  USP35 MUTATED                                                        6
  USP35 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  USP35 MUTATED                                                   1
  USP35 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  USP35 MUTATED                                                                   0
  USP35 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  USP35 MUTATED                                                    0
  USP35 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  USP35 MUTATED                                                  1
  USP35 WILD-TYPE                                               60
D482V9, multiclass
                                                                   clus
vv                                                                  USP35 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  USP35 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP35 MUTATED     6   1   0   0
  USP35 WILD-TYPE 305  13  15  24
D482V10, multiclass
    clus
vv   USP35 MUTATED USP35 WILD-TYPE
  R0             6             305
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D482V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  USP35 MUTATED       3                         0
  USP35 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP35 MUTATED                                           0     4
  USP35 WILD-TYPE                                         1   239
D482V12, multiclass
                                           clus
vv                                          USP35 MUTATED USP35 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D482V13, binary
                 cls
clus                0   1
  USP35 MUTATED     0   7
  USP35 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP35 MUTATED      0    7
  USP35 WILD-TYPE    4  303
                        clus
vv                       USP35 MUTATED USP35 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(483) Variable = ZFP36L1 MUTATION ANALYSIS
D483V1, survival
                   sevent
clus2                 0   1
  ZFP36L1 MUTATED     3   1
  ZFP36L1 WILD-TYPE 227 138
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
                4               365 
  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE 
                1               138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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             14.17 
[1] "11.8 - 74.5 (41.5)" "0.0 - 122.3 (14.2)"
[1] "hr=" "2.9"
D483V2, 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       2       15       40       30        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFP36L1 MUTATED           0          2          0          0        1
  ZFP36L1 WILD-TYPE         3         68         53         32       37
D483V3, multiclass
            clus
vv           ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZFP36L1 MUTATED     0   0   2   3
  ZFP36L1 WILD-TYPE  22  92 171  94
D483V4, multiclass
    clus
vv   ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  T1               0                22
  T2               0                92
  T3               2               171
  T4               3                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
  ZFP36L1 MUTATED     2   3   0   0
  ZFP36L1 WILD-TYPE 116 101  77  77
D483V5, multiclass
    clus
vv   ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  N0               2               116
  N1               3               101
  N2               0                77
  N3               0                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"
D483V6, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     4   1
  ZFP36L1 WILD-TYPE 342  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      4    1
  ZFP36L1 WILD-TYPE  342   28
   clus
vv  ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  0               4               342
  1               1                28
[1] 2 2
[1] FALSE
D483V7, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     2   3
  ZFP36L1 WILD-TYPE 143 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      2    3
  ZFP36L1 WILD-TYPE  143  245
        clus
vv       ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  FEMALE               2               143
  MALE                 3               245
[1] 2 2
[1] FALSE
D483V8, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     4   1
  ZFP36L1 WILD-TYPE 288  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      4    1
  ZFP36L1 WILD-TYPE  288   58
     clus
vv    ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  NO                4               288
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZFP36L1 MUTATED                                          0
  ZFP36L1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZFP36L1 MUTATED                                       1
  ZFP36L1 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZFP36L1 MUTATED                                                        2
  ZFP36L1 WILD-TYPE                                                    156
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZFP36L1 MUTATED                                                   1
  ZFP36L1 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZFP36L1 MUTATED                                                                   1
  ZFP36L1 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZFP36L1 MUTATED                                                    0
  ZFP36L1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZFP36L1 MUTATED                                                  0
  ZFP36L1 WILD-TYPE                                               61
D483V9, multiclass
                                                                   clus
vv                                                                  ZFP36L1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  ZFP36L1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZFP36L1 MUTATED     4   0   0   0
  ZFP36L1 WILD-TYPE 307  14  15  24
D483V10, multiclass
    clus
vv   ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  R0               4               307
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D483V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ZFP36L1 MUTATED       1                         0
  ZFP36L1 WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZFP36L1 MUTATED                                           0     4
  ZFP36L1 WILD-TYPE                                         1   239
D483V12, multiclass
                                           clus
vv                                          ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D483V13, binary
                   cls
clus                  0   1
  ZFP36L1 MUTATED     1   3
  ZFP36L1 WILD-TYPE   3 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L1 MUTATED      1    3
  ZFP36L1 WILD-TYPE    3  307
                        clus
vv                       ZFP36L1 MUTATED ZFP36L1 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               3               307
[1] 2 2
[1] FALSE

Clustering(484) Variable = RASAL2 MUTATION ANALYSIS
D484V1, survival
                  sevent
clus2                0   1
  RASAL2 MUTATED    13   5
  RASAL2 WILD-TYPE 217 134
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              18              351 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
               5              134 
$`RASAL2 MUTATED`
TCGA-BR-4188 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8078 
        7.43         9.34         9.67        34.68        30.90        29.59 
TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-5723 
       32.25         1.12        31.96         9.01        18.97       105.07 
TCGA-D7-5579 TCGA-D7-A6EY TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-A4GN TCGA-VQ-A8P2 
       20.91        11.44        21.27        11.08        29.98        38.14 

$`RASAL2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-4191 
        9.47         9.44         6.61         6.97         4.64        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-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-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-4469 
       14.01        29.98        19.07        12.03         0.00         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-D7-6518 
       69.04        21.07         7.99        25.71        12.66        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-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 

  RASAL2 MUTATED RASAL2 WILD-TYPE 
            1.12             0.00 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
          105.07           122.30 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
           21.09            14.07 
[1] "1.1 - 105.1 (21.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D484V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RASAL2 MUTATED         0        0        1        1         4         3
  RASAL2 WILD-TYPE       2       15       39       29        33        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RASAL2 MUTATED           0          3          2          0        2
  RASAL2 WILD-TYPE         3         67         51         32       36
D484V3, multiclass
            clus
vv           RASAL2 MUTATED RASAL2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               4               33
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              2               51
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RASAL2 MUTATED     0   3   7   6
  RASAL2 WILD-TYPE  22  89 166  91
D484V4, multiclass
    clus
vv   RASAL2 MUTATED RASAL2 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              7              166
  T4              6               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
  RASAL2 MUTATED     7   5   3   3
  RASAL2 WILD-TYPE 111  99  74  74
D484V5, multiclass
    clus
vv   RASAL2 MUTATED RASAL2 WILD-TYPE
  N0              7              111
  N1              5               99
  N2              3               74
  N3              3               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"
D484V6, binary
                  cls
clus                 0   1
  RASAL2 MUTATED    17   2
  RASAL2 WILD-TYPE 329  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED     17    2
  RASAL2 WILD-TYPE  329   27
   clus
vv  RASAL2 MUTATED RASAL2 WILD-TYPE
  0             17              329
  1              2               27
[1] 2 2
[1] FALSE
D484V7, binary
                  cls
clus                 0   1
  RASAL2 MUTATED     9  10
  RASAL2 WILD-TYPE 136 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED      9   10
  RASAL2 WILD-TYPE  136  238
        clus
vv       RASAL2 MUTATED RASAL2 WILD-TYPE
  FEMALE              9              136
  MALE               10              238
[1] 2 2
[1] FALSE
D484V8, binary
                  cls
clus                 0   1
  RASAL2 MUTATED    15   3
  RASAL2 WILD-TYPE 277  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED     15    3
  RASAL2 WILD-TYPE  277   56
     clus
vv    RASAL2 MUTATED RASAL2 WILD-TYPE
  NO              15              277
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RASAL2 MUTATED                                          0
  RASAL2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RASAL2 MUTATED                                       1
  RASAL2 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RASAL2 MUTATED                                                       10
  RASAL2 WILD-TYPE                                                    148
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RASAL2 MUTATED                                                   3
  RASAL2 WILD-TYPE                                                18
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RASAL2 MUTATED                                                                   2
  RASAL2 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RASAL2 MUTATED                                                    0
  RASAL2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RASAL2 MUTATED                                                  3
  RASAL2 WILD-TYPE                                               58
D484V9, multiclass
                                                                   clus
vv                                                                  RASAL2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  RASAL2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RASAL2 MUTATED    14   1   1   3
  RASAL2 WILD-TYPE 297  13  14  21
D484V10, multiclass
    clus
vv   RASAL2 MUTATED RASAL2 WILD-TYPE
  R0             14              297
  R1              1               13
  R2              1               14
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D484V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RASAL2 MUTATED       2                         1
  RASAL2 WILD-TYPE    85                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RASAL2 MUTATED                                           0    13
  RASAL2 WILD-TYPE                                         1   230
D484V12, multiclass
                                           clus
vv                                          RASAL2 MUTATED RASAL2 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D484V13, binary
                  cls
clus                 0   1
  RASAL2 MUTATED     1  14
  RASAL2 WILD-TYPE   3 296
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED      1   14
  RASAL2 WILD-TYPE    3  296
                        clus
vv                       RASAL2 MUTATED RASAL2 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             14              296
[1] 2 2
[1] FALSE

Clustering(485) Variable = GTF3C1 MUTATION ANALYSIS
D485V1, survival
                  sevent
clus2                0   1
  GTF3C1 MUTATED    19  12
  GTF3C1 WILD-TYPE 211 127
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
              31              338 
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
              12              127 
$`GTF3C1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7704 
       26.70         6.97        30.90        34.68        36.16        35.24 
TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8369 TCGA-BR-8372 TCGA-BR-8382 
       35.84        32.25         0.26        14.04        31.27        25.05 
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-CD-5801 TCGA-CD-8536 
        1.12        28.14        20.65        16.14        13.18        12.43 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A4YV TCGA-D7-A6EY 
        6.58         1.02         6.02       105.07         5.92        11.44 
TCGA-F1-6874 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-IN-A6RL 
       14.47        26.47        22.32        22.68        29.98        13.35 
TCGA-VQ-A8P2 
       38.14 

$`GTF3C1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       21.90         9.21        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-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
        4.31         3.32        11.80        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-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-A4PE TCGA-BR-A4PF 
       28.34         0.66        32.52        13.51        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       21.44         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-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-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-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-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-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-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-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 

  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
            0.26             0.00 
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
          105.07           122.30 
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
          22.320           14.055 
[1] "0.3 - 105.1 (22.3)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D485V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GTF3C1 MUTATED         0        1        4        3         4         6
  GTF3C1 WILD-TYPE       2       14       36       27        33        46
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GTF3C1 MUTATED           0          5          3          3        3
  GTF3C1 WILD-TYPE         3         65         50         29       35
D485V3, multiclass
            clus
vv           GTF3C1 MUTATED GTF3C1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                4               36
  STAGE II                3               27
  STAGE IIA               4               33
  STAGE IIB               6               46
  STAGE III               0                3
  STAGE IIIA              5               65
  STAGE IIIB              3               50
  STAGE IIIC              3               29
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GTF3C1 MUTATED     2   8  13  11
  GTF3C1 WILD-TYPE  20  84 160  86
D485V4, multiclass
    clus
vv   GTF3C1 MUTATED GTF3C1 WILD-TYPE
  T1              2               20
  T2              8               84
  T3             13              160
  T4             11               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
  GTF3C1 MUTATED    15  10   2   6
  GTF3C1 WILD-TYPE 103  94  75  71
D485V5, multiclass
    clus
vv   GTF3C1 MUTATED GTF3C1 WILD-TYPE
  N0             15              103
  N1             10               94
  N2              2               75
  N3              6               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"
D485V6, binary
                  cls
clus                 0   1
  GTF3C1 MUTATED    32   1
  GTF3C1 WILD-TYPE 314  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C1 MUTATED     32    1
  GTF3C1 WILD-TYPE  314   28
   clus
vv  GTF3C1 MUTATED GTF3C1 WILD-TYPE
  0             32              314
  1              1               28
[1] 2 2
[1] FALSE
D485V7, binary
                  cls
clus                 0   1
  GTF3C1 MUTATED    21  14
  GTF3C1 WILD-TYPE 124 234
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C1 MUTATED     21   14
  GTF3C1 WILD-TYPE  124  234
        clus
vv       GTF3C1 MUTATED GTF3C1 WILD-TYPE
  FEMALE             21              124
  MALE               14              234
[1] 2 2
[1] FALSE
D485V8, binary
                  cls
clus                 0   1
  GTF3C1 MUTATED    29   1
  GTF3C1 WILD-TYPE 263  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C1 MUTATED     29    1
  GTF3C1 WILD-TYPE  263   58
     clus
vv    GTF3C1 MUTATED GTF3C1 WILD-TYPE
  NO              29              263
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GTF3C1 MUTATED                                          1
  GTF3C1 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GTF3C1 MUTATED                                       4
  GTF3C1 WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GTF3C1 MUTATED                                                       22
  GTF3C1 WILD-TYPE                                                    136
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GTF3C1 MUTATED                                                   1
  GTF3C1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GTF3C1 MUTATED                                                                   3
  GTF3C1 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GTF3C1 MUTATED                                                    1
  GTF3C1 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GTF3C1 MUTATED                                                  3
  GTF3C1 WILD-TYPE                                               58
D485V9, multiclass
                                                                   clus
vv                                                                  GTF3C1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  GTF3C1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         136
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GTF3C1 MUTATED    26   0   1   6
  GTF3C1 WILD-TYPE 285  14  14  18
D485V10, multiclass
    clus
vv   GTF3C1 MUTATED GTF3C1 WILD-TYPE
  R0             26              285
  R1              0               14
  R2              1               14
  RX              6               18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D485V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GTF3C1 MUTATED       6                         0
  GTF3C1 WILD-TYPE    81                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GTF3C1 MUTATED                                           0    26
  GTF3C1 WILD-TYPE                                         1   217
D485V12, multiclass
                                           clus
vv                                          GTF3C1 MUTATED GTF3C1 WILD-TYPE
  ASIAN                                                  6               81
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 26              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D485V13, binary
                  cls
clus                 0   1
  GTF3C1 MUTATED     0  31
  GTF3C1 WILD-TYPE   4 279
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C1 MUTATED      0   31
  GTF3C1 WILD-TYPE    4  279
                        clus
vv                       GTF3C1 MUTATED GTF3C1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             31              279
[1] 2 2
[1] FALSE

Clustering(486) Variable = RPS20 MUTATION ANALYSIS
D486V1, survival
                 sevent
clus2               0   1
  RPS20 MUTATED     2   1
  RPS20 WILD-TYPE 228 138
  RPS20 MUTATED RPS20 WILD-TYPE 
              3             366 
  RPS20 MUTATED RPS20 WILD-TYPE 
              1             138 
$`RPS20 MUTATED`
TCGA-BR-8284 TCGA-D7-8573 TCGA-D7-8574 
        8.05        19.50        17.19 

$`RPS20 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-8575 TCGA-D7-8576 
       11.31        12.33        24.72        16.80        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 

  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           14.22 
[1] "8.1 - 19.5 (17.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1"  
D486V2, 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       2       15       40       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPS20 MUTATED           0          1          0          1        0
  RPS20 WILD-TYPE         3         69         53         31       38
D486V3, multiclass
            clus
vv           RPS20 MUTATED RPS20 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RPS20 MUTATED     0   1   2   1
  RPS20 WILD-TYPE  22  91 171  96
D486V4, multiclass
    clus
vv   RPS20 MUTATED RPS20 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             2             171
  T4             1              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
  RPS20 MUTATED     1   0   0   2
  RPS20 WILD-TYPE 117 104  77  75
D486V5, multiclass
    clus
vv   RPS20 MUTATED RPS20 WILD-TYPE
  N0             1             117
  N1             0             104
  N2             0              77
  N3             2              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"
D486V6, binary
                 cls
clus                0   1
  RPS20 MUTATED     3   0
  RPS20 WILD-TYPE 343  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS20 MUTATED      3    0
  RPS20 WILD-TYPE  343   29
   clus
vv  RPS20 MUTATED RPS20 WILD-TYPE
  0             3             343
  1             0              29
[1] 2 2
[1] FALSE
D486V7, binary
                 cls
clus                0   1
  RPS20 MUTATED     2   2
  RPS20 WILD-TYPE 143 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS20 MUTATED      2    2
  RPS20 WILD-TYPE  143  246
        clus
vv       RPS20 MUTATED RPS20 WILD-TYPE
  FEMALE             2             143
  MALE               2             246
[1] 2 2
[1] FALSE
D486V8, binary
                 cls
clus                0   1
  RPS20 MUTATED     3   0
  RPS20 WILD-TYPE 289  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS20 MUTATED      3    0
  RPS20 WILD-TYPE  289   59
     clus
vv    RPS20 MUTATED RPS20 WILD-TYPE
  NO              3             289
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RPS20 MUTATED                                          0
  RPS20 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RPS20 MUTATED                                       0
  RPS20 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RPS20 MUTATED                                                        2
  RPS20 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RPS20 MUTATED                                                   0
  RPS20 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RPS20 MUTATED                                                                   1
  RPS20 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RPS20 MUTATED                                                    0
  RPS20 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RPS20 MUTATED                                                  1
  RPS20 WILD-TYPE                                               60
D486V9, multiclass
                                                                   clus
vv                                                                  RPS20 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  RPS20 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RPS20 MUTATED     3   0   0   1
  RPS20 WILD-TYPE 308  14  15  23
D486V10, multiclass
    clus
vv   RPS20 MUTATED RPS20 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D486V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RPS20 MUTATED       0                         0
  RPS20 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RPS20 MUTATED                                           0     4
  RPS20 WILD-TYPE                                         1   239
D486V12, multiclass
                                           clus
vv                                          RPS20 MUTATED RPS20 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D486V13, binary
                 cls
clus                0   1
  RPS20 MUTATED     0   4
  RPS20 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPS20 MUTATED      0    4
  RPS20 WILD-TYPE    4  306
                        clus
vv                       RPS20 MUTATED RPS20 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(487) Variable = KIAA0748 MUTATION ANALYSIS
D487V1, survival
                    sevent
clus2                  0   1
  KIAA0748 MUTATED    10   5
  KIAA0748 WILD-TYPE 220 134
  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
                15                354 
  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
                 5                134 
$`KIAA0748 MUTATED`
TCGA-BR-4267 TCGA-BR-6453 TCGA-BR-6458 TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8368 
        6.18        15.95        19.33        44.94        32.25         4.31 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4437 TCGA-CG-5732 TCGA-FP-A4BE 
       12.82        12.43         6.58         8.05        69.04        11.08 
TCGA-HU-A4GQ TCGA-HU-A4H8 TCGA-R5-A7ZI 
        0.10        14.07        74.53 

$`KIAA0748 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
             12.82              14.45 
[1] "0.1 - 74.5 (12.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D487V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0748 MUTATED         0        0        4        2         4         2
  KIAA0748 WILD-TYPE       2       15       36       28        33        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0748 MUTATED           0          1          0          1        2
  KIAA0748 WILD-TYPE         3         69         53         31       36
D487V3, multiclass
            clus
vv           KIAA0748 MUTATED KIAA0748 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  4                 36
  STAGE II                  2                 28
  STAGE IIA                 4                 33
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                0                 53
  STAGE IIIC                1                 31
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0748 MUTATED     1   6   6   3
  KIAA0748 WILD-TYPE  21  86 167  94
D487V4, multiclass
    clus
vv   KIAA0748 MUTATED KIAA0748 WILD-TYPE
  T1                1                 21
  T2                6                 86
  T3                6                167
  T4                3                 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
  KIAA0748 MUTATED     8   6   1   1
  KIAA0748 WILD-TYPE 110  98  76  76
D487V5, multiclass
    clus
vv   KIAA0748 MUTATED KIAA0748 WILD-TYPE
  N0                8                110
  N1                6                 98
  N2                1                 76
  N3                1                 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"
D487V6, binary
                    cls
clus                   0   1
  KIAA0748 MUTATED    15   1
  KIAA0748 WILD-TYPE 331  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0748 MUTATED     15    1
  KIAA0748 WILD-TYPE  331   28
   clus
vv  KIAA0748 MUTATED KIAA0748 WILD-TYPE
  0               15                331
  1                1                 28
[1] 2 2
[1] FALSE
D487V7, binary
                    cls
clus                   0   1
  KIAA0748 MUTATED     6  10
  KIAA0748 WILD-TYPE 139 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0748 MUTATED      6   10
  KIAA0748 WILD-TYPE  139  238
        clus
vv       KIAA0748 MUTATED KIAA0748 WILD-TYPE
  FEMALE                6                139
  MALE                 10                238
[1] 2 2
[1] FALSE
D487V8, binary
                    cls
clus                   0   1
  KIAA0748 MUTATED    15   1
  KIAA0748 WILD-TYPE 277  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0748 MUTATED     15    1
  KIAA0748 WILD-TYPE  277   58
     clus
vv    KIAA0748 MUTATED KIAA0748 WILD-TYPE
  NO                15                277
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA0748 MUTATED                                          0
  KIAA0748 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA0748 MUTATED                                       2
  KIAA0748 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0748 MUTATED                                                       10
  KIAA0748 WILD-TYPE                                                    148
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA0748 MUTATED                                                   0
  KIAA0748 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0748 MUTATED                                                                   2
  KIAA0748 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA0748 MUTATED                                                    0
  KIAA0748 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA0748 MUTATED                                                  2
  KIAA0748 WILD-TYPE                                               59
D487V9, multiclass
                                                                   clus
vv                                                                  KIAA0748 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  KIAA0748 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0748 MUTATED    14   0   0   1
  KIAA0748 WILD-TYPE 297  14  15  23
D487V10, multiclass
    clus
vv   KIAA0748 MUTATED KIAA0748 WILD-TYPE
  R0               14                297
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D487V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0748 MUTATED       5                         1
  KIAA0748 WILD-TYPE    82                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0748 MUTATED                                           0     8
  KIAA0748 WILD-TYPE                                         1   235
D487V12, multiclass
                                           clus
vv                                          KIAA0748 MUTATED KIAA0748 WILD-TYPE
  ASIAN                                                    5                 82
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    8                235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D487V13, binary
                    cls
clus                   0   1
  KIAA0748 MUTATED     1  13
  KIAA0748 WILD-TYPE   3 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0748 MUTATED      1   13
  KIAA0748 WILD-TYPE    3  297
                        clus
vv                       KIAA0748 MUTATED KIAA0748 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               13                297
[1] 2 2
[1] FALSE

Clustering(488) Variable = USP1 MUTATION ANALYSIS
D488V1, survival
                sevent
clus2              0   1
  USP1 MUTATED     4   1
  USP1 WILD-TYPE 226 138
  USP1 MUTATED USP1 WILD-TYPE 
             5            364 
  USP1 MUTATED USP1 WILD-TYPE 
             1            138 
$`USP1 MUTATED`
TCGA-BR-8078 TCGA-BR-8382 TCGA-BR-8680 TCGA-CG-5728 TCGA-D7-A4YY 
       29.59        25.05        31.96        65.10        13.78 

$`USP1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  USP1 MUTATED USP1 WILD-TYPE 
         13.78           0.00 
  USP1 MUTATED USP1 WILD-TYPE 
          65.1          122.3 
  USP1 MUTATED USP1 WILD-TYPE 
         29.59          14.12 
[1] "13.8 - 65.1 (29.6)" "0.0 - 122.3 (14.1)"
[1] "hr=" "3.1"
D488V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP1 MUTATED         0        0        1        0         0         1
  USP1 WILD-TYPE       2       15       39       30        37        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  USP1 MUTATED           0          0          1          1        1
  USP1 WILD-TYPE         3         70         52         31       37
D488V3, multiclass
            clus
vv           USP1 MUTATED USP1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  USP1 MUTATED     0   1   1   3
  USP1 WILD-TYPE  22  91 172  94
D488V4, multiclass
    clus
vv   USP1 MUTATED USP1 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            1            172
  T4            3             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
  USP1 MUTATED     2   0   1   2
  USP1 WILD-TYPE 116 104  76  75
D488V5, multiclass
    clus
vv   USP1 MUTATED USP1 WILD-TYPE
  N0            2            116
  N1            0            104
  N2            1             76
  N3            2             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"
D488V6, binary
                cls
clus               0   1
  USP1 MUTATED     4   1
  USP1 WILD-TYPE 342  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      4    1
  USP1 WILD-TYPE  342   28
   clus
vv  USP1 MUTATED USP1 WILD-TYPE
  0            4            342
  1            1             28
[1] 2 2
[1] FALSE
D488V7, binary
                cls
clus               0   1
  USP1 MUTATED     3   2
  USP1 WILD-TYPE 142 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      3    2
  USP1 WILD-TYPE  142  246
        clus
vv       USP1 MUTATED USP1 WILD-TYPE
  FEMALE            3            142
  MALE              2            246
[1] 2 2
[1] FALSE
D488V8, binary
                cls
clus               0   1
  USP1 MUTATED     3   1
  USP1 WILD-TYPE 289  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      3    1
  USP1 WILD-TYPE  289   58
     clus
vv    USP1 MUTATED USP1 WILD-TYPE
  NO             3            289
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  USP1 MUTATED                                          0
  USP1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  USP1 MUTATED                                       0
  USP1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  USP1 MUTATED                                                        3
  USP1 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  USP1 MUTATED                                                   0
  USP1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  USP1 MUTATED                                                                   1
  USP1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  USP1 MUTATED                                                    0
  USP1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  USP1 MUTATED                                                  1
  USP1 WILD-TYPE                                               60
D488V9, multiclass
                                                                   clus
vv                                                                  USP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  USP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  USP1 MUTATED     5   0   0   0
  USP1 WILD-TYPE 306  14  15  24
D488V10, multiclass
    clus
vv   USP1 MUTATED USP1 WILD-TYPE
  R0            5            306
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D488V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  USP1 MUTATED       1                         0
  USP1 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP1 MUTATED                                           0     3
  USP1 WILD-TYPE                                         1   240
D488V12, multiclass
                                           clus
vv                                          USP1 MUTATED USP1 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D488V13, binary
                cls
clus               0   1
  USP1 MUTATED     0   4
  USP1 WILD-TYPE   4 306
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      0    4
  USP1 WILD-TYPE    4  306
                        clus
vv                       USP1 MUTATED USP1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            4            306
[1] 2 2
[1] FALSE

Clustering(489) Variable = BRMS1 MUTATION ANALYSIS
D489V1, survival
                 sevent
clus2               0   1
  BRMS1 MUTATED     4   2
  BRMS1 WILD-TYPE 226 137
  BRMS1 MUTATED BRMS1 WILD-TYPE 
              6             363 
  BRMS1 MUTATED BRMS1 WILD-TYPE 
              2             137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  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           14.27 
[1] "8.0 - 34.7 (21.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D489V2, 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       2       15       39       30        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BRMS1 MUTATED           0          0          0          0        0
  BRMS1 WILD-TYPE         3         70         53         32       38
D489V3, multiclass
            clus
vv           BRMS1 MUTATED BRMS1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BRMS1 MUTATED     1   1   2   1
  BRMS1 WILD-TYPE  21  91 171  96
D489V4, multiclass
    clus
vv   BRMS1 MUTATED BRMS1 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             2             171
  T4             1              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
  BRMS1 MUTATED     2   4   0   0
  BRMS1 WILD-TYPE 116 100  77  77
D489V5, multiclass
    clus
vv   BRMS1 MUTATED BRMS1 WILD-TYPE
  N0             2             116
  N1             4             100
  N2             0              77
  N3             0              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"
D489V6, binary
                 cls
clus                0   1
  BRMS1 MUTATED     5   0
  BRMS1 WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRMS1 MUTATED      5    0
  BRMS1 WILD-TYPE  341   29
   clus
vv  BRMS1 MUTATED BRMS1 WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D489V7, binary
                 cls
clus                0   1
  BRMS1 MUTATED     3   3
  BRMS1 WILD-TYPE 142 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRMS1 MUTATED      3    3
  BRMS1 WILD-TYPE  142  245
        clus
vv       BRMS1 MUTATED BRMS1 WILD-TYPE
  FEMALE             3             142
  MALE               3             245
[1] 2 2
[1] FALSE
D489V8, binary
                 cls
clus                0   1
  BRMS1 MUTATED     5   1
  BRMS1 WILD-TYPE 287  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRMS1 MUTATED      5    1
  BRMS1 WILD-TYPE  287   58
     clus
vv    BRMS1 MUTATED BRMS1 WILD-TYPE
  NO              5             287
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BRMS1 MUTATED                                          0
  BRMS1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BRMS1 MUTATED                                       0
  BRMS1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BRMS1 MUTATED                                                        3
  BRMS1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BRMS1 MUTATED                                                   0
  BRMS1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BRMS1 MUTATED                                                                   1
  BRMS1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BRMS1 MUTATED                                                    0
  BRMS1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BRMS1 MUTATED                                                  2
  BRMS1 WILD-TYPE                                               59
D489V9, multiclass
                                                                   clus
vv                                                                  BRMS1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  BRMS1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BRMS1 MUTATED     4   0   0   1
  BRMS1 WILD-TYPE 307  14  15  23
D489V10, multiclass
    clus
vv   BRMS1 MUTATED BRMS1 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D489V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BRMS1 MUTATED       2                         0
  BRMS1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRMS1 MUTATED                                           0     4
  BRMS1 WILD-TYPE                                         1   239
D489V12, multiclass
                                           clus
vv                                          BRMS1 MUTATED BRMS1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D489V13, binary
                 cls
clus                0   1
  BRMS1 MUTATED     0   6
  BRMS1 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRMS1 MUTATED      0    6
  BRMS1 WILD-TYPE    4  304
                        clus
vv                       BRMS1 MUTATED BRMS1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(490) Variable = RNASEL MUTATION ANALYSIS
D490V1, survival
                  sevent
clus2                0   1
  RNASEL MUTATED     6   0
  RNASEL WILD-TYPE 224 139
  RNASEL MUTATED RNASEL WILD-TYPE 
               6              363 
  RNASEL MUTATED RNASEL WILD-TYPE 
               0              139 
$`RNASEL MUTATED`
TCGA-B7-5818 TCGA-BR-8360 TCGA-BR-8680 TCGA-CG-4305 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       11.70         6.18        31.96        15.95        19.73        38.14 

$`RNASEL WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  RNASEL MUTATED RNASEL WILD-TYPE 
            6.18             0.00 
  RNASEL MUTATED RNASEL WILD-TYPE 
           38.14           122.30 
  RNASEL MUTATED RNASEL WILD-TYPE 
           17.84            14.17 
[1] "6.2 - 38.1 (17.8)"  "0.0 - 122.3 (14.2)"
[1] "hr="     "9200000"
D490V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RNASEL MUTATED         0        0        1        1         1         0
  RNASEL WILD-TYPE       2       15       39       29        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNASEL MUTATED           0          2          0          0        1
  RNASEL WILD-TYPE         3         68         53         32       37
D490V3, multiclass
            clus
vv           RNASEL MUTATED RNASEL WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNASEL MUTATED     0   2   2   2
  RNASEL WILD-TYPE  22  90 171  95
D490V4, multiclass
    clus
vv   RNASEL MUTATED RNASEL WILD-TYPE
  T1              0               22
  T2              2               90
  T3              2              171
  T4              2               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
  RNASEL MUTATED     2   2   2   0
  RNASEL WILD-TYPE 116 102  75  77
D490V5, multiclass
    clus
vv   RNASEL MUTATED RNASEL WILD-TYPE
  N0              2              116
  N1              2              102
  N2              2               75
  N3              0               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"
D490V6, binary
                  cls
clus                 0   1
  RNASEL MUTATED     5   1
  RNASEL WILD-TYPE 341  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASEL MUTATED      5    1
  RNASEL WILD-TYPE  341   28
   clus
vv  RNASEL MUTATED RNASEL WILD-TYPE
  0              5              341
  1              1               28
[1] 2 2
[1] FALSE
D490V7, binary
                  cls
clus                 0   1
  RNASEL MUTATED     1   5
  RNASEL WILD-TYPE 144 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASEL MUTATED      1    5
  RNASEL WILD-TYPE  144  243
        clus
vv       RNASEL MUTATED RNASEL WILD-TYPE
  FEMALE              1              144
  MALE                5              243
[1] 2 2
[1] FALSE
D490V8, binary
                  cls
clus                 0   1
  RNASEL MUTATED     5   1
  RNASEL WILD-TYPE 287  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASEL MUTATED      5    1
  RNASEL WILD-TYPE  287   58
     clus
vv    RNASEL MUTATED RNASEL WILD-TYPE
  NO               5              287
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RNASEL MUTATED                                          0
  RNASEL WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RNASEL MUTATED                                       1
  RNASEL WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RNASEL MUTATED                                                        1
  RNASEL WILD-TYPE                                                    157
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RNASEL MUTATED                                                   1
  RNASEL WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RNASEL MUTATED                                                                   1
  RNASEL WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RNASEL MUTATED                                                    0
  RNASEL WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RNASEL MUTATED                                                  2
  RNASEL WILD-TYPE                                               59
D490V9, multiclass
                                                                   clus
vv                                                                  RNASEL MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  RNASEL WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RNASEL MUTATED     6   0   0   0
  RNASEL WILD-TYPE 305  14  15  24
D490V10, multiclass
    clus
vv   RNASEL MUTATED RNASEL WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D490V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RNASEL MUTATED       1                         0
  RNASEL WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RNASEL MUTATED                                           0     4
  RNASEL WILD-TYPE                                         1   239
D490V12, multiclass
                                           clus
vv                                          RNASEL MUTATED RNASEL WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D490V13, binary
                  cls
clus                 0   1
  RNASEL MUTATED     0   4
  RNASEL WILD-TYPE   4 306
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASEL MUTATED      0    4
  RNASEL WILD-TYPE    4  306
                        clus
vv                       RNASEL MUTATED RNASEL WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              306
[1] 2 2
[1] FALSE

Clustering(491) Variable = TIMP3 MUTATION ANALYSIS
D491V1, survival
                 sevent
clus2               0   1
  TIMP3 MUTATED     7   0
  TIMP3 WILD-TYPE 223 139
  TIMP3 MUTATED TIMP3 WILD-TYPE 
              7             362 
  TIMP3 MUTATED TIMP3 WILD-TYPE 
              0             139 
$`TIMP3 MUTATED`
TCGA-B7-A5TI TCGA-BR-8487 TCGA-BR-A4J4 TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4GU 
       19.56         1.12         0.53        24.20         6.51         6.58 
TCGA-VQ-A8P3 
       37.22 

$`TIMP3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  TIMP3 MUTATED TIMP3 WILD-TYPE 
           0.53            0.00 
  TIMP3 MUTATED TIMP3 WILD-TYPE 
          37.22          122.30 
  TIMP3 MUTATED TIMP3 WILD-TYPE 
           6.58           14.35 
[1] "0.5 - 37.2 (6.6)"   "0.0 - 122.3 (14.3)"
[1] "hr="     "9100000"
D491V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TIMP3 MUTATED         0        1        0        0         2         1
  TIMP3 WILD-TYPE       2       14       40       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TIMP3 MUTATED           0          2          1          1        0
  TIMP3 WILD-TYPE         3         68         52         31       38
D491V3, multiclass
            clus
vv           TIMP3 MUTATED TIMP3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TIMP3 MUTATED     1   0   5   3
  TIMP3 WILD-TYPE  21  92 168  94
D491V4, multiclass
    clus
vv   TIMP3 MUTATED TIMP3 WILD-TYPE
  T1             1              21
  T2             0              92
  T3             5             168
  T4             3              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
  TIMP3 MUTATED     3   3   1   1
  TIMP3 WILD-TYPE 115 101  76  76
D491V5, multiclass
    clus
vv   TIMP3 MUTATED TIMP3 WILD-TYPE
  N0             3             115
  N1             3             101
  N2             1              76
  N3             1              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"
D491V6, binary
                 cls
clus                0   1
  TIMP3 MUTATED     8   0
  TIMP3 WILD-TYPE 338  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIMP3 MUTATED      8    0
  TIMP3 WILD-TYPE  338   29
   clus
vv  TIMP3 MUTATED TIMP3 WILD-TYPE
  0             8             338
  1             0              29
[1] 2 2
[1] FALSE
D491V7, binary
                 cls
clus                0   1
  TIMP3 MUTATED     3   6
  TIMP3 WILD-TYPE 142 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIMP3 MUTATED      3    6
  TIMP3 WILD-TYPE  142  242
        clus
vv       TIMP3 MUTATED TIMP3 WILD-TYPE
  FEMALE             3             142
  MALE               6             242
[1] 2 2
[1] FALSE
D491V8, binary
                 cls
clus                0   1
  TIMP3 MUTATED     5   2
  TIMP3 WILD-TYPE 287  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIMP3 MUTATED      5    2
  TIMP3 WILD-TYPE  287   57
     clus
vv    TIMP3 MUTATED TIMP3 WILD-TYPE
  NO              5             287
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TIMP3 MUTATED                                          0
  TIMP3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TIMP3 MUTATED                                       2
  TIMP3 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TIMP3 MUTATED                                                        4
  TIMP3 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TIMP3 MUTATED                                                   0
  TIMP3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TIMP3 MUTATED                                                                   0
  TIMP3 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TIMP3 MUTATED                                                    0
  TIMP3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TIMP3 MUTATED                                                  3
  TIMP3 WILD-TYPE                                               58
D491V9, multiclass
                                                                   clus
vv                                                                  TIMP3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  TIMP3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TIMP3 MUTATED     6   1   0   1
  TIMP3 WILD-TYPE 305  13  15  23
D491V10, multiclass
    clus
vv   TIMP3 MUTATED TIMP3 WILD-TYPE
  R0             6             305
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D491V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TIMP3 MUTATED       4                         0
  TIMP3 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TIMP3 MUTATED                                           0     4
  TIMP3 WILD-TYPE                                         1   239
D491V12, multiclass
                                           clus
vv                                          TIMP3 MUTATED TIMP3 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D491V13, binary
                 cls
clus                0   1
  TIMP3 MUTATED     0   7
  TIMP3 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIMP3 MUTATED      0    7
  TIMP3 WILD-TYPE    4  303
                        clus
vv                       TIMP3 MUTATED TIMP3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(492) Variable = RELT MUTATION ANALYSIS
D492V1, survival
                sevent
clus2              0   1
  RELT MUTATED     5   2
  RELT WILD-TYPE 225 137
  RELT MUTATED RELT WILD-TYPE 
             7            362 
  RELT MUTATED RELT WILD-TYPE 
             2            137 
$`RELT MUTATED`
TCGA-BR-8078 TCGA-BR-8487 TCGA-D7-A6EY TCGA-HF-7134 TCGA-HU-A4GQ TCGA-HU-A4GT 
       29.59         1.12        11.44        52.21         0.10         6.51 
TCGA-HU-A4GU 
        6.58 

$`RELT WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        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-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-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        8.98        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 

  RELT MUTATED RELT WILD-TYPE 
           0.1            0.0 
  RELT MUTATED RELT WILD-TYPE 
         52.21         122.30 
  RELT MUTATED RELT WILD-TYPE 
          6.58          14.45 
[1] "0.1 - 52.2 (6.6)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D492V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RELT MUTATED         0        1        0        0         2         2
  RELT WILD-TYPE       2       14       40       30        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RELT MUTATED           0          0          1          1        0
  RELT WILD-TYPE         3         70         52         31       38
D492V3, multiclass
            clus
vv           RELT MUTATED RELT WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RELT MUTATED     1   0   4   2
  RELT WILD-TYPE  21  92 169  95
D492V4, multiclass
    clus
vv   RELT MUTATED RELT WILD-TYPE
  T1            1             21
  T2            0             92
  T3            4            169
  T4            2             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
  RELT MUTATED     4   1   1   1
  RELT WILD-TYPE 114 103  76  76
D492V5, multiclass
    clus
vv   RELT MUTATED RELT WILD-TYPE
  N0            4            114
  N1            1            103
  N2            1             76
  N3            1             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"
D492V6, binary
                cls
clus               0   1
  RELT MUTATED     7   0
  RELT WILD-TYPE 339  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELT MUTATED      7    0
  RELT WILD-TYPE  339   29
   clus
vv  RELT MUTATED RELT WILD-TYPE
  0            7            339
  1            0             29
[1] 2 2
[1] FALSE
D492V7, binary
                cls
clus               0   1
  RELT MUTATED     4   3
  RELT WILD-TYPE 141 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELT MUTATED      4    3
  RELT WILD-TYPE  141  245
        clus
vv       RELT MUTATED RELT WILD-TYPE
  FEMALE            4            141
  MALE              3            245
[1] 2 2
[1] FALSE
D492V8, binary
                cls
clus               0   1
  RELT MUTATED     7   0
  RELT WILD-TYPE 285  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELT MUTATED      7    0
  RELT WILD-TYPE  285   59
     clus
vv    RELT MUTATED RELT WILD-TYPE
  NO             7            285
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RELT MUTATED                                          0
  RELT WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RELT MUTATED                                       1
  RELT WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RELT MUTATED                                                        2
  RELT WILD-TYPE                                                    156
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RELT MUTATED                                                   0
  RELT WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RELT MUTATED                                                                   1
  RELT WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RELT MUTATED                                                    0
  RELT WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RELT MUTATED                                                  3
  RELT WILD-TYPE                                               58
D492V9, multiclass
                                                                   clus
vv                                                                  RELT MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  RELT WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RELT MUTATED     7   0   0   0
  RELT WILD-TYPE 304  14  15  24
D492V10, multiclass
    clus
vv   RELT MUTATED RELT WILD-TYPE
  R0            7            304
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D492V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RELT MUTATED       3                         0
  RELT WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RELT MUTATED                                           0     3
  RELT WILD-TYPE                                         1   240
D492V12, multiclass
                                           clus
vv                                          RELT MUTATED RELT WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D492V13, binary
                cls
clus               0   1
  RELT MUTATED     0   6
  RELT WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELT MUTATED      0    6
  RELT WILD-TYPE    4  304
                        clus
vv                       RELT MUTATED RELT WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(493) Variable = HAUS3 MUTATION ANALYSIS
D493V1, survival
                 sevent
clus2               0   1
  HAUS3 MUTATED     6   4
  HAUS3 WILD-TYPE 224 135
  HAUS3 MUTATED HAUS3 WILD-TYPE 
             10             359 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
              4             135 
$`HAUS3 MUTATED`
TCGA-CG-4460 TCGA-BR-4191 TCGA-BR-6452 TCGA-BR-8363 TCGA-CD-5813 TCGA-CG-5721 
       21.99        18.35        34.68         0.26        12.39         6.02 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-MX-A5UJ TCGA-R5-A7ZI 
        6.51         6.58        19.73        74.53 

$`HAUS3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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 

  HAUS3 MUTATED HAUS3 WILD-TYPE 
           0.26            0.00 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
          74.53          122.30 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
          15.37           14.27 
[1] "0.3 - 74.5 (15.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D493V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HAUS3 MUTATED         1        0        1        1         2         1
  HAUS3 WILD-TYPE       1       15       39       29        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HAUS3 MUTATED           0          1          0          0        3
  HAUS3 WILD-TYPE         3         69         53         32       35
D493V3, multiclass
            clus
vv           HAUS3 MUTATED HAUS3 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HAUS3 MUTATED     1   1   5   3
  HAUS3 WILD-TYPE  21  91 168  94
D493V4, multiclass
    clus
vv   HAUS3 MUTATED HAUS3 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             5             168
  T4             3              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
  HAUS3 MUTATED     4   6   1   0
  HAUS3 WILD-TYPE 114  98  76  77
D493V5, multiclass
    clus
vv   HAUS3 MUTATED HAUS3 WILD-TYPE
  N0             4             114
  N1             6              98
  N2             1              76
  N3             0              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"
D493V6, binary
                 cls
clus                0   1
  HAUS3 MUTATED     8   2
  HAUS3 WILD-TYPE 338  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      8    2
  HAUS3 WILD-TYPE  338   27
   clus
vv  HAUS3 MUTATED HAUS3 WILD-TYPE
  0             8             338
  1             2              27
[1] 2 2
[1] FALSE
D493V7, binary
                 cls
clus                0   1
  HAUS3 MUTATED     6   5
  HAUS3 WILD-TYPE 139 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      6    5
  HAUS3 WILD-TYPE  139  243
        clus
vv       HAUS3 MUTATED HAUS3 WILD-TYPE
  FEMALE             6             139
  MALE               5             243
[1] 2 2
[1] FALSE
D493V8, binary
                 cls
clus                0   1
  HAUS3 MUTATED    11   0
  HAUS3 WILD-TYPE 281  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED     11    0
  HAUS3 WILD-TYPE  281   59
     clus
vv    HAUS3 MUTATED HAUS3 WILD-TYPE
  NO             11             281
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HAUS3 MUTATED                                          0
  HAUS3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HAUS3 MUTATED                                       2
  HAUS3 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HAUS3 MUTATED                                                        4
  HAUS3 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HAUS3 MUTATED                                                   1
  HAUS3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HAUS3 MUTATED                                                                   2
  HAUS3 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HAUS3 MUTATED                                                    0
  HAUS3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HAUS3 MUTATED                                                  2
  HAUS3 WILD-TYPE                                               59
D493V9, multiclass
                                                                   clus
vv                                                                  HAUS3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  HAUS3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HAUS3 MUTATED     8   0   1   1
  HAUS3 WILD-TYPE 303  14  14  23
D493V10, multiclass
    clus
vv   HAUS3 MUTATED HAUS3 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D493V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HAUS3 MUTATED       3                         1
  HAUS3 WILD-TYPE    84                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HAUS3 MUTATED                                           0     5
  HAUS3 WILD-TYPE                                         1   238
D493V12, multiclass
                                           clus
vv                                          HAUS3 MUTATED HAUS3 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D493V13, binary
                 cls
clus                0   1
  HAUS3 MUTATED     1   8
  HAUS3 WILD-TYPE   3 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      1    8
  HAUS3 WILD-TYPE    3  302
                        clus
vv                       HAUS3 MUTATED HAUS3 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(494) Variable = CCDC150 MUTATION ANALYSIS
D494V1, survival
                   sevent
clus2                 0   1
  CCDC150 MUTATED     7   0
  CCDC150 WILD-TYPE 223 139
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                7               362 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
                0               139 
$`CCDC150 MUTATED`
TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8372 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 
       34.68         6.18        31.27        30.51        22.32        22.68 
TCGA-VQ-A8P2 
       38.14 

$`CCDC150 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  CCDC150 MUTATED CCDC150 WILD-TYPE 
             6.18              0.00 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
            38.14            122.30 
  CCDC150 MUTATED CCDC150 WILD-TYPE 
            30.51             14.07 
[1] "6.2 - 38.1 (30.5)"  "0.0 - 122.3 (14.1)"
[1] "hr="     "2.5e+07"
D494V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC150 MUTATED         1        0        1        0         2         2
  CCDC150 WILD-TYPE       1       15       39       30        35        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC150 MUTATED           0          1          0          2        0
  CCDC150 WILD-TYPE         3         69         53         30       38
D494V3, multiclass
            clus
vv           CCDC150 MUTATED CCDC150 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               2                30
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC150 MUTATED     1   1   3   4
  CCDC150 WILD-TYPE  21  91 170  93
D494V4, multiclass
    clus
vv   CCDC150 MUTATED CCDC150 WILD-TYPE
  T1               1                21
  T2               1                91
  T3               3               170
  T4               4                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
  CCDC150 MUTATED     4   3   0   2
  CCDC150 WILD-TYPE 114 101  77  75
D494V5, multiclass
    clus
vv   CCDC150 MUTATED CCDC150 WILD-TYPE
  N0               4               114
  N1               3               101
  N2               0                77
  N3               2                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"
D494V6, binary
                   cls
clus                  0   1
  CCDC150 MUTATED     9   0
  CCDC150 WILD-TYPE 337  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      9    0
  CCDC150 WILD-TYPE  337   29
   clus
vv  CCDC150 MUTATED CCDC150 WILD-TYPE
  0               9               337
  1               0                29
[1] 2 2
[1] FALSE
D494V7, binary
                   cls
clus                  0   1
  CCDC150 MUTATED     5   5
  CCDC150 WILD-TYPE 140 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      5    5
  CCDC150 WILD-TYPE  140  243
        clus
vv       CCDC150 MUTATED CCDC150 WILD-TYPE
  FEMALE               5               140
  MALE                 5               243
[1] 2 2
[1] FALSE
D494V8, binary
                   cls
clus                  0   1
  CCDC150 MUTATED     6   2
  CCDC150 WILD-TYPE 286  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      6    2
  CCDC150 WILD-TYPE  286   57
     clus
vv    CCDC150 MUTATED CCDC150 WILD-TYPE
  NO                6               286
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CCDC150 MUTATED                                          0
  CCDC150 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CCDC150 MUTATED                                       2
  CCDC150 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC150 MUTATED                                                        4
  CCDC150 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CCDC150 MUTATED                                                   2
  CCDC150 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC150 MUTATED                                                                   2
  CCDC150 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CCDC150 MUTATED                                                    0
  CCDC150 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CCDC150 MUTATED                                                  0
  CCDC150 WILD-TYPE                                               61
D494V9, multiclass
                                                                   clus
vv                                                                  CCDC150 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  CCDC150 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC150 MUTATED     7   1   0   1
  CCDC150 WILD-TYPE 304  13  15  23
D494V10, multiclass
    clus
vv   CCDC150 MUTATED CCDC150 WILD-TYPE
  R0               7               304
  R1               1                13
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D494V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CCDC150 MUTATED       2                         1
  CCDC150 WILD-TYPE    85                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC150 MUTATED                                           0     5
  CCDC150 WILD-TYPE                                         1   238
D494V12, multiclass
                                           clus
vv                                          CCDC150 MUTATED CCDC150 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D494V13, binary
                   cls
clus                  0   1
  CCDC150 MUTATED     0   7
  CCDC150 WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC150 MUTATED      0    7
  CCDC150 WILD-TYPE    4  303
                        clus
vv                       CCDC150 MUTATED CCDC150 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(495) Variable = GLIPR1L2 MUTATION ANALYSIS
D495V1, survival
                    sevent
clus2                  0   1
  GLIPR1L2 MUTATED     5   7
  GLIPR1L2 WILD-TYPE 225 132
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
                12                357 
  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE 
                 7                132 
$`GLIPR1L2 MUTATED`
TCGA-BR-4201 TCGA-BR-6566 TCGA-CD-5801 TCGA-CD-8536 TCGA-CG-4465 TCGA-CG-5718 
       30.90        32.78        13.18        12.43         9.01        36.00 
TCGA-D7-6527 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-A4GQ TCGA-IN-7808 TCGA-VQ-A8P2 
       10.26        21.27        11.08         0.10         3.45        38.14 

$`GLIPR1L2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         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-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        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-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-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-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 

  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             14.430 
[1] "0.1 - 38.1 (12.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.6"
D495V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GLIPR1L2 MUTATED         0        0        1        3         2         0
  GLIPR1L2 WILD-TYPE       2       15       39       27        35        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLIPR1L2 MUTATED           0          2          1          1        1
  GLIPR1L2 WILD-TYPE         3         68         52         31       37
D495V3, multiclass
            clus
vv           GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  3                 27
  STAGE IIA                 2                 35
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                1                 52
  STAGE IIIC                1                 31
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  GLIPR1L2 MUTATED     0   4   6   3
  GLIPR1L2 WILD-TYPE  22  88 167  94
D495V4, multiclass
    clus
vv   GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  T1                0                 22
  T2                4                 88
  T3                6                167
  T4                3                 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
  GLIPR1L2 MUTATED     4   4   1   3
  GLIPR1L2 WILD-TYPE 114 100  76  74
D495V5, multiclass
    clus
vv   GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  N0                4                114
  N1                4                100
  N2                1                 76
  N3                3                 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"
D495V6, binary
                    cls
clus                   0   1
  GLIPR1L2 MUTATED    11   2
  GLIPR1L2 WILD-TYPE 335  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GLIPR1L2 MUTATED     11    2
  GLIPR1L2 WILD-TYPE  335   27
   clus
vv  GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  0               11                335
  1                2                 27
[1] 2 2
[1] FALSE
D495V7, binary
                    cls
clus                   0   1
  GLIPR1L2 MUTATED     4   9
  GLIPR1L2 WILD-TYPE 141 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GLIPR1L2 MUTATED      4    9
  GLIPR1L2 WILD-TYPE  141  239
        clus
vv       GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  FEMALE                4                141
  MALE                  9                239
[1] 2 2
[1] FALSE
D495V8, binary
                    cls
clus                   0   1
  GLIPR1L2 MUTATED     7   4
  GLIPR1L2 WILD-TYPE 285  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GLIPR1L2 MUTATED      7    4
  GLIPR1L2 WILD-TYPE  285   55
     clus
vv    GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  NO                 7                285
  YES                4                 55
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GLIPR1L2 MUTATED                                          0
  GLIPR1L2 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GLIPR1L2 MUTATED                                       2
  GLIPR1L2 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GLIPR1L2 MUTATED                                                        5
  GLIPR1L2 WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GLIPR1L2 MUTATED                                                   2
  GLIPR1L2 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GLIPR1L2 MUTATED                                                                   2
  GLIPR1L2 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GLIPR1L2 MUTATED                                                    1
  GLIPR1L2 WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GLIPR1L2 MUTATED                                                  1
  GLIPR1L2 WILD-TYPE                                               60
D495V9, multiclass
                                                                   clus
vv                                                                  GLIPR1L2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  GLIPR1L2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  GLIPR1L2 MUTATED    10   0   1   1
  GLIPR1L2 WILD-TYPE 301  14  14  23
D495V10, multiclass
    clus
vv   GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  R0               10                301
  R1                0                 14
  R2                1                 14
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D495V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  GLIPR1L2 MUTATED       3                         1
  GLIPR1L2 WILD-TYPE    84                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GLIPR1L2 MUTATED                                           0     6
  GLIPR1L2 WILD-TYPE                                         1   237
D495V12, multiclass
                                           clus
vv                                          GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D495V13, binary
                    cls
clus                   0   1
  GLIPR1L2 MUTATED     1   8
  GLIPR1L2 WILD-TYPE   3 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GLIPR1L2 MUTATED      1    8
  GLIPR1L2 WILD-TYPE    3  302
                        clus
vv                       GLIPR1L2 MUTATED GLIPR1L2 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO                8                302
[1] 2 2
[1] FALSE

Clustering(496) Variable = ZNF23 MUTATION ANALYSIS
D496V1, survival
                 sevent
clus2               0   1
  ZNF23 MUTATED     2   1
  ZNF23 WILD-TYPE 228 138
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              3             366 
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              1             138 
$`ZNF23 MUTATED`
TCGA-BR-4256 TCGA-BR-8372 TCGA-FP-A4BE 
        9.34        31.27        11.08 

$`ZNF23 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  ZNF23 MUTATED ZNF23 WILD-TYPE 
           9.34            0.00 
  ZNF23 MUTATED ZNF23 WILD-TYPE 
          31.27          122.30 
  ZNF23 MUTATED ZNF23 WILD-TYPE 
          11.08           14.35 
[1] "9.3 - 31.3 (11.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D496V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF23 MUTATED         0        0        0        0         1         0
  ZNF23 WILD-TYPE       2       15       40       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF23 MUTATED           0          0          0          1        0
  ZNF23 WILD-TYPE         3         70         53         31       38
D496V3, multiclass
[1] "Remove cluster labels:" "ZNF23 MUTATED"         
clus
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              2             370 
     TCGA-CG-4444      TCGA-CG-4460      TCGA-CG-4475      TCGA-CG-4476 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5716      TCGA-CG-5727      TCGA-EQ-A4SO      TCGA-F1-6177 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-FP-A8CX      TCGA-HF-7131      TCGA-KB-A93G      TCGA-MX-A663 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-B7-A5TI      TCGA-B7-A5TJ 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-B7-A5TK      TCGA-B7-A5TN      TCGA-BR-4183      TCGA-BR-4184 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4267      TCGA-BR-4279 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-4280      TCGA-BR-4361      TCGA-BR-4368      TCGA-BR-6452 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6453      TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6457      TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6565      TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6707      TCGA-BR-6709      TCGA-BR-6710      TCGA-BR-6801 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6802      TCGA-BR-6803      TCGA-BR-6852      TCGA-BR-7196 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7704      TCGA-BR-7707 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8060      TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8081      TCGA-BR-8284      TCGA-BR-8285      TCGA-BR-8286 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8289      TCGA-BR-8291      TCGA-BR-8295      TCGA-BR-8297 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8360      TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8365      TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8369      TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8373 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J5      TCGA-BR-A4J6 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4J7      TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QL      TCGA-BR-A4QM 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-5798      TCGA-CD-5799      TCGA-CD-5800      TCGA-CD-5801 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-5802      TCGA-CD-5803      TCGA-CD-5813      TCGA-CD-8524 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-8525      TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-8529      TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-8533      TCGA-CD-8534      TCGA-CD-8535      TCGA-CD-8536 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-A486      TCGA-CD-A487      TCGA-CD-A489      TCGA-CD-A48A 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-A48C      TCGA-CD-A4MG      TCGA-CD-A4MH      TCGA-CD-A4MI 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-A4MJ      TCGA-CG-4300      TCGA-CG-4301      TCGA-CG-4304 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4305      TCGA-CG-4306      TCGA-CG-4436      TCGA-CG-4437 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4438      TCGA-CG-4440      TCGA-CG-4441      TCGA-CG-4442 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4443      TCGA-CG-4449      TCGA-CG-4455      TCGA-CG-4462 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4465      TCGA-CG-4466      TCGA-CG-4469      TCGA-CG-4474 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4477      TCGA-CG-5717      TCGA-CG-5718      TCGA-CG-5719 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5720      TCGA-CG-5721      TCGA-CG-5722      TCGA-CG-5723 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5724      TCGA-CG-5725      TCGA-CG-5726      TCGA-CG-5728 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5730      TCGA-CG-5732      TCGA-CG-5733      TCGA-CG-5734 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6520      TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6525 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-8570      TCGA-D7-8572      TCGA-D7-8573      TCGA-D7-8574 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-8575      TCGA-D7-8576      TCGA-D7-8578      TCGA-D7-8579 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-A4YT      TCGA-D7-A4YU      TCGA-D7-A4YV      TCGA-D7-A4YX 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-A4YY      TCGA-D7-A4Z0      TCGA-D7-A6ET      TCGA-D7-A6EV 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-A6EX      TCGA-D7-A6EY      TCGA-D7-A6EZ      TCGA-D7-A6F0 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-A6F2      TCGA-D7-A747      TCGA-D7-A748      TCGA-D7-A74A 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-A74B      TCGA-EQ-5647      TCGA-EQ-8122      TCGA-F1-6874 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-F1-6875      TCGA-F1-A448      TCGA-F1-A72C      TCGA-FP-7735 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-FP-7829      TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-FP-8209      TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-FP-A4BF      TCGA-HF-7132      TCGA-HF-7133      TCGA-HF-7134 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HF-7136      TCGA-HF-A5NB      TCGA-HJ-7597      TCGA-HU-8243 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-8244      TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-8608      TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4G6      TCGA-HU-A4G8      TCGA-HU-A4G9      TCGA-HU-A4GC 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4GD      TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GJ 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4GN      TCGA-HU-A4GP      TCGA-HU-A4GQ      TCGA-HU-A4GT 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4GU      TCGA-HU-A4GX      TCGA-HU-A4GY      TCGA-HU-A4H0 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4H2      TCGA-HU-A4H3      TCGA-HU-A4H4      TCGA-HU-A4H5 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4H6      TCGA-HU-A4H8      TCGA-HU-A4HB      TCGA-HU-A4HD 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IN-7806      TCGA-IN-8462      TCGA-IN-8663      TCGA-IN-A6RI 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IN-A6RJ      TCGA-IN-A6RL      TCGA-IN-A6RN      TCGA-IN-A6RO 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IN-A6RP      TCGA-IN-A6RR      TCGA-IN-A6RS      TCGA-IN-A7NR 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IN-A7NT      TCGA-IN-A7NU      TCGA-IN-AB1V      TCGA-IN-AB1X 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IP-7968      TCGA-KB-A6F5      TCGA-KB-A6F7      TCGA-KB-A93J 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-MX-A5UG      TCGA-MX-A5UJ      TCGA-MX-A666      TCGA-R5-A7O7 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-R5-A7ZE      TCGA-R5-A7ZF      TCGA-R5-A7ZI      TCGA-R5-A7ZR 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-R5-A804      TCGA-R5-A805      TCGA-RD-A7BS      TCGA-RD-A7BT 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-RD-A7BW      TCGA-RD-A7C1      TCGA-RD-A8MV      TCGA-RD-A8MW 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-RD-A8N0      TCGA-RD-A8N1      TCGA-RD-A8N2      TCGA-RD-A8N4 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-RD-A8N5      TCGA-RD-A8N6      TCGA-RD-A8N9      TCGA-SW-A7EA 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-SW-A7EB      TCGA-VQ-A8DL      TCGA-VQ-A8DT      TCGA-VQ-A8DU 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VQ-A8DV      TCGA-VQ-A8DZ      TCGA-VQ-A8E2      TCGA-VQ-A8E7 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VQ-A8P2      TCGA-VQ-A8P3      TCGA-VQ-A8PE      TCGA-VQ-A8PK 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VQ-A8PM      TCGA-VQ-A8PQ      TCGA-VQ-A91Q      TCGA-VQ-A91U 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VQ-A91V      TCGA-VQ-A92D      TCGA-VQ-A94T      TCGA-VQ-AA64 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VQ-AA68      TCGA-VQ-AA69      TCGA-VQ-AA6A      TCGA-VQ-AA6B 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VQ-AA6F      TCGA-VQ-AA6G      TCGA-VQ-AA6I      TCGA-VQ-AA6J 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VQ-AA6K      TCGA-ZA-A8F6 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
                 vv
clus               T1  T2  T3  T4
  ZNF23 MUTATED     0   0   1   1
  ZNF23 WILD-TYPE  22  92 172  96
D496V4, multiclass
[1] "Remove cluster labels:" "ZNF23 MUTATED"         
clus
  ZNF23 MUTATED ZNF23 WILD-TYPE 
              2             382 
     TCGA-CG-4444      TCGA-CG-4460      TCGA-CG-4475      TCGA-CG-4476 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5716      TCGA-CG-5727      TCGA-EQ-A4SO      TCGA-F1-6177 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-FP-A8CX      TCGA-HF-7131      TCGA-KB-A93G      TCGA-MX-A663 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-B7-A5TI      TCGA-B7-A5TJ 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-B7-A5TK      TCGA-B7-A5TN      TCGA-BR-4183      TCGA-BR-4184 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-4201      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4267 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292      TCGA-BR-4294 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4363      TCGA-BR-4368 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453      TCGA-BR-6454 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457      TCGA-BR-6458 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565      TCGA-BR-6566 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707      TCGA-BR-6709 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-7704      TCGA-BR-7707      TCGA-BR-7715      TCGA-BR-7716 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-7717      TCGA-BR-7722      TCGA-BR-7723      TCGA-BR-7851 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-7901      TCGA-BR-7957      TCGA-BR-7958      TCGA-BR-7959 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8058      TCGA-BR-8059      TCGA-BR-8060      TCGA-BR-8077 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8078      TCGA-BR-8080      TCGA-BR-8081      TCGA-BR-8284 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8285      TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8295      TCGA-BR-8297      TCGA-BR-8360      TCGA-BR-8361 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8371      TCGA-BR-8373      TCGA-BR-8380      TCGA-BR-8381 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483      TCGA-BR-8484 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487      TCGA-BR-8588 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591      TCGA-BR-8592 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678      TCGA-BR-8679 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683      TCGA-BR-8686 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T      TCGA-BR-A44U 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ      TCGA-BR-A4CR 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV      TCGA-BR-A4IY 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2      TCGA-BR-A4J4 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4J5      TCGA-BR-A4J6      TCGA-BR-A4J7      TCGA-BR-A4J8 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5798      TCGA-CD-5799 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-5800      TCGA-CD-5801      TCGA-CD-5802      TCGA-CD-5803 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-5804      TCGA-CD-5813      TCGA-CD-8524      TCGA-CD-8525 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528      TCGA-CD-8529 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532      TCGA-CD-8533 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-8534      TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A486 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-A487      TCGA-CD-A489      TCGA-CD-A48A      TCGA-CD-A48C 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CD-A4MG      TCGA-CD-A4MH      TCGA-CD-A4MI      TCGA-CD-A4MJ 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4300      TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4306      TCGA-CG-4436      TCGA-CG-4437      TCGA-CG-4438 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4440      TCGA-CG-4441      TCGA-CG-4442      TCGA-CG-4443 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4449      TCGA-CG-4455      TCGA-CG-4462      TCGA-CG-4465 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-4466      TCGA-CG-4469      TCGA-CG-4474      TCGA-CG-4477 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5717      TCGA-CG-5718      TCGA-CG-5719      TCGA-CG-5720 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5721      TCGA-CG-5722      TCGA-CG-5723      TCGA-CG-5724 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5725      TCGA-CG-5726      TCGA-CG-5728      TCGA-CG-5730 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-CG-5732      TCGA-CG-5733      TCGA-CG-5734      TCGA-D7-5577 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518      TCGA-D7-6519 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522      TCGA-D7-6524 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572      TCGA-D7-8573 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576      TCGA-D7-8578 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU      TCGA-D7-A4YV 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0      TCGA-D7-A6ET 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-A6EV      TCGA-D7-A6EX      TCGA-D7-A6EY      TCGA-D7-A6EZ 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-A6F0      TCGA-D7-A6F2      TCGA-D7-A747      TCGA-D7-A748 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-D7-A74A      TCGA-D7-A74B      TCGA-EQ-5647      TCGA-EQ-8122 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-F1-6874      TCGA-F1-6875      TCGA-F1-A448      TCGA-F1-A72C 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-FP-7735      TCGA-FP-7829      TCGA-FP-7916      TCGA-FP-7998 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-FP-8099      TCGA-FP-8209      TCGA-FP-8210      TCGA-FP-8211 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-FP-8631      TCGA-FP-A4BF      TCGA-FP-A9TM      TCGA-HF-7132 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HF-7133      TCGA-HF-7134      TCGA-HF-7136      TCGA-HF-A5NB 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HJ-7597      TCGA-HU-8238      TCGA-HU-8243      TCGA-HU-8244 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4G8      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GJ      TCGA-HU-A4GN 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4GP      TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4GX      TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4H3      TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-HU-A4H8      TCGA-HU-A4HB      TCGA-HU-A4HD      TCGA-IN-7806 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IN-7808      TCGA-IN-8462      TCGA-IN-8663      TCGA-IN-A6RI 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IN-A6RJ      TCGA-IN-A6RL      TCGA-IN-A6RN      TCGA-IN-A6RO 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IN-A6RP      TCGA-IN-A6RR      TCGA-IN-A6RS      TCGA-IN-A7NR 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IN-A7NT      TCGA-IN-A7NU      TCGA-IN-AB1V      TCGA-IN-AB1X 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-IP-7968      TCGA-KB-A6F5      TCGA-KB-A6F7      TCGA-KB-A93J 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-MX-A5UG      TCGA-MX-A5UJ      TCGA-MX-A666      TCGA-R5-A7O7 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-R5-A7ZE      TCGA-R5-A7ZF      TCGA-R5-A7ZI      TCGA-R5-A7ZR 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-R5-A804      TCGA-R5-A805      TCGA-RD-A7BS      TCGA-RD-A7BT 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-RD-A7BW      TCGA-RD-A7C1      TCGA-RD-A8MV      TCGA-RD-A8MW 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-RD-A8N0      TCGA-RD-A8N1      TCGA-RD-A8N2      TCGA-RD-A8N4 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-RD-A8N5      TCGA-RD-A8N6      TCGA-RD-A8N9      TCGA-SW-A7EA 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-SW-A7EB      TCGA-VQ-A8DL      TCGA-VQ-A8DT      TCGA-VQ-A8DU 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VQ-A8DV      TCGA-VQ-A8DZ      TCGA-VQ-A8E2      TCGA-VQ-A8E7 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VQ-A8P2      TCGA-VQ-A8P3      TCGA-VQ-A8PE      TCGA-VQ-A8PK 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VQ-A8PM      TCGA-VQ-A8PQ      TCGA-VQ-A91Q      TCGA-VQ-A91U 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VQ-A91V      TCGA-VQ-A92D      TCGA-VQ-A94T      TCGA-VQ-AA64 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VQ-AA68      TCGA-VQ-AA69      TCGA-VQ-AA6A      TCGA-VQ-AA6B 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VQ-AA6F      TCGA-VQ-AA6G      TCGA-VQ-AA6I      TCGA-VQ-AA6J 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
     TCGA-VQ-AA6K      TCGA-ZA-A8F6 
"ZNF23 WILD-TYPE" "ZNF23 WILD-TYPE" 
                 vv
clus               N0  N1  N2  N3
  ZNF23 MUTATED     1   1   0   1
  ZNF23 WILD-TYPE 117 103  77  76
D496V5, multiclass
    clus
vv   ZNF23 MUTATED ZNF23 WILD-TYPE
  N0             1             117
  N1             1             103
  N2             0              77
  N3             1              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"
D496V6, binary
                 cls
clus                0   1
  ZNF23 MUTATED     3   0
  ZNF23 WILD-TYPE 343  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF23 MUTATED      3    0
  ZNF23 WILD-TYPE  343   29
   clus
vv  ZNF23 MUTATED ZNF23 WILD-TYPE
  0             3             343
  1             0              29
[1] 2 2
[1] FALSE
D496V7, binary
                 cls
clus                0   1
  ZNF23 MUTATED     0   3
  ZNF23 WILD-TYPE 145 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF23 MUTATED      0    3
  ZNF23 WILD-TYPE  145  245
        clus
vv       ZNF23 MUTATED ZNF23 WILD-TYPE
  FEMALE             0             145
  MALE               3             245
[1] 2 2
[1] FALSE
D496V8, binary
                 cls
clus                0   1
  ZNF23 MUTATED     2   1
  ZNF23 WILD-TYPE 290  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF23 MUTATED      2    1
  ZNF23 WILD-TYPE  290   58
     clus
vv    ZNF23 MUTATED ZNF23 WILD-TYPE
  NO              2             290
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF23 MUTATED                                          0
  ZNF23 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF23 MUTATED                                       0
  ZNF23 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF23 MUTATED                                                        3
  ZNF23 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF23 MUTATED                                                   0
  ZNF23 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF23 MUTATED                                                                   0
  ZNF23 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF23 MUTATED                                                    0
  ZNF23 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF23 MUTATED                                                  0
  ZNF23 WILD-TYPE                                               61
D496V9, multiclass
                                                                   clus
vv                                                                  ZNF23 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  ZNF23 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZNF23 MUTATED     2   0   0   1
  ZNF23 WILD-TYPE 309  14  15  23
D496V10, multiclass
    clus
vv   ZNF23 MUTATED ZNF23 WILD-TYPE
  R0             2             309
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D496V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZNF23 MUTATED       0                         1
  ZNF23 WILD-TYPE    87                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF23 MUTATED                                           0     2
  ZNF23 WILD-TYPE                                         1   241
D496V12, multiclass
                                           clus
vv                                          ZNF23 MUTATED ZNF23 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D496V13, binary
                 cls
clus                0   1
  ZNF23 MUTATED     0   3
  ZNF23 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF23 MUTATED      0    3
  ZNF23 WILD-TYPE    4  307
                        clus
vv                       ZNF23 MUTATED ZNF23 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(497) Variable = OSGEPL1 MUTATION ANALYSIS
D497V1, survival
                   sevent
clus2                 0   1
  OSGEPL1 MUTATED     2   2
  OSGEPL1 WILD-TYPE 228 137
  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE 
                4               365 
  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE 
                2               137 
$`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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        5.79         0.92        48.79        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 

  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE 
             5.46              0.00 
  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE 
             65.1             122.3 
  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE 
            16.64             14.27 
[1] "5.5 - 65.1 (16.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D497V2, 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       2       15       39       30        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSGEPL1 MUTATED           0          1          0          0        0
  OSGEPL1 WILD-TYPE         3         69         53         32       38
D497V3, multiclass
            clus
vv           OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  OSGEPL1 MUTATED     0   1   2   1
  OSGEPL1 WILD-TYPE  22  91 171  96
D497V4, multiclass
    clus
vv   OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  T1               0                22
  T2               1                91
  T3               2               171
  T4               1                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
  OSGEPL1 MUTATED     3   0   1   0
  OSGEPL1 WILD-TYPE 115 104  76  77
D497V5, multiclass
    clus
vv   OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  N0               3               115
  N1               0               104
  N2               1                76
  N3               0                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"
D497V6, binary
                   cls
clus                  0   1
  OSGEPL1 MUTATED     4   0
  OSGEPL1 WILD-TYPE 342  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSGEPL1 MUTATED      4    0
  OSGEPL1 WILD-TYPE  342   29
   clus
vv  OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  0               4               342
  1               0                29
[1] 2 2
[1] FALSE
D497V7, binary
                   cls
clus                  0   1
  OSGEPL1 MUTATED     2   2
  OSGEPL1 WILD-TYPE 143 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSGEPL1 MUTATED      2    2
  OSGEPL1 WILD-TYPE  143  246
        clus
vv       OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  FEMALE               2               143
  MALE                 2               246
[1] 2 2
[1] FALSE
D497V8, binary
                   cls
clus                  0   1
  OSGEPL1 MUTATED     3   0
  OSGEPL1 WILD-TYPE 289  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSGEPL1 MUTATED      3    0
  OSGEPL1 WILD-TYPE  289   59
     clus
vv    OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  NO                3               289
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OSGEPL1 MUTATED                                          0
  OSGEPL1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OSGEPL1 MUTATED                                       2
  OSGEPL1 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OSGEPL1 MUTATED                                                        0
  OSGEPL1 WILD-TYPE                                                    158
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OSGEPL1 MUTATED                                                   0
  OSGEPL1 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OSGEPL1 MUTATED                                                                   1
  OSGEPL1 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OSGEPL1 MUTATED                                                    0
  OSGEPL1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OSGEPL1 MUTATED                                                  1
  OSGEPL1 WILD-TYPE                                               60
D497V9, multiclass
                                                                   clus
vv                                                                  OSGEPL1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  OSGEPL1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          158
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  OSGEPL1 MUTATED     3   0   0   0
  OSGEPL1 WILD-TYPE 308  14  15  24
D497V10, multiclass
    clus
vv   OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  R0               3               308
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D497V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  OSGEPL1 MUTATED       1                         0
  OSGEPL1 WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OSGEPL1 MUTATED                                           0     2
  OSGEPL1 WILD-TYPE                                         1   241
D497V12, multiclass
                                           clus
vv                                          OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D497V13, binary
                   cls
clus                  0   1
  OSGEPL1 MUTATED     0   2
  OSGEPL1 WILD-TYPE   4 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSGEPL1 MUTATED      0    2
  OSGEPL1 WILD-TYPE    4  308
                        clus
vv                       OSGEPL1 MUTATED OSGEPL1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               2               308
[1] 2 2
[1] FALSE

Clustering(498) Variable = EFHA2 MUTATION ANALYSIS
D498V1, survival
                 sevent
clus2               0   1
  EFHA2 MUTATED    11   3
  EFHA2 WILD-TYPE 219 136
  EFHA2 MUTATED EFHA2 WILD-TYPE 
             14             355 
  EFHA2 MUTATED EFHA2 WILD-TYPE 
              3             136 
$`EFHA2 MUTATED`
TCGA-B7-A5TI TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8487 
       19.56        34.68        35.84        14.43        32.25         1.12 
TCGA-BR-8591 TCGA-CD-8536 TCGA-CG-4438 TCGA-CG-5726 TCGA-D7-A6EY TCGA-HU-A4GN 
       28.14        12.43        54.08        28.96        11.44        29.98 
TCGA-HU-A4H8 TCGA-R5-A7ZI 
       14.07        74.53 

$`EFHA2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-4440 
       27.02        15.95         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-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-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-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 

  EFHA2 MUTATED EFHA2 WILD-TYPE 
           1.12            0.00 
  EFHA2 MUTATED EFHA2 WILD-TYPE 
          74.53          122.30 
  EFHA2 MUTATED EFHA2 WILD-TYPE 
          28.55           14.04 
[1] "1.1 - 74.5 (28.6)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "2.6"
D498V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EFHA2 MUTATED         0        1        2        1         3         1
  EFHA2 WILD-TYPE       2       14       38       29        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFHA2 MUTATED           1          0          1          2        2
  EFHA2 WILD-TYPE         2         70         52         30       36
D498V3, multiclass
            clus
vv           EFHA2 MUTATED EFHA2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EFHA2 MUTATED     2   2   4   6
  EFHA2 WILD-TYPE  20  90 169  91
D498V4, multiclass
    clus
vv   EFHA2 MUTATED EFHA2 WILD-TYPE
  T1             2              20
  T2             2              90
  T3             4             169
  T4             6              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
  EFHA2 MUTATED     6   4   1   3
  EFHA2 WILD-TYPE 112 100  76  74
D498V5, multiclass
    clus
vv   EFHA2 MUTATED EFHA2 WILD-TYPE
  N0             6             112
  N1             4             100
  N2             1              76
  N3             3              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"
D498V6, binary
                 cls
clus                0   1
  EFHA2 MUTATED    13   1
  EFHA2 WILD-TYPE 333  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA2 MUTATED     13    1
  EFHA2 WILD-TYPE  333   28
   clus
vv  EFHA2 MUTATED EFHA2 WILD-TYPE
  0            13             333
  1             1              28
[1] 2 2
[1] FALSE
D498V7, binary
                 cls
clus                0   1
  EFHA2 MUTATED     6   8
  EFHA2 WILD-TYPE 139 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA2 MUTATED      6    8
  EFHA2 WILD-TYPE  139  240
        clus
vv       EFHA2 MUTATED EFHA2 WILD-TYPE
  FEMALE             6             139
  MALE               8             240
[1] 2 2
[1] FALSE
D498V8, binary
                 cls
clus                0   1
  EFHA2 MUTATED    12   0
  EFHA2 WILD-TYPE 280  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA2 MUTATED     12    0
  EFHA2 WILD-TYPE  280   59
     clus
vv    EFHA2 MUTATED EFHA2 WILD-TYPE
  NO             12             280
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EFHA2 MUTATED                                          0
  EFHA2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EFHA2 MUTATED                                       2
  EFHA2 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EFHA2 MUTATED                                                        6
  EFHA2 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EFHA2 MUTATED                                                   0
  EFHA2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EFHA2 MUTATED                                                                   3
  EFHA2 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EFHA2 MUTATED                                                    0
  EFHA2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EFHA2 MUTATED                                                  3
  EFHA2 WILD-TYPE                                               58
D498V9, multiclass
                                                                   clus
vv                                                                  EFHA2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  EFHA2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EFHA2 MUTATED    13   0   0   0
  EFHA2 WILD-TYPE 298  14  15  24
D498V10, multiclass
    clus
vv   EFHA2 MUTATED EFHA2 WILD-TYPE
  R0            13             298
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D498V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EFHA2 MUTATED       3                         0
  EFHA2 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EFHA2 MUTATED                                           0     9
  EFHA2 WILD-TYPE                                         1   234
D498V12, multiclass
                                           clus
vv                                          EFHA2 MUTATED EFHA2 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D498V13, binary
                 cls
clus                0   1
  EFHA2 MUTATED     1  11
  EFHA2 WILD-TYPE   3 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA2 MUTATED      1   11
  EFHA2 WILD-TYPE    3  299
                        clus
vv                       EFHA2 MUTATED EFHA2 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(499) Variable = CDH24 MUTATION ANALYSIS
D499V1, survival
                 sevent
clus2               0   1
  CDH24 MUTATED     9   3
  CDH24 WILD-TYPE 221 136
  CDH24 MUTATED CDH24 WILD-TYPE 
             12             357 
  CDH24 MUTATED CDH24 WILD-TYPE 
              3             136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-F1-6875 
        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-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-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-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 

  CDH24 MUTATED CDH24 WILD-TYPE 
           1.12            0.00 
  CDH24 MUTATED CDH24 WILD-TYPE 
          35.84          122.30 
  CDH24 MUTATED CDH24 WILD-TYPE 
          19.99           14.04 
[1] "1.1 - 35.8 (20.0)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.8"
D499V2, 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       2       14       38       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDH24 MUTATED           2          2          0          2        0
  CDH24 WILD-TYPE         1         68         53         30       38
D499V3, multiclass
            clus
vv           CDH24 MUTATED CDH24 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              2               1
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDH24 MUTATED     1   4   2   5
  CDH24 WILD-TYPE  21  88 171  92
D499V4, multiclass
    clus
vv   CDH24 MUTATED CDH24 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             2             171
  T4             5              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
  CDH24 MUTATED     5   6   3   0
  CDH24 WILD-TYPE 113  98  74  77
D499V5, multiclass
    clus
vv   CDH24 MUTATED CDH24 WILD-TYPE
  N0             5             113
  N1             6              98
  N2             3              74
  N3             0              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"
D499V6, binary
                 cls
clus                0   1
  CDH24 MUTATED    14   0
  CDH24 WILD-TYPE 332  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED     14    0
  CDH24 WILD-TYPE  332   29
   clus
vv  CDH24 MUTATED CDH24 WILD-TYPE
  0            14             332
  1             0              29
[1] 2 2
[1] FALSE
D499V7, binary
                 cls
clus                0   1
  CDH24 MUTATED     8   6
  CDH24 WILD-TYPE 137 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED      8    6
  CDH24 WILD-TYPE  137  242
        clus
vv       CDH24 MUTATED CDH24 WILD-TYPE
  FEMALE             8             137
  MALE               6             242
[1] 2 2
[1] FALSE
D499V8, binary
                 cls
clus                0   1
  CDH24 MUTATED    13   0
  CDH24 WILD-TYPE 279  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED     13    0
  CDH24 WILD-TYPE  279   59
     clus
vv    CDH24 MUTATED CDH24 WILD-TYPE
  NO             13             279
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CDH24 MUTATED                                          0
  CDH24 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CDH24 MUTATED                                       1
  CDH24 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDH24 MUTATED                                                        7
  CDH24 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CDH24 MUTATED                                                   0
  CDH24 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDH24 MUTATED                                                                   3
  CDH24 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CDH24 MUTATED                                                    0
  CDH24 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CDH24 MUTATED                                                  3
  CDH24 WILD-TYPE                                               58
D499V9, multiclass
                                                                   clus
vv                                                                  CDH24 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  CDH24 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDH24 MUTATED    11   0   0   3
  CDH24 WILD-TYPE 300  14  15  21
D499V10, multiclass
    clus
vv   CDH24 MUTATED CDH24 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D499V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CDH24 MUTATED       3                         0
  CDH24 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDH24 MUTATED                                           0    11
  CDH24 WILD-TYPE                                         1   232
D499V12, multiclass
                                           clus
vv                                          CDH24 MUTATED CDH24 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D499V13, binary
                 cls
clus                0   1
  CDH24 MUTATED     0  14
  CDH24 WILD-TYPE   4 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED      0   14
  CDH24 WILD-TYPE    4  296
                        clus
vv                       CDH24 MUTATED CDH24 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(500) Variable = C6ORF150 MUTATION ANALYSIS
D500V1, survival
                    sevent
clus2                  0   1
  C6ORF150 MUTATED     6   1
  C6ORF150 WILD-TYPE 224 138
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 7                362 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 1                138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        9.47         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-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-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-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-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 

  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              14.45 
[1] "1.1 - 32.0 (9.7)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.9"
D500V2, 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       2       15       39       30        36        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF150 MUTATED           0          1          0          0        1
  C6ORF150 WILD-TYPE         3         69         53         32       37
D500V3, multiclass
            clus
vv           C6ORF150 MUTATED C6ORF150 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 3                 49
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                0                 53
  STAGE IIIC                0                 32
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C6ORF150 MUTATED     0   1   3   3
  C6ORF150 WILD-TYPE  22  91 170  94
D500V4, multiclass
    clus
vv   C6ORF150 MUTATED C6ORF150 WILD-TYPE
  T1                0                 22
  T2                1                 91
  T3                3                170
  T4                3                 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
  C6ORF150 MUTATED     3   2   1   0
  C6ORF150 WILD-TYPE 115 102  76  77
D500V5, multiclass
    clus
vv   C6ORF150 MUTATED C6ORF150 WILD-TYPE
  N0                3                115
  N1                2                102
  N2                1                 76
  N3                0                 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"
D500V6, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     7   1
  C6ORF150 WILD-TYPE 339  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      7    1
  C6ORF150 WILD-TYPE  339   28
   clus
vv  C6ORF150 MUTATED C6ORF150 WILD-TYPE
  0                7                339
  1                1                 28
[1] 2 2
[1] FALSE
D500V7, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     5   3
  C6ORF150 WILD-TYPE 140 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      5    3
  C6ORF150 WILD-TYPE  140  245
        clus
vv       C6ORF150 MUTATED C6ORF150 WILD-TYPE
  FEMALE                5                140
  MALE                  3                245
[1] 2 2
[1] FALSE
D500V8, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     7   0
  C6ORF150 WILD-TYPE 285  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      7    0
  C6ORF150 WILD-TYPE  285   59
     clus
vv    C6ORF150 MUTATED C6ORF150 WILD-TYPE
  NO                 7                285
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C6ORF150 MUTATED                                          0
  C6ORF150 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C6ORF150 MUTATED                                       2
  C6ORF150 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C6ORF150 MUTATED                                                        5
  C6ORF150 WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C6ORF150 MUTATED                                                   0
  C6ORF150 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C6ORF150 MUTATED                                                                   0
  C6ORF150 WILD-TYPE                                                                68
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C6ORF150 MUTATED                                                    0
  C6ORF150 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C6ORF150 MUTATED                                                  1
  C6ORF150 WILD-TYPE                                               60
D500V9, multiclass
                                                                   clus
vv                                                                  C6ORF150 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  C6ORF150 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C6ORF150 MUTATED     5   0   0   2
  C6ORF150 WILD-TYPE 306  14  15  22
D500V10, multiclass
    clus
vv   C6ORF150 MUTATED C6ORF150 WILD-TYPE
  R0                5                306
  R1                0                 14
  R2                0                 15
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D500V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C6ORF150 MUTATED       2                         0
  C6ORF150 WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C6ORF150 MUTATED                                           0     6
  C6ORF150 WILD-TYPE                                         1   237
D500V12, multiclass
                                           clus
vv                                          C6ORF150 MUTATED C6ORF150 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D500V13, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     0   8
  C6ORF150 WILD-TYPE   4 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      0    8
  C6ORF150 WILD-TYPE    4  302
                        clus
vv                       C6ORF150 MUTATED C6ORF150 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                8                302
[1] 2 2
[1] FALSE

Clustering(501) Variable = MGA MUTATION ANALYSIS
D501V1, survival
               sevent
clus2             0   1
  MGA MUTATED    17   9
  MGA WILD-TYPE 213 130
  MGA MUTATED MGA WILD-TYPE 
           26           343 
  MGA MUTATED MGA WILD-TYPE 
            9           130 
$`MGA MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-6852 
       11.70         6.97        30.90        34.68        30.90        44.94 
TCGA-BR-8360 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-5801 TCGA-CD-8531 TCGA-CG-4465 
        6.18        27.12        31.96        13.18        12.59         9.01 
TCGA-CG-5725 TCGA-CG-5726 TCGA-D7-A4YY TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-A4BE 
       15.02        28.96        13.78        14.47        21.27        11.08 
TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-IN-A6RL 
       26.47        22.32         0.10        29.00        14.07        13.35 
TCGA-SW-A7EA TCGA-VQ-A8P2 
       19.04        38.14 

$`MGA WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-6803 TCGA-BR-7196 TCGA-BR-7197 
       12.16         8.98        40.21        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-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-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-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-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-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-A72C TCGA-FP-7735 
        7.13         0.62         7.99        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-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-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-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 

  MGA MUTATED MGA WILD-TYPE 
          0.1           0.0 
  MGA MUTATED MGA WILD-TYPE 
        44.94        122.30 
  MGA MUTATED MGA WILD-TYPE 
        17.03         14.07 
[1] "0.1 - 44.9 (17.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D501V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MGA MUTATED         0        2        6        0         4         1
  MGA WILD-TYPE       2       13       34       30        33        51
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MGA MUTATED           0          6          3          2        2
  MGA WILD-TYPE         3         64         50         30       36
D501V3, multiclass
            clus
vv           MGA MUTATED MGA WILD-TYPE
  STAGE I              0             2
  STAGE IA             2            13
  STAGE IB             6            34
  STAGE II             0            30
  STAGE IIA            4            33
  STAGE IIB            1            51
  STAGE III            0             3
  STAGE IIIA           6            64
  STAGE IIIB           3            50
  STAGE IIIC           2            30
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MGA MUTATED     3   7  10   7
  MGA WILD-TYPE  19  85 163  90
D501V4, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  T1           3            19
  T2           7            85
  T3          10           163
  T4           7            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
  MGA MUTATED    12   8   3   4
  MGA WILD-TYPE 106  96  74  73
D501V5, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  N0          12           106
  N1           8            96
  N2           3            74
  N3           4            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"
D501V6, binary
               cls
clus              0   1
  MGA MUTATED    24   2
  MGA WILD-TYPE 322  27
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     24    2
  MGA WILD-TYPE  322   27
   clus
vv  MGA MUTATED MGA WILD-TYPE
  0          24           322
  1           2            27
[1] 2 2
[1] FALSE
D501V7, binary
               cls
clus              0   1
  MGA MUTATED    10  18
  MGA WILD-TYPE 135 230
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     10   18
  MGA WILD-TYPE  135  230
        clus
vv       MGA MUTATED MGA WILD-TYPE
  FEMALE          10           135
  MALE            18           230
[1] 2 2
[1] FALSE
D501V8, binary
               cls
clus              0   1
  MGA MUTATED    18   6
  MGA WILD-TYPE 274  53
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     18    6
  MGA WILD-TYPE  274   53
     clus
vv    MGA MUTATED MGA WILD-TYPE
  NO           18           274
  YES           6            53
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MGA MUTATED                                          1
  MGA WILD-TYPE                                        7
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MGA MUTATED                                       6
  MGA WILD-TYPE                                    64
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MGA MUTATED                                                       13
  MGA WILD-TYPE                                                    145
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MGA MUTATED                                                   2
  MGA WILD-TYPE                                                19
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MGA MUTATED                                                                   3
  MGA WILD-TYPE                                                                65
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MGA MUTATED                                                    0
  MGA WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MGA MUTATED                                                  3
  MGA WILD-TYPE                                               58
D501V9, multiclass
                                                                   clus
vv                                                                  MGA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                     13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            3
                                                                   clus
vv                                                                  MGA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  MGA MUTATED    24   0   1   3
  MGA WILD-TYPE 287  14  14  21
D501V10, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  R0          24           287
  R1           0            14
  R2           1            14
  RX           3            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D501V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  MGA MUTATED       8                         1
  MGA WILD-TYPE    79                         8
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MGA MUTATED                                           0    16
  MGA WILD-TYPE                                         1   227
D501V12, multiclass
                                           clus
vv                                          MGA MUTATED MGA WILD-TYPE
  ASIAN                                               8            79
  BLACK OR AFRICAN AMERICAN                           1             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              16           227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D501V13, binary
               cls
clus              0   1
  MGA MUTATED     1  23
  MGA WILD-TYPE   3 287
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED      1   23
  MGA WILD-TYPE    3  287
                        clus
vv                       MGA MUTATED MGA WILD-TYPE
  HISPANIC OR LATINO               1             3
  NOT HISPANIC OR LATINO          23           287
[1] 2 2
[1] FALSE

Clustering(502) Variable = SH3RF1 MUTATION ANALYSIS
D502V1, survival
                  sevent
clus2                0   1
  SH3RF1 MUTATED     7   4
  SH3RF1 WILD-TYPE 223 135
  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
              11              358 
  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
               4              135 
$`SH3RF1 MUTATED`
TCGA-BR-4201 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8487 TCGA-CG-5723 
       30.90        35.84        29.59         0.26         1.12       105.07 
TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4H4 TCGA-VQ-A8P2 
       11.44        22.32         0.10        23.84        38.14 

$`SH3RF1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
             0.1              0.0 
  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
          105.07           122.30 
  SH3RF1 MUTATED SH3RF1 WILD-TYPE 
           23.84            14.12 
[1] "0.1 - 105.1 (23.8)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D502V2, 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       2       15       38       29        36        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SH3RF1 MUTATED           0          1          1          1        0
  SH3RF1 WILD-TYPE         3         69         52         31       38
D502V3, multiclass
            clus
vv           SH3RF1 MUTATED SH3RF1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SH3RF1 MUTATED     0   5   2   4
  SH3RF1 WILD-TYPE  22  87 171  93
D502V4, multiclass
    clus
vv   SH3RF1 MUTATED SH3RF1 WILD-TYPE
  T1              0               22
  T2              5               87
  T3              2              171
  T4              4               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
  SH3RF1 MUTATED     5   2   2   1
  SH3RF1 WILD-TYPE 113 102  75  76
D502V5, multiclass
    clus
vv   SH3RF1 MUTATED SH3RF1 WILD-TYPE
  N0              5              113
  N1              2              102
  N2              2               75
  N3              1               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"
D502V6, binary
                  cls
clus                 0   1
  SH3RF1 MUTATED    12   0
  SH3RF1 WILD-TYPE 334  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3RF1 MUTATED     12    0
  SH3RF1 WILD-TYPE  334   29
   clus
vv  SH3RF1 MUTATED SH3RF1 WILD-TYPE
  0             12              334
  1              0               29
[1] 2 2
[1] FALSE
D502V7, binary
                  cls
clus                 0   1
  SH3RF1 MUTATED     9   3
  SH3RF1 WILD-TYPE 136 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3RF1 MUTATED      9    3
  SH3RF1 WILD-TYPE  136  245
        clus
vv       SH3RF1 MUTATED SH3RF1 WILD-TYPE
  FEMALE              9              136
  MALE                3              245
[1] 2 2
[1] FALSE
D502V8, binary
                  cls
clus                 0   1
  SH3RF1 MUTATED    10   1
  SH3RF1 WILD-TYPE 282  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3RF1 MUTATED     10    1
  SH3RF1 WILD-TYPE  282   58
     clus
vv    SH3RF1 MUTATED SH3RF1 WILD-TYPE
  NO              10              282
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SH3RF1 MUTATED                                          0
  SH3RF1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SH3RF1 MUTATED                                       1
  SH3RF1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SH3RF1 MUTATED                                                        7
  SH3RF1 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SH3RF1 MUTATED                                                   1
  SH3RF1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SH3RF1 MUTATED                                                                   0
  SH3RF1 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SH3RF1 MUTATED                                                    0
  SH3RF1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SH3RF1 MUTATED                                                  3
  SH3RF1 WILD-TYPE                                               58
D502V9, multiclass
                                                                   clus
vv                                                                  SH3RF1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  SH3RF1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SH3RF1 MUTATED    10   0   0   2
  SH3RF1 WILD-TYPE 301  14  15  22
D502V10, multiclass
    clus
vv   SH3RF1 MUTATED SH3RF1 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D502V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SH3RF1 MUTATED       3                         0
  SH3RF1 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SH3RF1 MUTATED                                           0     8
  SH3RF1 WILD-TYPE                                         1   235
D502V12, multiclass
                                           clus
vv                                          SH3RF1 MUTATED SH3RF1 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D502V13, binary
                  cls
clus                 0   1
  SH3RF1 MUTATED     0  10
  SH3RF1 WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3RF1 MUTATED      0   10
  SH3RF1 WILD-TYPE    4  300
                        clus
vv                       SH3RF1 MUTATED SH3RF1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(503) Variable = HTR1E MUTATION ANALYSIS
D503V1, survival
                 sevent
clus2               0   1
  HTR1E MUTATED     7   5
  HTR1E WILD-TYPE 223 134
  HTR1E MUTATED HTR1E WILD-TYPE 
             12             357 
  HTR1E MUTATED HTR1E WILD-TYPE 
              5             134 
$`HTR1E MUTATED`
TCGA-BR-4184 TCGA-BR-7704 TCGA-BR-8360 TCGA-BR-8680 TCGA-CD-8527 TCGA-CG-5733 
        6.97        35.24         6.18        31.96         7.17        21.07 
TCGA-F1-A448 TCGA-HF-7132 TCGA-HU-A4GX TCGA-IN-8663 TCGA-VQ-A8P3 TCGA-VQ-AA6G 
       21.27        77.29        20.25         3.39        37.22        26.04 

$`HTR1E WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
          21.17           14.07 
[1] "3.4 - 77.3 (21.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D503V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HTR1E MUTATED         0        0        0        3         2         1
  HTR1E WILD-TYPE       2       15       40       27        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HTR1E MUTATED           0          3          1          1        1
  HTR1E WILD-TYPE         3         67         52         31       37
D503V3, multiclass
            clus
vv           HTR1E MUTATED HTR1E WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               3              27
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HTR1E MUTATED     0   4   5   3
  HTR1E WILD-TYPE  22  88 168  94
D503V4, multiclass
    clus
vv   HTR1E MUTATED HTR1E WILD-TYPE
  T1             0              22
  T2             4              88
  T3             5             168
  T4             3              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
  HTR1E MUTATED     3   4   4   1
  HTR1E WILD-TYPE 115 100  73  76
D503V5, multiclass
    clus
vv   HTR1E MUTATED HTR1E WILD-TYPE
  N0             3             115
  N1             4             100
  N2             4              73
  N3             1              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"
D503V6, binary
                 cls
clus                0   1
  HTR1E MUTATED    10   1
  HTR1E WILD-TYPE 336  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1E MUTATED     10    1
  HTR1E WILD-TYPE  336   28
   clus
vv  HTR1E MUTATED HTR1E WILD-TYPE
  0            10             336
  1             1              28
[1] 2 2
[1] FALSE
D503V7, binary
                 cls
clus                0   1
  HTR1E MUTATED     4   8
  HTR1E WILD-TYPE 141 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1E MUTATED      4    8
  HTR1E WILD-TYPE  141  240
        clus
vv       HTR1E MUTATED HTR1E WILD-TYPE
  FEMALE             4             141
  MALE               8             240
[1] 2 2
[1] FALSE
D503V8, binary
                 cls
clus                0   1
  HTR1E MUTATED     9   3
  HTR1E WILD-TYPE 283  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1E MUTATED      9    3
  HTR1E WILD-TYPE  283   56
     clus
vv    HTR1E MUTATED HTR1E WILD-TYPE
  NO              9             283
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HTR1E MUTATED                                          0
  HTR1E WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HTR1E MUTATED                                       1
  HTR1E WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HTR1E MUTATED                                                        2
  HTR1E WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HTR1E MUTATED                                                   2
  HTR1E WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HTR1E MUTATED                                                                   5
  HTR1E WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HTR1E MUTATED                                                    0
  HTR1E WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HTR1E MUTATED                                                  2
  HTR1E WILD-TYPE                                               59
D503V9, multiclass
                                                                   clus
vv                                                                  HTR1E MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  HTR1E WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HTR1E MUTATED    11   0   0   1
  HTR1E WILD-TYPE 300  14  15  23
D503V10, multiclass
    clus
vv   HTR1E MUTATED HTR1E WILD-TYPE
  R0            11             300
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D503V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HTR1E MUTATED       3                         0
  HTR1E WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HTR1E MUTATED                                           0     7
  HTR1E WILD-TYPE                                         1   236
D503V12, multiclass
                                           clus
vv                                          HTR1E MUTATED HTR1E WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D503V13, binary
                 cls
clus                0   1
  HTR1E MUTATED     1   7
  HTR1E WILD-TYPE   3 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR1E MUTATED      1    7
  HTR1E WILD-TYPE    3  303
                        clus
vv                       HTR1E MUTATED HTR1E WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(504) Variable = FLNB MUTATION ANALYSIS
D504V1, survival
                sevent
clus2              0   1
  FLNB MUTATED    15  10
  FLNB WILD-TYPE 215 129
  FLNB MUTATED FLNB WILD-TYPE 
            25            344 
  FLNB MUTATED FLNB WILD-TYPE 
            10            129 
$`FLNB MUTATED`
TCGA-BR-4184 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8487 
        6.97        14.43         9.60         4.31        25.05         1.12 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4CS TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI 
       28.14        31.96         1.48        12.43         6.58        11.77 
TCGA-CG-5721 TCGA-CG-5733 TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GT 
        6.02        21.07        26.47        22.68        29.98         6.51 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-IN-A6RN TCGA-IN-A6RR TCGA-KB-A6F7 TCGA-VQ-A8P2 
       20.25        29.00        19.53         6.74        63.62        38.14 
TCGA-VQ-A8P3 
       37.22 

$`FLNB WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-A4GP 
        3.25        22.75        25.81        11.77        21.37         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-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.44        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-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 

  FLNB MUTATED FLNB WILD-TYPE 
          1.12           0.00 
  FLNB MUTATED FLNB WILD-TYPE 
         63.62         122.30 
  FLNB MUTATED FLNB WILD-TYPE 
         19.53          14.12 
[1] "1.1 - 63.6 (19.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D504V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FLNB MUTATED         0        0        3        1         5         2
  FLNB WILD-TYPE       2       15       37       29        32        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FLNB MUTATED           1          7          0          6        2
  FLNB WILD-TYPE         2         63         53         26       36
D504V3, multiclass
            clus
vv           FLNB MUTATED FLNB WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              3             37
  STAGE II              1             29
  STAGE IIA             5             32
  STAGE IIB             2             50
  STAGE III             1              2
  STAGE IIIA            7             63
  STAGE IIIB            0             53
  STAGE IIIC            6             26
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FLNB MUTATED     2   4   8  13
  FLNB WILD-TYPE  20  88 165  84
D504V4, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  T1            2             20
  T2            4             88
  T3            8            165
  T4           13             84
[1] 4 2
[1] TRUE
[1] "dimension of 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  11   4   5
  FLNB WILD-TYPE 110  93  73  72
D504V5, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  N0            8            110
  N1           11             93
  N2            4             73
  N3            5             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"
D504V6, binary
                cls
clus               0   1
  FLNB MUTATED    25   1
  FLNB WILD-TYPE 321  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     25    1
  FLNB WILD-TYPE  321   28
   clus
vv  FLNB MUTATED FLNB WILD-TYPE
  0           25            321
  1            1             28
[1] 2 2
[1] FALSE
D504V7, binary
                cls
clus               0   1
  FLNB MUTATED    14  14
  FLNB WILD-TYPE 131 234
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     14   14
  FLNB WILD-TYPE  131  234
        clus
vv       FLNB MUTATED FLNB WILD-TYPE
  FEMALE           14            131
  MALE             14            234
[1] 2 2
[1] FALSE
D504V8, binary
                cls
clus               0   1
  FLNB MUTATED    22   3
  FLNB WILD-TYPE 270  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     22    3
  FLNB WILD-TYPE  270   56
     clus
vv    FLNB MUTATED FLNB WILD-TYPE
  NO            22            270
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FLNB MUTATED                                          1
  FLNB WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FLNB MUTATED                                       4
  FLNB WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FLNB MUTATED                                                       12
  FLNB WILD-TYPE                                                    146
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FLNB MUTATED                                                   2
  FLNB WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FLNB MUTATED                                                                   5
  FLNB WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FLNB MUTATED                                                    0
  FLNB WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FLNB MUTATED                                                  4
  FLNB WILD-TYPE                                               57
D504V9, multiclass
                                                                   clus
vv                                                                  FLNB MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  FLNB WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FLNB MUTATED    22   0   0   3
  FLNB WILD-TYPE 289  14  15  21
D504V10, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  R0           22            289
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D504V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FLNB MUTATED       9                         0
  FLNB WILD-TYPE    78                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FLNB MUTATED                                           0    16
  FLNB WILD-TYPE                                         1   227
D504V12, multiclass
                                           clus
vv                                          FLNB MUTATED FLNB WILD-TYPE
  ASIAN                                                9             78
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               16            227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D504V13, binary
                cls
clus               0   1
  FLNB MUTATED     0  23
  FLNB WILD-TYPE   4 287
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED      0   23
  FLNB WILD-TYPE    4  287
                        clus
vv                       FLNB MUTATED FLNB WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           23            287
[1] 2 2
[1] FALSE

Clustering(505) Variable = NCAPH MUTATION ANALYSIS
D505V1, survival
                 sevent
clus2               0   1
  NCAPH MUTATED     6   3
  NCAPH WILD-TYPE 224 136
  NCAPH MUTATED NCAPH WILD-TYPE 
              9             360 
  NCAPH MUTATED NCAPH WILD-TYPE 
              3             136 
$`NCAPH MUTATED`
TCGA-BR-4184 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5730 TCGA-FP-A4BE 
        6.97         6.02       105.07        28.96         4.01        11.08 
TCGA-HF-A5NB TCGA-HU-A4GQ TCGA-VQ-A8P2 
       30.51         0.10        38.14 

$`NCAPH WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
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-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-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 

  NCAPH MUTATED NCAPH WILD-TYPE 
            0.1             0.0 
  NCAPH MUTATED NCAPH WILD-TYPE 
         105.07          122.30 
  NCAPH MUTATED NCAPH WILD-TYPE 
          11.08           14.35 
[1] "0.1 - 105.1 (11.1)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D505V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NCAPH MUTATED         0        1        0        1         1         0
  NCAPH WILD-TYPE       2       14       40       29        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NCAPH MUTATED           0          3          0          3        2
  NCAPH WILD-TYPE         3         67         53         29       36
D505V3, multiclass
            clus
vv           NCAPH MUTATED NCAPH WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NCAPH MUTATED     1   2   2   6
  NCAPH WILD-TYPE  21  90 171  91
D505V4, multiclass
    clus
vv   NCAPH MUTATED NCAPH WILD-TYPE
  T1             1              21
  T2             2              90
  T3             2             171
  T4             6              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
  NCAPH MUTATED     3   5   1   2
  NCAPH WILD-TYPE 115  99  76  75
D505V5, multiclass
    clus
vv   NCAPH MUTATED NCAPH WILD-TYPE
  N0             3             115
  N1             5              99
  N2             1              76
  N3             2              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"
D505V6, binary
                 cls
clus                0   1
  NCAPH MUTATED    10   1
  NCAPH WILD-TYPE 336  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCAPH MUTATED     10    1
  NCAPH WILD-TYPE  336   28
   clus
vv  NCAPH MUTATED NCAPH WILD-TYPE
  0            10             336
  1             1              28
[1] 2 2
[1] FALSE
D505V7, binary
                 cls
clus                0   1
  NCAPH MUTATED     4   8
  NCAPH WILD-TYPE 141 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCAPH MUTATED      4    8
  NCAPH WILD-TYPE  141  240
        clus
vv       NCAPH MUTATED NCAPH WILD-TYPE
  FEMALE             4             141
  MALE               8             240
[1] 2 2
[1] FALSE
D505V8, binary
                 cls
clus                0   1
  NCAPH MUTATED     4   3
  NCAPH WILD-TYPE 288  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCAPH MUTATED      4    3
  NCAPH WILD-TYPE  288   56
     clus
vv    NCAPH MUTATED NCAPH WILD-TYPE
  NO              4             288
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NCAPH MUTATED                                          0
  NCAPH WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NCAPH MUTATED                                       1
  NCAPH WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NCAPH MUTATED                                                        5
  NCAPH WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NCAPH MUTATED                                                   2
  NCAPH WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NCAPH MUTATED                                                                   3
  NCAPH WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NCAPH MUTATED                                                    0
  NCAPH WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NCAPH MUTATED                                                  1
  NCAPH WILD-TYPE                                               60
D505V9, multiclass
                                                                   clus
vv                                                                  NCAPH MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  NCAPH WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NCAPH MUTATED     7   1   1   3
  NCAPH WILD-TYPE 304  13  14  21
D505V10, multiclass
    clus
vv   NCAPH MUTATED NCAPH WILD-TYPE
  R0             7             304
  R1             1              13
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D505V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NCAPH MUTATED       1                         1
  NCAPH WILD-TYPE    86                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NCAPH MUTATED                                           0     4
  NCAPH WILD-TYPE                                         1   239
D505V12, multiclass
                                           clus
vv                                          NCAPH MUTATED NCAPH WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D505V13, binary
                 cls
clus                0   1
  NCAPH MUTATED     0   5
  NCAPH WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCAPH MUTATED      0    5
  NCAPH WILD-TYPE    4  305
                        clus
vv                       NCAPH MUTATED NCAPH WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(506) Variable = SLFN13 MUTATION ANALYSIS
D506V1, survival
                  sevent
clus2                0   1
  SLFN13 MUTATED     5   1
  SLFN13 WILD-TYPE 225 138
  SLFN13 MUTATED SLFN13 WILD-TYPE 
               6              363 
  SLFN13 MUTATED SLFN13 WILD-TYPE 
               1              138 
$`SLFN13 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8589 TCGA-CG-5721 TCGA-VQ-A8PM 
       34.68        29.59         6.18        27.12         6.02         1.87 

$`SLFN13 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  SLFN13 MUTATED SLFN13 WILD-TYPE 
            1.87             0.00 
  SLFN13 MUTATED SLFN13 WILD-TYPE 
           34.68           122.30 
  SLFN13 MUTATED SLFN13 WILD-TYPE 
           16.65            14.27 
[1] "1.9 - 34.7 (16.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.2"
D506V2, 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       1       15       39       30        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLFN13 MUTATED           0          0          1          0        2
  SLFN13 WILD-TYPE         3         70         52         32       36
D506V3, multiclass
            clus
vv           SLFN13 MUTATED SLFN13 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLFN13 MUTATED     1   1   2   4
  SLFN13 WILD-TYPE  21  91 171  93
D506V4, multiclass
    clus
vv   SLFN13 MUTATED SLFN13 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              2              171
  T4              4               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
  SLFN13 MUTATED     4   4   0   1
  SLFN13 WILD-TYPE 114 100  77  76
D506V5, multiclass
    clus
vv   SLFN13 MUTATED SLFN13 WILD-TYPE
  N0              4              114
  N1              4              100
  N2              0               77
  N3              1               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"
D506V6, binary
                  cls
clus                 0   1
  SLFN13 MUTATED     8   0
  SLFN13 WILD-TYPE 338  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLFN13 MUTATED      8    0
  SLFN13 WILD-TYPE  338   29
   clus
vv  SLFN13 MUTATED SLFN13 WILD-TYPE
  0              8              338
  1              0               29
[1] 2 2
[1] FALSE
D506V7, binary
                  cls
clus                 0   1
  SLFN13 MUTATED     3   6
  SLFN13 WILD-TYPE 142 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLFN13 MUTATED      3    6
  SLFN13 WILD-TYPE  142  242
        clus
vv       SLFN13 MUTATED SLFN13 WILD-TYPE
  FEMALE              3              142
  MALE                6              242
[1] 2 2
[1] FALSE
D506V8, binary
                  cls
clus                 0   1
  SLFN13 MUTATED     7   0
  SLFN13 WILD-TYPE 285  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLFN13 MUTATED      7    0
  SLFN13 WILD-TYPE  285   59
     clus
vv    SLFN13 MUTATED SLFN13 WILD-TYPE
  NO               7              285
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLFN13 MUTATED                                          1
  SLFN13 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLFN13 MUTATED                                       0
  SLFN13 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLFN13 MUTATED                                                        5
  SLFN13 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLFN13 MUTATED                                                   0
  SLFN13 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLFN13 MUTATED                                                                   3
  SLFN13 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLFN13 MUTATED                                                    0
  SLFN13 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLFN13 MUTATED                                                  0
  SLFN13 WILD-TYPE                                               61
D506V9, multiclass
                                                                   clus
vv                                                                  SLFN13 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  SLFN13 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SLFN13 MUTATED     8   0   0   1
  SLFN13 WILD-TYPE 303  14  15  23
D506V10, multiclass
    clus
vv   SLFN13 MUTATED SLFN13 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D506V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SLFN13 MUTATED       0                         1
  SLFN13 WILD-TYPE    87                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLFN13 MUTATED                                           0     6
  SLFN13 WILD-TYPE                                         1   237
D506V12, multiclass
                                           clus
vv                                          SLFN13 MUTATED SLFN13 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D506V13, binary
                  cls
clus                 0   1
  SLFN13 MUTATED     0   6
  SLFN13 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLFN13 MUTATED      0    6
  SLFN13 WILD-TYPE    4  304
                        clus
vv                       SLFN13 MUTATED SLFN13 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(507) Variable = GATA3 MUTATION ANALYSIS
D507V1, survival
                 sevent
clus2               0   1
  GATA3 MUTATED     9   6
  GATA3 WILD-TYPE 221 133
  GATA3 MUTATED GATA3 WILD-TYPE 
             15             354 
  GATA3 MUTATED GATA3 WILD-TYPE 
              6             133 
$`GATA3 MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7958 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8382 
       34.68        36.16        29.56         0.26         4.31        25.05 
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-8687 TCGA-CG-4469 TCGA-EQ-5647 
        1.12        28.14        31.96         8.22         7.07         0.62 
TCGA-HU-8244 TCGA-HU-A4GQ TCGA-VQ-A8P2 
       24.39         0.10        38.14 

$`GATA3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        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-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-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-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-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-D7-6818 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-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-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8249 
       52.21        30.51        26.47         1.51         5.92        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 

  GATA3 MUTATED GATA3 WILD-TYPE 
            0.1             0.0 
  GATA3 MUTATED GATA3 WILD-TYPE 
          38.14          122.30 
  GATA3 MUTATED GATA3 WILD-TYPE 
          24.39           14.22 
[1] "0.1 - 38.1 (24.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D507V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GATA3 MUTATED         0        2        2        0         2         0
  GATA3 WILD-TYPE       2       13       38       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GATA3 MUTATED           0          1          1          5        3
  GATA3 WILD-TYPE         3         69         52         27       35
D507V3, multiclass
            clus
vv           GATA3 MUTATED GATA3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             5              27
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GATA3 MUTATED     3   2   3   9
  GATA3 WILD-TYPE  19  90 170  88
D507V4, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  T1             3              19
  T2             2              90
  T3             3             170
  T4             9              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
  GATA3 MUTATED     7   1   3   5
  GATA3 WILD-TYPE 111 103  74  72
D507V5, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  N0             7             111
  N1             1             103
  N2             3              74
  N3             5              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"
D507V6, binary
                 cls
clus                0   1
  GATA3 MUTATED    16   2
  GATA3 WILD-TYPE 330  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     16    2
  GATA3 WILD-TYPE  330   27
   clus
vv  GATA3 MUTATED GATA3 WILD-TYPE
  0            16             330
  1             2              27
[1] 2 2
[1] FALSE
D507V7, binary
                 cls
clus                0   1
  GATA3 MUTATED    10   8
  GATA3 WILD-TYPE 135 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     10    8
  GATA3 WILD-TYPE  135  240
        clus
vv       GATA3 MUTATED GATA3 WILD-TYPE
  FEMALE            10             135
  MALE               8             240
[1] 2 2
[1] FALSE
D507V8, binary
                 cls
clus                0   1
  GATA3 MUTATED    14   1
  GATA3 WILD-TYPE 278  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     14    1
  GATA3 WILD-TYPE  278   58
     clus
vv    GATA3 MUTATED GATA3 WILD-TYPE
  NO             14             278
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GATA3 MUTATED                                          0
  GATA3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GATA3 MUTATED                                       0
  GATA3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GATA3 MUTATED                                                       12
  GATA3 WILD-TYPE                                                    146
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GATA3 MUTATED                                                   1
  GATA3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GATA3 MUTATED                                                                   1
  GATA3 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GATA3 MUTATED                                                    1
  GATA3 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GATA3 MUTATED                                                  3
  GATA3 WILD-TYPE                                               58
D507V9, multiclass
                                                                   clus
vv                                                                  GATA3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  GATA3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GATA3 MUTATED    12   3   1   2
  GATA3 WILD-TYPE 299  11  14  22
D507V10, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  R0            12             299
  R1             3              11
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D507V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GATA3 MUTATED       3                         0
  GATA3 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GATA3 MUTATED                                           0    14
  GATA3 WILD-TYPE                                         1   229
D507V12, multiclass
                                           clus
vv                                          GATA3 MUTATED GATA3 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D507V13, binary
                 cls
clus                0   1
  GATA3 MUTATED     0  16
  GATA3 WILD-TYPE   4 294
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED      0   16
  GATA3 WILD-TYPE    4  294
                        clus
vv                       GATA3 MUTATED GATA3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            16             294
[1] 2 2
[1] FALSE

Clustering(508) Variable = RDBP MUTATION ANALYSIS
D508V1, survival
                sevent
clus2              0   1
  RDBP MUTATED     6   3
  RDBP WILD-TYPE 224 136
  RDBP MUTATED RDBP WILD-TYPE 
             9            360 
  RDBP MUTATED RDBP WILD-TYPE 
             3            136 
$`RDBP MUTATED`
TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-8531 TCGA-CD-A4MG TCGA-HU-A4GQ 
        0.26         1.12        28.14        12.59         6.58         0.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-VQ-A8P2 
       29.00        23.84        38.14 

$`RDBP WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  RDBP MUTATED RDBP WILD-TYPE 
           0.1            0.0 
  RDBP MUTATED RDBP WILD-TYPE 
         38.14         122.30 
  RDBP MUTATED RDBP WILD-TYPE 
         12.59          14.35 
[1] "0.1 - 38.1 (12.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D508V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RDBP MUTATED         0        0        1        0         2         1
  RDBP WILD-TYPE       2       15       39       30        35        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RDBP MUTATED           0          2          0          3        0
  RDBP WILD-TYPE         3         68         53         29       38
D508V3, multiclass
            clus
vv           RDBP MUTATED RDBP WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            3             29
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RDBP MUTATED     0   2   3   4
  RDBP WILD-TYPE  22  90 170  93
D508V4, multiclass
    clus
vv   RDBP MUTATED RDBP WILD-TYPE
  T1            0             22
  T2            2             90
  T3            3            170
  T4            4             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
  RDBP MUTATED     3   3   2   2
  RDBP WILD-TYPE 115 101  75  75
D508V5, multiclass
    clus
vv   RDBP MUTATED RDBP WILD-TYPE
  N0            3            115
  N1            3            101
  N2            2             75
  N3            2             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"
D508V6, binary
                cls
clus               0   1
  RDBP MUTATED    10   0
  RDBP WILD-TYPE 336  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED     10    0
  RDBP WILD-TYPE  336   29
   clus
vv  RDBP MUTATED RDBP WILD-TYPE
  0           10            336
  1            0             29
[1] 2 2
[1] FALSE
D508V7, binary
                cls
clus               0   1
  RDBP MUTATED     6   4
  RDBP WILD-TYPE 139 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      6    4
  RDBP WILD-TYPE  139  244
        clus
vv       RDBP MUTATED RDBP WILD-TYPE
  FEMALE            6            139
  MALE              4            244
[1] 2 2
[1] FALSE
D508V8, binary
                cls
clus               0   1
  RDBP MUTATED     6   2
  RDBP WILD-TYPE 286  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      6    2
  RDBP WILD-TYPE  286   57
     clus
vv    RDBP MUTATED RDBP WILD-TYPE
  NO             6            286
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RDBP MUTATED                                          0
  RDBP WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RDBP MUTATED                                       3
  RDBP WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RDBP MUTATED                                                        4
  RDBP WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RDBP MUTATED                                                   1
  RDBP WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RDBP MUTATED                                                                   0
  RDBP WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RDBP MUTATED                                                    0
  RDBP WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RDBP MUTATED                                                  2
  RDBP WILD-TYPE                                               59
D508V9, multiclass
                                                                   clus
vv                                                                  RDBP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  RDBP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RDBP MUTATED     8   0   0   1
  RDBP WILD-TYPE 303  14  15  23
D508V10, multiclass
    clus
vv   RDBP MUTATED RDBP WILD-TYPE
  R0            8            303
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D508V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RDBP MUTATED       5                         0
  RDBP WILD-TYPE    82                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RDBP MUTATED                                           0     5
  RDBP WILD-TYPE                                         1   238
D508V12, multiclass
                                           clus
vv                                          RDBP MUTATED RDBP WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D508V13, binary
                cls
clus               0   1
  RDBP MUTATED     0   9
  RDBP WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      0    9
  RDBP WILD-TYPE    4  301
                        clus
vv                       RDBP MUTATED RDBP WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(509) Variable = TNRC6C MUTATION ANALYSIS
D509V1, survival
                  sevent
clus2                0   1
  TNRC6C MUTATED     9   3
  TNRC6C WILD-TYPE 221 136
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              12              357 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               3              136 
$`TNRC6C MUTATED`
TCGA-CG-4444 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-A4QL TCGA-CG-4465 
       47.05        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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-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-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 

  TNRC6C MUTATED TNRC6C WILD-TYPE 
            6.02             0.00 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
           47.05           122.30 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
           23.51            14.07 
[1] "6.0 - 47.0 (23.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D509V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNRC6C MUTATED         1        1        4        0         4         0
  TNRC6C WILD-TYPE       1       14       36       30        33        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNRC6C MUTATED           0          1          1          0        2
  TNRC6C WILD-TYPE         3         69         52         32       36
D509V3, multiclass
            clus
vv           TNRC6C MUTATED TNRC6C WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                4               36
  STAGE II                0               30
  STAGE IIA               4               33
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TNRC6C MUTATED     3   4   5   2
  TNRC6C WILD-TYPE  19  88 168  95
D509V4, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  T1              3               19
  T2              4               88
  T3              5              168
  T4              2               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
  TNRC6C MUTATED     8   4   1   2
  TNRC6C WILD-TYPE 110 100  76  75
D509V5, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  N0              8              110
  N1              4              100
  N2              1               76
  N3              2               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"
D509V6, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    12   1
  TNRC6C WILD-TYPE 334  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     12    1
  TNRC6C WILD-TYPE  334   28
   clus
vv  TNRC6C MUTATED TNRC6C WILD-TYPE
  0             12              334
  1              1               28
[1] 2 2
[1] FALSE
D509V7, binary
                  cls
clus                 0   1
  TNRC6C MUTATED     9   6
  TNRC6C WILD-TYPE 136 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      9    6
  TNRC6C WILD-TYPE  136  242
        clus
vv       TNRC6C MUTATED TNRC6C WILD-TYPE
  FEMALE              9              136
  MALE                6              242
[1] 2 2
[1] FALSE
D509V8, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    10   2
  TNRC6C WILD-TYPE 282  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     10    2
  TNRC6C WILD-TYPE  282   57
     clus
vv    TNRC6C MUTATED TNRC6C WILD-TYPE
  NO              10              282
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TNRC6C MUTATED                                          1
  TNRC6C WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TNRC6C MUTATED                                       2
  TNRC6C WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNRC6C MUTATED                                                        7
  TNRC6C WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TNRC6C MUTATED                                                   0
  TNRC6C WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNRC6C MUTATED                                                                   2
  TNRC6C WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TNRC6C MUTATED                                                    0
  TNRC6C WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TNRC6C MUTATED                                                  3
  TNRC6C WILD-TYPE                                               58
D509V9, multiclass
                                                                   clus
vv                                                                  TNRC6C MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  TNRC6C WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TNRC6C MUTATED    13   0   1   1
  TNRC6C WILD-TYPE 298  14  14  23
D509V10, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  R0             13              298
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D509V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TNRC6C MUTATED       3                         2
  TNRC6C WILD-TYPE    84                         7
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNRC6C MUTATED                                           0     6
  TNRC6C WILD-TYPE                                         1   237
D509V12, multiclass
                                           clus
vv                                          TNRC6C MUTATED TNRC6C WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              2                7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D509V13, binary
                  cls
clus                 0   1
  TNRC6C MUTATED     0  11
  TNRC6C WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      0   11
  TNRC6C WILD-TYPE    4  299
                        clus
vv                       TNRC6C MUTATED TNRC6C WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(510) Variable = ZNF292 MUTATION ANALYSIS
D510V1, survival
                  sevent
clus2                0   1
  ZNF292 MUTATED    18   9
  ZNF292 WILD-TYPE 212 130
  ZNF292 MUTATED ZNF292 WILD-TYPE 
              27              342 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
               9              130 
$`ZNF292 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6802 
       21.99         6.97         9.34        34.68        32.78        30.90 
TCGA-BR-7703 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 
       36.16        32.25        29.42        31.27         1.12        28.14 
TCGA-BR-8680 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5721 
       31.96        12.59        12.43         6.58        11.77         6.02 
TCGA-D7-5577 TCGA-D7-A6EY TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4G8 
       25.71        11.44        11.08        30.51        26.47        22.68 
TCGA-HU-A4GX TCGA-VQ-A8P2 TCGA-VQ-A8PE 
       20.25        38.14        22.19 

$`ZNF292 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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 
            1.12             0.00 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
           38.14           122.30 
  ZNF292 MUTATED ZNF292 WILD-TYPE 
          22.680           14.055 
[1] "1.1 - 38.1 (22.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D510V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF292 MUTATED         0        1        2        2         5         2
  ZNF292 WILD-TYPE       2       14       38       28        32        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF292 MUTATED           0          6          2          4        3
  ZNF292 WILD-TYPE         3         64         51         28       35
D510V3, multiclass
            clus
vv           ZNF292 MUTATED ZNF292 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                2               28
  STAGE IIA               5               32
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              6               64
  STAGE IIIB              2               51
  STAGE IIIC              4               28
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF292 MUTATED     1   3  14   9
  ZNF292 WILD-TYPE  21  89 159  88
D510V4, multiclass
    clus
vv   ZNF292 MUTATED ZNF292 WILD-TYPE
  T1              1               21
  T2              3               89
  T3             14              159
  T4              9               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
  ZNF292 MUTATED    11   9   3   6
  ZNF292 WILD-TYPE 107  95  74  71
D510V5, multiclass
    clus
vv   ZNF292 MUTATED ZNF292 WILD-TYPE
  N0             11              107
  N1              9               95
  N2              3               74
  N3              6               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"
D510V6, binary
                  cls
clus                 0   1
  ZNF292 MUTATED    25   2
  ZNF292 WILD-TYPE 321  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF292 MUTATED     25    2
  ZNF292 WILD-TYPE  321   27
   clus
vv  ZNF292 MUTATED ZNF292 WILD-TYPE
  0             25              321
  1              2               27
[1] 2 2
[1] FALSE
D510V7, binary
                  cls
clus                 0   1
  ZNF292 MUTATED    13  16
  ZNF292 WILD-TYPE 132 232
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF292 MUTATED     13   16
  ZNF292 WILD-TYPE  132  232
        clus
vv       ZNF292 MUTATED ZNF292 WILD-TYPE
  FEMALE             13              132
  MALE               16              232
[1] 2 2
[1] FALSE
D510V8, binary
                  cls
clus                 0   1
  ZNF292 MUTATED    23   4
  ZNF292 WILD-TYPE 269  55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF292 MUTATED     23    4
  ZNF292 WILD-TYPE  269   55
     clus
vv    ZNF292 MUTATED ZNF292 WILD-TYPE
  NO              23              269
  YES              4               55
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF292 MUTATED                                          1
  ZNF292 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF292 MUTATED                                       4
  ZNF292 WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF292 MUTATED                                                       14
  ZNF292 WILD-TYPE                                                    144
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF292 MUTATED                                                   2
  ZNF292 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF292 MUTATED                                                                   3
  ZNF292 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF292 MUTATED                                                    1
  ZNF292 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF292 MUTATED                                                  4
  ZNF292 WILD-TYPE                                               57
D510V9, multiclass
                                                                   clus
vv                                                                  ZNF292 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  ZNF292 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF292 MUTATED    21   1   1   3
  ZNF292 WILD-TYPE 290  13  14  21
D510V10, multiclass
    clus
vv   ZNF292 MUTATED ZNF292 WILD-TYPE
  R0             21              290
  R1              1               13
  R2              1               14
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D510V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF292 MUTATED       7                         1
  ZNF292 WILD-TYPE    80                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF292 MUTATED                                           0    17
  ZNF292 WILD-TYPE                                         1   226
D510V12, multiclass
                                           clus
vv                                          ZNF292 MUTATED ZNF292 WILD-TYPE
  ASIAN                                                  7               80
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 17              226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D510V13, binary
                  cls
clus                 0   1
  ZNF292 MUTATED     0  23
  ZNF292 WILD-TYPE   4 287
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF292 MUTATED      0   23
  ZNF292 WILD-TYPE    4  287
                        clus
vv                       ZNF292 MUTATED ZNF292 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             23              287
[1] 2 2
[1] FALSE

Clustering(511) Variable = TPTE2 MUTATION ANALYSIS
D511V1, survival
                 sevent
clus2               0   1
  TPTE2 MUTATED     9   7
  TPTE2 WILD-TYPE 221 132
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             16             353 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              7             132 
$`TPTE2 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-8680 TCGA-BR-8690 
        6.97        34.68         9.17        35.24        31.96        10.68 
TCGA-CG-5721 TCGA-D7-A4Z0 TCGA-EQ-8122 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8243 
        6.02        14.76         7.99        52.21        26.47         5.92 
TCGA-HU-A4GU TCGA-HU-A4H6 TCGA-RD-A7BT TCGA-VQ-A8PK 
        6.58        21.17         8.61        17.85 

$`TPTE2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
           5.92            0.00 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
          52.21          122.30 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
          12.72           14.27 
[1] "5.9 - 52.2 (12.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D511V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TPTE2 MUTATED         0        1        1        1         1         4
  TPTE2 WILD-TYPE       2       14       39       29        36        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TPTE2 MUTATED           0          2          2          1        3
  TPTE2 WILD-TYPE         3         68         51         31       35
D511V3, multiclass
            clus
vv           TPTE2 MUTATED TPTE2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TPTE2 MUTATED     1   3   9   4
  TPTE2 WILD-TYPE  21  89 164  93
D511V4, multiclass
    clus
vv   TPTE2 MUTATED TPTE2 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             9             164
  T4             4              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
  TPTE2 MUTATED     5   4   3   4
  TPTE2 WILD-TYPE 113 100  74  73
D511V5, multiclass
    clus
vv   TPTE2 MUTATED TPTE2 WILD-TYPE
  N0             5             113
  N1             4             100
  N2             3              74
  N3             4              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"
D511V6, binary
                 cls
clus                0   1
  TPTE2 MUTATED    13   1
  TPTE2 WILD-TYPE 333  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED     13    1
  TPTE2 WILD-TYPE  333   28
   clus
vv  TPTE2 MUTATED TPTE2 WILD-TYPE
  0            13             333
  1             1              28
[1] 2 2
[1] FALSE
D511V7, binary
                 cls
clus                0   1
  TPTE2 MUTATED     8   9
  TPTE2 WILD-TYPE 137 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      8    9
  TPTE2 WILD-TYPE  137  239
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  FEMALE             8             137
  MALE               9             239
[1] 2 2
[1] FALSE
D511V8, binary
                 cls
clus                0   1
  TPTE2 MUTATED    14   2
  TPTE2 WILD-TYPE 278  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED     14    2
  TPTE2 WILD-TYPE  278   57
     clus
vv    TPTE2 MUTATED TPTE2 WILD-TYPE
  NO             14             278
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TPTE2 MUTATED                                          1
  TPTE2 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TPTE2 MUTATED                                       1
  TPTE2 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TPTE2 MUTATED                                                        5
  TPTE2 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TPTE2 MUTATED                                                   1
  TPTE2 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TPTE2 MUTATED                                                                   6
  TPTE2 WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TPTE2 MUTATED                                                    0
  TPTE2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TPTE2 MUTATED                                                  3
  TPTE2 WILD-TYPE                                               58
D511V9, multiclass
                                                                   clus
vv                                                                  TPTE2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  TPTE2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TPTE2 MUTATED    13   0   1   2
  TPTE2 WILD-TYPE 298  14  14  22
D511V10, multiclass
    clus
vv   TPTE2 MUTATED TPTE2 WILD-TYPE
  R0            13             298
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D511V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TPTE2 MUTATED       4                         0
  TPTE2 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TPTE2 MUTATED                                           1    10
  TPTE2 WILD-TYPE                                         0   233
D511V12, multiclass
                                           clus
vv                                          TPTE2 MUTATED TPTE2 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               0
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D511V13, binary
                 cls
clus                0   1
  TPTE2 MUTATED     0  14
  TPTE2 WILD-TYPE   4 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      0   14
  TPTE2 WILD-TYPE    4  296
                        clus
vv                       TPTE2 MUTATED TPTE2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(512) Variable = FBXO48 MUTATION ANALYSIS
D512V1, survival
                  sevent
clus2                0   1
  FBXO48 MUTATED     3   1
  FBXO48 WILD-TYPE 227 138
  FBXO48 MUTATED FBXO48 WILD-TYPE 
               4              365 
  FBXO48 MUTATED FBXO48 WILD-TYPE 
               1              138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-F1-6875 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-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 

  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           14.170 
[1] "11.1 - 35.2 (21.7)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.9"
D512V2, 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       2       14       38       29        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO48 MUTATED           0          0          0          0        0
  FBXO48 WILD-TYPE         3         70         53         32       38
D512V3, multiclass
            clus
vv           FBXO48 MUTATED FBXO48 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO48 MUTATED     1   2   2   0
  FBXO48 WILD-TYPE  21  90 171  97
D512V4, multiclass
    clus
vv   FBXO48 MUTATED FBXO48 WILD-TYPE
  T1              1               21
  T2              2               90
  T3              2              171
  T4              0               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
  FBXO48 MUTATED     5   0   0   0
  FBXO48 WILD-TYPE 113 104  77  77
D512V5, multiclass
    clus
vv   FBXO48 MUTATED FBXO48 WILD-TYPE
  N0              5              113
  N1              0              104
  N2              0               77
  N3              0               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"
D512V6, binary
                  cls
clus                 0   1
  FBXO48 MUTATED     5   0
  FBXO48 WILD-TYPE 341  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO48 MUTATED      5    0
  FBXO48 WILD-TYPE  341   29
   clus
vv  FBXO48 MUTATED FBXO48 WILD-TYPE
  0              5              341
  1              0               29
[1] 2 2
[1] FALSE
D512V7, binary
                  cls
clus                 0   1
  FBXO48 MUTATED     1   4
  FBXO48 WILD-TYPE 144 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO48 MUTATED      1    4
  FBXO48 WILD-TYPE  144  244
        clus
vv       FBXO48 MUTATED FBXO48 WILD-TYPE
  FEMALE              1              144
  MALE                4              244
[1] 2 2
[1] FALSE
D512V8, binary
                  cls
clus                 0   1
  FBXO48 MUTATED     2   1
  FBXO48 WILD-TYPE 290  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO48 MUTATED      2    1
  FBXO48 WILD-TYPE  290   58
     clus
vv    FBXO48 MUTATED FBXO48 WILD-TYPE
  NO               2              290
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FBXO48 MUTATED                                          0
  FBXO48 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FBXO48 MUTATED                                       0
  FBXO48 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBXO48 MUTATED                                                        1
  FBXO48 WILD-TYPE                                                    157
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FBXO48 MUTATED                                                   0
  FBXO48 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBXO48 MUTATED                                                                   4
  FBXO48 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FBXO48 MUTATED                                                    0
  FBXO48 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FBXO48 MUTATED                                                  0
  FBXO48 WILD-TYPE                                               61
D512V9, multiclass
                                                                   clus
vv                                                                  FBXO48 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  FBXO48 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FBXO48 MUTATED     5   0   0   0
  FBXO48 WILD-TYPE 306  14  15  24
D512V10, multiclass
    clus
vv   FBXO48 MUTATED FBXO48 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D512V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FBXO48 MUTATED       0                         1
  FBXO48 WILD-TYPE    87                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXO48 MUTATED                                           0     2
  FBXO48 WILD-TYPE                                         1   241
D512V12, multiclass
                                           clus
vv                                          FBXO48 MUTATED FBXO48 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D512V13, binary
                  cls
clus                 0   1
  FBXO48 MUTATED     0   3
  FBXO48 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO48 MUTATED      0    3
  FBXO48 WILD-TYPE    4  307
                        clus
vv                       FBXO48 MUTATED FBXO48 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(513) Variable = KRTAP5-5 MUTATION ANALYSIS
D513V1, survival
                    sevent
clus2                  0   1
  KRTAP5-5 MUTATED     5   1
  KRTAP5-5 WILD-TYPE 225 138
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 6                363 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 1                138 
$`KRTAP5-5 MUTATED`
TCGA-BR-8081 TCGA-CD-A4MJ TCGA-CG-5723 TCGA-CG-5726 TCGA-HU-A4G8 TCGA-HU-A4GT 
       32.25        12.62       105.07        28.96        22.68         6.51 

$`KRTAP5-5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-5724 TCGA-CG-5725 
        1.02         0.99         6.02         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-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 

  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
              6.51               0.00 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
            105.07             122.30 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
             25.82              14.17 
[1] "6.5 - 105.1 (25.8)" "0.0 - 122.3 (14.2)"
[1] "hr=" "3.4"
D513V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRTAP5-5 MUTATED         0        1        1        1         1         2
  KRTAP5-5 WILD-TYPE       2       14       39       29        36        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRTAP5-5 MUTATED           0          0          0          0        0
  KRTAP5-5 WILD-TYPE         3         70         53         32       38
D513V3, multiclass
            clus
vv           KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  1                 39
  STAGE II                  1                 29
  STAGE IIA                 1                 36
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                0                 53
  STAGE IIIC                0                 32
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KRTAP5-5 MUTATED     1   2   2   1
  KRTAP5-5 WILD-TYPE  21  90 171  96
D513V4, multiclass
    clus
vv   KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  T1                1                 21
  T2                2                 90
  T3                2                171
  T4                1                 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
  KRTAP5-5 MUTATED     4   2   0   0
  KRTAP5-5 WILD-TYPE 114 102  77  77
D513V5, multiclass
    clus
vv   KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  N0                4                114
  N1                2                102
  N2                0                 77
  N3                0                 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"
D513V6, binary
                    cls
clus                   0   1
  KRTAP5-5 MUTATED     6   0
  KRTAP5-5 WILD-TYPE 340  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      6    0
  KRTAP5-5 WILD-TYPE  340   29
   clus
vv  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  0                6                340
  1                0                 29
[1] 2 2
[1] FALSE
D513V7, binary
                    cls
clus                   0   1
  KRTAP5-5 MUTATED     3   3
  KRTAP5-5 WILD-TYPE 142 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      3    3
  KRTAP5-5 WILD-TYPE  142  245
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  FEMALE                3                142
  MALE                  3                245
[1] 2 2
[1] FALSE
D513V8, binary
                    cls
clus                   0   1
  KRTAP5-5 MUTATED     5   0
  KRTAP5-5 WILD-TYPE 287  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      5    0
  KRTAP5-5 WILD-TYPE  287   59
     clus
vv    KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  NO                 5                287
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KRTAP5-5 MUTATED                                          0
  KRTAP5-5 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KRTAP5-5 MUTATED                                       1
  KRTAP5-5 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KRTAP5-5 MUTATED                                                        3
  KRTAP5-5 WILD-TYPE                                                    155
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KRTAP5-5 MUTATED                                                   0
  KRTAP5-5 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KRTAP5-5 MUTATED                                                                   1
  KRTAP5-5 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KRTAP5-5 MUTATED                                                    0
  KRTAP5-5 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KRTAP5-5 MUTATED                                                  1
  KRTAP5-5 WILD-TYPE                                               60
D513V9, multiclass
                                                                   clus
vv                                                                  KRTAP5-5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  KRTAP5-5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KRTAP5-5 MUTATED     4   0   0   0
  KRTAP5-5 WILD-TYPE 307  14  15  24
D513V10, multiclass
    clus
vv   KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  R0                4                307
  R1                0                 14
  R2                0                 15
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D513V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KRTAP5-5 MUTATED       3                         0
  KRTAP5-5 WILD-TYPE    84                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KRTAP5-5 MUTATED                                           0     1
  KRTAP5-5 WILD-TYPE                                         1   242
D513V12, multiclass
                                           clus
vv                                          KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    1                242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D513V13, binary
                    cls
clus                   0   1
  KRTAP5-5 MUTATED     0   4
  KRTAP5-5 WILD-TYPE   4 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      0    4
  KRTAP5-5 WILD-TYPE    4  306
                        clus
vv                       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                4                306
[1] 2 2
[1] FALSE

Clustering(514) Variable = SERPINB12 MUTATION ANALYSIS
D514V1, survival
                     sevent
clus2                   0   1
  SERPINB12 MUTATED     4   0
  SERPINB12 WILD-TYPE 226 139
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
                  4                 365 
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
                  0                 139 
$`SERPINB12 MUTATED`
TCGA-BR-8286 TCGA-BR-8487 TCGA-HU-A4GH TCGA-HU-A4GN 
       29.42         1.12        11.77        29.98 

$`SERPINB12 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
               1.12                0.00 
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
              29.98              122.30 
  SERPINB12 MUTATED SERPINB12 WILD-TYPE 
             20.595              14.270 
[1] "1.1 - 30.0 (20.6)"  "0.0 - 122.3 (14.3)"
[1] "hr="     "9100000"
D514V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPINB12 MUTATED         0        1        0        1         2         0
  SERPINB12 WILD-TYPE       2       14       40       29        35        52
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB12 MUTATED           0          1          0          0        0
  SERPINB12 WILD-TYPE         3         69         53         32       38
D514V3, multiclass
            clus
vv           SERPINB12 MUTATED SERPINB12 WILD-TYPE
  STAGE I                    0                   2
  STAGE IA                   1                  14
  STAGE IB                   0                  40
  STAGE II                   1                  29
  STAGE IIA                  2                  35
  STAGE IIB                  0                  52
  STAGE III                  0                   3
  STAGE IIIA                 1                  69
  STAGE IIIB                 0                  53
  STAGE IIIC                 0                  32
  STAGE IV                   0                  38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  SERPINB12 MUTATED     1   2   2   1
  SERPINB12 WILD-TYPE  21  90 171  96
D514V4, multiclass
    clus
vv   SERPINB12 MUTATED SERPINB12 WILD-TYPE
  T1                 1                  21
  T2                 2                  90
  T3                 2                 171
  T4                 1                  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
  SERPINB12 MUTATED     4   1   0   0
  SERPINB12 WILD-TYPE 114 103  77  77
D514V5, multiclass
    clus
vv   SERPINB12 MUTATED SERPINB12 WILD-TYPE
  N0                 4                 114
  N1                 1                 103
  N2                 0                  77
  N3                 0                  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"
D514V6, binary
                     cls
clus                    0   1
  SERPINB12 MUTATED     6   0
  SERPINB12 WILD-TYPE 340  29
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB12 MUTATED      6    0
  SERPINB12 WILD-TYPE  340   29
   clus
vv  SERPINB12 MUTATED SERPINB12 WILD-TYPE
  0                 6                 340
  1                 0                  29
[1] 2 2
[1] FALSE
D514V7, binary
                     cls
clus                    0   1
  SERPINB12 MUTATED     3   3
  SERPINB12 WILD-TYPE 142 245
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB12 MUTATED      3    3
  SERPINB12 WILD-TYPE  142  245
        clus
vv       SERPINB12 MUTATED SERPINB12 WILD-TYPE
  FEMALE                 3                 142
  MALE                   3                 245
[1] 2 2
[1] FALSE
D514V8, binary
                     cls
clus                    0   1
  SERPINB12 MUTATED     4   0
  SERPINB12 WILD-TYPE 288  59
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB12 MUTATED      4    0
  SERPINB12 WILD-TYPE  288   59
     clus
vv    SERPINB12 MUTATED SERPINB12 WILD-TYPE
  NO                  4                 288
  YES                 0                  59
[1] 2 2
[1] FALSE
                     vv
clus                  STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SERPINB12 MUTATED                                          0
  SERPINB12 WILD-TYPE                                        8
                     vv
clus                  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SERPINB12 MUTATED                                       0
  SERPINB12 WILD-TYPE                                    70
                     vv
clus                  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SERPINB12 MUTATED                                                        4
  SERPINB12 WILD-TYPE                                                    154
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SERPINB12 MUTATED                                                   0
  SERPINB12 WILD-TYPE                                                21
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SERPINB12 MUTATED                                                                   0
  SERPINB12 WILD-TYPE                                                                68
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SERPINB12 MUTATED                                                    0
  SERPINB12 WILD-TYPE                                                  5
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SERPINB12 MUTATED                                                  2
  SERPINB12 WILD-TYPE                                               59
D514V9, multiclass
                                                                   clus
vv                                                                  SERPINB12 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  2
                                                                   clus
vv                                                                  SERPINB12 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                            8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                              70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                  21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                  5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                   59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  SERPINB12 MUTATED     4   0   0   2
  SERPINB12 WILD-TYPE 307  14  15  22
D514V10, multiclass
    clus
vv   SERPINB12 MUTATED SERPINB12 WILD-TYPE
  R0                 4                 307
  R1                 0                  14
  R2                 0                  15
  RX                 2                  22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D514V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN
  SERPINB12 MUTATED       2                         0
  SERPINB12 WILD-TYPE    85                         9
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SERPINB12 MUTATED                                           0     4
  SERPINB12 WILD-TYPE                                         1   239
D514V12, multiclass
                                           clus
vv                                          SERPINB12 MUTATED
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                     4
                                           clus
vv                                          SERPINB12 WILD-TYPE
  ASIAN                                                      85
  BLACK OR AFRICAN AMERICAN                                   9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   1
  WHITE                                                     239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D514V13, binary
                     cls
clus                    0   1
  SERPINB12 MUTATED     0   6
  SERPINB12 WILD-TYPE   4 304
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB12 MUTATED      0    6
  SERPINB12 WILD-TYPE    4  304
                        clus
vv                       SERPINB12 MUTATED SERPINB12 WILD-TYPE
  HISPANIC OR LATINO                     0                   4
  NOT HISPANIC OR LATINO                 6                 304
[1] 2 2
[1] FALSE

Clustering(515) Variable = TAF7L MUTATION ANALYSIS
D515V1, survival
                 sevent
clus2               0   1
  TAF7L MUTATED     6   3
  TAF7L WILD-TYPE 224 136
  TAF7L MUTATED TAF7L WILD-TYPE 
              9             360 
  TAF7L MUTATED TAF7L WILD-TYPE 
              3             136 
$`TAF7L MUTATED`
TCGA-BR-6852 TCGA-BR-8363 TCGA-BR-8382 TCGA-BR-8589 TCGA-CD-A4MJ TCGA-CG-5721 
       44.94         0.26        25.05        27.12        12.62         6.02 
TCGA-CG-5733 TCGA-D7-6524 TCGA-HU-A4H4 
       21.07        17.85        23.84 

$`TAF7L WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-D7-6525 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-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 

  TAF7L MUTATED TAF7L WILD-TYPE 
           0.26            0.00 
  TAF7L MUTATED TAF7L WILD-TYPE 
          44.94          122.30 
  TAF7L MUTATED TAF7L WILD-TYPE 
          21.07           14.12 
[1] "0.3 - 44.9 (21.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D515V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAF7L MUTATED         0        0        2        1         1         1
  TAF7L WILD-TYPE       2       15       38       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAF7L MUTATED           0          1          1          1        1
  TAF7L WILD-TYPE         3         69         52         31       37
D515V3, multiclass
            clus
vv           TAF7L MUTATED TAF7L WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TAF7L MUTATED     0   5   1   3
  TAF7L WILD-TYPE  22  87 172  94
D515V4, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  T1             0              22
  T2             5              87
  T3             1             172
  T4             3              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
  TAF7L MUTATED     3   3   2   1
  TAF7L WILD-TYPE 115 101  75  76
D515V5, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  N0             3             115
  N1             3             101
  N2             2              75
  N3             1              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"
D515V6, binary
                 cls
clus                0   1
  TAF7L MUTATED     9   0
  TAF7L WILD-TYPE 337  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED      9    0
  TAF7L WILD-TYPE  337   29
   clus
vv  TAF7L MUTATED TAF7L WILD-TYPE
  0             9             337
  1             0              29
[1] 2 2
[1] FALSE
D515V7, binary
                 cls
clus                0   1
  TAF7L MUTATED     5   4
  TAF7L WILD-TYPE 140 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED      5    4
  TAF7L WILD-TYPE  140  244
        clus
vv       TAF7L MUTATED TAF7L WILD-TYPE
  FEMALE             5             140
  MALE               4             244
[1] 2 2
[1] FALSE
D515V8, binary
                 cls
clus                0   1
  TAF7L MUTATED     9   0
  TAF7L WILD-TYPE 283  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED      9    0
  TAF7L WILD-TYPE  283   59
     clus
vv    TAF7L MUTATED TAF7L WILD-TYPE
  NO              9             283
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TAF7L MUTATED                                          0
  TAF7L WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TAF7L MUTATED                                       1
  TAF7L WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TAF7L MUTATED                                                        5
  TAF7L WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TAF7L MUTATED                                                   0
  TAF7L WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TAF7L MUTATED                                                                   2
  TAF7L WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TAF7L MUTATED                                                    0
  TAF7L WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TAF7L MUTATED                                                  1
  TAF7L WILD-TYPE                                               60
D515V9, multiclass
                                                                   clus
vv                                                                  TAF7L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  TAF7L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TAF7L MUTATED     7   1   0   0
  TAF7L WILD-TYPE 304  13  15  24
D515V10, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  R0             7             304
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D515V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TAF7L MUTATED       2                         0
  TAF7L WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAF7L MUTATED                                           0     5
  TAF7L WILD-TYPE                                         1   238
D515V12, multiclass
                                           clus
vv                                          TAF7L MUTATED TAF7L WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D515V13, binary
                 cls
clus                0   1
  TAF7L MUTATED     0   7
  TAF7L WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED      0    7
  TAF7L WILD-TYPE    4  303
                        clus
vv                       TAF7L MUTATED TAF7L WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(516) Variable = INTS12 MUTATION ANALYSIS
D516V1, survival
                  sevent
clus2                0   1
  INTS12 MUTATED     2   2
  INTS12 WILD-TYPE 228 137
  INTS12 MUTATED INTS12 WILD-TYPE 
               4              365 
  INTS12 MUTATED INTS12 WILD-TYPE 
               2              137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  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           14.170 
[1] "6.2 - 34.7 (15.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D516V2, 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       2       15       40       30        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INTS12 MUTATED           1          0          1          0        1
  INTS12 WILD-TYPE         2         70         52         32       37
D516V3, multiclass
            clus
vv           INTS12 MUTATED INTS12 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               1                2
  STAGE IIIA              0               70
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  INTS12 MUTATED     0   0   3   2
  INTS12 WILD-TYPE  22  92 170  95
D516V4, multiclass
    clus
vv   INTS12 MUTATED INTS12 WILD-TYPE
  T1              0               22
  T2              0               92
  T3              3              170
  T4              2               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
  INTS12 MUTATED     2   2   1   1
  INTS12 WILD-TYPE 116 102  76  76
D516V5, multiclass
    clus
vv   INTS12 MUTATED INTS12 WILD-TYPE
  N0              2              116
  N1              2              102
  N2              1               76
  N3              1               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"
D516V6, binary
                  cls
clus                 0   1
  INTS12 MUTATED     6   0
  INTS12 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INTS12 MUTATED      6    0
  INTS12 WILD-TYPE  340   29
   clus
vv  INTS12 MUTATED INTS12 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D516V7, binary
                  cls
clus                 0   1
  INTS12 MUTATED     4   2
  INTS12 WILD-TYPE 141 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INTS12 MUTATED      4    2
  INTS12 WILD-TYPE  141  246
        clus
vv       INTS12 MUTATED INTS12 WILD-TYPE
  FEMALE              4              141
  MALE                2              246
[1] 2 2
[1] FALSE
D516V8, binary
                  cls
clus                 0   1
  INTS12 MUTATED     4   0
  INTS12 WILD-TYPE 288  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INTS12 MUTATED      4    0
  INTS12 WILD-TYPE  288   59
     clus
vv    INTS12 MUTATED INTS12 WILD-TYPE
  NO               4              288
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  INTS12 MUTATED                                          0
  INTS12 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  INTS12 MUTATED                                       0
  INTS12 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  INTS12 MUTATED                                                        4
  INTS12 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  INTS12 MUTATED                                                   0
  INTS12 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  INTS12 MUTATED                                                                   2
  INTS12 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  INTS12 MUTATED                                                    0
  INTS12 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  INTS12 MUTATED                                                  0
  INTS12 WILD-TYPE                                               61
D516V9, multiclass
                                                                   clus
vv                                                                  INTS12 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  INTS12 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  INTS12 MUTATED     4   0   0   2
  INTS12 WILD-TYPE 307  14  15  22
D516V10, multiclass
    clus
vv   INTS12 MUTATED INTS12 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D516V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  INTS12 MUTATED       0                         0
  INTS12 WILD-TYPE    87                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INTS12 MUTATED                                           0     6
  INTS12 WILD-TYPE                                         1   237
D516V12, multiclass
                                           clus
vv                                          INTS12 MUTATED INTS12 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D516V13, binary
                  cls
clus                 0   1
  INTS12 MUTATED     0   6
  INTS12 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INTS12 MUTATED      0    6
  INTS12 WILD-TYPE    4  304
                        clus
vv                       INTS12 MUTATED INTS12 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(517) Variable = CTSA MUTATION ANALYSIS
D517V1, survival
                sevent
clus2              0   1
  CTSA MUTATED     3   2
  CTSA WILD-TYPE 227 137
  CTSA MUTATED CTSA WILD-TYPE 
             5            364 
  CTSA MUTATED CTSA WILD-TYPE 
             2            137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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          14.35 
[1] "7.0 - 105.1 (11.4)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D517V2, 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       2       15       40       28        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTSA MUTATED           0          1          1          0        0
  CTSA WILD-TYPE         3         69         52         32       38
D517V3, multiclass
            clus
vv           CTSA MUTATED CTSA WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              2             28
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTSA MUTATED     0   2   3   0
  CTSA WILD-TYPE  22  90 170  97
D517V4, multiclass
    clus
vv   CTSA MUTATED CTSA WILD-TYPE
  T1            0             22
  T2            2             90
  T3            3            170
  T4            0             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
  CTSA MUTATED     1   3   0   1
  CTSA WILD-TYPE 117 101  77  76
D517V5, multiclass
    clus
vv   CTSA MUTATED CTSA WILD-TYPE
  N0            1            117
  N1            3            101
  N2            0             77
  N3            1             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"
D517V6, binary
                cls
clus               0   1
  CTSA MUTATED     4   0
  CTSA WILD-TYPE 342  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      4    0
  CTSA WILD-TYPE  342   29
   clus
vv  CTSA MUTATED CTSA WILD-TYPE
  0            4            342
  1            0             29
[1] 2 2
[1] FALSE
D517V7, binary
                cls
clus               0   1
  CTSA MUTATED     1   4
  CTSA WILD-TYPE 144 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      1    4
  CTSA WILD-TYPE  144  244
        clus
vv       CTSA MUTATED CTSA WILD-TYPE
  FEMALE            1            144
  MALE              4            244
[1] 2 2
[1] FALSE
D517V8, binary
                cls
clus               0   1
  CTSA MUTATED     4   1
  CTSA WILD-TYPE 288  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      4    1
  CTSA WILD-TYPE  288   58
     clus
vv    CTSA MUTATED CTSA WILD-TYPE
  NO             4            288
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CTSA MUTATED                                          0
  CTSA WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CTSA MUTATED                                       0
  CTSA WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTSA MUTATED                                                        4
  CTSA WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CTSA MUTATED                                                   0
  CTSA WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTSA MUTATED                                                                   0
  CTSA WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CTSA MUTATED                                                    0
  CTSA WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CTSA MUTATED                                                  1
  CTSA WILD-TYPE                                               60
D517V9, multiclass
                                                                   clus
vv                                                                  CTSA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  CTSA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CTSA MUTATED     4   0   0   1
  CTSA WILD-TYPE 307  14  15  23
D517V10, multiclass
    clus
vv   CTSA MUTATED CTSA WILD-TYPE
  R0            4            307
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D517V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CTSA MUTATED       0                         1
  CTSA WILD-TYPE    87                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTSA MUTATED                                           0     2
  CTSA WILD-TYPE                                         1   241
D517V12, multiclass
                                           clus
vv                                          CTSA MUTATED CTSA WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D517V13, binary
                cls
clus               0   1
  CTSA MUTATED     0   3
  CTSA WILD-TYPE   4 307
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      0    3
  CTSA WILD-TYPE    4  307
                        clus
vv                       CTSA MUTATED CTSA WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            3            307
[1] 2 2
[1] FALSE

Clustering(518) Variable = C1QA MUTATION ANALYSIS
D518V1, survival
                sevent
clus2              0   1
  C1QA MUTATED     5   0
  C1QA WILD-TYPE 225 139
  C1QA MUTATED C1QA WILD-TYPE 
             5            364 
  C1QA MUTATED C1QA WILD-TYPE 
             0            139 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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          14.22 
[1] "1.1 - 105.1 (29.6)" "0.0 - 122.3 (14.2)"
[1] "hr="     "9500000"
D518V2, 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       2       15       39       29        35        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1QA MUTATED           0          0          0          0        0
  C1QA WILD-TYPE         3         70         53         32       38
D518V3, multiclass
            clus
vv           C1QA MUTATED C1QA WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  C1QA MUTATED     0   2   2   1
  C1QA WILD-TYPE  22  90 171  96
D518V4, multiclass
    clus
vv   C1QA MUTATED C1QA WILD-TYPE
  T1            0             22
  T2            2             90
  T3            2            171
  T4            1             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
  C1QA MUTATED     4   1   0   0
  C1QA WILD-TYPE 114 103  77  77
D518V5, multiclass
    clus
vv   C1QA MUTATED C1QA WILD-TYPE
  N0            4            114
  N1            1            103
  N2            0             77
  N3            0             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"
D518V6, binary
                cls
clus               0   1
  C1QA MUTATED     5   0
  C1QA WILD-TYPE 341  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QA MUTATED      5    0
  C1QA WILD-TYPE  341   29
   clus
vv  C1QA MUTATED C1QA WILD-TYPE
  0            5            341
  1            0             29
[1] 2 2
[1] FALSE
D518V7, binary
                cls
clus               0   1
  C1QA MUTATED     4   1
  C1QA WILD-TYPE 141 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QA MUTATED      4    1
  C1QA WILD-TYPE  141  247
        clus
vv       C1QA MUTATED C1QA WILD-TYPE
  FEMALE            4            141
  MALE              1            247
[1] 2 2
[1] FALSE
D518V8, binary
                cls
clus               0   1
  C1QA MUTATED     4   0
  C1QA WILD-TYPE 288  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QA MUTATED      4    0
  C1QA WILD-TYPE  288   59
     clus
vv    C1QA MUTATED C1QA WILD-TYPE
  NO             4            288
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C1QA MUTATED                                          0
  C1QA WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C1QA MUTATED                                       0
  C1QA WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C1QA MUTATED                                                        3
  C1QA WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C1QA MUTATED                                                   0
  C1QA WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C1QA MUTATED                                                                   1
  C1QA WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C1QA MUTATED                                                    0
  C1QA WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C1QA MUTATED                                                  1
  C1QA WILD-TYPE                                               60
D518V9, multiclass
                                                                   clus
vv                                                                  C1QA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  C1QA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  C1QA MUTATED     5   0   0   0
  C1QA WILD-TYPE 306  14  15  24
D518V10, multiclass
    clus
vv   C1QA MUTATED C1QA WILD-TYPE
  R0            5            306
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D518V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  C1QA MUTATED       1                         0
  C1QA WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C1QA MUTATED                                           0     2
  C1QA WILD-TYPE                                         1   241
D518V12, multiclass
                                           clus
vv                                          C1QA MUTATED C1QA WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D518V13, binary
                cls
clus               0   1
  C1QA MUTATED     0   3
  C1QA WILD-TYPE   4 307
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QA MUTATED      0    3
  C1QA WILD-TYPE    4  307
                        clus
vv                       C1QA MUTATED C1QA WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            3            307
[1] 2 2
[1] FALSE

Clustering(519) Variable = KCNN3 MUTATION ANALYSIS
D519V1, survival
                 sevent
clus2               0   1
  KCNN3 MUTATED     5   5
  KCNN3 WILD-TYPE 225 134
  KCNN3 MUTATED KCNN3 WILD-TYPE 
             10             359 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
              5             134 
$`KCNN3 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8680 TCGA-CD-A4MI 
        6.97         6.61        36.16        35.84        31.96        11.77 
TCGA-CG-4306 TCGA-D7-A6EY TCGA-HF-A5NB TCGA-HU-A4GU 
        1.02        11.44        30.51         6.58 

$`KCNN3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
          36.16          122.30 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
         11.605          14.430 
[1] "1.0 - 36.2 (11.6)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.4"
D519V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNN3 MUTATED         0        1        1        0         0         1
  KCNN3 WILD-TYPE       2       14       39       30        37        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNN3 MUTATED           1          2          1          1        2
  KCNN3 WILD-TYPE         2         68         52         31       36
D519V3, multiclass
            clus
vv           KCNN3 MUTATED KCNN3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNN3 MUTATED     1   2   5   2
  KCNN3 WILD-TYPE  21  90 168  95
D519V4, multiclass
    clus
vv   KCNN3 MUTATED KCNN3 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             5             168
  T4             2              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
  KCNN3 MUTATED     2   4   2   2
  KCNN3 WILD-TYPE 116 100  75  75
D519V5, multiclass
    clus
vv   KCNN3 MUTATED KCNN3 WILD-TYPE
  N0             2             116
  N1             4             100
  N2             2              75
  N3             2              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"
D519V6, binary
                 cls
clus                0   1
  KCNN3 MUTATED     7   2
  KCNN3 WILD-TYPE 339  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      7    2
  KCNN3 WILD-TYPE  339   27
   clus
vv  KCNN3 MUTATED KCNN3 WILD-TYPE
  0             7             339
  1             2              27
[1] 2 2
[1] FALSE
D519V7, binary
                 cls
clus                0   1
  KCNN3 MUTATED     4   6
  KCNN3 WILD-TYPE 141 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      4    6
  KCNN3 WILD-TYPE  141  242
        clus
vv       KCNN3 MUTATED KCNN3 WILD-TYPE
  FEMALE             4             141
  MALE               6             242
[1] 2 2
[1] FALSE
D519V8, binary
                 cls
clus                0   1
  KCNN3 MUTATED     8   1
  KCNN3 WILD-TYPE 284  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      8    1
  KCNN3 WILD-TYPE  284   58
     clus
vv    KCNN3 MUTATED KCNN3 WILD-TYPE
  NO              8             284
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KCNN3 MUTATED                                          0
  KCNN3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KCNN3 MUTATED                                       1
  KCNN3 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNN3 MUTATED                                                        5
  KCNN3 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KCNN3 MUTATED                                                   1
  KCNN3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNN3 MUTATED                                                                   0
  KCNN3 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KCNN3 MUTATED                                                    1
  KCNN3 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KCNN3 MUTATED                                                  2
  KCNN3 WILD-TYPE                                               59
D519V9, multiclass
                                                                   clus
vv                                                                  KCNN3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  KCNN3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCNN3 MUTATED     5   1   1   2
  KCNN3 WILD-TYPE 306  13  14  22
D519V10, multiclass
    clus
vv   KCNN3 MUTATED KCNN3 WILD-TYPE
  R0             5             306
  R1             1              13
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D519V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCNN3 MUTATED       3                         0
  KCNN3 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNN3 MUTATED                                           0     5
  KCNN3 WILD-TYPE                                         1   238
D519V12, multiclass
                                           clus
vv                                          KCNN3 MUTATED KCNN3 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D519V13, binary
                 cls
clus                0   1
  KCNN3 MUTATED     0   8
  KCNN3 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      0    8
  KCNN3 WILD-TYPE    4  302
                        clus
vv                       KCNN3 MUTATED KCNN3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(520) Variable = NPHS1 MUTATION ANALYSIS
D520V1, survival
                 sevent
clus2               0   1
  NPHS1 MUTATED    10   6
  NPHS1 WILD-TYPE 220 133
  NPHS1 MUTATED NPHS1 WILD-TYPE 
             16             353 
  NPHS1 MUTATED NPHS1 WILD-TYPE 
              6             133 
$`NPHS1 MUTATED`
TCGA-BR-8080 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-A4QL TCGA-CD-8529 TCGA-CD-8532 
        9.60         4.31        11.80        16.14        12.30        11.64 
TCGA-CD-8534 TCGA-CG-4305 TCGA-CG-5721 TCGA-D7-8573 TCGA-D7-A6EY TCGA-FP-8209 
       12.07        15.95         6.02        19.50        11.44        59.54 
TCGA-FP-A4BE TCGA-HU-A4GU TCGA-IN-A6RJ TCGA-VQ-A8P2 
       11.08         6.58        12.46        38.14 

$`NPHS1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
         11.935          14.660 
[1] "4.3 - 59.5 (11.9)"  "0.0 - 122.3 (14.7)"
[1] "hr=" "1.2"
D520V2, 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       2       14       38       27        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NPHS1 MUTATED           0          1          3          1        2
  NPHS1 WILD-TYPE         3         69         50         31       36
D520V3, multiclass
            clus
vv           NPHS1 MUTATED NPHS1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               3              27
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             3              50
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NPHS1 MUTATED     1   3   8   4
  NPHS1 WILD-TYPE  21  89 165  93
D520V4, multiclass
    clus
vv   NPHS1 MUTATED NPHS1 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             8             165
  T4             4              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
  NPHS1 MUTATED     8   4   0   4
  NPHS1 WILD-TYPE 110 100  77  73
D520V5, multiclass
    clus
vv   NPHS1 MUTATED NPHS1 WILD-TYPE
  N0             8             110
  N1             4             100
  N2             0              77
  N3             4              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"
D520V6, binary
                 cls
clus                0   1
  NPHS1 MUTATED    15   1
  NPHS1 WILD-TYPE 331  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHS1 MUTATED     15    1
  NPHS1 WILD-TYPE  331   28
   clus
vv  NPHS1 MUTATED NPHS1 WILD-TYPE
  0            15             331
  1             1              28
[1] 2 2
[1] FALSE
D520V7, binary
                 cls
clus                0   1
  NPHS1 MUTATED     4  12
  NPHS1 WILD-TYPE 141 236
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHS1 MUTATED      4   12
  NPHS1 WILD-TYPE  141  236
        clus
vv       NPHS1 MUTATED NPHS1 WILD-TYPE
  FEMALE             4             141
  MALE              12             236
[1] 2 2
[1] FALSE
D520V8, binary
                 cls
clus                0   1
  NPHS1 MUTATED    12   4
  NPHS1 WILD-TYPE 280  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHS1 MUTATED     12    4
  NPHS1 WILD-TYPE  280   55
     clus
vv    NPHS1 MUTATED NPHS1 WILD-TYPE
  NO             12             280
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NPHS1 MUTATED                                          0
  NPHS1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NPHS1 MUTATED                                       3
  NPHS1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NPHS1 MUTATED                                                        7
  NPHS1 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NPHS1 MUTATED                                                   3
  NPHS1 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NPHS1 MUTATED                                                                   1
  NPHS1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NPHS1 MUTATED                                                    0
  NPHS1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NPHS1 MUTATED                                                  2
  NPHS1 WILD-TYPE                                               59
D520V9, multiclass
                                                                   clus
vv                                                                  NPHS1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  NPHS1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NPHS1 MUTATED    16   0   0   0
  NPHS1 WILD-TYPE 295  14  15  24
D520V10, multiclass
    clus
vv   NPHS1 MUTATED NPHS1 WILD-TYPE
  R0            16             295
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D520V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NPHS1 MUTATED       4                         1
  NPHS1 WILD-TYPE    83                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NPHS1 MUTATED                                           0     9
  NPHS1 WILD-TYPE                                         1   234
D520V12, multiclass
                                           clus
vv                                          NPHS1 MUTATED NPHS1 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D520V13, binary
                 cls
clus                0   1
  NPHS1 MUTATED     0  13
  NPHS1 WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NPHS1 MUTATED      0   13
  NPHS1 WILD-TYPE    4  297
                        clus
vv                       NPHS1 MUTATED NPHS1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(521) Variable = HSP90B1 MUTATION ANALYSIS
D521V1, survival
                   sevent
clus2                 0   1
  HSP90B1 MUTATED     5   4
  HSP90B1 WILD-TYPE 225 135
  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
                9               360 
  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
                4               135 
$`HSP90B1 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-8680 TCGA-CG-5721 TCGA-D7-A6EY TCGA-HJ-7597 
       21.99         6.97        31.96         6.02        11.44        26.47 
TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4G9 
       22.82        22.68        24.20 

$`HSP90B1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-D7-6528 
       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-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-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-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-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 

  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
             6.02              0.00 
  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
            31.96            122.30 
  HSP90B1 MUTATED HSP90B1 WILD-TYPE 
            22.68             14.12 
[1] "6.0 - 32.0 (22.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D521V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HSP90B1 MUTATED         0        1        1        0         1         1
  HSP90B1 WILD-TYPE       2       14       39       30        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSP90B1 MUTATED           0          1          1          0        3
  HSP90B1 WILD-TYPE         3         69         52         32       35
D521V3, multiclass
            clus
vv           HSP90B1 MUTATED HSP90B1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 3                35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  HSP90B1 MUTATED     1   1   4   3
  HSP90B1 WILD-TYPE  21  91 169  94
D521V4, multiclass
    clus
vv   HSP90B1 MUTATED HSP90B1 WILD-TYPE
  T1               1                21
  T2               1                91
  T3               4               169
  T4               3                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
  HSP90B1 MUTATED     3   4   1   1
  HSP90B1 WILD-TYPE 115 100  76  76
D521V5, multiclass
    clus
vv   HSP90B1 MUTATED HSP90B1 WILD-TYPE
  N0               3               115
  N1               4               100
  N2               1                76
  N3               1                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"
D521V6, binary
                   cls
clus                  0   1
  HSP90B1 MUTATED     5   2
  HSP90B1 WILD-TYPE 341  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSP90B1 MUTATED      5    2
  HSP90B1 WILD-TYPE  341   27
   clus
vv  HSP90B1 MUTATED HSP90B1 WILD-TYPE
  0               5               341
  1               2                27
[1] 2 2
[1] FALSE
D521V7, binary
                   cls
clus                  0   1
  HSP90B1 MUTATED     6   3
  HSP90B1 WILD-TYPE 139 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSP90B1 MUTATED      6    3
  HSP90B1 WILD-TYPE  139  245
        clus
vv       HSP90B1 MUTATED HSP90B1 WILD-TYPE
  FEMALE               6               139
  MALE                 3               245
[1] 2 2
[1] FALSE
D521V8, binary
                   cls
clus                  0   1
  HSP90B1 MUTATED     9   0
  HSP90B1 WILD-TYPE 283  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSP90B1 MUTATED      9    0
  HSP90B1 WILD-TYPE  283   59
     clus
vv    HSP90B1 MUTATED HSP90B1 WILD-TYPE
  NO                9               283
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HSP90B1 MUTATED                                          1
  HSP90B1 WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HSP90B1 MUTATED                                       1
  HSP90B1 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HSP90B1 MUTATED                                                        1
  HSP90B1 WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HSP90B1 MUTATED                                                   0
  HSP90B1 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HSP90B1 MUTATED                                                                   2
  HSP90B1 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HSP90B1 MUTATED                                                    0
  HSP90B1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HSP90B1 MUTATED                                                  4
  HSP90B1 WILD-TYPE                                               57
D521V9, multiclass
                                                                   clus
vv                                                                  HSP90B1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                4
                                                                   clus
vv                                                                  HSP90B1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  HSP90B1 MUTATED     6   0   1   1
  HSP90B1 WILD-TYPE 305  14  14  23
D521V10, multiclass
    clus
vv   HSP90B1 MUTATED HSP90B1 WILD-TYPE
  R0               6               305
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D521V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  HSP90B1 MUTATED       4                         0
  HSP90B1 WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HSP90B1 MUTATED                                           0     3
  HSP90B1 WILD-TYPE                                         1   240
D521V12, multiclass
                                           clus
vv                                          HSP90B1 MUTATED HSP90B1 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D521V13, binary
                   cls
clus                  0   1
  HSP90B1 MUTATED     0   7
  HSP90B1 WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSP90B1 MUTATED      0    7
  HSP90B1 WILD-TYPE    4  303
                        clus
vv                       HSP90B1 MUTATED HSP90B1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(522) Variable = P2RY4 MUTATION ANALYSIS
D522V1, survival
                 sevent
clus2               0   1
  P2RY4 MUTATED     6   6
  P2RY4 WILD-TYPE 224 133
  P2RY4 MUTATED P2RY4 WILD-TYPE 
             12             357 
  P2RY4 MUTATED P2RY4 WILD-TYPE 
              6             133 
$`P2RY4 MUTATED`
TCGA-BR-4184 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8487 TCGA-CD-8524 
        6.97         0.69         8.05         2.20         1.12        12.76 
TCGA-CG-5726 TCGA-D7-8576 TCGA-FP-8209 TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H4 
       28.96        14.66        59.54        20.25         0.26        23.84 

$`P2RY4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
       14.43        11.44        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-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-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-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-D7-8578 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-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       17.06         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-A4H0 
       29.98         8.98         0.10         6.51         6.58         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 

  P2RY4 MUTATED P2RY4 WILD-TYPE 
           0.26            0.00 
  P2RY4 MUTATED P2RY4 WILD-TYPE 
          59.54          122.30 
  P2RY4 MUTATED P2RY4 WILD-TYPE 
         10.405          14.430 
[1] "0.3 - 59.5 (10.4)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.7"
D522V2, 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       2       14       39       29        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  P2RY4 MUTATED           0          2          2          2        0
  P2RY4 WILD-TYPE         3         68         51         30       38
D522V3, multiclass
            clus
vv           P2RY4 MUTATED P2RY4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  P2RY4 MUTATED     1   2   4   5
  P2RY4 WILD-TYPE  21  90 169  92
D522V4, multiclass
    clus
vv   P2RY4 MUTATED P2RY4 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             4             169
  T4             5              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
  P2RY4 MUTATED     5   3   2   2
  P2RY4 WILD-TYPE 113 101  75  75
D522V5, multiclass
    clus
vv   P2RY4 MUTATED P2RY4 WILD-TYPE
  N0             5             113
  N1             3             101
  N2             2              75
  N3             2              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"
D522V6, binary
                 cls
clus                0   1
  P2RY4 MUTATED    11   0
  P2RY4 WILD-TYPE 335  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY4 MUTATED     11    0
  P2RY4 WILD-TYPE  335   29
   clus
vv  P2RY4 MUTATED P2RY4 WILD-TYPE
  0            11             335
  1             0              29
[1] 2 2
[1] FALSE
D522V7, binary
                 cls
clus                0   1
  P2RY4 MUTATED     9   3
  P2RY4 WILD-TYPE 136 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY4 MUTATED      9    3
  P2RY4 WILD-TYPE  136  245
        clus
vv       P2RY4 MUTATED P2RY4 WILD-TYPE
  FEMALE             9             136
  MALE               3             245
[1] 2 2
[1] FALSE
D522V8, binary
                 cls
clus                0   1
  P2RY4 MUTATED     9   1
  P2RY4 WILD-TYPE 283  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY4 MUTATED      9    1
  P2RY4 WILD-TYPE  283   58
     clus
vv    P2RY4 MUTATED P2RY4 WILD-TYPE
  NO              9             283
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  P2RY4 MUTATED                                          0
  P2RY4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  P2RY4 MUTATED                                       3
  P2RY4 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  P2RY4 MUTATED                                                        3
  P2RY4 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  P2RY4 MUTATED                                                   0
  P2RY4 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  P2RY4 MUTATED                                                                   4
  P2RY4 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  P2RY4 MUTATED                                                    0
  P2RY4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  P2RY4 MUTATED                                                  2
  P2RY4 WILD-TYPE                                               59
D522V9, multiclass
                                                                   clus
vv                                                                  P2RY4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  P2RY4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  P2RY4 MUTATED    11   0   0   1
  P2RY4 WILD-TYPE 300  14  15  23
D522V10, multiclass
    clus
vv   P2RY4 MUTATED P2RY4 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D522V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  P2RY4 MUTATED       4                         0
  P2RY4 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  P2RY4 MUTATED                                           0     7
  P2RY4 WILD-TYPE                                         1   236
D522V12, multiclass
                                           clus
vv                                          P2RY4 MUTATED P2RY4 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D522V13, binary
                 cls
clus                0   1
  P2RY4 MUTATED     0  11
  P2RY4 WILD-TYPE   4 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY4 MUTATED      0   11
  P2RY4 WILD-TYPE    4  299
                        clus
vv                       P2RY4 MUTATED P2RY4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(523) Variable = LRFN3 MUTATION ANALYSIS
D523V1, survival
                 sevent
clus2               0   1
  LRFN3 MUTATED    16   4
  LRFN3 WILD-TYPE 214 135
  LRFN3 MUTATED LRFN3 WILD-TYPE 
             20             349 
  LRFN3 MUTATED LRFN3 WILD-TYPE 
              4             135 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-D7-5577 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-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-8604 
       26.47         1.51         5.92        24.39        28.96        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07        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-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-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 

  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          14.470 
[1] "0.8 - 44.9 (12.6)"  "0.0 - 122.3 (14.5)"
[1] "hr=" "1.7"
D523V2, 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       2       13       39       29        32        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRFN3 MUTATED           0          3          1          3        2
  LRFN3 WILD-TYPE         3         67         52         29       36
D523V3, multiclass
            clus
vv           LRFN3 MUTATED LRFN3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              5              32
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LRFN3 MUTATED     4   0  12   5
  LRFN3 WILD-TYPE  18  92 161  92
D523V4, multiclass
    clus
vv   LRFN3 MUTATED LRFN3 WILD-TYPE
  T1             4              18
  T2             0              92
  T3            12             161
  T4             5              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
  LRFN3 MUTATED    10   4   3   3
  LRFN3 WILD-TYPE 108 100  74  74
D523V5, multiclass
    clus
vv   LRFN3 MUTATED LRFN3 WILD-TYPE
  N0            10             108
  N1             4             100
  N2             3              74
  N3             3              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"
D523V6, binary
                 cls
clus                0   1
  LRFN3 MUTATED    19   2
  LRFN3 WILD-TYPE 327  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRFN3 MUTATED     19    2
  LRFN3 WILD-TYPE  327   27
   clus
vv  LRFN3 MUTATED LRFN3 WILD-TYPE
  0            19             327
  1             2              27
[1] 2 2
[1] FALSE
D523V7, binary
                 cls
clus                0   1
  LRFN3 MUTATED     9  13
  LRFN3 WILD-TYPE 136 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRFN3 MUTATED      9   13
  LRFN3 WILD-TYPE  136  235
        clus
vv       LRFN3 MUTATED LRFN3 WILD-TYPE
  FEMALE             9             136
  MALE              13             235
[1] 2 2
[1] FALSE
D523V8, binary
                 cls
clus                0   1
  LRFN3 MUTATED    14   3
  LRFN3 WILD-TYPE 278  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRFN3 MUTATED     14    3
  LRFN3 WILD-TYPE  278   56
     clus
vv    LRFN3 MUTATED LRFN3 WILD-TYPE
  NO             14             278
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LRFN3 MUTATED                                          0
  LRFN3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LRFN3 MUTATED                                       4
  LRFN3 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LRFN3 MUTATED                                                       11
  LRFN3 WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LRFN3 MUTATED                                                   2
  LRFN3 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LRFN3 MUTATED                                                                   2
  LRFN3 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LRFN3 MUTATED                                                    0
  LRFN3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LRFN3 MUTATED                                                  3
  LRFN3 WILD-TYPE                                               58
D523V9, multiclass
                                                                   clus
vv                                                                  LRFN3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  LRFN3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LRFN3 MUTATED    17   0   1   2
  LRFN3 WILD-TYPE 294  14  14  22
D523V10, multiclass
    clus
vv   LRFN3 MUTATED LRFN3 WILD-TYPE
  R0            17             294
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D523V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LRFN3 MUTATED      10                         0
  LRFN3 WILD-TYPE    77                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LRFN3 MUTATED                                           0    10
  LRFN3 WILD-TYPE                                         1   233
D523V12, multiclass
                                           clus
vv                                          LRFN3 MUTATED LRFN3 WILD-TYPE
  ASIAN                                                10              77
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D523V13, binary
                 cls
clus                0   1
  LRFN3 MUTATED     1  19
  LRFN3 WILD-TYPE   3 291
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRFN3 MUTATED      1   19
  LRFN3 WILD-TYPE    3  291
                        clus
vv                       LRFN3 MUTATED LRFN3 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            19             291
[1] 2 2
[1] FALSE

Clustering(524) Variable = SMARCB1 MUTATION ANALYSIS
D524V1, survival
                   sevent
clus2                 0   1
  SMARCB1 MUTATED     7   4
  SMARCB1 WILD-TYPE 223 135
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               11               358 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                4               135 
$`SMARCB1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8368 TCGA-CD-A4MI TCGA-CG-4305 
        6.97        30.90        34.68         4.31        11.77        15.95 
TCGA-F1-6874 TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-VQ-A8DT 
       14.47         0.10        29.00        14.07        48.79 

$`SMARCB1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-F1-6875 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-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-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-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 

  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
              0.1               0.0 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
            48.79            122.30 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
            14.47             14.22 
[1] "0.1 - 48.8 (14.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D524V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMARCB1 MUTATED         0        1        3        1         1         1
  SMARCB1 WILD-TYPE       2       14       37       29        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCB1 MUTATED           0          2          1          2        0
  SMARCB1 WILD-TYPE         3         68         52         30       38
D524V3, multiclass
            clus
vv           SMARCB1 MUTATED SMARCB1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 3                37
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               2                30
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SMARCB1 MUTATED     2   4   4   3
  SMARCB1 WILD-TYPE  20  88 169  94
D524V4, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  T1               2                20
  T2               4                88
  T3               4               169
  T4               3                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
  SMARCB1 MUTATED     5   4   1   2
  SMARCB1 WILD-TYPE 113 100  76  75
D524V5, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  N0               5               113
  N1               4               100
  N2               1                76
  N3               2                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"
D524V6, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    12   0
  SMARCB1 WILD-TYPE 334  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     12    0
  SMARCB1 WILD-TYPE  334   29
   clus
vv  SMARCB1 MUTATED SMARCB1 WILD-TYPE
  0              12               334
  1               0                29
[1] 2 2
[1] FALSE
D524V7, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     4   9
  SMARCB1 WILD-TYPE 141 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      4    9
  SMARCB1 WILD-TYPE  141  239
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  FEMALE               4               141
  MALE                 9               239
[1] 2 2
[1] FALSE
D524V8, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    10   2
  SMARCB1 WILD-TYPE 282  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     10    2
  SMARCB1 WILD-TYPE  282   57
     clus
vv    SMARCB1 MUTATED SMARCB1 WILD-TYPE
  NO               10               282
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SMARCB1 MUTATED                                          0
  SMARCB1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SMARCB1 MUTATED                                       1
  SMARCB1 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMARCB1 MUTATED                                                        7
  SMARCB1 WILD-TYPE                                                    151
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SMARCB1 MUTATED                                                   0
  SMARCB1 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMARCB1 MUTATED                                                                   3
  SMARCB1 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SMARCB1 MUTATED                                                    0
  SMARCB1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SMARCB1 MUTATED                                                  2
  SMARCB1 WILD-TYPE                                               59
D524V9, multiclass
                                                                   clus
vv                                                                  SMARCB1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  SMARCB1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SMARCB1 MUTATED    10   0   0   2
  SMARCB1 WILD-TYPE 301  14  15  22
D524V10, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  R0              10               301
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D524V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SMARCB1 MUTATED       5                         0
  SMARCB1 WILD-TYPE    82                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMARCB1 MUTATED                                           0     6
  SMARCB1 WILD-TYPE                                         1   237
D524V12, multiclass
                                           clus
vv                                          SMARCB1 MUTATED SMARCB1 WILD-TYPE
  ASIAN                                                   5                82
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D524V13, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     0  11
  SMARCB1 WILD-TYPE   4 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      0   11
  SMARCB1 WILD-TYPE    4  299
                        clus
vv                       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              11               299
[1] 2 2
[1] FALSE

Clustering(525) Variable = ITGA6 MUTATION ANALYSIS
D525V1, survival
                 sevent
clus2               0   1
  ITGA6 MUTATED     5   2
  ITGA6 WILD-TYPE 225 137
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              7             362 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              2             137 
$`ITGA6 MUTATED`
TCGA-B7-A5TI TCGA-BR-4280 TCGA-CD-A4MG TCGA-CG-5723 TCGA-D7-8573 TCGA-HU-8602 
       19.56         6.61         6.58       105.07        19.50        22.32 
TCGA-VQ-A8P2 
       38.14 

$`ITGA6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        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-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 

  ITGA6 MUTATED ITGA6 WILD-TYPE 
           6.58            0.00 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
         105.07          122.30 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
          19.56           14.12 
[1] "6.6 - 105.1 (19.6)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D525V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITGA6 MUTATED         0        0        1        1         2         1
  ITGA6 WILD-TYPE       2       15       39       29        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ITGA6 MUTATED           1          1          0          1        0
  ITGA6 WILD-TYPE         2         69         53         31       38
D525V3, multiclass
            clus
vv           ITGA6 MUTATED ITGA6 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGA6 MUTATED     0   3   2   3
  ITGA6 WILD-TYPE  22  89 171  94
D525V4, multiclass
    clus
vv   ITGA6 MUTATED ITGA6 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             2             171
  T4             3              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
  ITGA6 MUTATED     4   4   0   1
  ITGA6 WILD-TYPE 114 100  77  76
D525V5, multiclass
    clus
vv   ITGA6 MUTATED ITGA6 WILD-TYPE
  N0             4             114
  N1             4             100
  N2             0              77
  N3             1              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"
D525V6, binary
                 cls
clus                0   1
  ITGA6 MUTATED     9   0
  ITGA6 WILD-TYPE 337  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      9    0
  ITGA6 WILD-TYPE  337   29
   clus
vv  ITGA6 MUTATED ITGA6 WILD-TYPE
  0             9             337
  1             0              29
[1] 2 2
[1] FALSE
D525V7, binary
                 cls
clus                0   1
  ITGA6 MUTATED     3   6
  ITGA6 WILD-TYPE 142 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      3    6
  ITGA6 WILD-TYPE  142  242
        clus
vv       ITGA6 MUTATED ITGA6 WILD-TYPE
  FEMALE             3             142
  MALE               6             242
[1] 2 2
[1] FALSE
D525V8, binary
                 cls
clus                0   1
  ITGA6 MUTATED     6   1
  ITGA6 WILD-TYPE 286  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      6    1
  ITGA6 WILD-TYPE  286   58
     clus
vv    ITGA6 MUTATED ITGA6 WILD-TYPE
  NO              6             286
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ITGA6 MUTATED                                          0
  ITGA6 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ITGA6 MUTATED                                       3
  ITGA6 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ITGA6 MUTATED                                                        3
  ITGA6 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ITGA6 MUTATED                                                   1
  ITGA6 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ITGA6 MUTATED                                                                   1
  ITGA6 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ITGA6 MUTATED                                                    0
  ITGA6 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ITGA6 MUTATED                                                  1
  ITGA6 WILD-TYPE                                               60
D525V9, multiclass
                                                                   clus
vv                                                                  ITGA6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  ITGA6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ITGA6 MUTATED     5   0   0   2
  ITGA6 WILD-TYPE 306  14  15  22
D525V10, multiclass
    clus
vv   ITGA6 MUTATED ITGA6 WILD-TYPE
  R0             5             306
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D525V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ITGA6 MUTATED       2                         0
  ITGA6 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ITGA6 MUTATED                                           0     5
  ITGA6 WILD-TYPE                                         1   238
D525V12, multiclass
                                           clus
vv                                          ITGA6 MUTATED ITGA6 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D525V13, binary
                 cls
clus                0   1
  ITGA6 MUTATED     0   6
  ITGA6 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      0    6
  ITGA6 WILD-TYPE    4  304
                        clus
vv                       ITGA6 MUTATED ITGA6 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(526) Variable = TRIP11 MUTATION ANALYSIS
D526V1, survival
                  sevent
clus2                0   1
  TRIP11 MUTATED    11   2
  TRIP11 WILD-TYPE 219 137
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              13              356 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
               2              137 
$`TRIP11 MUTATED`
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8680 TCGA-CD-5800 
       36.16        35.24        29.59         4.31        31.96        13.15 
TCGA-CG-4466 TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5733 TCGA-HU-A4GQ TCGA-HU-A4GU 
       18.97         6.02        65.10        21.07         0.10         6.58 
TCGA-VQ-A8P2 
       38.14 

$`TRIP11 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
           21.07            14.12 
[1] "0.1 - 65.1 (21.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3"  
D526V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIP11 MUTATED         0        1        3        2         0         2
  TRIP11 WILD-TYPE       2       14       37       28        37        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIP11 MUTATED           0          2          0          1        2
  TRIP11 WILD-TYPE         3         68         53         31       36
D526V3, multiclass
            clus
vv           TRIP11 MUTATED TRIP11 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                3               37
  STAGE II                2               28
  STAGE IIA               0               37
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIP11 MUTATED     1   4   3   5
  TRIP11 WILD-TYPE  21  88 170  92
D526V4, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  T1              1               21
  T2              4               88
  T3              3              170
  T4              5               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
  TRIP11 MUTATED     7   3   3   0
  TRIP11 WILD-TYPE 111 101  74  77
D526V5, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  N0              7              111
  N1              3              101
  N2              3               74
  N3              0               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"
D526V6, binary
                  cls
clus                 0   1
  TRIP11 MUTATED    12   1
  TRIP11 WILD-TYPE 334  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED     12    1
  TRIP11 WILD-TYPE  334   28
   clus
vv  TRIP11 MUTATED TRIP11 WILD-TYPE
  0             12              334
  1              1               28
[1] 2 2
[1] FALSE
D526V7, binary
                  cls
clus                 0   1
  TRIP11 MUTATED     7   6
  TRIP11 WILD-TYPE 138 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED      7    6
  TRIP11 WILD-TYPE  138  242
        clus
vv       TRIP11 MUTATED TRIP11 WILD-TYPE
  FEMALE              7              138
  MALE                6              242
[1] 2 2
[1] FALSE
D526V8, binary
                  cls
clus                 0   1
  TRIP11 MUTATED    11   1
  TRIP11 WILD-TYPE 281  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED     11    1
  TRIP11 WILD-TYPE  281   58
     clus
vv    TRIP11 MUTATED TRIP11 WILD-TYPE
  NO              11              281
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TRIP11 MUTATED                                          0
  TRIP11 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TRIP11 MUTATED                                       1
  TRIP11 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRIP11 MUTATED                                                        2
  TRIP11 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TRIP11 MUTATED                                                   1
  TRIP11 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRIP11 MUTATED                                                                   5
  TRIP11 WILD-TYPE                                                                63
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TRIP11 MUTATED                                                    2
  TRIP11 WILD-TYPE                                                  3
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TRIP11 MUTATED                                                  2
  TRIP11 WILD-TYPE                                               59
D526V9, multiclass
                                                                   clus
vv                                                                  TRIP11 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  TRIP11 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIP11 MUTATED    13   0   0   0
  TRIP11 WILD-TYPE 298  14  15  24
D526V10, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  R0             13              298
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D526V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TRIP11 MUTATED       4                         0
  TRIP11 WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRIP11 MUTATED                                           0     5
  TRIP11 WILD-TYPE                                         1   238
D526V12, multiclass
                                           clus
vv                                          TRIP11 MUTATED TRIP11 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D526V13, binary
                  cls
clus                 0   1
  TRIP11 MUTATED     0   8
  TRIP11 WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED      0    8
  TRIP11 WILD-TYPE    4  302
                        clus
vv                       TRIP11 MUTATED TRIP11 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(527) Variable = PNPLA7 MUTATION ANALYSIS
D527V1, survival
                  sevent
clus2                0   1
  PNPLA7 MUTATED    15   5
  PNPLA7 WILD-TYPE 215 134
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
              20              349 
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
               5              134 
$`PNPLA7 MUTATED`
TCGA-BR-4201 TCGA-BR-6852 TCGA-BR-7901 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8363 
       30.90        44.94         3.45        29.59        31.10         0.26 
TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8589 TCGA-CG-4305 TCGA-CG-5723 TCGA-CG-5732 
       31.27         1.12        27.12        15.95       105.07        69.04 
TCGA-HF-7132 TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4H4 TCGA-HU-A4H8 
       77.29        29.98         8.98         0.10        23.84        14.07 
TCGA-IN-A6RP TCGA-VQ-A8P2 
        6.44        38.14 

$`PNPLA7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       11.77        21.37         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-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-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-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 

  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
             0.1              0.0 
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
          105.07           122.30 
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
          28.355           14.040 
[1] "0.1 - 105.1 (28.4)" "0.0 - 122.3 (14.0)"
[1] "hr=" "2.1"
D527V2, 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       2       15       38       27        33        48
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PNPLA7 MUTATED           0          2          1          4        1
  PNPLA7 WILD-TYPE         3         68         52         28       37
D527V3, multiclass
            clus
vv           PNPLA7 MUTATED PNPLA7 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                3               27
  STAGE IIA               4               33
  STAGE IIB               4               48
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              4               28
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PNPLA7 MUTATED     3   9   3   8
  PNPLA7 WILD-TYPE  19  83 170  89
D527V4, multiclass
    clus
vv   PNPLA7 MUTATED PNPLA7 WILD-TYPE
  T1              3               19
  T2              9               83
  T3              3              170
  T4              8               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
  PNPLA7 MUTATED     6   9   3   3
  PNPLA7 WILD-TYPE 112  95  74  74
D527V5, multiclass
    clus
vv   PNPLA7 MUTATED PNPLA7 WILD-TYPE
  N0              6              112
  N1              9               95
  N2              3               74
  N3              3               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"
D527V6, binary
                  cls
clus                 0   1
  PNPLA7 MUTATED    23   0
  PNPLA7 WILD-TYPE 323  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA7 MUTATED     23    0
  PNPLA7 WILD-TYPE  323   29
   clus
vv  PNPLA7 MUTATED PNPLA7 WILD-TYPE
  0             23              323
  1              0               29
[1] 2 2
[1] FALSE
D527V7, binary
                  cls
clus                 0   1
  PNPLA7 MUTATED    10  13
  PNPLA7 WILD-TYPE 135 235
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA7 MUTATED     10   13
  PNPLA7 WILD-TYPE  135  235
        clus
vv       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  FEMALE             10              135
  MALE               13              235
[1] 2 2
[1] FALSE
D527V8, binary
                  cls
clus                 0   1
  PNPLA7 MUTATED    18   3
  PNPLA7 WILD-TYPE 274  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA7 MUTATED     18    3
  PNPLA7 WILD-TYPE  274   56
     clus
vv    PNPLA7 MUTATED PNPLA7 WILD-TYPE
  NO              18              274
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PNPLA7 MUTATED                                          0
  PNPLA7 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PNPLA7 MUTATED                                       1
  PNPLA7 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PNPLA7 MUTATED                                                       14
  PNPLA7 WILD-TYPE                                                    144
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PNPLA7 MUTATED                                                   2
  PNPLA7 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PNPLA7 MUTATED                                                                   2
  PNPLA7 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PNPLA7 MUTATED                                                    0
  PNPLA7 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PNPLA7 MUTATED                                                  4
  PNPLA7 WILD-TYPE                                               57
D527V9, multiclass
                                                                   clus
vv                                                                  PNPLA7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  PNPLA7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PNPLA7 MUTATED    20   0   0   3
  PNPLA7 WILD-TYPE 291  14  15  21
D527V10, multiclass
    clus
vv   PNPLA7 MUTATED PNPLA7 WILD-TYPE
  R0             20              291
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D527V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PNPLA7 MUTATED       5                         0
  PNPLA7 WILD-TYPE    82                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PNPLA7 MUTATED                                           0    14
  PNPLA7 WILD-TYPE                                         1   229
D527V12, multiclass
                                           clus
vv                                          PNPLA7 MUTATED PNPLA7 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 14              229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D527V13, binary
                  cls
clus                 0   1
  PNPLA7 MUTATED     0  18
  PNPLA7 WILD-TYPE   4 292
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA7 MUTATED      0   18
  PNPLA7 WILD-TYPE    4  292
                        clus
vv                       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             18              292
[1] 2 2
[1] FALSE

Clustering(528) Variable = C7ORF49 MUTATION ANALYSIS
D528V1, survival
                   sevent
clus2                 0   1
  C7ORF49 MUTATED     6   1
  C7ORF49 WILD-TYPE 224 138
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
                7               362 
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
                1               138 
$`C7ORF49 MUTATED`
TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MJ TCGA-D7-A4YV TCGA-HU-A4G9 
       29.59         1.12        28.14        12.62         5.92        24.20 
TCGA-HU-A4GU 
        6.58 

$`C7ORF49 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
             1.12              0.00 
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
            29.59            122.30 
  C7ORF49 MUTATED C7ORF49 WILD-TYPE 
            12.62             14.35 
[1] "1.1 - 29.6 (12.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.4"
D528V2, 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       2       14       39       30        36        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF49 MUTATED           0          0          0          1        0
  C7ORF49 WILD-TYPE         3         70         53         31       38
D528V3, multiclass
            clus
vv           C7ORF49 MUTATED C7ORF49 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                3                49
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C7ORF49 MUTATED     1   1   3   2
  C7ORF49 WILD-TYPE  21  91 170  95
D528V4, multiclass
    clus
vv   C7ORF49 MUTATED C7ORF49 WILD-TYPE
  T1               1                21
  T2               1                91
  T3               3               170
  T4               2                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
  C7ORF49 MUTATED     4   2   0   1
  C7ORF49 WILD-TYPE 114 102  77  76
D528V5, multiclass
    clus
vv   C7ORF49 MUTATED C7ORF49 WILD-TYPE
  N0               4               114
  N1               2               102
  N2               0                77
  N3               1                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"
D528V6, binary
                   cls
clus                  0   1
  C7ORF49 MUTATED     7   0
  C7ORF49 WILD-TYPE 339  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF49 MUTATED      7    0
  C7ORF49 WILD-TYPE  339   29
   clus
vv  C7ORF49 MUTATED C7ORF49 WILD-TYPE
  0               7               339
  1               0                29
[1] 2 2
[1] FALSE
D528V7, binary
                   cls
clus                  0   1
  C7ORF49 MUTATED     4   3
  C7ORF49 WILD-TYPE 141 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF49 MUTATED      4    3
  C7ORF49 WILD-TYPE  141  245
        clus
vv       C7ORF49 MUTATED C7ORF49 WILD-TYPE
  FEMALE               4               141
  MALE                 3               245
[1] 2 2
[1] FALSE
D528V8, binary
                   cls
clus                  0   1
  C7ORF49 MUTATED     7   0
  C7ORF49 WILD-TYPE 285  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF49 MUTATED      7    0
  C7ORF49 WILD-TYPE  285   59
     clus
vv    C7ORF49 MUTATED C7ORF49 WILD-TYPE
  NO                7               285
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C7ORF49 MUTATED                                          0
  C7ORF49 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C7ORF49 MUTATED                                       1
  C7ORF49 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C7ORF49 MUTATED                                                        4
  C7ORF49 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C7ORF49 MUTATED                                                   0
  C7ORF49 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C7ORF49 MUTATED                                                                   0
  C7ORF49 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C7ORF49 MUTATED                                                    0
  C7ORF49 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C7ORF49 MUTATED                                                  2
  C7ORF49 WILD-TYPE                                               59
D528V9, multiclass
                                                                   clus
vv                                                                  C7ORF49 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  C7ORF49 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C7ORF49 MUTATED     6   0   0   0
  C7ORF49 WILD-TYPE 305  14  15  24
D528V10, multiclass
    clus
vv   C7ORF49 MUTATED C7ORF49 WILD-TYPE
  R0               6               305
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C7ORF49 MUTATED       3                         0
  C7ORF49 WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C7ORF49 MUTATED                                           0     4
  C7ORF49 WILD-TYPE                                         1   239
D528V12, multiclass
                                           clus
vv                                          C7ORF49 MUTATED C7ORF49 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V13, binary
                   cls
clus                  0   1
  C7ORF49 MUTATED     0   7
  C7ORF49 WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF49 MUTATED      0    7
  C7ORF49 WILD-TYPE    4  303
                        clus
vv                       C7ORF49 MUTATED C7ORF49 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(529) Variable = C14ORF50 MUTATION ANALYSIS
D529V1, survival
                    sevent
clus2                  0   1
  C14ORF50 MUTATED     3   5
  C14ORF50 WILD-TYPE 227 134
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 8                361 
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 5                134 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-6566 
       13.68        19.33        39.12        26.10         9.17        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       25.61        18.05        19.89         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-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-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-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 

  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             14.430 
[1] "0.3 - 65.1 (9.3)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.9"
D529V2, 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       2       15       38       30        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF50 MUTATED           0          0          1          0        2
  C14ORF50 WILD-TYPE         3         70         52         32       36
D529V3, multiclass
            clus
vv           C14ORF50 MUTATED C14ORF50 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  2                 38
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                1                 52
  STAGE IIIC                0                 32
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C14ORF50 MUTATED     0   3   4   1
  C14ORF50 WILD-TYPE  22  89 169  96
D529V4, multiclass
    clus
vv   C14ORF50 MUTATED C14ORF50 WILD-TYPE
  T1                0                 22
  T2                3                 89
  T3                4                169
  T4                1                 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
  C14ORF50 MUTATED     3   1   2   1
  C14ORF50 WILD-TYPE 115 103  75  76
D529V5, multiclass
    clus
vv   C14ORF50 MUTATED C14ORF50 WILD-TYPE
  N0                3                115
  N1                1                103
  N2                2                 75
  N3                1                 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"
D529V6, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     6   2
  C14ORF50 WILD-TYPE 340  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      6    2
  C14ORF50 WILD-TYPE  340   27
   clus
vv  C14ORF50 MUTATED C14ORF50 WILD-TYPE
  0                6                340
  1                2                 27
[1] 2 2
[1] FALSE
D529V7, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     6   2
  C14ORF50 WILD-TYPE 139 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      6    2
  C14ORF50 WILD-TYPE  139  246
        clus
vv       C14ORF50 MUTATED C14ORF50 WILD-TYPE
  FEMALE                6                139
  MALE                  2                246
[1] 2 2
[1] FALSE
D529V8, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     6   0
  C14ORF50 WILD-TYPE 286  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      6    0
  C14ORF50 WILD-TYPE  286   59
     clus
vv    C14ORF50 MUTATED C14ORF50 WILD-TYPE
  NO                 6                286
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C14ORF50 MUTATED                                          0
  C14ORF50 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C14ORF50 MUTATED                                       0
  C14ORF50 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C14ORF50 MUTATED                                                        4
  C14ORF50 WILD-TYPE                                                    154
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C14ORF50 MUTATED                                                   0
  C14ORF50 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C14ORF50 MUTATED                                                                   1
  C14ORF50 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C14ORF50 MUTATED                                                    0
  C14ORF50 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C14ORF50 MUTATED                                                  3
  C14ORF50 WILD-TYPE                                               58
D529V9, multiclass
                                                                   clus
vv                                                                  C14ORF50 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 3
                                                                   clus
vv                                                                  C14ORF50 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C14ORF50 MUTATED     5   1   1   1
  C14ORF50 WILD-TYPE 306  13  14  23
D529V10, multiclass
    clus
vv   C14ORF50 MUTATED C14ORF50 WILD-TYPE
  R0                5                306
  R1                1                 13
  R2                1                 14
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D529V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C14ORF50 MUTATED       2                         0
  C14ORF50 WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C14ORF50 MUTATED                                           0     4
  C14ORF50 WILD-TYPE                                         1   239
D529V12, multiclass
                                           clus
vv                                          C14ORF50 MUTATED C14ORF50 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D529V13, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     0   6
  C14ORF50 WILD-TYPE   4 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      0    6
  C14ORF50 WILD-TYPE    4  304
                        clus
vv                       C14ORF50 MUTATED C14ORF50 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                6                304
[1] 2 2
[1] FALSE

Clustering(530) Variable = PKN1 MUTATION ANALYSIS
D530V1, survival
                sevent
clus2              0   1
  PKN1 MUTATED     6   2
  PKN1 WILD-TYPE 224 137
  PKN1 MUTATED PKN1 WILD-TYPE 
             8            361 
  PKN1 MUTATED PKN1 WILD-TYPE 
             2            137 
$`PKN1 MUTATED`
TCGA-BR-4184 TCGA-BR-8372 TCGA-BR-A4QL TCGA-CG-4449 TCGA-CG-5721 TCGA-HU-A4GT 
        6.97        31.27        16.14        19.07         6.02         6.51 
TCGA-HU-A4H8 TCGA-MX-A5UJ 
       14.07        19.73 

$`PKN1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  PKN1 MUTATED PKN1 WILD-TYPE 
          6.02           0.00 
  PKN1 MUTATED PKN1 WILD-TYPE 
         31.27         122.30 
  PKN1 MUTATED PKN1 WILD-TYPE 
        15.105         14.270 
[1] "6.0 - 31.3 (15.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D530V2, 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       2       15       38       29        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PKN1 MUTATED           0          2          1          1        2
  PKN1 WILD-TYPE         3         68         52         31       36
D530V3, multiclass
            clus
vv           PKN1 MUTATED PKN1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PKN1 MUTATED     1   2   4   3
  PKN1 WILD-TYPE  21  90 169  94
D530V4, multiclass
    clus
vv   PKN1 MUTATED PKN1 WILD-TYPE
  T1            1             21
  T2            2             90
  T3            4            169
  T4            3             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
  PKN1 MUTATED     2   4   2   2
  PKN1 WILD-TYPE 116 100  75  75
D530V5, multiclass
    clus
vv   PKN1 MUTATED PKN1 WILD-TYPE
  N0            2            116
  N1            4            100
  N2            2             75
  N3            2             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"
D530V6, binary
                cls
clus               0   1
  PKN1 MUTATED     9   0
  PKN1 WILD-TYPE 337  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN1 MUTATED      9    0
  PKN1 WILD-TYPE  337   29
   clus
vv  PKN1 MUTATED PKN1 WILD-TYPE
  0            9            337
  1            0             29
[1] 2 2
[1] FALSE
D530V7, binary
                cls
clus               0   1
  PKN1 MUTATED     4   6
  PKN1 WILD-TYPE 141 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN1 MUTATED      4    6
  PKN1 WILD-TYPE  141  242
        clus
vv       PKN1 MUTATED PKN1 WILD-TYPE
  FEMALE            4            141
  MALE              6            242
[1] 2 2
[1] FALSE
D530V8, binary
                cls
clus               0   1
  PKN1 MUTATED     8   0
  PKN1 WILD-TYPE 284  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN1 MUTATED      8    0
  PKN1 WILD-TYPE  284   59
     clus
vv    PKN1 MUTATED PKN1 WILD-TYPE
  NO             8            284
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PKN1 MUTATED                                          0
  PKN1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PKN1 MUTATED                                       0
  PKN1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PKN1 MUTATED                                                        4
  PKN1 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PKN1 MUTATED                                                   1
  PKN1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PKN1 MUTATED                                                                   2
  PKN1 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PKN1 MUTATED                                                    0
  PKN1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PKN1 MUTATED                                                  3
  PKN1 WILD-TYPE                                               58
D530V9, multiclass
                                                                   clus
vv                                                                  PKN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  PKN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PKN1 MUTATED     8   0   0   2
  PKN1 WILD-TYPE 303  14  15  22
D530V10, multiclass
    clus
vv   PKN1 MUTATED PKN1 WILD-TYPE
  R0            8            303
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D530V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PKN1 MUTATED       2                         0
  PKN1 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PKN1 MUTATED                                           0     5
  PKN1 WILD-TYPE                                         1   238
D530V12, multiclass
                                           clus
vv                                          PKN1 MUTATED PKN1 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D530V13, binary
                cls
clus               0   1
  PKN1 MUTATED     0   7
  PKN1 WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKN1 MUTATED      0    7
  PKN1 WILD-TYPE    4  303
                        clus
vv                       PKN1 MUTATED PKN1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(531) Variable = ASAP2 MUTATION ANALYSIS
D531V1, survival
                 sevent
clus2               0   1
  ASAP2 MUTATED     8   5
  ASAP2 WILD-TYPE 222 134
  ASAP2 MUTATED ASAP2 WILD-TYPE 
             13             356 
  ASAP2 MUTATED ASAP2 WILD-TYPE 
              5             134 
$`ASAP2 MUTATED`
TCGA-EQ-A4SO TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8372 TCGA-BR-8589 TCGA-CD-8533 
       16.24         6.97        34.68        31.27        27.12        15.39 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-HU-A4GQ TCGA-HU-A4H4 
       65.10        21.07        11.31        11.44         0.10        23.84 
TCGA-RD-A7C1 
       16.67 

$`ASAP2 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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 
          16.67           14.07 
[1] "0.1 - 65.1 (16.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D531V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ASAP2 MUTATED         0        0        2        1         1         2
  ASAP2 WILD-TYPE       2       15       38       29        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ASAP2 MUTATED           0          3          3          2        1
  ASAP2 WILD-TYPE         3         67         50         30       37
D531V3, multiclass
            clus
vv           ASAP2 MUTATED ASAP2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             3              50
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ASAP2 MUTATED     0   4   5   6
  ASAP2 WILD-TYPE  22  88 168  91
D531V4, multiclass
    clus
vv   ASAP2 MUTATED ASAP2 WILD-TYPE
  T1             0              22
  T2             4              88
  T3             5             168
  T4             6              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
  ASAP2 MUTATED     5   4   5   2
  ASAP2 WILD-TYPE 113 100  72  75
D531V5, multiclass
    clus
vv   ASAP2 MUTATED ASAP2 WILD-TYPE
  N0             5             113
  N1             4             100
  N2             5              72
  N3             2              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"
D531V6, binary
                 cls
clus                0   1
  ASAP2 MUTATED    14   0
  ASAP2 WILD-TYPE 332  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASAP2 MUTATED     14    0
  ASAP2 WILD-TYPE  332   29
   clus
vv  ASAP2 MUTATED ASAP2 WILD-TYPE
  0            14             332
  1             0              29
[1] 2 2
[1] FALSE
D531V7, binary
                 cls
clus                0   1
  ASAP2 MUTATED     8   8
  ASAP2 WILD-TYPE 137 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASAP2 MUTATED      8    8
  ASAP2 WILD-TYPE  137  240
        clus
vv       ASAP2 MUTATED ASAP2 WILD-TYPE
  FEMALE             8             137
  MALE               8             240
[1] 2 2
[1] FALSE
D531V8, binary
                 cls
clus                0   1
  ASAP2 MUTATED    12   1
  ASAP2 WILD-TYPE 280  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASAP2 MUTATED     12    1
  ASAP2 WILD-TYPE  280   58
     clus
vv    ASAP2 MUTATED ASAP2 WILD-TYPE
  NO             12             280
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ASAP2 MUTATED                                          0
  ASAP2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ASAP2 MUTATED                                       1
  ASAP2 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ASAP2 MUTATED                                                        7
  ASAP2 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ASAP2 MUTATED                                                   0
  ASAP2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ASAP2 MUTATED                                                                   3
  ASAP2 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ASAP2 MUTATED                                                    0
  ASAP2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ASAP2 MUTATED                                                  4
  ASAP2 WILD-TYPE                                               57
D531V9, multiclass
                                                                   clus
vv                                                                  ASAP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  ASAP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ASAP2 MUTATED    13   0   0   3
  ASAP2 WILD-TYPE 298  14  15  21
D531V10, multiclass
    clus
vv   ASAP2 MUTATED ASAP2 WILD-TYPE
  R0            13             298
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D531V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ASAP2 MUTATED       3                         0
  ASAP2 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ASAP2 MUTATED                                           0    11
  ASAP2 WILD-TYPE                                         1   232
D531V12, multiclass
                                           clus
vv                                          ASAP2 MUTATED ASAP2 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D531V13, binary
                 cls
clus                0   1
  ASAP2 MUTATED     0  14
  ASAP2 WILD-TYPE   4 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASAP2 MUTATED      0   14
  ASAP2 WILD-TYPE    4  296
                        clus
vv                       ASAP2 MUTATED ASAP2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(532) Variable = FAM133A MUTATION ANALYSIS
D532V1, survival
                   sevent
clus2                 0   1
  FAM133A MUTATED     5   4
  FAM133A WILD-TYPE 225 135
  FAM133A MUTATED FAM133A WILD-TYPE 
                9               360 
  FAM133A MUTATED FAM133A WILD-TYPE 
                4               135 
$`FAM133A MUTATED`
TCGA-CG-4460 TCGA-BR-4201 TCGA-BR-6458 TCGA-BR-7707 TCGA-BR-8078 TCGA-CD-A4MG 
       21.99        30.90        19.33        35.84        29.59         6.58 
TCGA-CD-A4MJ TCGA-HU-A4H3 TCGA-VQ-A8P2 
       12.62        29.00        38.14 

$`FAM133A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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 

  FAM133A MUTATED FAM133A WILD-TYPE 
             6.58              0.00 
  FAM133A MUTATED FAM133A WILD-TYPE 
            38.14            122.30 
  FAM133A MUTATED FAM133A WILD-TYPE 
            29.00             14.07 
[1] "6.6 - 38.1 (29.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D532V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM133A MUTATED         0        0        2        0         1         2
  FAM133A WILD-TYPE       2       15       38       30        36        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM133A MUTATED           0          1          0          1        1
  FAM133A WILD-TYPE         3         69         53         31       37
D532V3, multiclass
            clus
vv           FAM133A MUTATED FAM133A WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM133A MUTATED     0   3   2   4
  FAM133A WILD-TYPE  22  89 171  93
D532V4, multiclass
    clus
vv   FAM133A MUTATED FAM133A WILD-TYPE
  T1               0                22
  T2               3                89
  T3               2               171
  T4               4                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
  FAM133A MUTATED     4   3   0   1
  FAM133A WILD-TYPE 114 101  77  76
D532V5, multiclass
    clus
vv   FAM133A MUTATED FAM133A WILD-TYPE
  N0               4               114
  N1               3               101
  N2               0                77
  N3               1                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"
D532V6, binary
                   cls
clus                  0   1
  FAM133A MUTATED     8   1
  FAM133A WILD-TYPE 338  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133A MUTATED      8    1
  FAM133A WILD-TYPE  338   28
   clus
vv  FAM133A MUTATED FAM133A WILD-TYPE
  0               8               338
  1               1                28
[1] 2 2
[1] FALSE
D532V7, binary
                   cls
clus                  0   1
  FAM133A MUTATED     6   3
  FAM133A WILD-TYPE 139 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133A MUTATED      6    3
  FAM133A WILD-TYPE  139  245
        clus
vv       FAM133A MUTATED FAM133A WILD-TYPE
  FEMALE               6               139
  MALE                 3               245
[1] 2 2
[1] FALSE
D532V8, binary
                   cls
clus                  0   1
  FAM133A MUTATED     7   1
  FAM133A WILD-TYPE 285  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133A MUTATED      7    1
  FAM133A WILD-TYPE  285   58
     clus
vv    FAM133A MUTATED FAM133A WILD-TYPE
  NO                7               285
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM133A MUTATED                                          0
  FAM133A WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM133A MUTATED                                       2
  FAM133A WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM133A MUTATED                                                        5
  FAM133A WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM133A MUTATED                                                   1
  FAM133A WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM133A MUTATED                                                                   1
  FAM133A WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM133A MUTATED                                                    0
  FAM133A WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM133A MUTATED                                                  0
  FAM133A WILD-TYPE                                               61
D532V9, multiclass
                                                                   clus
vv                                                                  FAM133A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  FAM133A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM133A MUTATED     5   0   1   1
  FAM133A WILD-TYPE 306  14  14  23
D532V10, multiclass
    clus
vv   FAM133A MUTATED FAM133A WILD-TYPE
  R0               5               306
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D532V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM133A MUTATED       3                         0
  FAM133A WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM133A MUTATED                                           0     5
  FAM133A WILD-TYPE                                         1   238
D532V12, multiclass
                                           clus
vv                                          FAM133A MUTATED FAM133A WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D532V13, binary
                   cls
clus                  0   1
  FAM133A MUTATED     0   7
  FAM133A WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133A MUTATED      0    7
  FAM133A WILD-TYPE    4  303
                        clus
vv                       FAM133A MUTATED FAM133A WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(533) Variable = METTL6 MUTATION ANALYSIS
D533V1, survival
                  sevent
clus2                0   1
  METTL6 MUTATED     2   2
  METTL6 WILD-TYPE 228 137
  METTL6 MUTATED METTL6 WILD-TYPE 
               4              365 
  METTL6 MUTATED METTL6 WILD-TYPE 
               2              137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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            14.17 
[1] "1.0 - 38.1 (31.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D533V2, 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       1       15       40       30        37        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  METTL6 MUTATED           0          1          0          0        2
  METTL6 WILD-TYPE         3         69         53         32       36
D533V3, multiclass
            clus
vv           METTL6 MUTATED METTL6 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  METTL6 MUTATED     1   1   1   2
  METTL6 WILD-TYPE  21  91 172  95
D533V4, multiclass
    clus
vv   METTL6 MUTATED METTL6 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              1              172
  T4              2               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
  METTL6 MUTATED     0   2   2   0
  METTL6 WILD-TYPE 118 102  75  77
D533V5, multiclass
    clus
vv   METTL6 MUTATED METTL6 WILD-TYPE
  N0              0              118
  N1              2              102
  N2              2               75
  N3              0               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"
D533V6, binary
                  cls
clus                 0   1
  METTL6 MUTATED     2   2
  METTL6 WILD-TYPE 344  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL6 MUTATED      2    2
  METTL6 WILD-TYPE  344   27
   clus
vv  METTL6 MUTATED METTL6 WILD-TYPE
  0              2              344
  1              2               27
[1] 2 2
[1] FALSE
D533V7, binary
                  cls
clus                 0   1
  METTL6 MUTATED     1   4
  METTL6 WILD-TYPE 144 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL6 MUTATED      1    4
  METTL6 WILD-TYPE  144  244
        clus
vv       METTL6 MUTATED METTL6 WILD-TYPE
  FEMALE              1              144
  MALE                4              244
[1] 2 2
[1] FALSE
D533V8, binary
                  cls
clus                 0   1
  METTL6 MUTATED     3   1
  METTL6 WILD-TYPE 289  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL6 MUTATED      3    1
  METTL6 WILD-TYPE  289   58
     clus
vv    METTL6 MUTATED METTL6 WILD-TYPE
  NO               3              289
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  METTL6 MUTATED                                          0
  METTL6 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  METTL6 MUTATED                                       0
  METTL6 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  METTL6 MUTATED                                                        3
  METTL6 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  METTL6 MUTATED                                                   1
  METTL6 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  METTL6 MUTATED                                                                   0
  METTL6 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  METTL6 MUTATED                                                    0
  METTL6 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  METTL6 MUTATED                                                  1
  METTL6 WILD-TYPE                                               60
D533V9, multiclass
                                                                   clus
vv                                                                  METTL6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  METTL6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  METTL6 MUTATED     3   0   1   1
  METTL6 WILD-TYPE 308  14  14  23
D533V10, multiclass
    clus
vv   METTL6 MUTATED METTL6 WILD-TYPE
  R0              3              308
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D533V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  METTL6 MUTATED       1                         1
  METTL6 WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  METTL6 MUTATED                                           0     2
  METTL6 WILD-TYPE                                         1   241
D533V12, multiclass
                                           clus
vv                                          METTL6 MUTATED METTL6 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D533V13, binary
                  cls
clus                 0   1
  METTL6 MUTATED     0   3
  METTL6 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL6 MUTATED      0    3
  METTL6 WILD-TYPE    4  307
                        clus
vv                       METTL6 MUTATED METTL6 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(534) Variable = EFHD1 MUTATION ANALYSIS
D534V1, survival
                 sevent
clus2               0   1
  EFHD1 MUTATED     5   1
  EFHD1 WILD-TYPE 225 138
  EFHD1 MUTATED EFHD1 WILD-TYPE 
              6             363 
  EFHD1 MUTATED EFHD1 WILD-TYPE 
              1             138 
$`EFHD1 MUTATED`
TCGA-BR-6452 TCGA-BR-A4QL TCGA-CG-5721 TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-VQ-A8P2 
       34.68        16.14         6.02         6.58        29.00        38.14 

$`EFHD1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        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 

  EFHD1 MUTATED EFHD1 WILD-TYPE 
           6.02            0.00 
  EFHD1 MUTATED EFHD1 WILD-TYPE 
          38.14          122.30 
  EFHD1 MUTATED EFHD1 WILD-TYPE 
          22.57           14.17 
[1] "6.0 - 38.1 (22.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.7"
D534V2, 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       2       15       40       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFHD1 MUTATED           0          1          1          1        1
  EFHD1 WILD-TYPE         3         69         52         31       37
D534V3, multiclass
            clus
vv           EFHD1 MUTATED EFHD1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EFHD1 MUTATED     0   0   3   3
  EFHD1 WILD-TYPE  22  92 170  94
D534V4, multiclass
    clus
vv   EFHD1 MUTATED EFHD1 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             3             170
  T4             3              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
  EFHD1 MUTATED     1   3   0   2
  EFHD1 WILD-TYPE 117 101  77  75
D534V5, multiclass
    clus
vv   EFHD1 MUTATED EFHD1 WILD-TYPE
  N0             1             117
  N1             3             101
  N2             0              77
  N3             2              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"
D534V6, binary
                 cls
clus                0   1
  EFHD1 MUTATED     6   0
  EFHD1 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHD1 MUTATED      6    0
  EFHD1 WILD-TYPE  340   29
   clus
vv  EFHD1 MUTATED EFHD1 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D534V7, binary
                 cls
clus                0   1
  EFHD1 MUTATED     3   3
  EFHD1 WILD-TYPE 142 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHD1 MUTATED      3    3
  EFHD1 WILD-TYPE  142  245
        clus
vv       EFHD1 MUTATED EFHD1 WILD-TYPE
  FEMALE             3             142
  MALE               3             245
[1] 2 2
[1] FALSE
D534V8, binary
                 cls
clus                0   1
  EFHD1 MUTATED     4   1
  EFHD1 WILD-TYPE 288  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHD1 MUTATED      4    1
  EFHD1 WILD-TYPE  288   58
     clus
vv    EFHD1 MUTATED EFHD1 WILD-TYPE
  NO              4             288
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EFHD1 MUTATED                                          0
  EFHD1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EFHD1 MUTATED                                       2
  EFHD1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EFHD1 MUTATED                                                        2
  EFHD1 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EFHD1 MUTATED                                                   1
  EFHD1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EFHD1 MUTATED                                                                   1
  EFHD1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EFHD1 MUTATED                                                    0
  EFHD1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EFHD1 MUTATED                                                  0
  EFHD1 WILD-TYPE                                               61
D534V9, multiclass
                                                                   clus
vv                                                                  EFHD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  EFHD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EFHD1 MUTATED     6   0   0   0
  EFHD1 WILD-TYPE 305  14  15  24
D534V10, multiclass
    clus
vv   EFHD1 MUTATED EFHD1 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EFHD1 MUTATED       2                         0
  EFHD1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EFHD1 MUTATED                                           0     3
  EFHD1 WILD-TYPE                                         1   240
D534V12, multiclass
                                           clus
vv                                          EFHD1 MUTATED EFHD1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V13, binary
                 cls
clus                0   1
  EFHD1 MUTATED     0   4
  EFHD1 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHD1 MUTATED      0    4
  EFHD1 WILD-TYPE    4  306
                        clus
vv                       EFHD1 MUTATED EFHD1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(535) Variable = VPS13A MUTATION ANALYSIS
D535V1, survival
                  sevent
clus2                0   1
  VPS13A MUTATED    24  10
  VPS13A WILD-TYPE 206 129
  VPS13A MUTATED VPS13A WILD-TYPE 
              34              335 
  VPS13A MUTATED VPS13A WILD-TYPE 
              10              129 
$`VPS13A MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7703 
        6.97         9.34         6.61        34.68        32.78        36.16 
TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-8078 TCGA-BR-8289 TCGA-BR-8361 TCGA-BR-8589 
       35.24        39.78        29.59         2.66        31.10        27.12 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4IY TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A487 
       28.14        31.96        12.89        16.14        12.43        12.30 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-5721 TCGA-CG-5723 
        6.58        12.62         1.02         8.05         6.02       105.07 
TCGA-CG-5728 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-A4YV TCGA-F1-6874 TCGA-HU-A4GN 
       65.10        25.71        20.91         5.92        14.47        29.98 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-VQ-A8P2 TCGA-VQ-AA6G 
       20.25        29.00        38.14        26.04 

$`VPS13A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        9.21        35.84        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-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-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-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-A486 TCGA-CD-A489 
       11.64        15.39        12.07        12.82         6.31        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-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         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-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-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99        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-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-F1-6875 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-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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       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 
           23.31            14.04 
[1] "1.0 - 105.1 (23.3)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.6"
D535V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VPS13A MUTATED         1        1        4        4         5         5
  VPS13A WILD-TYPE       1       14       36       26        32        47
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPS13A MUTATED           1          4          2          4        4
  VPS13A WILD-TYPE         2         66         51         28       34
D535V3, multiclass
            clus
vv           VPS13A MUTATED VPS13A WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                4               36
  STAGE II                4               26
  STAGE IIA               5               32
  STAGE IIB               5               47
  STAGE III               1                2
  STAGE IIIA              4               66
  STAGE IIIB              2               51
  STAGE IIIC              4               28
  STAGE IV                4               34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  VPS13A MUTATED     2   9  13  11
  VPS13A WILD-TYPE  20  83 160  86
D535V4, multiclass
    clus
vv   VPS13A MUTATED VPS13A WILD-TYPE
  T1              2               20
  T2              9               83
  T3             13              160
  T4             11               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
  VPS13A MUTATED    13  14   5   5
  VPS13A WILD-TYPE 105  90  72  72
D535V5, multiclass
    clus
vv   VPS13A MUTATED VPS13A WILD-TYPE
  N0             13              105
  N1             14               90
  N2              5               72
  N3              5               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"
D535V6, binary
                  cls
clus                 0   1
  VPS13A MUTATED    33   3
  VPS13A WILD-TYPE 313  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13A MUTATED     33    3
  VPS13A WILD-TYPE  313   26
   clus
vv  VPS13A MUTATED VPS13A WILD-TYPE
  0             33              313
  1              3               26
[1] 2 2
[1] FALSE
D535V7, binary
                  cls
clus                 0   1
  VPS13A MUTATED    15  23
  VPS13A WILD-TYPE 130 225
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13A MUTATED     15   23
  VPS13A WILD-TYPE  130  225
        clus
vv       VPS13A MUTATED VPS13A WILD-TYPE
  FEMALE             15              130
  MALE               23              225
[1] 2 2
[1] FALSE
D535V8, binary
                  cls
clus                 0   1
  VPS13A MUTATED    31   1
  VPS13A WILD-TYPE 261  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13A MUTATED     31    1
  VPS13A WILD-TYPE  261   58
     clus
vv    VPS13A MUTATED VPS13A WILD-TYPE
  NO              31              261
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  VPS13A MUTATED                                          0
  VPS13A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  VPS13A MUTATED                                       4
  VPS13A WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  VPS13A MUTATED                                                       19
  VPS13A WILD-TYPE                                                    139
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  VPS13A MUTATED                                                   2
  VPS13A WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  VPS13A MUTATED                                                                   8
  VPS13A WILD-TYPE                                                                60
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  VPS13A MUTATED                                                    1
  VPS13A WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  VPS13A MUTATED                                                  4
  VPS13A WILD-TYPE                                               57
D535V9, multiclass
                                                                   clus
vv                                                                  VPS13A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        19
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              8
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  VPS13A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         139
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               60
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  VPS13A MUTATED    29   1   1   5
  VPS13A WILD-TYPE 282  13  14  19
D535V10, multiclass
    clus
vv   VPS13A MUTATED VPS13A WILD-TYPE
  R0             29              282
  R1              1               13
  R2              1               14
  RX              5               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D535V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  VPS13A MUTATED       9                         1
  VPS13A WILD-TYPE    78                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  VPS13A MUTATED                                           0    22
  VPS13A WILD-TYPE                                         1   221
D535V12, multiclass
                                           clus
vv                                          VPS13A MUTATED VPS13A WILD-TYPE
  ASIAN                                                  9               78
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 22              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D535V13, binary
                  cls
clus                 0   1
  VPS13A MUTATED     0  30
  VPS13A WILD-TYPE   4 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13A MUTATED      0   30
  VPS13A WILD-TYPE    4  280
                        clus
vv                       VPS13A MUTATED VPS13A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             30              280
[1] 2 2
[1] FALSE

Clustering(536) Variable = ANKRD28 MUTATION ANALYSIS
D536V1, survival
                   sevent
clus2                 0   1
  ANKRD28 MUTATED     7   6
  ANKRD28 WILD-TYPE 223 133
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
               13               356 
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
                6               133 
$`ANKRD28 MUTATED`
TCGA-CG-4460 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-7717 TCGA-BR-8361 TCGA-BR-8366 
       21.99         9.34        34.68        18.15        31.10         0.95 
TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-A4GQ TCGA-MX-A5UG 
        1.12        16.14         6.02       105.07         0.10         3.72 
TCGA-MX-A5UJ 
       19.73 

$`ANKRD28 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-8363 
        2.66        19.96         2.20         7.40         6.18         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-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-A666 TCGA-R5-A7O7 
        2.53         5.56        63.62        36.95        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 

  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
              0.1               0.0 
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
           105.07            122.30 
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
            16.14             14.22 
[1] "0.1 - 105.1 (16.1)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D536V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKRD28 MUTATED         0        0        0        1         3         0
  ANKRD28 WILD-TYPE       2       15       40       29        34        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD28 MUTATED           0          2          1          2        3
  ANKRD28 WILD-TYPE         3         68         52         30       35
D536V3, multiclass
            clus
vv           ANKRD28 MUTATED ANKRD28 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 1                29
  STAGE IIA                3                34
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               2                30
  STAGE IV                 3                35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD28 MUTATED     0   1   6   5
  ANKRD28 WILD-TYPE  22  91 167  92
D536V4, multiclass
    clus
vv   ANKRD28 MUTATED ANKRD28 WILD-TYPE
  T1               0                22
  T2               1                91
  T3               6               167
  T4               5                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
  ANKRD28 MUTATED     3   6   3   1
  ANKRD28 WILD-TYPE 115  98  74  76
D536V5, multiclass
    clus
vv   ANKRD28 MUTATED ANKRD28 WILD-TYPE
  N0               3               115
  N1               6                98
  N2               3                74
  N3               1                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"
D536V6, binary
                   cls
clus                  0   1
  ANKRD28 MUTATED    12   1
  ANKRD28 WILD-TYPE 334  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD28 MUTATED     12    1
  ANKRD28 WILD-TYPE  334   28
   clus
vv  ANKRD28 MUTATED ANKRD28 WILD-TYPE
  0              12               334
  1               1                28
[1] 2 2
[1] FALSE
D536V7, binary
                   cls
clus                  0   1
  ANKRD28 MUTATED     7   6
  ANKRD28 WILD-TYPE 138 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD28 MUTATED      7    6
  ANKRD28 WILD-TYPE  138  242
        clus
vv       ANKRD28 MUTATED ANKRD28 WILD-TYPE
  FEMALE               7               138
  MALE                 6               242
[1] 2 2
[1] FALSE
D536V8, binary
                   cls
clus                  0   1
  ANKRD28 MUTATED    13   0
  ANKRD28 WILD-TYPE 279  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD28 MUTATED     13    0
  ANKRD28 WILD-TYPE  279   59
     clus
vv    ANKRD28 MUTATED ANKRD28 WILD-TYPE
  NO               13               279
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ANKRD28 MUTATED                                          0
  ANKRD28 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ANKRD28 MUTATED                                       1
  ANKRD28 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANKRD28 MUTATED                                                        8
  ANKRD28 WILD-TYPE                                                    150
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ANKRD28 MUTATED                                                   0
  ANKRD28 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANKRD28 MUTATED                                                                   2
  ANKRD28 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ANKRD28 MUTATED                                                    0
  ANKRD28 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ANKRD28 MUTATED                                                  2
  ANKRD28 WILD-TYPE                                               59
D536V9, multiclass
                                                                   clus
vv                                                                  ANKRD28 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  ANKRD28 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ANKRD28 MUTATED    11   0   1   1
  ANKRD28 WILD-TYPE 300  14  14  23
D536V10, multiclass
    clus
vv   ANKRD28 MUTATED ANKRD28 WILD-TYPE
  R0              11               300
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D536V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ANKRD28 MUTATED       2                         0
  ANKRD28 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANKRD28 MUTATED                                           0     8
  ANKRD28 WILD-TYPE                                         1   235
D536V12, multiclass
                                           clus
vv                                          ANKRD28 MUTATED ANKRD28 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D536V13, binary
                   cls
clus                  0   1
  ANKRD28 MUTATED     0  10
  ANKRD28 WILD-TYPE   4 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD28 MUTATED      0   10
  ANKRD28 WILD-TYPE    4  300
                        clus
vv                       ANKRD28 MUTATED ANKRD28 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              10               300
[1] 2 2
[1] FALSE

Clustering(537) Variable = OR5M3 MUTATION ANALYSIS
D537V1, survival
                 sevent
clus2               0   1
  OR5M3 MUTATED    12   5
  OR5M3 WILD-TYPE 218 134
  OR5M3 MUTATED OR5M3 WILD-TYPE 
             17             352 
  OR5M3 MUTATED OR5M3 WILD-TYPE 
              5             134 
$`OR5M3 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8297 TCGA-BR-8360 
        0.56        29.42         2.66        19.96         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-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-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-8529 
       12.39        12.76        12.59        12.53         7.17        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-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-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-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-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-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-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 

  OR5M3 MUTATED OR5M3 WILD-TYPE 
           1.12            0.00 
  OR5M3 MUTATED OR5M3 WILD-TYPE 
          77.29          122.30 
  OR5M3 MUTATED OR5M3 WILD-TYPE 
          15.02           14.22 
[1] "1.1 - 77.3 (15.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D537V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR5M3 MUTATED         0        0        4        1         3         4
  OR5M3 WILD-TYPE       2       15       36       29        34        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR5M3 MUTATED           0          3          0          2        1
  OR5M3 WILD-TYPE         3         67         53         30       37
D537V3, multiclass
            clus
vv           OR5M3 MUTATED OR5M3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               4              36
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR5M3 MUTATED     2   4   5   8
  OR5M3 WILD-TYPE  20  88 168  89
D537V4, multiclass
    clus
vv   OR5M3 MUTATED OR5M3 WILD-TYPE
  T1             2              20
  T2             4              88
  T3             5             168
  T4             8              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
  OR5M3 MUTATED     9   6   1   2
  OR5M3 WILD-TYPE 109  98  76  75
D537V5, multiclass
    clus
vv   OR5M3 MUTATED OR5M3 WILD-TYPE
  N0             9             109
  N1             6              98
  N2             1              76
  N3             2              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"
D537V6, binary
                 cls
clus                0   1
  OR5M3 MUTATED    18   1
  OR5M3 WILD-TYPE 328  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5M3 MUTATED     18    1
  OR5M3 WILD-TYPE  328   28
   clus
vv  OR5M3 MUTATED OR5M3 WILD-TYPE
  0            18             328
  1             1              28
[1] 2 2
[1] FALSE
D537V7, binary
                 cls
clus                0   1
  OR5M3 MUTATED    12   7
  OR5M3 WILD-TYPE 133 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5M3 MUTATED     12    7
  OR5M3 WILD-TYPE  133  241
        clus
vv       OR5M3 MUTATED OR5M3 WILD-TYPE
  FEMALE            12             133
  MALE               7             241
[1] 2 2
[1] FALSE
D537V8, binary
                 cls
clus                0   1
  OR5M3 MUTATED    14   4
  OR5M3 WILD-TYPE 278  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5M3 MUTATED     14    4
  OR5M3 WILD-TYPE  278   55
     clus
vv    OR5M3 MUTATED OR5M3 WILD-TYPE
  NO             14             278
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OR5M3 MUTATED                                          0
  OR5M3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OR5M3 MUTATED                                       2
  OR5M3 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OR5M3 MUTATED                                                        8
  OR5M3 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OR5M3 MUTATED                                                   1
  OR5M3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OR5M3 MUTATED                                                                   3
  OR5M3 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OR5M3 MUTATED                                                    0
  OR5M3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OR5M3 MUTATED                                                  5
  OR5M3 WILD-TYPE                                               56
D537V9, multiclass
                                                                   clus
vv                                                                  OR5M3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              5
                                                                   clus
vv                                                                  OR5M3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR5M3 MUTATED    18   0   0   1
  OR5M3 WILD-TYPE 293  14  15  23
D537V10, multiclass
    clus
vv   OR5M3 MUTATED OR5M3 WILD-TYPE
  R0            18             293
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D537V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OR5M3 MUTATED       5                         0
  OR5M3 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OR5M3 MUTATED                                           0    10
  OR5M3 WILD-TYPE                                         1   233
D537V12, multiclass
                                           clus
vv                                          OR5M3 MUTATED OR5M3 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D537V13, binary
                 cls
clus                0   1
  OR5M3 MUTATED     1  13
  OR5M3 WILD-TYPE   3 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5M3 MUTATED      1   13
  OR5M3 WILD-TYPE    3  297
                        clus
vv                       OR5M3 MUTATED OR5M3 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(538) Variable = EXPH5 MUTATION ANALYSIS
D538V1, survival
                 sevent
clus2               0   1
  EXPH5 MUTATED    10   3
  EXPH5 WILD-TYPE 220 136
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             13             356 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
              3             136 
$`EXPH5 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7723 TCGA-BR-8368 TCGA-BR-8589 
        6.97        34.68        32.78        28.73         4.31        27.12 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-6528 TCGA-HF-A5NB TCGA-HU-A4G8 
       12.43         6.58         6.02        15.22        30.51        22.68 
TCGA-VQ-A8P2 
       38.14 

$`EXPH5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-F1-6874 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-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 

  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           14.12 
[1] "4.3 - 38.1 (22.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D538V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EXPH5 MUTATED         0        0        2        1         3         1
  EXPH5 WILD-TYPE       2       15       38       29        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EXPH5 MUTATED           0          2          2          1        1
  EXPH5 WILD-TYPE         3         68         51         31       37
D538V3, multiclass
            clus
vv           EXPH5 MUTATED EXPH5 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EXPH5 MUTATED     1   2   7   4
  EXPH5 WILD-TYPE  21  90 166  93
D538V4, multiclass
    clus
vv   EXPH5 MUTATED EXPH5 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             7             166
  T4             4              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
  EXPH5 MUTATED     6   5   0   2
  EXPH5 WILD-TYPE 112  99  77  75
D538V5, multiclass
    clus
vv   EXPH5 MUTATED EXPH5 WILD-TYPE
  N0             6             112
  N1             5              99
  N2             0              77
  N3             2              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"
D538V6, binary
                 cls
clus                0   1
  EXPH5 MUTATED    14   0
  EXPH5 WILD-TYPE 332  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED     14    0
  EXPH5 WILD-TYPE  332   29
   clus
vv  EXPH5 MUTATED EXPH5 WILD-TYPE
  0            14             332
  1             0              29
[1] 2 2
[1] FALSE
D538V7, binary
                 cls
clus                0   1
  EXPH5 MUTATED     8   7
  EXPH5 WILD-TYPE 137 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED      8    7
  EXPH5 WILD-TYPE  137  241
        clus
vv       EXPH5 MUTATED EXPH5 WILD-TYPE
  FEMALE             8             137
  MALE               7             241
[1] 2 2
[1] FALSE
D538V8, binary
                 cls
clus                0   1
  EXPH5 MUTATED    11   2
  EXPH5 WILD-TYPE 281  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED     11    2
  EXPH5 WILD-TYPE  281   57
     clus
vv    EXPH5 MUTATED EXPH5 WILD-TYPE
  NO             11             281
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EXPH5 MUTATED                                          0
  EXPH5 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EXPH5 MUTATED                                       2
  EXPH5 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EXPH5 MUTATED                                                        9
  EXPH5 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EXPH5 MUTATED                                                   2
  EXPH5 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EXPH5 MUTATED                                                                   1
  EXPH5 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EXPH5 MUTATED                                                    0
  EXPH5 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EXPH5 MUTATED                                                  1
  EXPH5 WILD-TYPE                                               60
D538V9, multiclass
                                                                   clus
vv                                                                  EXPH5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  EXPH5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EXPH5 MUTATED     9   1   0   3
  EXPH5 WILD-TYPE 302  13  15  21
D538V10, multiclass
    clus
vv   EXPH5 MUTATED EXPH5 WILD-TYPE
  R0             9             302
  R1             1              13
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D538V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EXPH5 MUTATED       3                         0
  EXPH5 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EXPH5 MUTATED                                           0    10
  EXPH5 WILD-TYPE                                         1   233
D538V12, multiclass
                                           clus
vv                                          EXPH5 MUTATED EXPH5 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D538V13, binary
                 cls
clus                0   1
  EXPH5 MUTATED     0  12
  EXPH5 WILD-TYPE   4 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED      0   12
  EXPH5 WILD-TYPE    4  298
                        clus
vv                       EXPH5 MUTATED EXPH5 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(539) Variable = ABCB4 MUTATION ANALYSIS
D539V1, survival
                 sevent
clus2               0   1
  ABCB4 MUTATED    14   9
  ABCB4 WILD-TYPE 216 130
  ABCB4 MUTATED ABCB4 WILD-TYPE 
             23             346 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
              9             130 
$`ABCB4 MUTATED`
TCGA-CG-5727 TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8361 TCGA-BR-8589 
       79.07         6.97        44.94        36.16        31.10        27.12 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8527 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
       31.96        16.14         7.17        11.61         6.58        11.77 
TCGA-CG-4305 TCGA-CG-4469 TCGA-CG-5728 TCGA-D7-A4YY TCGA-D7-A6EY TCGA-F1-6874 
       15.95         7.07        65.10        13.78        11.44        14.47 
TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-VQ-A8PQ 
       11.08        77.29        20.25        23.84        15.65 

$`ABCB4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-7704 TCGA-BR-7707 TCGA-BR-7715 
       31.20        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-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-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-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-A4MH TCGA-CD-A4MJ 
        6.31        12.30        11.31        12.43        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-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-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-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-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-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-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 

  ABCB4 MUTATED ABCB4 WILD-TYPE 
           6.58            0.00 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
          79.07          122.30 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
          15.95           14.07 
[1] "6.6 - 79.1 (15.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D539V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCB4 MUTATED         0        1        2        4         3         3
  ABCB4 WILD-TYPE       2       14       38       26        34        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABCB4 MUTATED           0          2          4          2        4
  ABCB4 WILD-TYPE         3         68         49         30       34
D539V3, multiclass
            clus
vv           ABCB4 MUTATED ABCB4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               4              26
  STAGE IIA              3              34
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             4              49
  STAGE IIIC             2              30
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCB4 MUTATED     1   6  12   7
  ABCB4 WILD-TYPE  21  86 161  90
D539V4, multiclass
    clus
vv   ABCB4 MUTATED ABCB4 WILD-TYPE
  T1             1              21
  T2             6              86
  T3            12             161
  T4             7              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
  ABCB4 MUTATED     8   8   5   4
  ABCB4 WILD-TYPE 110  96  72  73
D539V5, multiclass
    clus
vv   ABCB4 MUTATED ABCB4 WILD-TYPE
  N0             8             110
  N1             8              96
  N2             5              72
  N3             4              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"
D539V6, binary
                 cls
clus                0   1
  ABCB4 MUTATED    22   2
  ABCB4 WILD-TYPE 324  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     22    2
  ABCB4 WILD-TYPE  324   27
   clus
vv  ABCB4 MUTATED ABCB4 WILD-TYPE
  0            22             324
  1             2              27
[1] 2 2
[1] FALSE
D539V7, binary
                 cls
clus                0   1
  ABCB4 MUTATED    12  14
  ABCB4 WILD-TYPE 133 234
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     12   14
  ABCB4 WILD-TYPE  133  234
        clus
vv       ABCB4 MUTATED ABCB4 WILD-TYPE
  FEMALE            12             133
  MALE              14             234
[1] 2 2
[1] FALSE
D539V8, binary
                 cls
clus                0   1
  ABCB4 MUTATED    19   3
  ABCB4 WILD-TYPE 273  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     19    3
  ABCB4 WILD-TYPE  273   56
     clus
vv    ABCB4 MUTATED ABCB4 WILD-TYPE
  NO             19             273
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ABCB4 MUTATED                                          0
  ABCB4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ABCB4 MUTATED                                       2
  ABCB4 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCB4 MUTATED                                                       12
  ABCB4 WILD-TYPE                                                    146
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ABCB4 MUTATED                                                   1
  ABCB4 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCB4 MUTATED                                                                   6
  ABCB4 WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ABCB4 MUTATED                                                    1
  ABCB4 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ABCB4 MUTATED                                                  4
  ABCB4 WILD-TYPE                                               57
D539V9, multiclass
                                                                   clus
vv                                                                  ABCB4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  ABCB4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCB4 MUTATED    18   1   1   3
  ABCB4 WILD-TYPE 293  13  14  21
D539V10, multiclass
    clus
vv   ABCB4 MUTATED ABCB4 WILD-TYPE
  R0            18             293
  R1             1              13
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D539V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCB4 MUTATED       7                         1
  ABCB4 WILD-TYPE    80                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCB4 MUTATED                                           0    13
  ABCB4 WILD-TYPE                                         1   230
D539V12, multiclass
                                           clus
vv                                          ABCB4 MUTATED ABCB4 WILD-TYPE
  ASIAN                                                 7              80
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D539V13, binary
                 cls
clus                0   1
  ABCB4 MUTATED     0  20
  ABCB4 WILD-TYPE   4 290
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED      0   20
  ABCB4 WILD-TYPE    4  290
                        clus
vv                       ABCB4 MUTATED ABCB4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            20             290
[1] 2 2
[1] FALSE

Clustering(540) Variable = HRNR MUTATION ANALYSIS
D540V1, survival
                sevent
clus2              0   1
  HRNR MUTATED    27  11
  HRNR WILD-TYPE 203 128
  HRNR MUTATED HRNR WILD-TYPE 
            38            331 
  HRNR MUTATED HRNR WILD-TYPE 
            11            128 
$`HRNR MUTATED`
TCGA-B7-A5TI TCGA-BR-6452 TCGA-BR-7715 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8078 
       19.56        34.68        33.63         3.45        29.56        29.59 
TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QI 
       25.05        31.96        32.58         0.72        20.65        21.44 
TCGA-BR-A4QM TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8532 TCGA-CD-A487 TCGA-CD-A4MG 
        5.13        12.39        12.76        11.64        12.30         6.58 
TCGA-CG-4304 TCGA-CG-4465 TCGA-CG-5723 TCGA-D7-6519 TCGA-D7-8572 TCGA-D7-A6EY 
       27.02         9.01       105.07        20.55        16.80        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-FP-7916 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE 
       20.32        15.65        14.07        13.58         0.56        11.08 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GX TCGA-HU-A4H6 TCGA-IN-A6RJ TCGA-VQ-A91V 
       22.68         3.25        20.25        21.17        12.46        42.64 
TCGA-VQ-A92D TCGA-VQ-AA6A 
       66.81        38.93 

$`HRNR WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7957 
       35.84        39.78        18.15        15.32        28.73         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-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-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-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-CD-5798 
       32.52        13.51        20.42         1.15        16.14        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-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-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-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-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        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-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-D7-6520 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-D7-6528 
       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-D7-8574 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-A747 TCGA-D7-A748 
       26.43        11.24        11.31        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-7998 TCGA-FP-8099 
       21.27        11.38         3.48        19.53        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       59.54         5.03         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-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-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-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        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-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       20.81         1.71        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 

  HRNR MUTATED HRNR WILD-TYPE 
          0.56           0.00 
  HRNR MUTATED HRNR WILD-TYPE 
        105.07         122.30 
  HRNR MUTATED HRNR WILD-TYPE 
        19.905         14.040 
[1] "0.6 - 105.1 (19.9)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.5"
D540V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HRNR MUTATED         1        1        4        4         5         8
  HRNR WILD-TYPE       1       14       36       26        32        44
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HRNR MUTATED           0          6          3          5        2
  HRNR WILD-TYPE         3         64         50         27       36
D540V3, multiclass
            clus
vv           HRNR MUTATED HRNR WILD-TYPE
  STAGE I               1              1
  STAGE IA              1             14
  STAGE IB              4             36
  STAGE II              4             26
  STAGE IIA             5             32
  STAGE IIB             8             44
  STAGE III             0              3
  STAGE IIIA            6             64
  STAGE IIIB            3             50
  STAGE IIIC            5             27
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HRNR MUTATED     3   7  18  13
  HRNR WILD-TYPE  19  85 155  84
D540V4, multiclass
    clus
vv   HRNR MUTATED HRNR WILD-TYPE
  T1            3             19
  T2            7             85
  T3           18            155
  T4           13             84
[1] 4 2
[1] TRUE
[1] "dimension of 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    17   9   9   6
  HRNR WILD-TYPE 101  95  68  71
D540V5, multiclass
    clus
vv   HRNR MUTATED HRNR WILD-TYPE
  N0           17            101
  N1            9             95
  N2            9             68
  N3            6             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"
D540V6, binary
                cls
clus               0   1
  HRNR MUTATED    36   2
  HRNR WILD-TYPE 310  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRNR MUTATED     36    2
  HRNR WILD-TYPE  310   27
   clus
vv  HRNR MUTATED HRNR WILD-TYPE
  0           36            310
  1            2             27
[1] 2 2
[1] FALSE
D540V7, binary
                cls
clus               0   1
  HRNR MUTATED    14  28
  HRNR WILD-TYPE 131 220
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRNR MUTATED     14   28
  HRNR WILD-TYPE  131  220
        clus
vv       HRNR MUTATED HRNR WILD-TYPE
  FEMALE           14            131
  MALE             28            220
[1] 2 2
[1] FALSE
D540V8, binary
                cls
clus               0   1
  HRNR MUTATED    30   5
  HRNR WILD-TYPE 262  54
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRNR MUTATED     30    5
  HRNR WILD-TYPE  262   54
     clus
vv    HRNR MUTATED HRNR WILD-TYPE
  NO            30            262
  YES            5             54
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HRNR MUTATED                                          0
  HRNR WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HRNR MUTATED                                       9
  HRNR WILD-TYPE                                    61
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HRNR MUTATED                                                       20
  HRNR WILD-TYPE                                                    138
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HRNR MUTATED                                                   2
  HRNR WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HRNR MUTATED                                                                   5
  HRNR WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HRNR MUTATED                                                    0
  HRNR WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HRNR MUTATED                                                  6
  HRNR WILD-TYPE                                               55
D540V9, multiclass
                                                                   clus
vv                                                                  HRNR MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      20
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             6
                                                                   clus
vv                                                                  HRNR WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         61
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       138
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HRNR MUTATED    33   1   1   2
  HRNR WILD-TYPE 278  13  14  22
D540V10, multiclass
    clus
vv   HRNR MUTATED HRNR WILD-TYPE
  R0           33            278
  R1            1             13
  R2            1             14
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D540V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  HRNR MUTATED      13                         2
  HRNR WILD-TYPE    74                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HRNR MUTATED                                           0    22
  HRNR WILD-TYPE                                         1   221
D540V12, multiclass
                                           clus
vv                                          HRNR MUTATED HRNR WILD-TYPE
  ASIAN                                               13             74
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               22            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D540V13, binary
                cls
clus               0   1
  HRNR MUTATED     0  35
  HRNR WILD-TYPE   4 275
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRNR MUTATED      0   35
  HRNR WILD-TYPE    4  275
                        clus
vv                       HRNR MUTATED HRNR WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           35            275
[1] 2 2
[1] FALSE

Clustering(541) Variable = BAHCC1 MUTATION ANALYSIS
D541V1, survival
                  sevent
clus2                0   1
  BAHCC1 MUTATED     5   6
  BAHCC1 WILD-TYPE 225 133
  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
              11              358 
  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
               6              133 
$`BAHCC1 MUTATED`
TCGA-CG-4460 TCGA-BR-4257 TCGA-BR-6455 TCGA-BR-8078 TCGA-BR-A4QL TCGA-CG-4441 
       21.99         9.67        13.87        29.59        16.14        14.01 
TCGA-CG-5726 TCGA-HU-8604 TCGA-HU-A4H4 TCGA-R5-A7ZI TCGA-VQ-A8P2 
       28.96        22.82        23.84        74.53        38.14 

$`BAHCC1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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 
            9.67             0.00 
  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
           74.53           122.30 
  BAHCC1 MUTATED BAHCC1 WILD-TYPE 
           22.82            14.07 
[1] "9.7 - 74.5 (22.8)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D541V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BAHCC1 MUTATED         0        1        0        0         1         4
  BAHCC1 WILD-TYPE       2       14       40       30        36        48
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BAHCC1 MUTATED           0          2          1          0        2
  BAHCC1 WILD-TYPE         3         68         52         32       36
D541V3, multiclass
            clus
vv           BAHCC1 MUTATED BAHCC1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               4               48
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BAHCC1 MUTATED     1   2   3   5
  BAHCC1 WILD-TYPE  21  90 170  92
D541V4, multiclass
    clus
vv   BAHCC1 MUTATED BAHCC1 WILD-TYPE
  T1              1               21
  T2              2               90
  T3              3              170
  T4              5               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
  BAHCC1 MUTATED     4   4   2   1
  BAHCC1 WILD-TYPE 114 100  75  76
D541V5, multiclass
    clus
vv   BAHCC1 MUTATED BAHCC1 WILD-TYPE
  N0              4              114
  N1              4              100
  N2              2               75
  N3              1               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"
D541V6, binary
                  cls
clus                 0   1
  BAHCC1 MUTATED    10   2
  BAHCC1 WILD-TYPE 336  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BAHCC1 MUTATED     10    2
  BAHCC1 WILD-TYPE  336   27
   clus
vv  BAHCC1 MUTATED BAHCC1 WILD-TYPE
  0             10              336
  1              2               27
[1] 2 2
[1] FALSE
D541V7, binary
                  cls
clus                 0   1
  BAHCC1 MUTATED     7   5
  BAHCC1 WILD-TYPE 138 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BAHCC1 MUTATED      7    5
  BAHCC1 WILD-TYPE  138  243
        clus
vv       BAHCC1 MUTATED BAHCC1 WILD-TYPE
  FEMALE              7              138
  MALE                5              243
[1] 2 2
[1] FALSE
D541V8, binary
                  cls
clus                 0   1
  BAHCC1 MUTATED     9   1
  BAHCC1 WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BAHCC1 MUTATED      9    1
  BAHCC1 WILD-TYPE  283   58
     clus
vv    BAHCC1 MUTATED BAHCC1 WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BAHCC1 MUTATED                                          0
  BAHCC1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BAHCC1 MUTATED                                       1
  BAHCC1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BAHCC1 MUTATED                                                        4
  BAHCC1 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BAHCC1 MUTATED                                                   1
  BAHCC1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BAHCC1 MUTATED                                                                   4
  BAHCC1 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BAHCC1 MUTATED                                                    0
  BAHCC1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BAHCC1 MUTATED                                                  2
  BAHCC1 WILD-TYPE                                               59
D541V9, multiclass
                                                                   clus
vv                                                                  BAHCC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  BAHCC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BAHCC1 MUTATED    10   0   1   1
  BAHCC1 WILD-TYPE 301  14  14  23
D541V10, multiclass
    clus
vv   BAHCC1 MUTATED BAHCC1 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D541V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  BAHCC1 MUTATED       2                         0
  BAHCC1 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BAHCC1 MUTATED                                           0     7
  BAHCC1 WILD-TYPE                                         1   236
D541V12, multiclass
                                           clus
vv                                          BAHCC1 MUTATED BAHCC1 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D541V13, binary
                  cls
clus                 0   1
  BAHCC1 MUTATED     1   7
  BAHCC1 WILD-TYPE   3 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BAHCC1 MUTATED      1    7
  BAHCC1 WILD-TYPE    3  303
                        clus
vv                       BAHCC1 MUTATED BAHCC1 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(542) Variable = C1RL MUTATION ANALYSIS
D542V1, survival
                sevent
clus2              0   1
  C1RL MUTATED     3   1
  C1RL WILD-TYPE 227 138
  C1RL MUTATED C1RL WILD-TYPE 
             4            365 
  C1RL MUTATED C1RL WILD-TYPE 
             1            138 
$`C1RL MUTATED`
TCGA-BR-6566 TCGA-BR-8487 TCGA-CD-A4MG TCGA-D7-A6F0 
       32.78         1.12         6.58        22.29 

$`C1RL WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  C1RL MUTATED C1RL WILD-TYPE 
          1.12           0.00 
  C1RL MUTATED C1RL WILD-TYPE 
         32.78         122.30 
  C1RL MUTATED C1RL WILD-TYPE 
        14.435         14.270 
[1] "1.1 - 32.8 (14.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D542V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C1RL MUTATED         0        0        1        0         3         0
  C1RL WILD-TYPE       2       15       39       30        34        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1RL MUTATED           0          1          0          0        0
  C1RL WILD-TYPE         3         69         53         32       38
D542V3, multiclass
            clus
vv           C1RL MUTATED C1RL WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             3             34
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  C1RL MUTATED     0   1   3   1
  C1RL WILD-TYPE  22  91 170  96
D542V4, multiclass
    clus
vv   C1RL MUTATED C1RL WILD-TYPE
  T1            0             22
  T2            1             91
  T3            3            170
  T4            1             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
  C1RL MUTATED     5   1   0   0
  C1RL WILD-TYPE 113 103  77  77
D542V5, multiclass
    clus
vv   C1RL MUTATED C1RL WILD-TYPE
  N0            5            113
  N1            1            103
  N2            0             77
  N3            0             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"
D542V6, binary
                cls
clus               0   1
  C1RL MUTATED     6   0
  C1RL WILD-TYPE 340  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1RL MUTATED      6    0
  C1RL WILD-TYPE  340   29
   clus
vv  C1RL MUTATED C1RL WILD-TYPE
  0            6            340
  1            0             29
[1] 2 2
[1] FALSE
D542V7, binary
                cls
clus               0   1
  C1RL MUTATED     5   1
  C1RL WILD-TYPE 140 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1RL MUTATED      5    1
  C1RL WILD-TYPE  140  247
        clus
vv       C1RL MUTATED C1RL WILD-TYPE
  FEMALE            5            140
  MALE              1            247
[1] 2 2
[1] FALSE
D542V8, binary
                cls
clus               0   1
  C1RL MUTATED     4   0
  C1RL WILD-TYPE 288  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1RL MUTATED      4    0
  C1RL WILD-TYPE  288   59
     clus
vv    C1RL MUTATED C1RL WILD-TYPE
  NO             4            288
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C1RL MUTATED                                          0
  C1RL WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C1RL MUTATED                                       1
  C1RL WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C1RL MUTATED                                                        4
  C1RL WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C1RL MUTATED                                                   0
  C1RL WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C1RL MUTATED                                                                   1
  C1RL WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C1RL MUTATED                                                    0
  C1RL WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C1RL MUTATED                                                  0
  C1RL WILD-TYPE                                               61
D542V9, multiclass
                                                                   clus
vv                                                                  C1RL MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  C1RL WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  C1RL MUTATED     3   0   0   2
  C1RL WILD-TYPE 308  14  15  22
D542V10, multiclass
    clus
vv   C1RL MUTATED C1RL WILD-TYPE
  R0            3            308
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D542V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  C1RL MUTATED       1                         0
  C1RL WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C1RL MUTATED                                           0     5
  C1RL WILD-TYPE                                         1   238
D542V12, multiclass
                                           clus
vv                                          C1RL MUTATED C1RL WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D542V13, binary
                cls
clus               0   1
  C1RL MUTATED     0   6
  C1RL WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1RL MUTATED      0    6
  C1RL WILD-TYPE    4  304
                        clus
vv                       C1RL MUTATED C1RL WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(543) Variable = USP21 MUTATION ANALYSIS
D543V1, survival
                 sevent
clus2               0   1
  USP21 MUTATED     8   5
  USP21 WILD-TYPE 222 134
  USP21 MUTATED USP21 WILD-TYPE 
             13             356 
  USP21 MUTATED USP21 WILD-TYPE 
              5             134 
$`USP21 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6852 TCGA-BR-8372 
       26.70         6.97         9.34         9.67        44.94        31.27 
TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-4466 TCGA-CG-5718 TCGA-D7-A74A TCGA-F1-6874 
        1.12        16.14        18.97        36.00        19.96        14.47 
TCGA-FP-A4BE 
       11.08 

$`USP21 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-6452 
        4.08         4.08         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-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-4469 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        9.01         7.07        30.97         6.97         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-A74B TCGA-EQ-5647 
       22.29        15.65         8.38         4.34         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-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 

  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           14.12 
[1] "1.1 - 44.9 (16.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D543V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP21 MUTATED         0        0        2        1         3         1
  USP21 WILD-TYPE       2       15       38       29        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  USP21 MUTATED           0          2          1          1        0
  USP21 WILD-TYPE         3         68         52         31       38
D543V3, multiclass
            clus
vv           USP21 MUTATED USP21 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP21 MUTATED     0   3   6   2
  USP21 WILD-TYPE  22  89 167  95
D543V4, multiclass
    clus
vv   USP21 MUTATED USP21 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             6             167
  T4             2              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
  USP21 MUTATED     6   3   1   2
  USP21 WILD-TYPE 112 101  76  75
D543V5, multiclass
    clus
vv   USP21 MUTATED USP21 WILD-TYPE
  N0             6             112
  N1             3             101
  N2             1              76
  N3             2              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"
D543V6, binary
                 cls
clus                0   1
  USP21 MUTATED    12   0
  USP21 WILD-TYPE 334  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP21 MUTATED     12    0
  USP21 WILD-TYPE  334   29
   clus
vv  USP21 MUTATED USP21 WILD-TYPE
  0            12             334
  1             0              29
[1] 2 2
[1] FALSE
D543V7, binary
                 cls
clus                0   1
  USP21 MUTATED     8   5
  USP21 WILD-TYPE 137 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP21 MUTATED      8    5
  USP21 WILD-TYPE  137  243
        clus
vv       USP21 MUTATED USP21 WILD-TYPE
  FEMALE             8             137
  MALE               5             243
[1] 2 2
[1] FALSE
D543V8, binary
                 cls
clus                0   1
  USP21 MUTATED    12   1
  USP21 WILD-TYPE 280  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP21 MUTATED     12    1
  USP21 WILD-TYPE  280   58
     clus
vv    USP21 MUTATED USP21 WILD-TYPE
  NO             12             280
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  USP21 MUTATED                                          0
  USP21 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  USP21 MUTATED                                       1
  USP21 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  USP21 MUTATED                                                        8
  USP21 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  USP21 MUTATED                                                   0
  USP21 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  USP21 MUTATED                                                                   3
  USP21 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  USP21 MUTATED                                                    0
  USP21 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  USP21 MUTATED                                                  1
  USP21 WILD-TYPE                                               60
D543V9, multiclass
                                                                   clus
vv                                                                  USP21 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  USP21 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP21 MUTATED    10   0   0   3
  USP21 WILD-TYPE 301  14  15  21
D543V10, multiclass
    clus
vv   USP21 MUTATED USP21 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D543V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  USP21 MUTATED       0                         1
  USP21 WILD-TYPE    87                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP21 MUTATED                                           0    10
  USP21 WILD-TYPE                                         1   233
D543V12, multiclass
                                           clus
vv                                          USP21 MUTATED USP21 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D543V13, binary
                 cls
clus                0   1
  USP21 MUTATED     0  11
  USP21 WILD-TYPE   4 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP21 MUTATED      0   11
  USP21 WILD-TYPE    4  299
                        clus
vv                       USP21 MUTATED USP21 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(544) Variable = ZBTB38 MUTATION ANALYSIS
D544V1, survival
                  sevent
clus2                0   1
  ZBTB38 MUTATED    13   7
  ZBTB38 WILD-TYPE 217 132
  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
              20              349 
  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
               7              132 
$`ZBTB38 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6455 
       21.99        26.70        19.56         9.34        34.68        13.87 
TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-A4J5 TCGA-BR-A4PE TCGA-BR-A4QL 
       29.59         0.26         1.12        28.34        20.42        16.14 
TCGA-CG-5721 TCGA-CG-5733 TCGA-HU-8249 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GT 
        6.02        21.07        28.96         5.59        22.68         6.51 
TCGA-HU-A4H4 TCGA-VQ-A8PK 
       23.84        17.85 

$`ZBTB38 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
        9.86        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-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-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-A4J6 
       12.89         8.98         0.72        14.17         0.53         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-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-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-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
       21.07         0.76        24.30        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-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-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 

  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
            0.26             0.00 
  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
           34.68           122.30 
  ZBTB38 MUTATED ZBTB38 WILD-TYPE 
           19.99            14.07 
[1] "0.3 - 34.7 (20.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D544V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZBTB38 MUTATED         0        0        2        0         3         6
  ZBTB38 WILD-TYPE       2       15       38       30        34        46
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB38 MUTATED           0          3          2          1        2
  ZBTB38 WILD-TYPE         3         67         51         31       36
D544V3, multiclass
            clus
vv           ZBTB38 MUTATED ZBTB38 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               6               46
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              2               51
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB38 MUTATED     0   5   8   6
  ZBTB38 WILD-TYPE  22  87 165  91
D544V4, multiclass
    clus
vv   ZBTB38 MUTATED ZBTB38 WILD-TYPE
  T1              0               22
  T2              5               87
  T3              8              165
  T4              6               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
  ZBTB38 MUTATED     7   6   4   3
  ZBTB38 WILD-TYPE 111  98  73  74
D544V5, multiclass
    clus
vv   ZBTB38 MUTATED ZBTB38 WILD-TYPE
  N0              7              111
  N1              6               98
  N2              4               73
  N3              3               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"
D544V6, binary
                  cls
clus                 0   1
  ZBTB38 MUTATED    19   1
  ZBTB38 WILD-TYPE 327  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB38 MUTATED     19    1
  ZBTB38 WILD-TYPE  327   28
   clus
vv  ZBTB38 MUTATED ZBTB38 WILD-TYPE
  0             19              327
  1              1               28
[1] 2 2
[1] FALSE
D544V7, binary
                  cls
clus                 0   1
  ZBTB38 MUTATED    12   8
  ZBTB38 WILD-TYPE 133 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB38 MUTATED     12    8
  ZBTB38 WILD-TYPE  133  240
        clus
vv       ZBTB38 MUTATED ZBTB38 WILD-TYPE
  FEMALE             12              133
  MALE                8              240
[1] 2 2
[1] FALSE
D544V8, binary
                  cls
clus                 0   1
  ZBTB38 MUTATED    20   0
  ZBTB38 WILD-TYPE 272  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB38 MUTATED     20    0
  ZBTB38 WILD-TYPE  272   59
     clus
vv    ZBTB38 MUTATED ZBTB38 WILD-TYPE
  NO              20              272
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZBTB38 MUTATED                                          0
  ZBTB38 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZBTB38 MUTATED                                       3
  ZBTB38 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZBTB38 MUTATED                                                        8
  ZBTB38 WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZBTB38 MUTATED                                                   1
  ZBTB38 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZBTB38 MUTATED                                                                   4
  ZBTB38 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZBTB38 MUTATED                                                    0
  ZBTB38 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZBTB38 MUTATED                                                  4
  ZBTB38 WILD-TYPE                                               57
D544V9, multiclass
                                                                   clus
vv                                                                  ZBTB38 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  ZBTB38 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZBTB38 MUTATED    16   0   1   1
  ZBTB38 WILD-TYPE 295  14  14  23
D544V10, multiclass
    clus
vv   ZBTB38 MUTATED ZBTB38 WILD-TYPE
  R0             16              295
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D544V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZBTB38 MUTATED       6                         0
  ZBTB38 WILD-TYPE    81                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZBTB38 MUTATED                                           0    11
  ZBTB38 WILD-TYPE                                         1   232
D544V12, multiclass
                                           clus
vv                                          ZBTB38 MUTATED ZBTB38 WILD-TYPE
  ASIAN                                                  6               81
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D544V13, binary
                  cls
clus                 0   1
  ZBTB38 MUTATED     0  16
  ZBTB38 WILD-TYPE   4 294
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB38 MUTATED      0   16
  ZBTB38 WILD-TYPE    4  294
                        clus
vv                       ZBTB38 MUTATED ZBTB38 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             16              294
[1] 2 2
[1] FALSE

Clustering(545) Variable = CBLN3 MUTATION ANALYSIS
D545V1, survival
                 sevent
clus2               0   1
  CBLN3 MUTATED     2   4
  CBLN3 WILD-TYPE 228 135
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              6             363 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              4             135 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-D7-8578 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-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 

  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          14.070 
[1] "4.3 - 38.1 (19.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D545V2, 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       2       14       38       30        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CBLN3 MUTATED           0          1          2          0        1
  CBLN3 WILD-TYPE         3         69         51         32       37
D545V3, multiclass
            clus
vv           CBLN3 MUTATED CBLN3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CBLN3 MUTATED     1   2   2   2
  CBLN3 WILD-TYPE  21  90 171  95
D545V4, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             2             171
  T4             2              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
  CBLN3 MUTATED     3   2   0   2
  CBLN3 WILD-TYPE 115 102  77  75
D545V5, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  N0             3             115
  N1             2             102
  N2             0              77
  N3             2              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"
D545V6, binary
                 cls
clus                0   1
  CBLN3 MUTATED     6   1
  CBLN3 WILD-TYPE 340  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      6    1
  CBLN3 WILD-TYPE  340   28
   clus
vv  CBLN3 MUTATED CBLN3 WILD-TYPE
  0             6             340
  1             1              28
[1] 2 2
[1] FALSE
D545V7, binary
                 cls
clus                0   1
  CBLN3 MUTATED     4   3
  CBLN3 WILD-TYPE 141 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      4    3
  CBLN3 WILD-TYPE  141  245
        clus
vv       CBLN3 MUTATED CBLN3 WILD-TYPE
  FEMALE             4             141
  MALE               3             245
[1] 2 2
[1] FALSE
D545V8, binary
                 cls
clus                0   1
  CBLN3 MUTATED     4   1
  CBLN3 WILD-TYPE 288  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      4    1
  CBLN3 WILD-TYPE  288   58
     clus
vv    CBLN3 MUTATED CBLN3 WILD-TYPE
  NO              4             288
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CBLN3 MUTATED                                          0
  CBLN3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CBLN3 MUTATED                                       0
  CBLN3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CBLN3 MUTATED                                                        2
  CBLN3 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CBLN3 MUTATED                                                   1
  CBLN3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CBLN3 MUTATED                                                                   3
  CBLN3 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CBLN3 MUTATED                                                    0
  CBLN3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CBLN3 MUTATED                                                  1
  CBLN3 WILD-TYPE                                               60
D545V9, multiclass
                                                                   clus
vv                                                                  CBLN3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  CBLN3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CBLN3 MUTATED     6   0   1   0
  CBLN3 WILD-TYPE 305  14  14  24
D545V10, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D545V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CBLN3 MUTATED       0                         0
  CBLN3 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CBLN3 MUTATED                                           0     4
  CBLN3 WILD-TYPE                                         1   239
D545V12, multiclass
                                           clus
vv                                          CBLN3 MUTATED CBLN3 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D545V13, binary
                 cls
clus                0   1
  CBLN3 MUTATED     0   3
  CBLN3 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      0    3
  CBLN3 WILD-TYPE    4  307
                        clus
vv                       CBLN3 MUTATED CBLN3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(546) Variable = AXIN2 MUTATION ANALYSIS
D546V1, survival
                 sevent
clus2               0   1
  AXIN2 MUTATED     9  10
  AXIN2 WILD-TYPE 221 129
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             19             350 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             10             129 
$`AXIN2 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-7957 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8487 
       21.99        34.68         9.07        29.59        31.10         1.12 
TCGA-BR-A4CQ TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4465 
       34.98        16.14        12.43         6.58        15.95         9.01 
TCGA-CG-5723 TCGA-D7-A4YV TCGA-D7-A6EY TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-RD-A7BW 
      105.07         5.92        11.44        19.73        18.21         5.13 
TCGA-RD-A8N6 
        8.94 

$`AXIN2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-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-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-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-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        14.04        45.67         8.52        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.60         9.24        11.05         8.61        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 

  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           14.22 
[1] "1.1 - 105.1 (15.9)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D546V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AXIN2 MUTATED         0        0        1        3         3         3
  AXIN2 WILD-TYPE       2       15       39       27        34        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AXIN2 MUTATED           0          4          2          1        3
  AXIN2 WILD-TYPE         3         66         51         31       35
D546V3, multiclass
            clus
vv           AXIN2 MUTATED AXIN2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               3              27
  STAGE IIA              3              34
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AXIN2 MUTATED     0   4  10   6
  AXIN2 WILD-TYPE  22  88 163  91
D546V4, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  T1             0              22
  T2             4              88
  T3            10             163
  T4             6              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
  AXIN2 MUTATED     7   5   4   4
  AXIN2 WILD-TYPE 111  99  73  73
D546V5, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  N0             7             111
  N1             5              99
  N2             4              73
  N3             4              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"
D546V6, binary
                 cls
clus                0   1
  AXIN2 MUTATED    17   3
  AXIN2 WILD-TYPE 329  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     17    3
  AXIN2 WILD-TYPE  329   26
   clus
vv  AXIN2 MUTATED AXIN2 WILD-TYPE
  0            17             329
  1             3              26
[1] 2 2
[1] FALSE
D546V7, binary
                 cls
clus                0   1
  AXIN2 MUTATED    14   6
  AXIN2 WILD-TYPE 131 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     14    6
  AXIN2 WILD-TYPE  131  242
        clus
vv       AXIN2 MUTATED AXIN2 WILD-TYPE
  FEMALE            14             131
  MALE               6             242
[1] 2 2
[1] FALSE
D546V8, binary
                 cls
clus                0   1
  AXIN2 MUTATED    18   1
  AXIN2 WILD-TYPE 274  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     18    1
  AXIN2 WILD-TYPE  274   58
     clus
vv    AXIN2 MUTATED AXIN2 WILD-TYPE
  NO             18             274
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AXIN2 MUTATED                                          0
  AXIN2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AXIN2 MUTATED                                       3
  AXIN2 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AXIN2 MUTATED                                                        9
  AXIN2 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AXIN2 MUTATED                                                   0
  AXIN2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AXIN2 MUTATED                                                                   4
  AXIN2 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AXIN2 MUTATED                                                    0
  AXIN2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AXIN2 MUTATED                                                  4
  AXIN2 WILD-TYPE                                               57
D546V9, multiclass
                                                                   clus
vv                                                                  AXIN2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  AXIN2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AXIN2 MUTATED    16   0   2   0
  AXIN2 WILD-TYPE 295  14  13  24
D546V10, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  R0            16             295
  R1             0              14
  R2             2              13
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D546V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AXIN2 MUTATED       2                         0
  AXIN2 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AXIN2 MUTATED                                           0    14
  AXIN2 WILD-TYPE                                         1   229
D546V12, multiclass
                                           clus
vv                                          AXIN2 MUTATED AXIN2 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D546V13, binary
                 cls
clus                0   1
  AXIN2 MUTATED     0  16
  AXIN2 WILD-TYPE   4 294
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED      0   16
  AXIN2 WILD-TYPE    4  294
                        clus
vv                       AXIN2 MUTATED AXIN2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            16             294
[1] 2 2
[1] FALSE

Clustering(547) Variable = CFI MUTATION ANALYSIS
D547V1, survival
               sevent
clus2             0   1
  CFI MUTATED    10   2
  CFI WILD-TYPE 220 137
  CFI MUTATED CFI WILD-TYPE 
           12           357 
  CFI MUTATED CFI WILD-TYPE 
            2           137 
$`CFI MUTATED`
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7715 TCGA-BR-8487 
        9.34         9.67        34.68        30.90        33.63         1.12 
TCGA-BR-8680 TCGA-CD-8529 TCGA-CG-4305 TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-VQ-A8P2 
       31.96        12.30        15.95         6.58        29.00        38.14 

$`CFI WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        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 

  CFI MUTATED CFI WILD-TYPE 
         1.12          0.00 
  CFI MUTATED CFI WILD-TYPE 
        38.14        122.30 
  CFI MUTATED CFI WILD-TYPE 
       22.475        14.170 
[1] "1.1 - 38.1 (22.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.7"
D547V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CFI MUTATED         0        0        0        1         3         1
  CFI WILD-TYPE       2       15       40       29        34        51
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CFI MUTATED           0          2          0          1        2
  CFI WILD-TYPE         3         68         53         31       36
D547V3, multiclass
            clus
vv           CFI MUTATED CFI WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             0            40
  STAGE II             1            29
  STAGE IIA            3            34
  STAGE IIB            1            51
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           0            53
  STAGE IIIC           1            31
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CFI MUTATED     0   1   5   4
  CFI WILD-TYPE  22  91 168  93
D547V4, multiclass
    clus
vv   CFI MUTATED CFI WILD-TYPE
  T1           0            22
  T2           1            91
  T3           5           168
  T4           4            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
  CFI MUTATED     4   5   2   1
  CFI WILD-TYPE 114  99  75  76
D547V5, multiclass
    clus
vv   CFI MUTATED CFI WILD-TYPE
  N0           4           114
  N1           5            99
  N2           2            75
  N3           1            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"
D547V6, binary
               cls
clus              0   1
  CFI MUTATED    11   2
  CFI WILD-TYPE 335  27
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFI MUTATED     11    2
  CFI WILD-TYPE  335   27
   clus
vv  CFI MUTATED CFI WILD-TYPE
  0          11           335
  1           2            27
[1] 2 2
[1] FALSE
D547V7, binary
               cls
clus              0   1
  CFI MUTATED     5   8
  CFI WILD-TYPE 140 240
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFI MUTATED      5    8
  CFI WILD-TYPE  140  240
        clus
vv       CFI MUTATED CFI WILD-TYPE
  FEMALE           5           140
  MALE             8           240
[1] 2 2
[1] FALSE
D547V8, binary
               cls
clus              0   1
  CFI MUTATED     9   2
  CFI WILD-TYPE 283  57
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFI MUTATED      9    2
  CFI WILD-TYPE  283   57
     clus
vv    CFI MUTATED CFI WILD-TYPE
  NO            9           283
  YES           2            57
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CFI MUTATED                                          0
  CFI WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CFI MUTATED                                       2
  CFI WILD-TYPE                                    68
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CFI MUTATED                                                        8
  CFI WILD-TYPE                                                    150
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CFI MUTATED                                                   2
  CFI WILD-TYPE                                                19
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CFI MUTATED                                                                   0
  CFI WILD-TYPE                                                                68
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CFI MUTATED                                                    0
  CFI WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CFI MUTATED                                                  1
  CFI WILD-TYPE                                               60
D547V9, multiclass
                                                                   clus
vv                                                                  CFI MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            1
                                                                   clus
vv                                                                  CFI WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  CFI MUTATED    10   0   0   3
  CFI WILD-TYPE 301  14  15  21
D547V10, multiclass
    clus
vv   CFI MUTATED CFI WILD-TYPE
  R0          10           301
  R1           0            14
  R2           0            15
  RX           3            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D547V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CFI MUTATED       4                         0
  CFI WILD-TYPE    83                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CFI MUTATED                                           0     8
  CFI WILD-TYPE                                         1   235
D547V12, multiclass
                                           clus
vv                                          CFI MUTATED CFI WILD-TYPE
  ASIAN                                               4            83
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               8           235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D547V13, binary
               cls
clus              0   1
  CFI MUTATED     0  11
  CFI WILD-TYPE   4 299
[1] "tbl2"
               cls
clus            [,1] [,2]
  CFI MUTATED      0   11
  CFI WILD-TYPE    4  299
                        clus
vv                       CFI MUTATED CFI WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          11           299
[1] 2 2
[1] FALSE

Clustering(548) Variable = UNC50 MUTATION ANALYSIS
D548V1, survival
                 sevent
clus2               0   1
  UNC50 MUTATED     3   0
  UNC50 WILD-TYPE 227 139
  UNC50 MUTATED UNC50 WILD-TYPE 
              3             366 
  UNC50 MUTATED UNC50 WILD-TYPE 
              0             139 
$`UNC50 MUTATED`
TCGA-BR-8368 TCGA-F1-A448 TCGA-FP-A4BE 
        4.31        21.27        11.08 

$`UNC50 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  UNC50 MUTATED UNC50 WILD-TYPE 
           4.31            0.00 
  UNC50 MUTATED UNC50 WILD-TYPE 
          21.27          122.30 
  UNC50 MUTATED UNC50 WILD-TYPE 
          11.08           14.35 
[1] "4.3 - 21.3 (11.1)"  "0.0 - 122.3 (14.3)"
[1] "hr="     "3300000"
D548V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UNC50 MUTATED         0        0        2        0         1         0
  UNC50 WILD-TYPE       2       15       38       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UNC50 MUTATED           0          0          1          0        0
  UNC50 WILD-TYPE         3         70         52         32       38
D548V3, multiclass
            clus
vv           UNC50 MUTATED UNC50 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UNC50 MUTATED     0   2   2   0
  UNC50 WILD-TYPE  22  90 171  97
D548V4, multiclass
    clus
vv   UNC50 MUTATED UNC50 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             2             171
  T4             0              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
  UNC50 MUTATED     3   0   0   1
  UNC50 WILD-TYPE 115 104  77  76
D548V5, multiclass
    clus
vv   UNC50 MUTATED UNC50 WILD-TYPE
  N0             3             115
  N1             0             104
  N2             0              77
  N3             1              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"
D548V6, binary
                 cls
clus                0   1
  UNC50 MUTATED     4   0
  UNC50 WILD-TYPE 342  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC50 MUTATED      4    0
  UNC50 WILD-TYPE  342   29
   clus
vv  UNC50 MUTATED UNC50 WILD-TYPE
  0             4             342
  1             0              29
[1] 2 2
[1] FALSE
D548V7, binary
                 cls
clus                0   1
  UNC50 MUTATED     1   3
  UNC50 WILD-TYPE 144 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC50 MUTATED      1    3
  UNC50 WILD-TYPE  144  245
        clus
vv       UNC50 MUTATED UNC50 WILD-TYPE
  FEMALE             1             144
  MALE               3             245
[1] 2 2
[1] FALSE
D548V8, binary
                 cls
clus                0   1
  UNC50 MUTATED     1   2
  UNC50 WILD-TYPE 291  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC50 MUTATED      1    2
  UNC50 WILD-TYPE  291   57
     clus
vv    UNC50 MUTATED UNC50 WILD-TYPE
  NO              1             291
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  UNC50 MUTATED                                          0
  UNC50 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  UNC50 MUTATED                                       0
  UNC50 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UNC50 MUTATED                                                        2
  UNC50 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  UNC50 MUTATED                                                   1
  UNC50 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UNC50 MUTATED                                                                   1
  UNC50 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  UNC50 MUTATED                                                    0
  UNC50 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  UNC50 MUTATED                                                  0
  UNC50 WILD-TYPE                                               61
D548V9, multiclass
                                                                   clus
vv                                                                  UNC50 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  UNC50 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  UNC50 MUTATED     4   0   0   0
  UNC50 WILD-TYPE 307  14  15  24
D548V10, multiclass
    clus
vv   UNC50 MUTATED UNC50 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D548V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  UNC50 MUTATED       0                         1
  UNC50 WILD-TYPE    87                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UNC50 MUTATED                                           0     2
  UNC50 WILD-TYPE                                         1   241
D548V12, multiclass
                                           clus
vv                                          UNC50 MUTATED UNC50 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D548V13, binary
                 cls
clus                0   1
  UNC50 MUTATED     1   2
  UNC50 WILD-TYPE   3 308
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC50 MUTATED      1    2
  UNC50 WILD-TYPE    3  308
                        clus
vv                       UNC50 MUTATED UNC50 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             2             308
[1] 2 2
[1] FALSE

Clustering(549) Variable = TH1L MUTATION ANALYSIS
D549V1, survival
                sevent
clus2              0   1
  TH1L MUTATED     9   2
  TH1L WILD-TYPE 221 137
  TH1L MUTATED TH1L WILD-TYPE 
            11            358 
  TH1L MUTATED TH1L WILD-TYPE 
             2            137 
$`TH1L MUTATED`
TCGA-FP-A8CX TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8680 TCGA-CD-8531 TCGA-CG-5721 
        0.23         6.97        30.90        31.96        12.59         6.02 
TCGA-CG-5723 TCGA-HU-8610 TCGA-HU-A4GN TCGA-HU-A4H0 TCGA-VQ-A8P2 
      105.07         0.76        29.98         2.10        38.14 

$`TH1L WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       47.05        21.99        22.98        79.07        16.24        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        22.82        21.07        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-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-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 

  TH1L MUTATED TH1L WILD-TYPE 
          0.23           0.00 
  TH1L MUTATED TH1L WILD-TYPE 
        105.07         122.30 
  TH1L MUTATED TH1L WILD-TYPE 
         12.59          14.35 
[1] "0.2 - 105.1 (12.6)" "0.0 - 122.3 (14.3)"
[1] "hr=" "2.3"
D549V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TH1L MUTATED         0        1        0        1         1         0
  TH1L WILD-TYPE       2       14       40       29        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TH1L MUTATED           0          3          0          2        2
  TH1L WILD-TYPE         3         67         53         30       36
D549V3, multiclass
            clus
vv           TH1L MUTATED TH1L WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TH1L MUTATED     1   3   2   5
  TH1L WILD-TYPE  21  89 171  92
D549V4, multiclass
    clus
vv   TH1L MUTATED TH1L WILD-TYPE
  T1            1             21
  T2            3             89
  T3            2            171
  T4            5             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
  TH1L MUTATED     1   6   1   2
  TH1L WILD-TYPE 117  98  76  75
D549V5, multiclass
    clus
vv   TH1L MUTATED TH1L WILD-TYPE
  N0            1            117
  N1            6             98
  N2            1             76
  N3            2             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"
D549V6, binary
                cls
clus               0   1
  TH1L MUTATED     8   1
  TH1L WILD-TYPE 338  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  TH1L MUTATED      8    1
  TH1L WILD-TYPE  338   28
   clus
vv  TH1L MUTATED TH1L WILD-TYPE
  0            8            338
  1            1             28
[1] 2 2
[1] FALSE
D549V7, binary
                cls
clus               0   1
  TH1L MUTATED     2   9
  TH1L WILD-TYPE 143 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  TH1L MUTATED      2    9
  TH1L WILD-TYPE  143  239
        clus
vv       TH1L MUTATED TH1L WILD-TYPE
  FEMALE            2            143
  MALE              9            239
[1] 2 2
[1] FALSE
D549V8, binary
                cls
clus               0   1
  TH1L MUTATED     8   2
  TH1L WILD-TYPE 284  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  TH1L MUTATED      8    2
  TH1L WILD-TYPE  284   57
     clus
vv    TH1L MUTATED TH1L WILD-TYPE
  NO             8            284
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TH1L MUTATED                                          1
  TH1L WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TH1L MUTATED                                       2
  TH1L WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TH1L MUTATED                                                        3
  TH1L WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TH1L MUTATED                                                   1
  TH1L WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TH1L MUTATED                                                                   1
  TH1L WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TH1L MUTATED                                                    0
  TH1L WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TH1L MUTATED                                                  3
  TH1L WILD-TYPE                                               58
D549V9, multiclass
                                                                   clus
vv                                                                  TH1L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  TH1L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TH1L MUTATED     9   0   0   2
  TH1L WILD-TYPE 302  14  15  22
D549V10, multiclass
    clus
vv   TH1L MUTATED TH1L WILD-TYPE
  R0            9            302
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D549V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TH1L MUTATED       5                         0
  TH1L WILD-TYPE    82                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TH1L MUTATED                                           0     4
  TH1L WILD-TYPE                                         1   239
D549V12, multiclass
                                           clus
vv                                          TH1L MUTATED TH1L WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D549V13, binary
                cls
clus               0   1
  TH1L MUTATED     0   8
  TH1L WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  TH1L MUTATED      0    8
  TH1L WILD-TYPE    4  302
                        clus
vv                       TH1L MUTATED TH1L WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(550) Variable = HEXDC MUTATION ANALYSIS
D550V1, survival
                 sevent
clus2               0   1
  HEXDC MUTATED     4   3
  HEXDC WILD-TYPE 226 136
  HEXDC MUTATED HEXDC WILD-TYPE 
              7             362 
  HEXDC MUTATED HEXDC WILD-TYPE 
              3             136 
$`HEXDC MUTATED`
TCGA-BR-8372 TCGA-CD-A4MI TCGA-CG-5726 TCGA-HF-7132 TCGA-HJ-7597 TCGA-IN-A6RN 
       31.27        11.77        28.96        77.29        26.47        19.53 
TCGA-VQ-A8P2 
       38.14 

$`HEXDC WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  HEXDC MUTATED HEXDC WILD-TYPE 
          11.77            0.00 
  HEXDC MUTATED HEXDC WILD-TYPE 
          77.29          122.30 
  HEXDC MUTATED HEXDC WILD-TYPE 
          28.96           14.07 
[1] "11.8 - 77.3 (29.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D550V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HEXDC MUTATED         0        1        1        1         1         0
  HEXDC WILD-TYPE       2       14       39       29        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HEXDC MUTATED           0          2          0          1        0
  HEXDC WILD-TYPE         3         68         53         31       38
D550V3, multiclass
            clus
vv           HEXDC MUTATED HEXDC WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HEXDC MUTATED     3   2   1   2
  HEXDC WILD-TYPE  19  90 172  95
D550V4, multiclass
    clus
vv   HEXDC MUTATED HEXDC WILD-TYPE
  T1             3              19
  T2             2              90
  T3             1             172
  T4             2              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
  HEXDC MUTATED     2   3   1   1
  HEXDC WILD-TYPE 116 101  76  76
D550V5, multiclass
    clus
vv   HEXDC MUTATED HEXDC WILD-TYPE
  N0             2             116
  N1             3             101
  N2             1              76
  N3             1              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"
D550V6, binary
                 cls
clus                0   1
  HEXDC MUTATED     7   0
  HEXDC WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HEXDC MUTATED      7    0
  HEXDC WILD-TYPE  339   29
   clus
vv  HEXDC MUTATED HEXDC WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D550V7, binary
                 cls
clus                0   1
  HEXDC MUTATED     3   5
  HEXDC WILD-TYPE 142 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HEXDC MUTATED      3    5
  HEXDC WILD-TYPE  142  243
        clus
vv       HEXDC MUTATED HEXDC WILD-TYPE
  FEMALE             3             142
  MALE               5             243
[1] 2 2
[1] FALSE
D550V8, binary
                 cls
clus                0   1
  HEXDC MUTATED     4   2
  HEXDC WILD-TYPE 288  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HEXDC MUTATED      4    2
  HEXDC WILD-TYPE  288   57
     clus
vv    HEXDC MUTATED HEXDC WILD-TYPE
  NO              4             288
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HEXDC MUTATED                                          1
  HEXDC WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HEXDC MUTATED                                       0
  HEXDC WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HEXDC MUTATED                                                        4
  HEXDC WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HEXDC MUTATED                                                   2
  HEXDC WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HEXDC MUTATED                                                                   1
  HEXDC WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HEXDC MUTATED                                                    0
  HEXDC WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HEXDC MUTATED                                                  0
  HEXDC WILD-TYPE                                               61
D550V9, multiclass
                                                                   clus
vv                                                                  HEXDC MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  HEXDC WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HEXDC MUTATED     6   0   0   1
  HEXDC WILD-TYPE 305  14  15  23
D550V10, multiclass
    clus
vv   HEXDC MUTATED HEXDC WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D550V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HEXDC MUTATED       1                         0
  HEXDC WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HEXDC MUTATED                                           0     5
  HEXDC WILD-TYPE                                         1   238
D550V12, multiclass
                                           clus
vv                                          HEXDC MUTATED HEXDC WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D550V13, binary
                 cls
clus                0   1
  HEXDC MUTATED     0   5
  HEXDC WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HEXDC MUTATED      0    5
  HEXDC WILD-TYPE    4  305
                        clus
vv                       HEXDC MUTATED HEXDC WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(551) Variable = SOS2 MUTATION ANALYSIS
D551V1, survival
                sevent
clus2              0   1
  SOS2 MUTATED    14   3
  SOS2 WILD-TYPE 216 136
  SOS2 MUTATED SOS2 WILD-TYPE 
            17            352 
  SOS2 MUTATED SOS2 WILD-TYPE 
             3            136 
$`SOS2 MUTATED`
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8080 
        9.34        34.68         9.17        35.84        29.59         9.60 
TCGA-BR-8081 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4PE TCGA-CD-8536 
       32.25        31.27         1.12        28.14        20.42        12.43 
TCGA-CG-4305 TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4HD 
       15.95        14.47        22.32         0.76        33.40 

$`SOS2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07        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-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-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 

  SOS2 MUTATED SOS2 WILD-TYPE 
          0.76           0.00 
  SOS2 MUTATED SOS2 WILD-TYPE 
         35.84         122.30 
  SOS2 MUTATED SOS2 WILD-TYPE 
         20.42          14.07 
[1] "0.8 - 35.8 (20.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.5"
D551V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SOS2 MUTATED         0        1        3        2         2         4
  SOS2 WILD-TYPE       2       14       37       28        35        48
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SOS2 MUTATED           0          1          0          3        0
  SOS2 WILD-TYPE         3         69         53         29       38
D551V3, multiclass
            clus
vv           SOS2 MUTATED SOS2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              3             37
  STAGE II              2             28
  STAGE IIA             2             35
  STAGE IIB             4             48
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            3             29
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SOS2 MUTATED     2   4   4   7
  SOS2 WILD-TYPE  20  88 169  90
D551V4, multiclass
    clus
vv   SOS2 MUTATED SOS2 WILD-TYPE
  T1            2             20
  T2            4             88
  T3            4            169
  T4            7             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
  SOS2 MUTATED    11   2   1   3
  SOS2 WILD-TYPE 107 102  76  74
D551V5, multiclass
    clus
vv   SOS2 MUTATED SOS2 WILD-TYPE
  N0           11            107
  N1            2            102
  N2            1             76
  N3            3             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"
D551V6, binary
                cls
clus               0   1
  SOS2 MUTATED    18   0
  SOS2 WILD-TYPE 328  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED     18    0
  SOS2 WILD-TYPE  328   29
   clus
vv  SOS2 MUTATED SOS2 WILD-TYPE
  0           18            328
  1            0             29
[1] 2 2
[1] FALSE
D551V7, binary
                cls
clus               0   1
  SOS2 MUTATED     9   9
  SOS2 WILD-TYPE 136 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED      9    9
  SOS2 WILD-TYPE  136  239
        clus
vv       SOS2 MUTATED SOS2 WILD-TYPE
  FEMALE            9            136
  MALE              9            239
[1] 2 2
[1] FALSE
D551V8, binary
                cls
clus               0   1
  SOS2 MUTATED    17   0
  SOS2 WILD-TYPE 275  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED     17    0
  SOS2 WILD-TYPE  275   59
     clus
vv    SOS2 MUTATED SOS2 WILD-TYPE
  NO            17            275
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SOS2 MUTATED                                          0
  SOS2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SOS2 MUTATED                                       1
  SOS2 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SOS2 MUTATED                                                       13
  SOS2 WILD-TYPE                                                    145
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SOS2 MUTATED                                                   1
  SOS2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SOS2 MUTATED                                                                   1
  SOS2 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SOS2 MUTATED                                                    0
  SOS2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SOS2 MUTATED                                                  2
  SOS2 WILD-TYPE                                               59
D551V9, multiclass
                                                                   clus
vv                                                                  SOS2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  SOS2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SOS2 MUTATED    16   0   0   2
  SOS2 WILD-TYPE 295  14  15  22
D551V10, multiclass
    clus
vv   SOS2 MUTATED SOS2 WILD-TYPE
  R0           16            295
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D551V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SOS2 MUTATED       4                         0
  SOS2 WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SOS2 MUTATED                                           0    13
  SOS2 WILD-TYPE                                         1   230
D551V12, multiclass
                                           clus
vv                                          SOS2 MUTATED SOS2 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D551V13, binary
                cls
clus               0   1
  SOS2 MUTATED     0  17
  SOS2 WILD-TYPE   4 293
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS2 MUTATED      0   17
  SOS2 WILD-TYPE    4  293
                        clus
vv                       SOS2 MUTATED SOS2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           17            293
[1] 2 2
[1] FALSE

Clustering(552) Variable = SPOCD1 MUTATION ANALYSIS
D552V1, survival
                  sevent
clus2                0   1
  SPOCD1 MUTATED     8   2
  SPOCD1 WILD-TYPE 222 137
  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
              10              359 
  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
               2              137 
$`SPOCD1 MUTATED`
TCGA-BR-4184 TCGA-BR-6453 TCGA-BR-7707 TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5728 
        6.97        15.95        35.84        11.77         6.02        65.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-MX-A5UJ TCGA-R5-A7ZI 
        6.51        20.25        19.73        74.53 

$`SPOCD1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
            6.02             0.00 
  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
           74.53           122.30 
  SPOCD1 MUTATED SPOCD1 WILD-TYPE 
           17.84            14.17 
[1] "6.0 - 74.5 (17.8)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.3"
D552V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPOCD1 MUTATED         0        1        2        0         2         0
  SPOCD1 WILD-TYPE       2       14       38       30        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPOCD1 MUTATED           0          4          0          1        2
  SPOCD1 WILD-TYPE         3         66         53         31       36
D552V3, multiclass
            clus
vv           SPOCD1 MUTATED SPOCD1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SPOCD1 MUTATED     1   3   4   4
  SPOCD1 WILD-TYPE  21  89 169  93
D552V4, multiclass
    clus
vv   SPOCD1 MUTATED SPOCD1 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              4              169
  T4              4               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
  SPOCD1 MUTATED     5   5   2   0
  SPOCD1 WILD-TYPE 113  99  75  77
D552V5, multiclass
    clus
vv   SPOCD1 MUTATED SPOCD1 WILD-TYPE
  N0              5              113
  N1              5               99
  N2              2               75
  N3              0               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"
D552V6, binary
                  cls
clus                 0   1
  SPOCD1 MUTATED    11   1
  SPOCD1 WILD-TYPE 335  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPOCD1 MUTATED     11    1
  SPOCD1 WILD-TYPE  335   28
   clus
vv  SPOCD1 MUTATED SPOCD1 WILD-TYPE
  0             11              335
  1              1               28
[1] 2 2
[1] FALSE
D552V7, binary
                  cls
clus                 0   1
  SPOCD1 MUTATED     8   5
  SPOCD1 WILD-TYPE 137 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPOCD1 MUTATED      8    5
  SPOCD1 WILD-TYPE  137  243
        clus
vv       SPOCD1 MUTATED SPOCD1 WILD-TYPE
  FEMALE              8              137
  MALE                5              243
[1] 2 2
[1] FALSE
D552V8, binary
                  cls
clus                 0   1
  SPOCD1 MUTATED     9   1
  SPOCD1 WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPOCD1 MUTATED      9    1
  SPOCD1 WILD-TYPE  283   58
     clus
vv    SPOCD1 MUTATED SPOCD1 WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SPOCD1 MUTATED                                          0
  SPOCD1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SPOCD1 MUTATED                                       2
  SPOCD1 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPOCD1 MUTATED                                                        7
  SPOCD1 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SPOCD1 MUTATED                                                   0
  SPOCD1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPOCD1 MUTATED                                                                   2
  SPOCD1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SPOCD1 MUTATED                                                    0
  SPOCD1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SPOCD1 MUTATED                                                  2
  SPOCD1 WILD-TYPE                                               59
D552V9, multiclass
                                                                   clus
vv                                                                  SPOCD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  SPOCD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SPOCD1 MUTATED     9   0   0   3
  SPOCD1 WILD-TYPE 302  14  15  21
D552V10, multiclass
    clus
vv   SPOCD1 MUTATED SPOCD1 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D552V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SPOCD1 MUTATED       4                         0
  SPOCD1 WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPOCD1 MUTATED                                           0     7
  SPOCD1 WILD-TYPE                                         1   236
D552V12, multiclass
                                           clus
vv                                          SPOCD1 MUTATED SPOCD1 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D552V13, binary
                  cls
clus                 0   1
  SPOCD1 MUTATED     1  10
  SPOCD1 WILD-TYPE   3 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPOCD1 MUTATED      1   10
  SPOCD1 WILD-TYPE    3  300
                        clus
vv                       SPOCD1 MUTATED SPOCD1 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(553) Variable = STX2 MUTATION ANALYSIS
D553V1, survival
                sevent
clus2              0   1
  STX2 MUTATED     4   2
  STX2 WILD-TYPE 226 137
  STX2 MUTATED STX2 WILD-TYPE 
             6            363 
  STX2 MUTATED STX2 WILD-TYPE 
             2            137 
$`STX2 MUTATED`
TCGA-BR-8680 TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4H8 TCGA-VQ-A8P2 
       31.96        11.44        22.32         0.10        14.07        38.14 

$`STX2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  STX2 MUTATED STX2 WILD-TYPE 
           0.1            0.0 
  STX2 MUTATED STX2 WILD-TYPE 
         38.14         122.30 
  STX2 MUTATED STX2 WILD-TYPE 
        18.195         14.270 
[1] "0.1 - 38.1 (18.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D553V2, 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       2       15       39       30        37        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STX2 MUTATED           0          1          1          1        1
  STX2 WILD-TYPE         3         69         52         31       37
D553V3, multiclass
            clus
vv           STX2 MUTATED STX2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  STX2 MUTATED     1   0   1   4
  STX2 WILD-TYPE  21  92 172  93
D553V4, multiclass
    clus
vv   STX2 MUTATED STX2 WILD-TYPE
  T1            1             21
  T2            0             92
  T3            1            172
  T4            4             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
  STX2 MUTATED     1   2   2   1
  STX2 WILD-TYPE 117 102  75  76
D553V5, multiclass
    clus
vv   STX2 MUTATED STX2 WILD-TYPE
  N0            1            117
  N1            2            102
  N2            2             75
  N3            1             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"
D553V6, binary
                cls
clus               0   1
  STX2 MUTATED     5   1
  STX2 WILD-TYPE 341  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX2 MUTATED      5    1
  STX2 WILD-TYPE  341   28
   clus
vv  STX2 MUTATED STX2 WILD-TYPE
  0            5            341
  1            1             28
[1] 2 2
[1] FALSE
D553V7, binary
                cls
clus               0   1
  STX2 MUTATED     2   4
  STX2 WILD-TYPE 143 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX2 MUTATED      2    4
  STX2 WILD-TYPE  143  244
        clus
vv       STX2 MUTATED STX2 WILD-TYPE
  FEMALE            2            143
  MALE              4            244
[1] 2 2
[1] FALSE
D553V8, binary
                cls
clus               0   1
  STX2 MUTATED     5   1
  STX2 WILD-TYPE 287  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX2 MUTATED      5    1
  STX2 WILD-TYPE  287   58
     clus
vv    STX2 MUTATED STX2 WILD-TYPE
  NO             5            287
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  STX2 MUTATED                                          0
  STX2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  STX2 MUTATED                                       1
  STX2 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  STX2 MUTATED                                                        0
  STX2 WILD-TYPE                                                    158
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  STX2 MUTATED                                                   1
  STX2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  STX2 MUTATED                                                                   0
  STX2 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  STX2 MUTATED                                                    0
  STX2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  STX2 MUTATED                                                  4
  STX2 WILD-TYPE                                               57
D553V9, multiclass
                                                                   clus
vv                                                                  STX2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       0
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  STX2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       158
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  STX2 MUTATED     6   0   0   0
  STX2 WILD-TYPE 305  14  15  24
D553V10, multiclass
    clus
vv   STX2 MUTATED STX2 WILD-TYPE
  R0            6            305
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D553V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  STX2 MUTATED       4                         0
  STX2 WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  STX2 MUTATED                                           0     2
  STX2 WILD-TYPE                                         1   241
D553V12, multiclass
                                           clus
vv                                          STX2 MUTATED STX2 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D553V13, binary
                cls
clus               0   1
  STX2 MUTATED     0   5
  STX2 WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX2 MUTATED      0    5
  STX2 WILD-TYPE    4  305
                        clus
vv                       STX2 MUTATED STX2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(554) Variable = SMAD7 MUTATION ANALYSIS
D554V1, survival
                 sevent
clus2               0   1
  SMAD7 MUTATED     3   1
  SMAD7 WILD-TYPE 227 138
  SMAD7 MUTATED SMAD7 WILD-TYPE 
              4             365 
  SMAD7 MUTATED SMAD7 WILD-TYPE 
              1             138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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          14.270 
[1] "6.6 - 36.2 (18.9)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.7"
D554V2, 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       2       14       38       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMAD7 MUTATED           0          0          0          0        1
  SMAD7 WILD-TYPE         3         70         53         32       37
D554V3, multiclass
            clus
vv           SMAD7 MUTATED SMAD7 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMAD7 MUTATED     2   1   1   2
  SMAD7 WILD-TYPE  20  91 172  95
D554V4, multiclass
    clus
vv   SMAD7 MUTATED SMAD7 WILD-TYPE
  T1             2              20
  T2             1              91
  T3             1             172
  T4             2              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
  SMAD7 MUTATED     4   1   1   0
  SMAD7 WILD-TYPE 114 103  76  77
D554V5, multiclass
    clus
vv   SMAD7 MUTATED SMAD7 WILD-TYPE
  N0             4             114
  N1             1             103
  N2             1              76
  N3             0              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"
D554V6, binary
                 cls
clus                0   1
  SMAD7 MUTATED     7   0
  SMAD7 WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD7 MUTATED      7    0
  SMAD7 WILD-TYPE  339   29
   clus
vv  SMAD7 MUTATED SMAD7 WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D554V7, binary
                 cls
clus                0   1
  SMAD7 MUTATED     2   5
  SMAD7 WILD-TYPE 143 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD7 MUTATED      2    5
  SMAD7 WILD-TYPE  143  243
        clus
vv       SMAD7 MUTATED SMAD7 WILD-TYPE
  FEMALE             2             143
  MALE               5             243
[1] 2 2
[1] FALSE
D554V8, binary
                 cls
clus                0   1
  SMAD7 MUTATED     5   0
  SMAD7 WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD7 MUTATED      5    0
  SMAD7 WILD-TYPE  287   59
     clus
vv    SMAD7 MUTATED SMAD7 WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SMAD7 MUTATED                                          0
  SMAD7 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SMAD7 MUTATED                                       1
  SMAD7 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMAD7 MUTATED                                                        2
  SMAD7 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SMAD7 MUTATED                                                   0
  SMAD7 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMAD7 MUTATED                                                                   1
  SMAD7 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SMAD7 MUTATED                                                    2
  SMAD7 WILD-TYPE                                                  3
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SMAD7 MUTATED                                                  1
  SMAD7 WILD-TYPE                                               60
D554V9, multiclass
                                                                   clus
vv                                                                  SMAD7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  SMAD7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SMAD7 MUTATED     4   0   0   2
  SMAD7 WILD-TYPE 307  14  15  22
D554V10, multiclass
    clus
vv   SMAD7 MUTATED SMAD7 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D554V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SMAD7 MUTATED       3                         0
  SMAD7 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMAD7 MUTATED                                           0     4
  SMAD7 WILD-TYPE                                         1   239
D554V12, multiclass
                                           clus
vv                                          SMAD7 MUTATED SMAD7 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D554V13, binary
                 cls
clus                0   1
  SMAD7 MUTATED     0   7
  SMAD7 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD7 MUTATED      0    7
  SMAD7 WILD-TYPE    4  303
                        clus
vv                       SMAD7 MUTATED SMAD7 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(555) Variable = GNPNAT1 MUTATION ANALYSIS
D555V1, survival
                   sevent
clus2                 0   1
  GNPNAT1 MUTATED     4   1
  GNPNAT1 WILD-TYPE 226 138
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
                5               364 
  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE 
                1               138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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             14.22 
[1] "6.0 - 65.1 (15.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.1"
D555V2, 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       2       15       38       30        37        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GNPNAT1 MUTATED           0          2          0          0        1
  GNPNAT1 WILD-TYPE         3         68         53         32       37
D555V3, multiclass
            clus
vv           GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                0                37
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GNPNAT1 MUTATED     0   4   0   2
  GNPNAT1 WILD-TYPE  22  88 173  95
D555V4, multiclass
    clus
vv   GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  T1               0                22
  T2               4                88
  T3               0               173
  T4               2                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
  GNPNAT1 MUTATED     3   3   0   0
  GNPNAT1 WILD-TYPE 115 101  77  77
D555V5, multiclass
    clus
vv   GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  N0               3               115
  N1               3               101
  N2               0                77
  N3               0                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"
D555V6, binary
                   cls
clus                  0   1
  GNPNAT1 MUTATED     6   0
  GNPNAT1 WILD-TYPE 340  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GNPNAT1 MUTATED      6    0
  GNPNAT1 WILD-TYPE  340   29
   clus
vv  GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  0               6               340
  1               0                29
[1] 2 2
[1] FALSE
D555V7, binary
                   cls
clus                  0   1
  GNPNAT1 MUTATED     2   4
  GNPNAT1 WILD-TYPE 143 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GNPNAT1 MUTATED      2    4
  GNPNAT1 WILD-TYPE  143  244
        clus
vv       GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  FEMALE               2               143
  MALE                 4               244
[1] 2 2
[1] FALSE
D555V8, binary
                   cls
clus                  0   1
  GNPNAT1 MUTATED     4   0
  GNPNAT1 WILD-TYPE 288  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GNPNAT1 MUTATED      4    0
  GNPNAT1 WILD-TYPE  288   59
     clus
vv    GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  NO                4               288
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GNPNAT1 MUTATED                                          0
  GNPNAT1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GNPNAT1 MUTATED                                       0
  GNPNAT1 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GNPNAT1 MUTATED                                                        3
  GNPNAT1 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GNPNAT1 MUTATED                                                   0
  GNPNAT1 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GNPNAT1 MUTATED                                                                   2
  GNPNAT1 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GNPNAT1 MUTATED                                                    0
  GNPNAT1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GNPNAT1 MUTATED                                                  1
  GNPNAT1 WILD-TYPE                                               60
D555V9, multiclass
                                                                   clus
vv                                                                  GNPNAT1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  GNPNAT1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GNPNAT1 MUTATED     5   0   0   1
  GNPNAT1 WILD-TYPE 306  14  15  23
D555V10, multiclass
    clus
vv   GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  R0               5               306
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D555V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  GNPNAT1 MUTATED       0                         0
  GNPNAT1 WILD-TYPE    87                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GNPNAT1 MUTATED                                           0     4
  GNPNAT1 WILD-TYPE                                         1   239
D555V12, multiclass
                                           clus
vv                                          GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  ASIAN                                                   0                87
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D555V13, binary
                   cls
clus                  0   1
  GNPNAT1 MUTATED     0   4
  GNPNAT1 WILD-TYPE   4 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GNPNAT1 MUTATED      0    4
  GNPNAT1 WILD-TYPE    4  306
                        clus
vv                       GNPNAT1 MUTATED GNPNAT1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4               306
[1] 2 2
[1] FALSE

Clustering(556) Variable = ALDH2 MUTATION ANALYSIS
D556V1, survival
                 sevent
clus2               0   1
  ALDH2 MUTATED     8   4
  ALDH2 WILD-TYPE 222 135
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             12             357 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
              4             135 
$`ALDH2 MUTATED`
TCGA-BR-4184 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8591 TCGA-BR-A4QL 
        6.97        36.16        35.84        29.59        28.14        16.14 
TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 TCGA-HU-8602 TCGA-HU-A4GU TCGA-VQ-A8P2 
        1.02         6.02        28.96        22.32         6.58        38.14 

$`ALDH2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  ALDH2 MUTATED ALDH2 WILD-TYPE 
           1.02            0.00 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
          38.14          122.30 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
          25.23           14.07 
[1] "1.0 - 38.1 (25.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D556V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ALDH2 MUTATED         0        2        1        0         0         3
  ALDH2 WILD-TYPE       2       13       39       30        37        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ALDH2 MUTATED           0          3          1          1        2
  ALDH2 WILD-TYPE         3         67         52         31       36
D556V3, multiclass
            clus
vv           ALDH2 MUTATED ALDH2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALDH2 MUTATED     2   1   4   6
  ALDH2 WILD-TYPE  20  91 169  91
D556V4, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  T1             2              20
  T2             1              91
  T3             4             169
  T4             6              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
  ALDH2 MUTATED     6   4   1   2
  ALDH2 WILD-TYPE 112 100  76  75
D556V5, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  N0             6             112
  N1             4             100
  N2             1              76
  N3             2              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"
D556V6, binary
                 cls
clus                0   1
  ALDH2 MUTATED    11   1
  ALDH2 WILD-TYPE 335  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED     11    1
  ALDH2 WILD-TYPE  335   28
   clus
vv  ALDH2 MUTATED ALDH2 WILD-TYPE
  0            11             335
  1             1              28
[1] 2 2
[1] FALSE
D556V7, binary
                 cls
clus                0   1
  ALDH2 MUTATED     5   8
  ALDH2 WILD-TYPE 140 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      5    8
  ALDH2 WILD-TYPE  140  240
        clus
vv       ALDH2 MUTATED ALDH2 WILD-TYPE
  FEMALE             5             140
  MALE               8             240
[1] 2 2
[1] FALSE
D556V8, binary
                 cls
clus                0   1
  ALDH2 MUTATED     9   1
  ALDH2 WILD-TYPE 283  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      9    1
  ALDH2 WILD-TYPE  283   58
     clus
vv    ALDH2 MUTATED ALDH2 WILD-TYPE
  NO              9             283
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ALDH2 MUTATED                                          0
  ALDH2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ALDH2 MUTATED                                       2
  ALDH2 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ALDH2 MUTATED                                                        7
  ALDH2 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ALDH2 MUTATED                                                   1
  ALDH2 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ALDH2 MUTATED                                                                   2
  ALDH2 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ALDH2 MUTATED                                                    1
  ALDH2 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ALDH2 MUTATED                                                  0
  ALDH2 WILD-TYPE                                               61
D556V9, multiclass
                                                                   clus
vv                                                                  ALDH2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  ALDH2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ALDH2 MUTATED    10   0   1   2
  ALDH2 WILD-TYPE 301  14  14  22
D556V10, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D556V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ALDH2 MUTATED       2                         0
  ALDH2 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ALDH2 MUTATED                                           0     8
  ALDH2 WILD-TYPE                                         1   235
D556V12, multiclass
                                           clus
vv                                          ALDH2 MUTATED ALDH2 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D556V13, binary
                 cls
clus                0   1
  ALDH2 MUTATED     0   9
  ALDH2 WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      0    9
  ALDH2 WILD-TYPE    4  301
                        clus
vv                       ALDH2 MUTATED ALDH2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(557) Variable = TMEM55A MUTATION ANALYSIS
D557V1, survival
                   sevent
clus2                 0   1
  TMEM55A MUTATED     1   1
  TMEM55A WILD-TYPE 229 138
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                2               367 
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                1               138 
$`TMEM55A MUTATED`
TCGA-BR-8361 TCGA-CD-A4MI 
       31.10        11.77 

$`TMEM55A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  TMEM55A MUTATED TMEM55A WILD-TYPE 
            11.77              0.00 
  TMEM55A MUTATED TMEM55A WILD-TYPE 
             31.1             122.3 
  TMEM55A MUTATED TMEM55A WILD-TYPE 
           21.435            14.270 
[1] "11.8 - 31.1 (21.4)" "0.0 - 122.3 (14.3)"
[1] "Remove cluster labels:" "TMEM55A MUTATED"       
D557V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM55A MUTATED         0        0        0        0         0         0
  TMEM55A WILD-TYPE       2       15       40       30        37        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM55A MUTATED           0          1          0          1        0
  TMEM55A WILD-TYPE         3         69         53         31       38
D557V3, multiclass
[1] "Remove cluster labels:" "TMEM55A MUTATED"       
clus
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                2               370 
       TCGA-CG-4444        TCGA-CG-4460        TCGA-CG-4475        TCGA-CG-4476 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5727        TCGA-EQ-A4SO        TCGA-F1-6177 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-A8CX        TCGA-HF-7131        TCGA-KB-A93G        TCGA-MX-A663 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-B7-A5TI        TCGA-B7-A5TJ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-B7-A5TK        TCGA-B7-A5TN        TCGA-BR-4183        TCGA-BR-4184 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4267        TCGA-BR-4279 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4280        TCGA-BR-4361        TCGA-BR-4368        TCGA-BR-6452 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8058        TCGA-BR-8059 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8060        TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8081        TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8289        TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8297 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8360        TCGA-BR-8363        TCGA-BR-8364        TCGA-BR-8365 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8366        TCGA-BR-8367        TCGA-BR-8368        TCGA-BR-8369 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8370        TCGA-BR-8371        TCGA-BR-8372        TCGA-BR-8373 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8380        TCGA-BR-8381        TCGA-BR-8382        TCGA-BR-8384 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8483        TCGA-BR-8484        TCGA-BR-8485        TCGA-BR-8486 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8487        TCGA-BR-8588        TCGA-BR-8589        TCGA-BR-8590 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8591        TCGA-BR-8592        TCGA-BR-8676        TCGA-BR-8677 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8678        TCGA-BR-8679        TCGA-BR-8680        TCGA-BR-8682 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8683        TCGA-BR-8686        TCGA-BR-8687        TCGA-BR-8690 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A44T        TCGA-BR-A44U        TCGA-BR-A452        TCGA-BR-A453 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4CQ        TCGA-BR-A4CR        TCGA-BR-A4CS        TCGA-BR-A4IU 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ        TCGA-BR-A4J1 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J5        TCGA-BR-A4J6 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4J7        TCGA-BR-A4J8        TCGA-BR-A4PD        TCGA-BR-A4PE 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-BR-A4QM 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5813        TCGA-CD-8524 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8525        TCGA-CD-8526        TCGA-CD-8527        TCGA-CD-8528 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8529        TCGA-CD-8530        TCGA-CD-8531        TCGA-CD-8532 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8533        TCGA-CD-8534        TCGA-CD-8535        TCGA-CD-8536 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-A486        TCGA-CD-A487        TCGA-CD-A489        TCGA-CD-A48A 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-A48C        TCGA-CD-A4MG        TCGA-CD-A4MH        TCGA-CD-A4MJ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4462        TCGA-CG-4465 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4477 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5728        TCGA-CG-5730 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6520 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-D7-8570 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8572        TCGA-D7-8573        TCGA-D7-8574        TCGA-D7-8575 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8576        TCGA-D7-8578        TCGA-D7-8579        TCGA-D7-A4YT 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A4YU        TCGA-D7-A4YV        TCGA-D7-A4YX        TCGA-D7-A4YY 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A4Z0        TCGA-D7-A6ET        TCGA-D7-A6EV        TCGA-D7-A6EX 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A6EY        TCGA-D7-A6EZ        TCGA-D7-A6F0        TCGA-D7-A6F2 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A747        TCGA-D7-A748        TCGA-D7-A74A        TCGA-D7-A74B 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6874        TCGA-F1-6875 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-F1-A448        TCGA-F1-A72C        TCGA-FP-7735        TCGA-FP-7829 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631        TCGA-FP-A4BE 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-A4BF        TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HF-7136        TCGA-HF-A5NB        TCGA-HJ-7597        TCGA-HU-8243 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8244        TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8608        TCGA-HU-8610        TCGA-HU-A4G2        TCGA-HU-A4G3 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4G6        TCGA-HU-A4G8        TCGA-HU-A4G9        TCGA-HU-A4GC 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GD        TCGA-HU-A4GF        TCGA-HU-A4GH        TCGA-HU-A4GJ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GN        TCGA-HU-A4GP        TCGA-HU-A4GQ        TCGA-HU-A4GT 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GU        TCGA-HU-A4GX        TCGA-HU-A4GY        TCGA-HU-A4H0 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4H2        TCGA-HU-A4H3        TCGA-HU-A4H4        TCGA-HU-A4H5 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4H6        TCGA-HU-A4H8        TCGA-HU-A4HB        TCGA-HU-A4HD 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-8462        TCGA-IN-8663        TCGA-IN-A6RI 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-A6RJ        TCGA-IN-A6RL        TCGA-IN-A6RN        TCGA-IN-A6RO 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-A6RP        TCGA-IN-A6RR        TCGA-IN-A6RS        TCGA-IN-A7NR 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-A7NT        TCGA-IN-A7NU        TCGA-IN-AB1V        TCGA-IN-AB1X 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IP-7968        TCGA-KB-A6F5        TCGA-KB-A6F7        TCGA-KB-A93J 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-MX-A5UG        TCGA-MX-A5UJ        TCGA-MX-A666        TCGA-R5-A7O7 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-R5-A7ZE        TCGA-R5-A7ZF        TCGA-R5-A7ZI        TCGA-R5-A7ZR 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-R5-A804        TCGA-R5-A805        TCGA-RD-A7BS        TCGA-RD-A7BT 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-RD-A7BW        TCGA-RD-A7C1        TCGA-RD-A8MV        TCGA-RD-A8MW 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-RD-A8N0        TCGA-RD-A8N1        TCGA-RD-A8N2        TCGA-RD-A8N4 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-RD-A8N5        TCGA-RD-A8N6        TCGA-RD-A8N9        TCGA-SW-A7EA 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-SW-A7EB        TCGA-VQ-A8DL        TCGA-VQ-A8DT        TCGA-VQ-A8DU 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A8DV        TCGA-VQ-A8DZ        TCGA-VQ-A8E2        TCGA-VQ-A8E7 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A8P2        TCGA-VQ-A8P3        TCGA-VQ-A8PE        TCGA-VQ-A8PK 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A8PM        TCGA-VQ-A8PQ        TCGA-VQ-A91Q        TCGA-VQ-A91U 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A91V        TCGA-VQ-A92D        TCGA-VQ-A94T        TCGA-VQ-AA64 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-AA68        TCGA-VQ-AA69        TCGA-VQ-AA6A        TCGA-VQ-AA6B 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-AA6F        TCGA-VQ-AA6G        TCGA-VQ-AA6I        TCGA-VQ-AA6J 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-AA6K        TCGA-ZA-A8F6 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
                   vv
clus                 T1  T2  T3  T4
  TMEM55A MUTATED     0   0   1   1
  TMEM55A WILD-TYPE  22  92 172  96
D557V4, multiclass
[1] "Remove cluster labels:" "TMEM55A MUTATED"       
clus
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                2               382 
       TCGA-CG-4444        TCGA-CG-4460        TCGA-CG-4475        TCGA-CG-4476 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5727        TCGA-EQ-A4SO        TCGA-F1-6177 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-A8CX        TCGA-HF-7131        TCGA-KB-A93G        TCGA-MX-A663 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-B7-A5TI        TCGA-B7-A5TJ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-B7-A5TK        TCGA-B7-A5TN        TCGA-BR-4183        TCGA-BR-4184 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4201        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4267 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4363        TCGA-BR-4368 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4371        TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958        TCGA-BR-7959 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8058        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8297        TCGA-BR-8360        TCGA-BR-8363 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8364        TCGA-BR-8365        TCGA-BR-8366        TCGA-BR-8367 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8368        TCGA-BR-8369        TCGA-BR-8370        TCGA-BR-8371 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8372        TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8382        TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8484 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8485        TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8589        TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8676        TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8680        TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8687        TCGA-BR-8690        TCGA-BR-A44T        TCGA-BR-A44U 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A452        TCGA-BR-A453        TCGA-BR-A4CQ        TCGA-BR-A4CR 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4CS        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J7        TCGA-BR-A4J8 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4PD        TCGA-BR-A4PE        TCGA-BR-A4PF        TCGA-BR-A4QI 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4QL        TCGA-BR-A4QM        TCGA-CD-5798        TCGA-CD-5799 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-5804        TCGA-CD-5813        TCGA-CD-8524        TCGA-CD-8525 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8526        TCGA-CD-8527        TCGA-CD-8528        TCGA-CD-8529 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8530        TCGA-CD-8531        TCGA-CD-8532        TCGA-CD-8533 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8534        TCGA-CD-8535        TCGA-CD-8536        TCGA-CD-A486 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-A487        TCGA-CD-A489        TCGA-CD-A48A        TCGA-CD-A48C 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-A4MG        TCGA-CD-A4MH        TCGA-CD-A4MJ        TCGA-CG-4300 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4449 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5717 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8570        TCGA-D7-8572        TCGA-D7-8573        TCGA-D7-8574 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8575        TCGA-D7-8576        TCGA-D7-8578        TCGA-D7-8579 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A4YT        TCGA-D7-A4YU        TCGA-D7-A4YV        TCGA-D7-A4YX 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A4YY        TCGA-D7-A4Z0        TCGA-D7-A6ET        TCGA-D7-A6EV 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A6EX        TCGA-D7-A6EY        TCGA-D7-A6EZ        TCGA-D7-A6F0 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A6F2        TCGA-D7-A747        TCGA-D7-A748        TCGA-D7-A74A 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A74B        TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6874 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-F1-6875        TCGA-F1-A448        TCGA-F1-A72C        TCGA-FP-7735 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-A4BE        TCGA-FP-A4BF        TCGA-FP-A9TM        TCGA-HF-7132 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136        TCGA-HF-A5NB 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HJ-7597        TCGA-HU-8238        TCGA-HU-8243        TCGA-HU-8244 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604        TCGA-HU-8608 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8610        TCGA-HU-A4G2        TCGA-HU-A4G3        TCGA-HU-A4G6 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4G8        TCGA-HU-A4G9        TCGA-HU-A4GC        TCGA-HU-A4GD 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GF        TCGA-HU-A4GH        TCGA-HU-A4GJ        TCGA-HU-A4GN 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GP        TCGA-HU-A4GQ        TCGA-HU-A4GT        TCGA-HU-A4GU 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GX        TCGA-HU-A4GY        TCGA-HU-A4H0        TCGA-HU-A4H2 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4H3        TCGA-HU-A4H4        TCGA-HU-A4H5        TCGA-HU-A4H6 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4H8        TCGA-HU-A4HB        TCGA-HU-A4HD        TCGA-IN-7806 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-7808        TCGA-IN-8462        TCGA-IN-8663        TCGA-IN-A6RI 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-A6RJ        TCGA-IN-A6RL        TCGA-IN-A6RN        TCGA-IN-A6RO 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-A6RP        TCGA-IN-A6RR        TCGA-IN-A6RS        TCGA-IN-A7NR 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-A7NT        TCGA-IN-A7NU        TCGA-IN-AB1V        TCGA-IN-AB1X 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IP-7968        TCGA-KB-A6F5        TCGA-KB-A6F7        TCGA-KB-A93J 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-MX-A5UG        TCGA-MX-A5UJ        TCGA-MX-A666        TCGA-R5-A7O7 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-R5-A7ZE        TCGA-R5-A7ZF        TCGA-R5-A7ZI        TCGA-R5-A7ZR 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-R5-A804        TCGA-R5-A805        TCGA-RD-A7BS        TCGA-RD-A7BT 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-RD-A7BW        TCGA-RD-A7C1        TCGA-RD-A8MV        TCGA-RD-A8MW 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-RD-A8N0        TCGA-RD-A8N1        TCGA-RD-A8N2        TCGA-RD-A8N4 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-RD-A8N5        TCGA-RD-A8N6        TCGA-RD-A8N9        TCGA-SW-A7EA 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-SW-A7EB        TCGA-VQ-A8DL        TCGA-VQ-A8DT        TCGA-VQ-A8DU 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A8DV        TCGA-VQ-A8DZ        TCGA-VQ-A8E2        TCGA-VQ-A8E7 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A8P2        TCGA-VQ-A8P3        TCGA-VQ-A8PE        TCGA-VQ-A8PK 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A8PM        TCGA-VQ-A8PQ        TCGA-VQ-A91Q        TCGA-VQ-A91U 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A91V        TCGA-VQ-A92D        TCGA-VQ-A94T        TCGA-VQ-AA64 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-AA68        TCGA-VQ-AA69        TCGA-VQ-AA6A        TCGA-VQ-AA6B 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-AA6F        TCGA-VQ-AA6G        TCGA-VQ-AA6I        TCGA-VQ-AA6J 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-AA6K        TCGA-ZA-A8F6 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
                   vv
clus                 N0  N1  N2  N3
  TMEM55A MUTATED     0   2   1   0
  TMEM55A WILD-TYPE 118 102  76  77
D557V5, multiclass
    clus
vv   TMEM55A MUTATED TMEM55A WILD-TYPE
  N0               0               118
  N1               2               102
  N2               1                76
  N3               0                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"
D557V6, binary
                   cls
clus                  0   1
  TMEM55A MUTATED     3   0
  TMEM55A WILD-TYPE 343  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM55A MUTATED      3    0
  TMEM55A WILD-TYPE  343   29
   clus
vv  TMEM55A MUTATED TMEM55A WILD-TYPE
  0               3               343
  1               0                29
[1] 2 2
[1] FALSE
D557V7, binary
                   cls
clus                  0   1
  TMEM55A MUTATED     2   1
  TMEM55A WILD-TYPE 143 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM55A MUTATED      2    1
  TMEM55A WILD-TYPE  143  247
        clus
vv       TMEM55A MUTATED TMEM55A WILD-TYPE
  FEMALE               2               143
  MALE                 1               247
[1] 2 2
[1] FALSE
D557V8, binary
                   cls
clus                  0   1
  TMEM55A MUTATED     2   0
  TMEM55A WILD-TYPE 290  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM55A MUTATED      2    0
  TMEM55A WILD-TYPE  290   59
     clus
vv    TMEM55A MUTATED TMEM55A WILD-TYPE
  NO                2               290
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TMEM55A MUTATED                                          0
  TMEM55A WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TMEM55A MUTATED                                       0
  TMEM55A WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM55A MUTATED                                                        3
  TMEM55A WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TMEM55A MUTATED                                                   0
  TMEM55A WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM55A MUTATED                                                                   0
  TMEM55A WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TMEM55A MUTATED                                                    0
  TMEM55A WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TMEM55A MUTATED                                                  0
  TMEM55A WILD-TYPE                                               61
D557V9, multiclass
                                                                   clus
vv                                                                  TMEM55A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  TMEM55A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM55A MUTATED     1   0   0   1
  TMEM55A WILD-TYPE 310  14  15  23
D557V10, multiclass
[1] "Remove cluster labels:" "TMEM55A MUTATED"       
clus
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                2               362 
       TCGA-CG-4444        TCGA-CG-4460        TCGA-CG-4475        TCGA-CG-4476 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5727        TCGA-EQ-A4SO        TCGA-F1-6177 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-A8CX        TCGA-HF-7131        TCGA-KB-A93G        TCGA-MX-A663 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4363 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4368        TCGA-BR-4369        TCGA-BR-4370 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4371        TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958        TCGA-BR-7959 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8058        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8297        TCGA-BR-8360        TCGA-BR-8363 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8364        TCGA-BR-8365        TCGA-BR-8366        TCGA-BR-8367 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8368        TCGA-BR-8369        TCGA-BR-8370        TCGA-BR-8371 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8372        TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8382        TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8484 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8485        TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8589        TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8676        TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8680        TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8687        TCGA-BR-8690        TCGA-BR-A44T        TCGA-BR-A44U 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A452        TCGA-BR-A453        TCGA-BR-A4CQ        TCGA-BR-A4CR 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4CS        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J7        TCGA-BR-A4J8 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4PD        TCGA-BR-A4PE        TCGA-BR-A4PF        TCGA-BR-A4QI 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4QL        TCGA-BR-A4QM        TCGA-CD-5800        TCGA-CD-5801 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-5804        TCGA-CD-8524        TCGA-CD-8525        TCGA-CD-8526 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8527        TCGA-CD-8528        TCGA-CD-8529        TCGA-CD-8530 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8531        TCGA-CD-8532        TCGA-CD-8533        TCGA-CD-8534 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8535        TCGA-CD-8536        TCGA-CD-A487        TCGA-CG-4300 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4449 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5717 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8570        TCGA-D7-8572        TCGA-D7-8573        TCGA-D7-8574 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8575        TCGA-D7-8576        TCGA-D7-8578        TCGA-D7-8579 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A4YT        TCGA-D7-A4YU        TCGA-D7-A4YV        TCGA-D7-A4YX 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A4YY        TCGA-D7-A4Z0        TCGA-D7-A6ET        TCGA-D7-A6EV 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A6EX        TCGA-D7-A6EY        TCGA-D7-A6EZ        TCGA-D7-A6F0 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A6F2        TCGA-D7-A747        TCGA-D7-A748        TCGA-D7-A74A 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A74B        TCGA-EQ-5647        TCGA-F1-6874        TCGA-F1-6875 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-F1-A448        TCGA-F1-A72C        TCGA-FP-7735        TCGA-FP-7829 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8211 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-8631        TCGA-FP-A4BE        TCGA-FP-A4BF        TCGA-FP-A9TM 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HF-A5NB        TCGA-HJ-7597        TCGA-HU-8238        TCGA-HU-8243 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8244        TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8608        TCGA-HU-8610        TCGA-HU-A4G2        TCGA-HU-A4G3 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4G6        TCGA-HU-A4G9        TCGA-HU-A4GC        TCGA-HU-A4GD 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GF        TCGA-HU-A4GH        TCGA-HU-A4GJ        TCGA-HU-A4GN 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GP        TCGA-HU-A4GQ        TCGA-HU-A4GT        TCGA-HU-A4GU 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GX        TCGA-HU-A4GY        TCGA-HU-A4H0        TCGA-HU-A4H2 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4H3        TCGA-HU-A4H4        TCGA-HU-A4H5        TCGA-HU-A4H6 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4H8        TCGA-HU-A4HB        TCGA-HU-A4HD        TCGA-IN-7806 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-8462        TCGA-IN-8663        TCGA-IN-A6RI        TCGA-IN-A6RJ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-A6RL        TCGA-IN-A6RN        TCGA-IN-A6RO        TCGA-IN-A6RP 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-A6RR        TCGA-IN-A6RS        TCGA-IN-A7NR        TCGA-IN-A7NT 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-A7NU        TCGA-IN-AB1V        TCGA-IN-AB1X        TCGA-IP-7968 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-KB-A6F5        TCGA-KB-A6F7        TCGA-KB-A93J        TCGA-MX-A5UG 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-MX-A5UJ        TCGA-R5-A7ZI        TCGA-RD-A7BS        TCGA-RD-A7BT 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-RD-A7BW        TCGA-RD-A7C1        TCGA-RD-A8MV        TCGA-RD-A8MW 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-RD-A8N0        TCGA-RD-A8N1        TCGA-RD-A8N2        TCGA-RD-A8N4 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-RD-A8N5        TCGA-RD-A8N6        TCGA-RD-A8N9        TCGA-SW-A7EA 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-SW-A7EB        TCGA-VQ-A8DL        TCGA-VQ-A8DT        TCGA-VQ-A8DU 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A8DV        TCGA-VQ-A8DZ        TCGA-VQ-A8E2        TCGA-VQ-A8E7 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A8P2        TCGA-VQ-A8P3        TCGA-VQ-A8PE        TCGA-VQ-A8PK 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A8PM        TCGA-VQ-A8PQ        TCGA-VQ-A91Q        TCGA-VQ-A91U 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A91V        TCGA-VQ-A92D        TCGA-VQ-A94T        TCGA-VQ-AA64 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-AA68        TCGA-VQ-AA69        TCGA-VQ-AA6A        TCGA-VQ-AA6B 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-AA6F        TCGA-VQ-AA6G        TCGA-VQ-AA6I        TCGA-VQ-AA6J 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-AA6K        TCGA-ZA-A8F6 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
D557V11, continuous
[1] "Remove cluster labels:" "TMEM55A MUTATED"       
clus
  TMEM55A MUTATED TMEM55A WILD-TYPE 
                2               341 
       TCGA-CG-4444        TCGA-CG-4460        TCGA-CG-4475        TCGA-CG-4476 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5727        TCGA-EQ-A4SO        TCGA-F1-6177        TCGA-FP-A8CX 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HF-7131        TCGA-KB-A93G        TCGA-MX-A663        TCGA-B7-5816 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-B7-A5TI        TCGA-BR-4183        TCGA-BR-4184        TCGA-BR-4188 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4191        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4361 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-4368        TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958        TCGA-BR-7959 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8058        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8297        TCGA-BR-8360        TCGA-BR-8363 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8364        TCGA-BR-8365        TCGA-BR-8366        TCGA-BR-8367 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8368        TCGA-BR-8369        TCGA-BR-8370        TCGA-BR-8371 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8372        TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8382        TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8484 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8485        TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8589        TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8676        TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8680        TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-8687        TCGA-BR-8690        TCGA-BR-A44T        TCGA-BR-A44U 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A452        TCGA-BR-A453        TCGA-BR-A4CQ        TCGA-BR-A4CR 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4CS        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4PD 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4PE        TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-BR-A4QM        TCGA-CD-5804        TCGA-CD-8525        TCGA-CD-8526 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CD-8531        TCGA-CD-8535        TCGA-CD-A487        TCGA-CG-4301 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4436        TCGA-CG-4437 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4462 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4474 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5728 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-D7-8570        TCGA-D7-8572 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8573        TCGA-D7-8574        TCGA-D7-8575        TCGA-D7-8576 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-8578        TCGA-D7-8579        TCGA-D7-A4YT        TCGA-D7-A4YU 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A4YV        TCGA-D7-A4YX        TCGA-D7-A4YY        TCGA-D7-A4Z0 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A6ET        TCGA-D7-A6EV        TCGA-D7-A6EX        TCGA-D7-A6EY 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A6EZ        TCGA-D7-A6F0        TCGA-D7-A6F2        TCGA-D7-A747 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-D7-A748        TCGA-D7-A74A        TCGA-D7-A74B        TCGA-EQ-5647 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6874        TCGA-F1-6875        TCGA-F1-A448 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-F1-A72C        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8210 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-8211        TCGA-FP-8631        TCGA-FP-A4BE        TCGA-FP-A4BF 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-FP-A9TM        TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HF-7136        TCGA-HF-A5NB        TCGA-HJ-7597        TCGA-HU-8238 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8243        TCGA-HU-8244        TCGA-HU-8249        TCGA-HU-8602 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-8604        TCGA-HU-8608        TCGA-HU-8610        TCGA-HU-A4G2 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4G3        TCGA-HU-A4G6        TCGA-HU-A4G8        TCGA-HU-A4G9 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GC        TCGA-HU-A4GD        TCGA-HU-A4GF        TCGA-HU-A4GH 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GJ        TCGA-HU-A4GN        TCGA-HU-A4GP        TCGA-HU-A4GQ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4GT        TCGA-HU-A4GU        TCGA-HU-A4GX        TCGA-HU-A4GY 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4H0        TCGA-HU-A4H2        TCGA-HU-A4H3        TCGA-HU-A4H4 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4H5        TCGA-HU-A4H6        TCGA-HU-A4H8        TCGA-HU-A4HB 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-HU-A4HD        TCGA-IN-7806        TCGA-IN-7808        TCGA-IN-8462 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-8663        TCGA-IN-A6RI        TCGA-IN-A6RJ        TCGA-IN-A6RL 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-A6RN        TCGA-IN-A6RO        TCGA-IN-A6RP        TCGA-IN-A6RR 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-A6RS        TCGA-IN-A7NR        TCGA-IN-A7NT        TCGA-IN-A7NU 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-IN-AB1V        TCGA-IN-AB1X        TCGA-IP-7968        TCGA-KB-A6F5 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-KB-A6F7        TCGA-KB-A93J        TCGA-MX-A5UG        TCGA-MX-A5UJ 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-R5-A7ZI        TCGA-RD-A7BS        TCGA-RD-A7BT        TCGA-RD-A7BW 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-RD-A7C1        TCGA-RD-A8MV        TCGA-RD-A8MW        TCGA-RD-A8N0 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-RD-A8N1        TCGA-RD-A8N2        TCGA-RD-A8N4        TCGA-RD-A8N5 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-RD-A8N6        TCGA-RD-A8N9        TCGA-SW-A7EA        TCGA-SW-A7EB 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A8DL        TCGA-VQ-A8DT        TCGA-VQ-A8DU        TCGA-VQ-A8DV 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A8DZ        TCGA-VQ-A8E2        TCGA-VQ-A8E7        TCGA-VQ-A8P2 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A8P3        TCGA-VQ-A8PE        TCGA-VQ-A8PK        TCGA-VQ-A8PM 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A8PQ        TCGA-VQ-A91Q        TCGA-VQ-A91U        TCGA-VQ-A91V 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-A92D        TCGA-VQ-A94T        TCGA-VQ-AA64        TCGA-VQ-AA68 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-AA69        TCGA-VQ-AA6A        TCGA-VQ-AA6B        TCGA-VQ-AA6F 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-VQ-AA6G        TCGA-VQ-AA6I        TCGA-VQ-AA6J        TCGA-VQ-AA6K 
"TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" "TMEM55A WILD-TYPE" 
       TCGA-ZA-A8F6 
"TMEM55A WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM55A MUTATED       1                         0
  TMEM55A WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM55A MUTATED                                           0     2
  TMEM55A WILD-TYPE                                         1   241
D557V12, multiclass
                                           clus
vv                                          TMEM55A MUTATED TMEM55A WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D557V13, binary
                   cls
clus                  0   1
  TMEM55A MUTATED     0   3
  TMEM55A WILD-TYPE   4 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM55A MUTATED      0    3
  TMEM55A WILD-TYPE    4  307
                        clus
vv                       TMEM55A MUTATED TMEM55A WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               3               307
[1] 2 2
[1] FALSE

Clustering(558) Variable = SPATA5L1 MUTATION ANALYSIS
D558V1, survival
                    sevent
clus2                  0   1
  SPATA5L1 MUTATED     5   1
  SPATA5L1 WILD-TYPE 225 138
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
                 6                363 
  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE 
                 1                138 
$`SPATA5L1 MUTATED`
TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8680 TCGA-CG-5728 TCGA-HU-A4GQ TCGA-HU-A4H0 
       44.94        29.59        31.96        65.10         0.10         2.10 

$`SPATA5L1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
        8.98         6.51         6.58        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-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 

  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             14.170 
[1] "0.1 - 65.1 (30.8)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3"  
D558V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPATA5L1 MUTATED         0        0        1        0         1         1
  SPATA5L1 WILD-TYPE       2       15       39       30        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPATA5L1 MUTATED           0          0          0          2        1
  SPATA5L1 WILD-TYPE         3         70         53         30       37
D558V3, multiclass
            clus
vv           SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                0                 53
  STAGE IIIC                2                 30
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SPATA5L1 MUTATED     0   1   1   4
  SPATA5L1 WILD-TYPE  22  91 172  93
D558V4, multiclass
    clus
vv   SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  T1                0                 22
  T2                1                 91
  T3                1                172
  T4                4                 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
  SPATA5L1 MUTATED     3   0   2   1
  SPATA5L1 WILD-TYPE 115 104  75  76
D558V5, multiclass
    clus
vv   SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  N0                3                115
  N1                0                104
  N2                2                 75
  N3                1                 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"
D558V6, binary
                    cls
clus                   0   1
  SPATA5L1 MUTATED     5   1
  SPATA5L1 WILD-TYPE 341  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SPATA5L1 MUTATED      5    1
  SPATA5L1 WILD-TYPE  341   28
   clus
vv  SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  0                5                341
  1                1                 28
[1] 2 2
[1] FALSE
D558V7, binary
                    cls
clus                   0   1
  SPATA5L1 MUTATED     3   3
  SPATA5L1 WILD-TYPE 142 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SPATA5L1 MUTATED      3    3
  SPATA5L1 WILD-TYPE  142  245
        clus
vv       SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  FEMALE                3                142
  MALE                  3                245
[1] 2 2
[1] FALSE
D558V8, binary
                    cls
clus                   0   1
  SPATA5L1 MUTATED     5   0
  SPATA5L1 WILD-TYPE 287  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SPATA5L1 MUTATED      5    0
  SPATA5L1 WILD-TYPE  287   59
     clus
vv    SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  NO                 5                287
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SPATA5L1 MUTATED                                          0
  SPATA5L1 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SPATA5L1 MUTATED                                       1
  SPATA5L1 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPATA5L1 MUTATED                                                        2
  SPATA5L1 WILD-TYPE                                                    156
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SPATA5L1 MUTATED                                                   0
  SPATA5L1 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPATA5L1 MUTATED                                                                   1
  SPATA5L1 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SPATA5L1 MUTATED                                                    0
  SPATA5L1 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SPATA5L1 MUTATED                                                  2
  SPATA5L1 WILD-TYPE                                               59
D558V9, multiclass
                                                                   clus
vv                                                                  SPATA5L1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  SPATA5L1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SPATA5L1 MUTATED     6   0   0   0
  SPATA5L1 WILD-TYPE 305  14  15  24
D558V10, multiclass
    clus
vv   SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  R0                6                305
  R1                0                 14
  R2                0                 15
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D558V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SPATA5L1 MUTATED       3                         0
  SPATA5L1 WILD-TYPE    84                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPATA5L1 MUTATED                                           0     2
  SPATA5L1 WILD-TYPE                                         1   241
D558V12, multiclass
                                           clus
vv                                          SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    2                241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D558V13, binary
                    cls
clus                   0   1
  SPATA5L1 MUTATED     0   5
  SPATA5L1 WILD-TYPE   4 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SPATA5L1 MUTATED      0    5
  SPATA5L1 WILD-TYPE    4  305
                        clus
vv                       SPATA5L1 MUTATED SPATA5L1 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                5                305
[1] 2 2
[1] FALSE

Clustering(559) Variable = CDC42EP1 MUTATION ANALYSIS
D559V1, survival
                    sevent
clus2                  0   1
  CDC42EP1 MUTATED     3   1
  CDC42EP1 WILD-TYPE 227 138
  CDC42EP1 MUTATED CDC42EP1 WILD-TYPE 
                 4                365 
  CDC42EP1 MUTATED CDC42EP1 WILD-TYPE 
                 1                138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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             14.270 
[1] "5.9 - 31.1 (18.5)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.6"
D559V2, 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       2       15       40       30        37        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC42EP1 MUTATED           0          0          0          2        0
  CDC42EP1 WILD-TYPE         3         70         53         30       38
D559V3, multiclass
            clus
vv           CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 0                 37
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                0                 53
  STAGE IIIC                2                 30
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CDC42EP1 MUTATED     0   0   2   2
  CDC42EP1 WILD-TYPE  22  92 171  95
D559V4, multiclass
    clus
vv   CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  T1                0                 22
  T2                0                 92
  T3                2                171
  T4                2                 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
  CDC42EP1 MUTATED     0   2   1   1
  CDC42EP1 WILD-TYPE 118 102  76  76
D559V5, multiclass
    clus
vv   CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  N0                0                118
  N1                2                102
  N2                1                 76
  N3                1                 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"
D559V6, binary
                    cls
clus                   0   1
  CDC42EP1 MUTATED     4   0
  CDC42EP1 WILD-TYPE 342  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42EP1 MUTATED      4    0
  CDC42EP1 WILD-TYPE  342   29
   clus
vv  CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  0                4                342
  1                0                 29
[1] 2 2
[1] FALSE
D559V7, binary
                    cls
clus                   0   1
  CDC42EP1 MUTATED     3   1
  CDC42EP1 WILD-TYPE 142 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42EP1 MUTATED      3    1
  CDC42EP1 WILD-TYPE  142  247
        clus
vv       CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  FEMALE                3                142
  MALE                  1                247
[1] 2 2
[1] FALSE
D559V8, binary
                    cls
clus                   0   1
  CDC42EP1 MUTATED     3   1
  CDC42EP1 WILD-TYPE 289  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42EP1 MUTATED      3    1
  CDC42EP1 WILD-TYPE  289   58
     clus
vv    CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  NO                 3                289
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CDC42EP1 MUTATED                                          0
  CDC42EP1 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CDC42EP1 MUTATED                                       1
  CDC42EP1 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDC42EP1 MUTATED                                                        1
  CDC42EP1 WILD-TYPE                                                    157
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CDC42EP1 MUTATED                                                   1
  CDC42EP1 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDC42EP1 MUTATED                                                                   0
  CDC42EP1 WILD-TYPE                                                                68
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CDC42EP1 MUTATED                                                    0
  CDC42EP1 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CDC42EP1 MUTATED                                                  1
  CDC42EP1 WILD-TYPE                                               60
D559V9, multiclass
                                                                   clus
vv                                                                  CDC42EP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  CDC42EP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  CDC42EP1 MUTATED     3   1   0   0
  CDC42EP1 WILD-TYPE 308  13  15  24
D559V10, multiclass
    clus
vv   CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  R0                3                308
  R1                1                 13
  R2                0                 15
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  CDC42EP1 MUTATED       1                         0
  CDC42EP1 WILD-TYPE    86                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDC42EP1 MUTATED                                           0     2
  CDC42EP1 WILD-TYPE                                         1   241
D559V12, multiclass
                                           clus
vv                                          CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    2                241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V13, binary
                    cls
clus                   0   1
  CDC42EP1 MUTATED     0   3
  CDC42EP1 WILD-TYPE   4 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42EP1 MUTATED      0    3
  CDC42EP1 WILD-TYPE    4  307
                        clus
vv                       CDC42EP1 MUTATED CDC42EP1 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                3                307
[1] 2 2
[1] FALSE

Clustering(560) Variable = SPATA20 MUTATION ANALYSIS
D560V1, survival
                   sevent
clus2                 0   1
  SPATA20 MUTATED    10   7
  SPATA20 WILD-TYPE 220 132
  SPATA20 MUTATED SPATA20 WILD-TYPE 
               17               352 
  SPATA20 MUTATED SPATA20 WILD-TYPE 
                7               132 
$`SPATA20 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8284 TCGA-BR-8368 
        6.61        34.68        35.84        14.43         8.05         4.31 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-A4MG TCGA-CG-4306 TCGA-D7-8572 TCGA-D7-8574 
       12.53        12.39         6.58         1.02        16.80        17.19 
TCGA-D7-A4YY TCGA-D7-A74A TCGA-FP-8209 TCGA-HU-A4GQ TCGA-HU-A4H3 
       13.78        19.96        59.54         0.10        29.00 

$`SPATA20 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-8527 TCGA-CD-8528 
       12.10        12.39        12.76        12.59         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-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-D7-8573 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-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-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-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       17.06         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 

  SPATA20 MUTATED SPATA20 WILD-TYPE 
              0.1               0.0 
  SPATA20 MUTATED SPATA20 WILD-TYPE 
            59.54            122.30 
  SPATA20 MUTATED SPATA20 WILD-TYPE 
            13.78             14.37 
[1] "0.1 - 59.5 (13.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D560V2, 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       2       15       37       29        35        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPATA20 MUTATED           2          3          1          3        1
  SPATA20 WILD-TYPE         1         67         52         29       37
D560V3, multiclass
            clus
vv           SPATA20 MUTATED SPATA20 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 3                37
  STAGE II                 1                29
  STAGE IIA                2                35
  STAGE IIB                1                51
  STAGE III                2                 1
  STAGE IIIA               3                67
  STAGE IIIB               1                52
  STAGE IIIC               3                29
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SPATA20 MUTATED     0   6   7   4
  SPATA20 WILD-TYPE  22  86 166  93
D560V4, multiclass
    clus
vv   SPATA20 MUTATED SPATA20 WILD-TYPE
  T1               0                22
  T2               6                86
  T3               7               166
  T4               4                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
  SPATA20 MUTATED     6   3   4   4
  SPATA20 WILD-TYPE 112 101  73  73
D560V5, multiclass
    clus
vv   SPATA20 MUTATED SPATA20 WILD-TYPE
  N0               6               112
  N1               3               101
  N2               4                73
  N3               4                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"
D560V6, binary
                   cls
clus                  0   1
  SPATA20 MUTATED    16   1
  SPATA20 WILD-TYPE 330  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA20 MUTATED     16    1
  SPATA20 WILD-TYPE  330   28
   clus
vv  SPATA20 MUTATED SPATA20 WILD-TYPE
  0              16               330
  1               1                28
[1] 2 2
[1] FALSE
D560V7, binary
                   cls
clus                  0   1
  SPATA20 MUTATED     8   9
  SPATA20 WILD-TYPE 137 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA20 MUTATED      8    9
  SPATA20 WILD-TYPE  137  239
        clus
vv       SPATA20 MUTATED SPATA20 WILD-TYPE
  FEMALE               8               137
  MALE                 9               239
[1] 2 2
[1] FALSE
D560V8, binary
                   cls
clus                  0   1
  SPATA20 MUTATED    12   3
  SPATA20 WILD-TYPE 280  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA20 MUTATED     12    3
  SPATA20 WILD-TYPE  280   56
     clus
vv    SPATA20 MUTATED SPATA20 WILD-TYPE
  NO               12               280
  YES               3                56
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SPATA20 MUTATED                                          0
  SPATA20 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SPATA20 MUTATED                                       4
  SPATA20 WILD-TYPE                                    66
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPATA20 MUTATED                                                        8
  SPATA20 WILD-TYPE                                                    150
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SPATA20 MUTATED                                                   0
  SPATA20 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPATA20 MUTATED                                                                   3
  SPATA20 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SPATA20 MUTATED                                                    0
  SPATA20 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SPATA20 MUTATED                                                  2
  SPATA20 WILD-TYPE                                               59
D560V9, multiclass
                                                                   clus
vv                                                                  SPATA20 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  SPATA20 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SPATA20 MUTATED    14   0   1   1
  SPATA20 WILD-TYPE 297  14  14  23
D560V10, multiclass
    clus
vv   SPATA20 MUTATED SPATA20 WILD-TYPE
  R0              14               297
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D560V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SPATA20 MUTATED       5                         0
  SPATA20 WILD-TYPE    82                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPATA20 MUTATED                                           0    11
  SPATA20 WILD-TYPE                                         1   232
D560V12, multiclass
                                           clus
vv                                          SPATA20 MUTATED SPATA20 WILD-TYPE
  ASIAN                                                   5                82
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D560V13, binary
                   cls
clus                  0   1
  SPATA20 MUTATED     0  16
  SPATA20 WILD-TYPE   4 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA20 MUTATED      0   16
  SPATA20 WILD-TYPE    4  294
                        clus
vv                       SPATA20 MUTATED SPATA20 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              16               294
[1] 2 2
[1] FALSE

Clustering(561) Variable = KIN MUTATION ANALYSIS
D561V1, survival
               sevent
clus2             0   1
  KIN MUTATED     6   1
  KIN WILD-TYPE 224 138
  KIN MUTATED KIN WILD-TYPE 
            7           362 
  KIN MUTATED KIN WILD-TYPE 
            1           138 
$`KIN MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-8680 TCGA-D7-A4YV 
       34.68        44.94        32.25         1.12        31.96         5.92 
TCGA-HF-7132 
       77.29 

$`KIN WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  KIN MUTATED KIN WILD-TYPE 
         1.12          0.00 
  KIN MUTATED KIN WILD-TYPE 
        77.29        122.30 
  KIN MUTATED KIN WILD-TYPE 
        32.25         14.12 
[1] "1.1 - 77.3 (32.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "4.1"
D561V2, 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       2       15       40       29        34        50
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIN MUTATED           0          0          0          0        1
  KIN WILD-TYPE         3         70         53         32       37
D561V3, multiclass
            clus
vv           KIN MUTATED KIN WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             0            40
  STAGE II             1            29
  STAGE IIA            3            34
  STAGE IIB            2            50
  STAGE III            0             3
  STAGE IIIA           0            70
  STAGE IIIB           0            53
  STAGE IIIC           0            32
  STAGE IV             1            37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  KIN MUTATED     0   1   4   2
  KIN WILD-TYPE  22  91 169  95
D561V4, multiclass
    clus
vv   KIN MUTATED KIN WILD-TYPE
  T1           0            22
  T2           1            91
  T3           4           169
  T4           2            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
  KIN MUTATED     4   2   1   0
  KIN WILD-TYPE 114 102  76  77
D561V5, multiclass
    clus
vv   KIN MUTATED KIN WILD-TYPE
  N0           4           114
  N1           2           102
  N2           1            76
  N3           0            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"
D561V6, binary
               cls
clus              0   1
  KIN MUTATED     6   1
  KIN WILD-TYPE 340  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIN MUTATED      6    1
  KIN WILD-TYPE  340   28
   clus
vv  KIN MUTATED KIN WILD-TYPE
  0           6           340
  1           1            28
[1] 2 2
[1] FALSE
D561V7, binary
               cls
clus              0   1
  KIN MUTATED     5   2
  KIN WILD-TYPE 140 246
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIN MUTATED      5    2
  KIN WILD-TYPE  140  246
        clus
vv       KIN MUTATED KIN WILD-TYPE
  FEMALE           5           140
  MALE             2           246
[1] 2 2
[1] FALSE
D561V8, binary
               cls
clus              0   1
  KIN MUTATED     6   1
  KIN WILD-TYPE 286  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIN MUTATED      6    1
  KIN WILD-TYPE  286   58
     clus
vv    KIN MUTATED KIN WILD-TYPE
  NO            6           286
  YES           1            58
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIN MUTATED                                          0
  KIN WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIN MUTATED                                       0
  KIN WILD-TYPE                                    70
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIN MUTATED                                                        4
  KIN WILD-TYPE                                                    154
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIN MUTATED                                                   1
  KIN WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIN MUTATED                                                                   0
  KIN WILD-TYPE                                                                68
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIN MUTATED                                                    0
  KIN WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIN MUTATED                                                  2
  KIN WILD-TYPE                                               59
D561V9, multiclass
                                                                   clus
vv                                                                  KIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            2
                                                                   clus
vv                                                                  KIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  KIN MUTATED     7   0   0   0
  KIN WILD-TYPE 304  14  15  24
D561V10, multiclass
    clus
vv   KIN MUTATED KIN WILD-TYPE
  R0           7           304
  R1           0            14
  R2           0            15
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D561V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  KIN MUTATED       1                         0
  KIN WILD-TYPE    86                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIN MUTATED                                           0     5
  KIN WILD-TYPE                                         1   238
D561V12, multiclass
                                           clus
vv                                          KIN MUTATED KIN WILD-TYPE
  ASIAN                                               1            86
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               5           238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D561V13, binary
               cls
clus              0   1
  KIN MUTATED     0   6
  KIN WILD-TYPE   4 304
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIN MUTATED      0    6
  KIN WILD-TYPE    4  304
                        clus
vv                       KIN MUTATED KIN WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           6           304
[1] 2 2
[1] FALSE

Clustering(562) Variable = TMEM87B MUTATION ANALYSIS
D562V1, survival
                   sevent
clus2                 0   1
  TMEM87B MUTATED     4   1
  TMEM87B WILD-TYPE 226 138
  TMEM87B MUTATED TMEM87B WILD-TYPE 
                5               364 
  TMEM87B MUTATED TMEM87B WILD-TYPE 
                1               138 
$`TMEM87B MUTATED`
TCGA-BR-4184 TCGA-BR-8368 TCGA-BR-8372 TCGA-CG-5721 TCGA-VQ-A8P2 
        6.97         4.31        31.27         6.02        38.14 

$`TMEM87B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  TMEM87B MUTATED TMEM87B WILD-TYPE 
             4.31              0.00 
  TMEM87B MUTATED TMEM87B WILD-TYPE 
            38.14            122.30 
  TMEM87B MUTATED TMEM87B WILD-TYPE 
             6.97             14.35 
[1] "4.3 - 38.1 (7.0)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "1.7"
D562V2, 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       2       15       39       30        37        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM87B MUTATED           0          2          0          1        1
  TMEM87B WILD-TYPE         3         68         53         31       37
D562V3, multiclass
            clus
vv           TMEM87B MUTATED TMEM87B WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                0                37
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM87B MUTATED     0   1   1   3
  TMEM87B WILD-TYPE  22  91 172  94
D562V4, multiclass
    clus
vv   TMEM87B MUTATED TMEM87B WILD-TYPE
  T1               0                22
  T2               1                91
  T3               1               172
  T4               3                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
  TMEM87B MUTATED     1   3   0   1
  TMEM87B WILD-TYPE 117 101  77  76
D562V5, multiclass
    clus
vv   TMEM87B MUTATED TMEM87B WILD-TYPE
  N0               1               117
  N1               3               101
  N2               0                77
  N3               1                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"
D562V6, binary
                   cls
clus                  0   1
  TMEM87B MUTATED     4   0
  TMEM87B WILD-TYPE 342  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM87B MUTATED      4    0
  TMEM87B WILD-TYPE  342   29
   clus
vv  TMEM87B MUTATED TMEM87B WILD-TYPE
  0               4               342
  1               0                29
[1] 2 2
[1] FALSE
D562V7, binary
                   cls
clus                  0   1
  TMEM87B MUTATED     1   4
  TMEM87B WILD-TYPE 144 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM87B MUTATED      1    4
  TMEM87B WILD-TYPE  144  244
        clus
vv       TMEM87B MUTATED TMEM87B WILD-TYPE
  FEMALE               1               144
  MALE                 4               244
[1] 2 2
[1] FALSE
D562V8, binary
                   cls
clus                  0   1
  TMEM87B MUTATED     4   1
  TMEM87B WILD-TYPE 288  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM87B MUTATED      4    1
  TMEM87B WILD-TYPE  288   58
     clus
vv    TMEM87B MUTATED TMEM87B WILD-TYPE
  NO                4               288
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TMEM87B MUTATED                                          0
  TMEM87B WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TMEM87B MUTATED                                       0
  TMEM87B WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM87B MUTATED                                                        3
  TMEM87B WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TMEM87B MUTATED                                                   1
  TMEM87B WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM87B MUTATED                                                                   1
  TMEM87B WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TMEM87B MUTATED                                                    0
  TMEM87B WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TMEM87B MUTATED                                                  0
  TMEM87B WILD-TYPE                                               61
D562V9, multiclass
                                                                   clus
vv                                                                  TMEM87B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  TMEM87B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM87B MUTATED     4   0   0   1
  TMEM87B WILD-TYPE 307  14  15  23
D562V10, multiclass
    clus
vv   TMEM87B MUTATED TMEM87B WILD-TYPE
  R0               4               307
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D562V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM87B MUTATED       0                         0
  TMEM87B WILD-TYPE    87                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM87B MUTATED                                           0     4
  TMEM87B WILD-TYPE                                         1   239
D562V12, multiclass
                                           clus
vv                                          TMEM87B MUTATED TMEM87B WILD-TYPE
  ASIAN                                                   0                87
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D562V13, binary
                   cls
clus                  0   1
  TMEM87B MUTATED     0   3
  TMEM87B WILD-TYPE   4 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM87B MUTATED      0    3
  TMEM87B WILD-TYPE    4  307
                        clus
vv                       TMEM87B MUTATED TMEM87B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               3               307
[1] 2 2
[1] FALSE

Clustering(563) Variable = SP100 MUTATION ANALYSIS
D563V1, survival
                 sevent
clus2               0   1
  SP100 MUTATED    11   7
  SP100 WILD-TYPE 219 132
  SP100 MUTATED SP100 WILD-TYPE 
             18             351 
  SP100 MUTATED SP100 WILD-TYPE 
              7             132 
$`SP100 MUTATED`
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-6456 TCGA-BR-8361 TCGA-BR-8382 
       26.70        11.70        19.56        17.29        31.10        25.05 
TCGA-CD-5813 TCGA-CD-A4MG TCGA-CG-4466 TCGA-CG-5721 TCGA-CG-5728 TCGA-HU-A4G9 
       12.39         6.58        18.97         6.02        65.10        24.20 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-IN-A6RL TCGA-VQ-A8DL TCGA-VQ-A8DU 
        6.58        20.25        14.07        13.35         0.92         5.46 

$`SP100 WILD-TYPE`
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-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
       20.15         9.86        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-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-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-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-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-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-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-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-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-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         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-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-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-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 

  SP100 MUTATED SP100 WILD-TYPE 
           0.92            0.00 
  SP100 MUTATED SP100 WILD-TYPE 
           65.1           122.3 
  SP100 MUTATED SP100 WILD-TYPE 
          15.68           14.27 
[1] "0.9 - 65.1 (15.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D563V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SP100 MUTATED         0        1        4        1         2         3
  SP100 WILD-TYPE       2       14       36       29        35        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SP100 MUTATED           0          2          0          4        1
  SP100 WILD-TYPE         3         68         53         28       37
D563V3, multiclass
            clus
vv           SP100 MUTATED SP100 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               4              36
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             4              28
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SP100 MUTATED     2   4   6   6
  SP100 WILD-TYPE  20  88 167  91
D563V4, multiclass
    clus
vv   SP100 MUTATED SP100 WILD-TYPE
  T1             2              20
  T2             4              88
  T3             6             167
  T4             6              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
  SP100 MUTATED     8   5   3   2
  SP100 WILD-TYPE 110  99  74  75
D563V5, multiclass
    clus
vv   SP100 MUTATED SP100 WILD-TYPE
  N0             8             110
  N1             5              99
  N2             3              74
  N3             2              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"
D563V6, binary
                 cls
clus                0   1
  SP100 MUTATED    18   0
  SP100 WILD-TYPE 328  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP100 MUTATED     18    0
  SP100 WILD-TYPE  328   29
   clus
vv  SP100 MUTATED SP100 WILD-TYPE
  0            18             328
  1             0              29
[1] 2 2
[1] FALSE
D563V7, binary
                 cls
clus                0   1
  SP100 MUTATED     9   9
  SP100 WILD-TYPE 136 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP100 MUTATED      9    9
  SP100 WILD-TYPE  136  239
        clus
vv       SP100 MUTATED SP100 WILD-TYPE
  FEMALE             9             136
  MALE               9             239
[1] 2 2
[1] FALSE
D563V8, binary
                 cls
clus                0   1
  SP100 MUTATED    17   0
  SP100 WILD-TYPE 275  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP100 MUTATED     17    0
  SP100 WILD-TYPE  275   59
     clus
vv    SP100 MUTATED SP100 WILD-TYPE
  NO             17             275
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SP100 MUTATED                                          0
  SP100 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SP100 MUTATED                                       6
  SP100 WILD-TYPE                                    64
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SP100 MUTATED                                                        4
  SP100 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SP100 MUTATED                                                   1
  SP100 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SP100 MUTATED                                                                   3
  SP100 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SP100 MUTATED                                                    0
  SP100 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SP100 MUTATED                                                  4
  SP100 WILD-TYPE                                               57
D563V9, multiclass
                                                                   clus
vv                                                                  SP100 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  SP100 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SP100 MUTATED    15   0   0   0
  SP100 WILD-TYPE 296  14  15  24
D563V10, multiclass
    clus
vv   SP100 MUTATED SP100 WILD-TYPE
  R0            15             296
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SP100 MUTATED       6                         0
  SP100 WILD-TYPE    81                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SP100 MUTATED                                           0     9
  SP100 WILD-TYPE                                         1   234
D563V12, multiclass
                                           clus
vv                                          SP100 MUTATED SP100 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V13, binary
                 cls
clus                0   1
  SP100 MUTATED     0  13
  SP100 WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP100 MUTATED      0   13
  SP100 WILD-TYPE    4  297
                        clus
vv                       SP100 MUTATED SP100 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(564) Variable = SOAT1 MUTATION ANALYSIS
D564V1, survival
                 sevent
clus2               0   1
  SOAT1 MUTATED     7   3
  SOAT1 WILD-TYPE 223 136
  SOAT1 MUTATED SOAT1 WILD-TYPE 
             10             359 
  SOAT1 MUTATED SOAT1 WILD-TYPE 
              3             136 
$`SOAT1 MUTATED`
TCGA-CG-4460 TCGA-BR-7703 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4465 
       21.99        36.16        27.12        28.14        16.14         9.01 
TCGA-HF-7132 TCGA-R5-A7ZI TCGA-SW-A7EA TCGA-VQ-A8P2 
       77.29        74.53        19.04        38.14 

$`SOAT1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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 

  SOAT1 MUTATED SOAT1 WILD-TYPE 
           9.01            0.00 
  SOAT1 MUTATED SOAT1 WILD-TYPE 
          77.29          122.30 
  SOAT1 MUTATED SOAT1 WILD-TYPE 
          27.63           14.04 
[1] "9.0 - 77.3 (27.6)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "2.2"
D564V2, 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       2       14       39       29        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SOAT1 MUTATED           0          1          2          1        3
  SOAT1 WILD-TYPE         3         69         51         31       35
D564V3, multiclass
            clus
vv           SOAT1 MUTATED SOAT1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SOAT1 MUTATED     1   2   1   6
  SOAT1 WILD-TYPE  21  90 172  91
D564V4, multiclass
    clus
vv   SOAT1 MUTATED SOAT1 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             1             172
  T4             6              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
  SOAT1 MUTATED     2   5   0   3
  SOAT1 WILD-TYPE 116  99  77  74
D564V5, multiclass
    clus
vv   SOAT1 MUTATED SOAT1 WILD-TYPE
  N0             2             116
  N1             5              99
  N2             0              77
  N3             3              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"
D564V6, binary
                 cls
clus                0   1
  SOAT1 MUTATED     7   3
  SOAT1 WILD-TYPE 339  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOAT1 MUTATED      7    3
  SOAT1 WILD-TYPE  339   26
   clus
vv  SOAT1 MUTATED SOAT1 WILD-TYPE
  0             7             339
  1             3              26
[1] 2 2
[1] FALSE
D564V7, binary
                 cls
clus                0   1
  SOAT1 MUTATED     5   5
  SOAT1 WILD-TYPE 140 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOAT1 MUTATED      5    5
  SOAT1 WILD-TYPE  140  243
        clus
vv       SOAT1 MUTATED SOAT1 WILD-TYPE
  FEMALE             5             140
  MALE               5             243
[1] 2 2
[1] FALSE
D564V8, binary
                 cls
clus                0   1
  SOAT1 MUTATED     7   2
  SOAT1 WILD-TYPE 285  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOAT1 MUTATED      7    2
  SOAT1 WILD-TYPE  285   57
     clus
vv    SOAT1 MUTATED SOAT1 WILD-TYPE
  NO              7             285
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SOAT1 MUTATED                                          0
  SOAT1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SOAT1 MUTATED                                       3
  SOAT1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SOAT1 MUTATED                                                        3
  SOAT1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SOAT1 MUTATED                                                   2
  SOAT1 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SOAT1 MUTATED                                                                   1
  SOAT1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SOAT1 MUTATED                                                    1
  SOAT1 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SOAT1 MUTATED                                                  0
  SOAT1 WILD-TYPE                                               61
D564V9, multiclass
                                                                   clus
vv                                                                  SOAT1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  SOAT1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SOAT1 MUTATED     8   0   2   0
  SOAT1 WILD-TYPE 303  14  13  24
D564V10, multiclass
    clus
vv   SOAT1 MUTATED SOAT1 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             2              13
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D564V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SOAT1 MUTATED       0                         0
  SOAT1 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SOAT1 MUTATED                                           0     7
  SOAT1 WILD-TYPE                                         1   236
D564V12, multiclass
                                           clus
vv                                          SOAT1 MUTATED SOAT1 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D564V13, binary
                 cls
clus                0   1
  SOAT1 MUTATED     1   5
  SOAT1 WILD-TYPE   3 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SOAT1 MUTATED      1    5
  SOAT1 WILD-TYPE    3  305
                        clus
vv                       SOAT1 MUTATED SOAT1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(565) Variable = IL7R MUTATION ANALYSIS
D565V1, survival
                sevent
clus2              0   1
  IL7R MUTATED     8   5
  IL7R WILD-TYPE 222 134
  IL7R MUTATED IL7R WILD-TYPE 
            13            356 
  IL7R MUTATED IL7R WILD-TYPE 
             5            134 
$`IL7R MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-8591 TCGA-BR-8680 
       30.90        34.68         9.21        35.24        28.14        31.96 
TCGA-BR-A4J4 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5733 TCGA-HU-A4GH 
        0.53        16.14         6.58         9.01        21.07        11.77 
TCGA-VQ-A8P2 
       38.14 

$`IL7R WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17        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-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-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-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-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 

  IL7R MUTATED IL7R WILD-TYPE 
          0.53           0.00 
  IL7R MUTATED IL7R WILD-TYPE 
         38.14         122.30 
  IL7R MUTATED IL7R WILD-TYPE 
         21.07          14.12 
[1] "0.5 - 38.1 (21.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D565V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IL7R MUTATED         0        1        0        2         2         0
  IL7R WILD-TYPE       2       14       40       28        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL7R MUTATED           0          2          2          1        2
  IL7R WILD-TYPE         3         68         51         31       36
D565V3, multiclass
            clus
vv           IL7R MUTATED IL7R WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              0             40
  STAGE II              2             28
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            2             51
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IL7R MUTATED     1   2   6   5
  IL7R WILD-TYPE  21  90 167  92
D565V4, multiclass
    clus
vv   IL7R MUTATED IL7R WILD-TYPE
  T1            1             21
  T2            2             90
  T3            6            167
  T4            5             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
  IL7R MUTATED     5   1   3   3
  IL7R WILD-TYPE 113 103  74  74
D565V5, multiclass
    clus
vv   IL7R MUTATED IL7R WILD-TYPE
  N0            5            113
  N1            1            103
  N2            3             74
  N3            3             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"
D565V6, binary
                cls
clus               0   1
  IL7R MUTATED    11   2
  IL7R WILD-TYPE 335  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL7R MUTATED     11    2
  IL7R WILD-TYPE  335   27
   clus
vv  IL7R MUTATED IL7R WILD-TYPE
  0           11            335
  1            2             27
[1] 2 2
[1] FALSE
D565V7, binary
                cls
clus               0   1
  IL7R MUTATED     6   8
  IL7R WILD-TYPE 139 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL7R MUTATED      6    8
  IL7R WILD-TYPE  139  240
        clus
vv       IL7R MUTATED IL7R WILD-TYPE
  FEMALE            6            139
  MALE              8            240
[1] 2 2
[1] FALSE
D565V8, binary
                cls
clus               0   1
  IL7R MUTATED    10   1
  IL7R WILD-TYPE 282  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL7R MUTATED     10    1
  IL7R WILD-TYPE  282   58
     clus
vv    IL7R MUTATED IL7R WILD-TYPE
  NO            10            282
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IL7R MUTATED                                          0
  IL7R WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IL7R MUTATED                                       2
  IL7R WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IL7R MUTATED                                                        7
  IL7R WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IL7R MUTATED                                                   1
  IL7R WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IL7R MUTATED                                                                   2
  IL7R WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IL7R MUTATED                                                    0
  IL7R WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IL7R MUTATED                                                  2
  IL7R WILD-TYPE                                               59
D565V9, multiclass
                                                                   clus
vv                                                                  IL7R MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  IL7R WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IL7R MUTATED    10   0   1   2
  IL7R WILD-TYPE 301  14  14  22
D565V10, multiclass
    clus
vv   IL7R MUTATED IL7R WILD-TYPE
  R0           10            301
  R1            0             14
  R2            1             14
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D565V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IL7R MUTATED       4                         0
  IL7R WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IL7R MUTATED                                           0     8
  IL7R WILD-TYPE                                         1   235
D565V12, multiclass
                                           clus
vv                                          IL7R MUTATED IL7R WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D565V13, binary
                cls
clus               0   1
  IL7R MUTATED     0  11
  IL7R WILD-TYPE   4 299
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL7R MUTATED      0   11
  IL7R WILD-TYPE    4  299
                        clus
vv                       IL7R MUTATED IL7R WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           11            299
[1] 2 2
[1] FALSE

Clustering(566) Variable = KRT222 MUTATION ANALYSIS
D566V1, survival
                  sevent
clus2                0   1
  KRT222 MUTATED     5   3
  KRT222 WILD-TYPE 225 136
  KRT222 MUTATED KRT222 WILD-TYPE 
               8              361 
  KRT222 MUTATED KRT222 WILD-TYPE 
               3              136 
$`KRT222 MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8487 TCGA-D7-A6EY TCGA-HF-7132 
        6.97         9.34        34.68         1.12        11.44        77.29 
TCGA-HU-A4GH TCGA-VQ-A8P2 
       11.77        38.14 

$`KRT222 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  KRT222 MUTATED KRT222 WILD-TYPE 
            1.12             0.00 
  KRT222 MUTATED KRT222 WILD-TYPE 
           77.29           122.30 
  KRT222 MUTATED KRT222 WILD-TYPE 
          11.605           14.430 
[1] "1.1 - 77.3 (11.6)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D566V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KRT222 MUTATED         0        1        0        1         2         0
  KRT222 WILD-TYPE       2       14       40       29        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRT222 MUTATED           0          2          1          0        0
  KRT222 WILD-TYPE         3         68         52         32       38
D566V3, multiclass
            clus
vv           KRT222 MUTATED KRT222 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KRT222 MUTATED     1   1   4   1
  KRT222 WILD-TYPE  21  91 169  96
D566V4, multiclass
    clus
vv   KRT222 MUTATED KRT222 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              4              169
  T4              1               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
  KRT222 MUTATED     3   4   0   1
  KRT222 WILD-TYPE 115 100  77  76
D566V5, multiclass
    clus
vv   KRT222 MUTATED KRT222 WILD-TYPE
  N0              3              115
  N1              4              100
  N2              0               77
  N3              1               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"
D566V6, binary
                  cls
clus                 0   1
  KRT222 MUTATED     7   0
  KRT222 WILD-TYPE 339  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      7    0
  KRT222 WILD-TYPE  339   29
   clus
vv  KRT222 MUTATED KRT222 WILD-TYPE
  0              7              339
  1              0               29
[1] 2 2
[1] FALSE
D566V7, binary
                  cls
clus                 0   1
  KRT222 MUTATED     3   5
  KRT222 WILD-TYPE 142 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      3    5
  KRT222 WILD-TYPE  142  243
        clus
vv       KRT222 MUTATED KRT222 WILD-TYPE
  FEMALE              3              142
  MALE                5              243
[1] 2 2
[1] FALSE
D566V8, binary
                  cls
clus                 0   1
  KRT222 MUTATED     6   2
  KRT222 WILD-TYPE 286  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      6    2
  KRT222 WILD-TYPE  286   57
     clus
vv    KRT222 MUTATED KRT222 WILD-TYPE
  NO               6              286
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KRT222 MUTATED                                          0
  KRT222 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KRT222 MUTATED                                       0
  KRT222 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KRT222 MUTATED                                                        4
  KRT222 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KRT222 MUTATED                                                   2
  KRT222 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KRT222 MUTATED                                                                   0
  KRT222 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KRT222 MUTATED                                                    0
  KRT222 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KRT222 MUTATED                                                  2
  KRT222 WILD-TYPE                                               59
D566V9, multiclass
                                                                   clus
vv                                                                  KRT222 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  KRT222 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KRT222 MUTATED     6   0   0   2
  KRT222 WILD-TYPE 305  14  15  22
D566V10, multiclass
    clus
vv   KRT222 MUTATED KRT222 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D566V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KRT222 MUTATED       1                         0
  KRT222 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KRT222 MUTATED                                           0     6
  KRT222 WILD-TYPE                                         1   237
D566V12, multiclass
                                           clus
vv                                          KRT222 MUTATED KRT222 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D566V13, binary
                  cls
clus                 0   1
  KRT222 MUTATED     0   6
  KRT222 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      0    6
  KRT222 WILD-TYPE    4  304
                        clus
vv                       KRT222 MUTATED KRT222 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(567) Variable = AP2A2 MUTATION ANALYSIS
D567V1, survival
                 sevent
clus2               0   1
  AP2A2 MUTATED     5   7
  AP2A2 WILD-TYPE 225 132
  AP2A2 MUTATED AP2A2 WILD-TYPE 
             12             357 
  AP2A2 MUTATED AP2A2 WILD-TYPE 
              7             132 
$`AP2A2 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7717 TCGA-BR-8081 TCGA-BR-A4QL TCGA-CD-A4MI 
       30.90        34.68        18.15        32.25        16.14        11.77 
TCGA-D7-A6EY TCGA-HJ-7597 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-MX-A5UJ TCGA-VQ-A8DT 
       11.44        26.47         0.10         6.58        19.73        48.79 

$`AP2A2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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 

  AP2A2 MUTATED AP2A2 WILD-TYPE 
            0.1             0.0 
  AP2A2 MUTATED AP2A2 WILD-TYPE 
          48.79          122.30 
  AP2A2 MUTATED AP2A2 WILD-TYPE 
          18.94           14.07 
[1] "0.1 - 48.8 (18.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D567V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AP2A2 MUTATED         0        0        2        0         1         2
  AP2A2 WILD-TYPE       2       15       38       30        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AP2A2 MUTATED           0          2          3          1        1
  AP2A2 WILD-TYPE         3         68         50         31       37
D567V3, multiclass
            clus
vv           AP2A2 MUTATED AP2A2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             3              50
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AP2A2 MUTATED     0   3   7   3
  AP2A2 WILD-TYPE  22  89 166  94
D567V4, multiclass
    clus
vv   AP2A2 MUTATED AP2A2 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             7             166
  T4             3              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
  AP2A2 MUTATED     4   3   2   3
  AP2A2 WILD-TYPE 114 101  75  74
D567V5, multiclass
    clus
vv   AP2A2 MUTATED AP2A2 WILD-TYPE
  N0             4             114
  N1             3             101
  N2             2              75
  N3             3              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"
D567V6, binary
                 cls
clus                0   1
  AP2A2 MUTATED    13   0
  AP2A2 WILD-TYPE 333  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP2A2 MUTATED     13    0
  AP2A2 WILD-TYPE  333   29
   clus
vv  AP2A2 MUTATED AP2A2 WILD-TYPE
  0            13             333
  1             0              29
[1] 2 2
[1] FALSE
D567V7, binary
                 cls
clus                0   1
  AP2A2 MUTATED     8   6
  AP2A2 WILD-TYPE 137 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP2A2 MUTATED      8    6
  AP2A2 WILD-TYPE  137  242
        clus
vv       AP2A2 MUTATED AP2A2 WILD-TYPE
  FEMALE             8             137
  MALE               6             242
[1] 2 2
[1] FALSE
D567V8, binary
                 cls
clus                0   1
  AP2A2 MUTATED    11   1
  AP2A2 WILD-TYPE 281  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP2A2 MUTATED     11    1
  AP2A2 WILD-TYPE  281   58
     clus
vv    AP2A2 MUTATED AP2A2 WILD-TYPE
  NO             11             281
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AP2A2 MUTATED                                          1
  AP2A2 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AP2A2 MUTATED                                       1
  AP2A2 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AP2A2 MUTATED                                                        7
  AP2A2 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AP2A2 MUTATED                                                   0
  AP2A2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AP2A2 MUTATED                                                                   2
  AP2A2 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AP2A2 MUTATED                                                    0
  AP2A2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AP2A2 MUTATED                                                  3
  AP2A2 WILD-TYPE                                               58
D567V9, multiclass
                                                                   clus
vv                                                                  AP2A2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  AP2A2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AP2A2 MUTATED    11   0   0   2
  AP2A2 WILD-TYPE 300  14  15  22
D567V10, multiclass
    clus
vv   AP2A2 MUTATED AP2A2 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D567V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AP2A2 MUTATED       3                         0
  AP2A2 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AP2A2 MUTATED                                           0     9
  AP2A2 WILD-TYPE                                         1   234
D567V12, multiclass
                                           clus
vv                                          AP2A2 MUTATED AP2A2 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D567V13, binary
                 cls
clus                0   1
  AP2A2 MUTATED     0  12
  AP2A2 WILD-TYPE   4 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP2A2 MUTATED      0   12
  AP2A2 WILD-TYPE    4  298
                        clus
vv                       AP2A2 MUTATED AP2A2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(568) Variable = RUSC2 MUTATION ANALYSIS
D568V1, survival
                 sevent
clus2               0   1
  RUSC2 MUTATED    10   8
  RUSC2 WILD-TYPE 220 131
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             18             351 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
              8             131 
$`RUSC2 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8284 
       21.99        26.70         6.61        34.68        29.59         8.05 
TCGA-BR-8487 TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-5579 
        1.12        11.77         1.02         6.02        65.10        20.91 
TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4H4 TCGA-VQ-AA64 
       77.29        26.47        22.68         0.10        23.84        18.41 

$`RUSC2 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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-D7-6518 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-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-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-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-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 

  RUSC2 MUTATED RUSC2 WILD-TYPE 
            0.1             0.0 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
          77.29          122.30 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
          21.45           14.07 
[1] "0.1 - 77.3 (21.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D568V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RUSC2 MUTATED         1        0        2        1         2         4
  RUSC2 WILD-TYPE       1       15       38       29        35        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RUSC2 MUTATED           1          2          1          2        3
  RUSC2 WILD-TYPE         2         68         52         30       35
D568V3, multiclass
            clus
vv           RUSC2 MUTATED RUSC2 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              4              48
  STAGE III              1               2
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RUSC2 MUTATED     1   5   8   6
  RUSC2 WILD-TYPE  21  87 165  91
D568V4, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  T1             1              21
  T2             5              87
  T3             8             165
  T4             6              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
  RUSC2 MUTATED     6   7   5   1
  RUSC2 WILD-TYPE 112  97  72  76
D568V5, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  N0             6             112
  N1             7              97
  N2             5              72
  N3             1              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"
D568V6, binary
                 cls
clus                0   1
  RUSC2 MUTATED    15   2
  RUSC2 WILD-TYPE 331  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED     15    2
  RUSC2 WILD-TYPE  331   27
   clus
vv  RUSC2 MUTATED RUSC2 WILD-TYPE
  0            15             331
  1             2              27
[1] 2 2
[1] FALSE
D568V7, binary
                 cls
clus                0   1
  RUSC2 MUTATED    12   8
  RUSC2 WILD-TYPE 133 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED     12    8
  RUSC2 WILD-TYPE  133  240
        clus
vv       RUSC2 MUTATED RUSC2 WILD-TYPE
  FEMALE            12             133
  MALE               8             240
[1] 2 2
[1] FALSE
D568V8, binary
                 cls
clus                0   1
  RUSC2 MUTATED    15   2
  RUSC2 WILD-TYPE 277  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED     15    2
  RUSC2 WILD-TYPE  277   57
     clus
vv    RUSC2 MUTATED RUSC2 WILD-TYPE
  NO             15             277
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RUSC2 MUTATED                                          1
  RUSC2 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RUSC2 MUTATED                                       2
  RUSC2 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RUSC2 MUTATED                                                        8
  RUSC2 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RUSC2 MUTATED                                                   2
  RUSC2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RUSC2 MUTATED                                                                   5
  RUSC2 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RUSC2 MUTATED                                                    0
  RUSC2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RUSC2 MUTATED                                                  2
  RUSC2 WILD-TYPE                                               59
D568V9, multiclass
                                                                   clus
vv                                                                  RUSC2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  RUSC2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RUSC2 MUTATED    13   1   2   2
  RUSC2 WILD-TYPE 298  13  13  22
D568V10, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  R0            13             298
  R1             1              13
  R2             2              13
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D568V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RUSC2 MUTATED       4                         1
  RUSC2 WILD-TYPE    83                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RUSC2 MUTATED                                           0    10
  RUSC2 WILD-TYPE                                         1   233
D568V12, multiclass
                                           clus
vv                                          RUSC2 MUTATED RUSC2 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D568V13, binary
                 cls
clus                0   1
  RUSC2 MUTATED     0  14
  RUSC2 WILD-TYPE   4 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED      0   14
  RUSC2 WILD-TYPE    4  296
                        clus
vv                       RUSC2 MUTATED RUSC2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(569) Variable = FAM186B MUTATION ANALYSIS
D569V1, survival
                   sevent
clus2                 0   1
  FAM186B MUTATED     6   6
  FAM186B WILD-TYPE 224 133
  FAM186B MUTATED FAM186B WILD-TYPE 
               12               357 
  FAM186B MUTATED FAM186B WILD-TYPE 
                6               133 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        26.70        11.70        11.01         9.47 
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-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-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-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-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 

  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            14.660 
[1] "0.0 - 30.9 (9.6)"   "0.1 - 122.3 (14.7)"
[1] "hr=" "2"  
D569V2, 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       2       15       39       30        34        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM186B MUTATED           0          1          1          1        1
  FAM186B WILD-TYPE         3         69         52         31       37
D569V3, multiclass
            clus
vv           FAM186B MUTATED FAM186B WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                3                34
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM186B MUTATED     0   2   7   3
  FAM186B WILD-TYPE  22  90 166  94
D569V4, multiclass
    clus
vv   FAM186B MUTATED FAM186B WILD-TYPE
  T1               0                22
  T2               2                90
  T3               7               166
  T4               3                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
  FAM186B MUTATED     5   1   0   3
  FAM186B WILD-TYPE 113 103  77  74
D569V5, multiclass
    clus
vv   FAM186B MUTATED FAM186B WILD-TYPE
  N0               5               113
  N1               1               103
  N2               0                77
  N3               3                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"
D569V6, binary
                   cls
clus                  0   1
  FAM186B MUTATED    10   1
  FAM186B WILD-TYPE 336  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM186B MUTATED     10    1
  FAM186B WILD-TYPE  336   28
   clus
vv  FAM186B MUTATED FAM186B WILD-TYPE
  0              10               336
  1               1                28
[1] 2 2
[1] FALSE
D569V7, binary
                   cls
clus                  0   1
  FAM186B MUTATED     8   5
  FAM186B WILD-TYPE 137 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM186B MUTATED      8    5
  FAM186B WILD-TYPE  137  243
        clus
vv       FAM186B MUTATED FAM186B WILD-TYPE
  FEMALE               8               137
  MALE                 5               243
[1] 2 2
[1] FALSE
D569V8, binary
                   cls
clus                  0   1
  FAM186B MUTATED    11   0
  FAM186B WILD-TYPE 281  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM186B MUTATED     11    0
  FAM186B WILD-TYPE  281   59
     clus
vv    FAM186B MUTATED FAM186B WILD-TYPE
  NO               11               281
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM186B MUTATED                                          0
  FAM186B WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM186B MUTATED                                       4
  FAM186B WILD-TYPE                                    66
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM186B MUTATED                                                        6
  FAM186B WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM186B MUTATED                                                   0
  FAM186B WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM186B MUTATED                                                                   1
  FAM186B WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM186B MUTATED                                                    0
  FAM186B WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM186B MUTATED                                                  2
  FAM186B WILD-TYPE                                               59
D569V9, multiclass
                                                                   clus
vv                                                                  FAM186B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  FAM186B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM186B MUTATED     5   0   1   4
  FAM186B WILD-TYPE 306  14  14  20
D569V10, multiclass
    clus
vv   FAM186B MUTATED FAM186B WILD-TYPE
  R0               5               306
  R1               0                14
  R2               1                14
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D569V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM186B MUTATED       3                         0
  FAM186B WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM186B MUTATED                                           0     9
  FAM186B WILD-TYPE                                         1   234
D569V12, multiclass
                                           clus
vv                                          FAM186B MUTATED FAM186B WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D569V13, binary
                   cls
clus                  0   1
  FAM186B MUTATED     0  12
  FAM186B WILD-TYPE   4 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM186B MUTATED      0   12
  FAM186B WILD-TYPE    4  298
                        clus
vv                       FAM186B MUTATED FAM186B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              12               298
[1] 2 2
[1] FALSE

Clustering(570) Variable = MEGF8 MUTATION ANALYSIS
D570V1, survival
                 sevent
clus2               0   1
  MEGF8 MUTATED    19   7
  MEGF8 WILD-TYPE 211 132
  MEGF8 MUTATED MEGF8 WILD-TYPE 
             26             343 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
              7             132 
$`MEGF8 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6566 
       21.99        26.70        19.56         9.67        34.68        32.78 
TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8487 
       44.94        29.59        32.25         4.31        25.05         1.12 
TCGA-CD-A4MG TCGA-CG-4466 TCGA-CG-5728 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HU-A4G8 
        6.58        18.97        65.10         5.92        11.08        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-R5-A7ZI 
       24.20         0.10         6.58         2.10        29.00        74.53 
TCGA-VQ-A8DV TCGA-VQ-A8P2 
       13.25        38.14 

$`MEGF8 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
        9.86        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-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-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-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-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-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-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-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-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-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-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-A4GT TCGA-HU-A4GX 
       11.77        21.37        29.98         8.98         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26        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-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-A8P3 TCGA-VQ-A8PE 
        5.46        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 

  MEGF8 MUTATED MEGF8 WILD-TYPE 
            0.1             0.0 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
          74.53          122.30 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
         22.335          14.070 
[1] "0.1 - 74.5 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D570V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MEGF8 MUTATED         0        1        4        0         6         6
  MEGF8 WILD-TYPE       2       14       36       30        31        46
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MEGF8 MUTATED           0          2          0          5        3
  MEGF8 WILD-TYPE         3         68         53         27       35
D570V3, multiclass
            clus
vv           MEGF8 MUTATED MEGF8 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               4              36
  STAGE II               0              30
  STAGE IIA              6              31
  STAGE IIB              6              46
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             5              27
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MEGF8 MUTATED     1   4   9  13
  MEGF8 WILD-TYPE  21  88 164  84
D570V4, multiclass
    clus
vv   MEGF8 MUTATED MEGF8 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             9             164
  T4            13              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2  N3
  MEGF8 MUTATED    15   7   2   4
  MEGF8 WILD-TYPE 103  97  75  73
D570V5, multiclass
    clus
vv   MEGF8 MUTATED MEGF8 WILD-TYPE
  N0            15             103
  N1             7              97
  N2             2              75
  N3             4              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"
D570V6, binary
                 cls
clus                0   1
  MEGF8 MUTATED    28   2
  MEGF8 WILD-TYPE 318  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED     28    2
  MEGF8 WILD-TYPE  318   27
   clus
vv  MEGF8 MUTATED MEGF8 WILD-TYPE
  0            28             318
  1             2              27
[1] 2 2
[1] FALSE
D570V7, binary
                 cls
clus                0   1
  MEGF8 MUTATED    22   8
  MEGF8 WILD-TYPE 123 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED     22    8
  MEGF8 WILD-TYPE  123  240
        clus
vv       MEGF8 MUTATED MEGF8 WILD-TYPE
  FEMALE            22             123
  MALE               8             240
[1] 2 2
[1] FALSE
D570V8, binary
                 cls
clus                0   1
  MEGF8 MUTATED    22   2
  MEGF8 WILD-TYPE 270  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED     22    2
  MEGF8 WILD-TYPE  270   57
     clus
vv    MEGF8 MUTATED MEGF8 WILD-TYPE
  NO             22             270
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MEGF8 MUTATED                                          0
  MEGF8 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MEGF8 MUTATED                                       8
  MEGF8 WILD-TYPE                                    62
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MEGF8 MUTATED                                                       14
  MEGF8 WILD-TYPE                                                    144
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MEGF8 MUTATED                                                   1
  MEGF8 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MEGF8 MUTATED                                                                   4
  MEGF8 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MEGF8 MUTATED                                                    0
  MEGF8 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MEGF8 MUTATED                                                  3
  MEGF8 WILD-TYPE                                               58
D570V9, multiclass
                                                                   clus
vv                                                                  MEGF8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  MEGF8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          62
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MEGF8 MUTATED    21   0   1   5
  MEGF8 WILD-TYPE 290  14  14  19
D570V10, multiclass
    clus
vv   MEGF8 MUTATED MEGF8 WILD-TYPE
  R0            21             290
  R1             0              14
  R2             1              14
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D570V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MEGF8 MUTATED       7                         1
  MEGF8 WILD-TYPE    80                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MEGF8 MUTATED                                           0    19
  MEGF8 WILD-TYPE                                         1   224
D570V12, multiclass
                                           clus
vv                                          MEGF8 MUTATED MEGF8 WILD-TYPE
  ASIAN                                                 7              80
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                19             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D570V13, binary
                 cls
clus                0   1
  MEGF8 MUTATED     1  24
  MEGF8 WILD-TYPE   3 286
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED      1   24
  MEGF8 WILD-TYPE    3  286
                        clus
vv                       MEGF8 MUTATED MEGF8 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            24             286
[1] 2 2
[1] FALSE

Clustering(571) Variable = CTSD MUTATION ANALYSIS
D571V1, survival
                sevent
clus2              0   1
  CTSD MUTATED     6   2
  CTSD WILD-TYPE 224 137
  CTSD MUTATED CTSD WILD-TYPE 
             8            361 
  CTSD MUTATED CTSD WILD-TYPE 
             2            137 
$`CTSD MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8059 TCGA-BR-8368 TCGA-CD-A4MG TCGA-D7-6820 
       34.68        32.78        14.43         4.31         6.58        11.31 
TCGA-HU-8602 TCGA-HU-A4GN 
       22.32        29.98 

$`CTSD WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-D7-6822 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-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-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 

  CTSD MUTATED CTSD WILD-TYPE 
          4.31           0.00 
  CTSD MUTATED CTSD WILD-TYPE 
         34.68         122.30 
  CTSD MUTATED CTSD WILD-TYPE 
        18.375         14.170 
[1] "4.3 - 34.7 (18.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.7"
D571V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTSD MUTATED         0        0        1        0         4         2
  CTSD WILD-TYPE       2       15       39       30        33        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTSD MUTATED           1          0          0          0        0
  CTSD WILD-TYPE         2         70         53         32       38
D571V3, multiclass
            clus
vv           CTSD MUTATED CTSD WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             4             33
  STAGE IIB             2             50
  STAGE III             1              2
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTSD MUTATED     0   3   3   2
  CTSD WILD-TYPE  22  89 170  95
D571V4, multiclass
    clus
vv   CTSD MUTATED CTSD WILD-TYPE
  T1            0             22
  T2            3             89
  T3            3            170
  T4            2             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
  CTSD MUTATED     5   3   0   0
  CTSD WILD-TYPE 113 101  77  77
D571V5, multiclass
    clus
vv   CTSD MUTATED CTSD WILD-TYPE
  N0            5            113
  N1            3            101
  N2            0             77
  N3            0             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"
D571V6, binary
                cls
clus               0   1
  CTSD MUTATED     8   0
  CTSD WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSD MUTATED      8    0
  CTSD WILD-TYPE  338   29
   clus
vv  CTSD MUTATED CTSD WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D571V7, binary
                cls
clus               0   1
  CTSD MUTATED     4   4
  CTSD WILD-TYPE 141 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSD MUTATED      4    4
  CTSD WILD-TYPE  141  244
        clus
vv       CTSD MUTATED CTSD WILD-TYPE
  FEMALE            4            141
  MALE              4            244
[1] 2 2
[1] FALSE
D571V8, binary
                cls
clus               0   1
  CTSD MUTATED     8   0
  CTSD WILD-TYPE 284  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSD MUTATED      8    0
  CTSD WILD-TYPE  284   59
     clus
vv    CTSD MUTATED CTSD WILD-TYPE
  NO             8            284
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CTSD MUTATED                                          0
  CTSD WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CTSD MUTATED                                       2
  CTSD WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTSD MUTATED                                                        3
  CTSD WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CTSD MUTATED                                                   0
  CTSD WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTSD MUTATED                                                                   1
  CTSD WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CTSD MUTATED                                                    0
  CTSD WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CTSD MUTATED                                                  2
  CTSD WILD-TYPE                                               59
D571V9, multiclass
                                                                   clus
vv                                                                  CTSD MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  CTSD WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CTSD MUTATED     7   0   0   0
  CTSD WILD-TYPE 304  14  15  24
D571V10, multiclass
    clus
vv   CTSD MUTATED CTSD WILD-TYPE
  R0            7            304
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D571V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CTSD MUTATED       3                         0
  CTSD WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTSD MUTATED                                           0     5
  CTSD WILD-TYPE                                         1   238
D571V12, multiclass
                                           clus
vv                                          CTSD MUTATED CTSD WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D571V13, binary
                cls
clus               0   1
  CTSD MUTATED     0   8
  CTSD WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSD MUTATED      0    8
  CTSD WILD-TYPE    4  302
                        clus
vv                       CTSD MUTATED CTSD WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(572) Variable = UBQLN2 MUTATION ANALYSIS
D572V1, survival
                  sevent
clus2                0   1
  UBQLN2 MUTATED     5   0
  UBQLN2 WILD-TYPE 225 139
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               5              364 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               0              139 
$`UBQLN2 MUTATED`
TCGA-BR-6802 TCGA-CD-8536 TCGA-CG-5723 TCGA-HU-A4G9 TCGA-IN-A7NT 
       30.90        12.43       105.07        24.20        10.62 

$`UBQLN2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
           10.62             0.00 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
          105.07           122.30 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
           24.20            14.22 
[1] "10.6 - 105.1 (24.2)" "0.0 - 122.3 (14.2)" 
[1] "hr="     "9300000"
D572V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UBQLN2 MUTATED         0        1        1        2         0         1
  UBQLN2 WILD-TYPE       2       14       39       28        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UBQLN2 MUTATED           0          2          0          0        0
  UBQLN2 WILD-TYPE         3         68         53         32       38
D572V3, multiclass
            clus
vv           UBQLN2 MUTATED UBQLN2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UBQLN2 MUTATED     1   2   3   1
  UBQLN2 WILD-TYPE  21  90 170  96
D572V4, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  T1              1               21
  T2              2               90
  T3              3              170
  T4              1               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
  UBQLN2 MUTATED     4   2   1   0
  UBQLN2 WILD-TYPE 114 102  76  77
D572V5, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  N0              4              114
  N1              2              102
  N2              1               76
  N3              0               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"
D572V6, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     6   0
  UBQLN2 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      6    0
  UBQLN2 WILD-TYPE  340   29
   clus
vv  UBQLN2 MUTATED UBQLN2 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D572V7, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     4   3
  UBQLN2 WILD-TYPE 141 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      4    3
  UBQLN2 WILD-TYPE  141  245
        clus
vv       UBQLN2 MUTATED UBQLN2 WILD-TYPE
  FEMALE              4              141
  MALE                3              245
[1] 2 2
[1] FALSE
D572V8, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     5   1
  UBQLN2 WILD-TYPE 287  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      5    1
  UBQLN2 WILD-TYPE  287   58
     clus
vv    UBQLN2 MUTATED UBQLN2 WILD-TYPE
  NO               5              287
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  UBQLN2 MUTATED                                          0
  UBQLN2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  UBQLN2 MUTATED                                       0
  UBQLN2 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UBQLN2 MUTATED                                                        6
  UBQLN2 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  UBQLN2 MUTATED                                                   0
  UBQLN2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UBQLN2 MUTATED                                                                   0
  UBQLN2 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  UBQLN2 MUTATED                                                    0
  UBQLN2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  UBQLN2 MUTATED                                                  1
  UBQLN2 WILD-TYPE                                               60
D572V9, multiclass
                                                                   clus
vv                                                                  UBQLN2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  UBQLN2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  UBQLN2 MUTATED     6   0   0   1
  UBQLN2 WILD-TYPE 305  14  15  23
D572V10, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D572V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  UBQLN2 MUTATED       2                         0
  UBQLN2 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UBQLN2 MUTATED                                           0     3
  UBQLN2 WILD-TYPE                                         1   240
D572V12, multiclass
                                           clus
vv                                          UBQLN2 MUTATED UBQLN2 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D572V13, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     0   5
  UBQLN2 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      0    5
  UBQLN2 WILD-TYPE    4  305
                        clus
vv                       UBQLN2 MUTATED UBQLN2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(573) Variable = FNDC4 MUTATION ANALYSIS
D573V1, survival
                 sevent
clus2               0   1
  FNDC4 MUTATED     3   2
  FNDC4 WILD-TYPE 227 137
  FNDC4 MUTATED FNDC4 WILD-TYPE 
              5             364 
  FNDC4 MUTATED FNDC4 WILD-TYPE 
              2             137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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           14.22 
[1] "5.1 - 54.1 (16.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1"  
D573V2, 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       2       15       40       30        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FNDC4 MUTATED           0          2          1          0        0
  FNDC4 WILD-TYPE         3         68         52         32       38
D573V3, multiclass
            clus
vv           FNDC4 MUTATED FNDC4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FNDC4 MUTATED     0   1   4   1
  FNDC4 WILD-TYPE  22  91 169  96
D573V4, multiclass
    clus
vv   FNDC4 MUTATED FNDC4 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             4             169
  T4             1              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
  FNDC4 MUTATED     2   1   2   1
  FNDC4 WILD-TYPE 116 103  75  76
D573V5, multiclass
    clus
vv   FNDC4 MUTATED FNDC4 WILD-TYPE
  N0             2             116
  N1             1             103
  N2             2              75
  N3             1              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"
D573V6, binary
                 cls
clus                0   1
  FNDC4 MUTATED     6   0
  FNDC4 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC4 MUTATED      6    0
  FNDC4 WILD-TYPE  340   29
   clus
vv  FNDC4 MUTATED FNDC4 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D573V7, binary
                 cls
clus                0   1
  FNDC4 MUTATED     2   4
  FNDC4 WILD-TYPE 143 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC4 MUTATED      2    4
  FNDC4 WILD-TYPE  143  244
        clus
vv       FNDC4 MUTATED FNDC4 WILD-TYPE
  FEMALE             2             143
  MALE               4             244
[1] 2 2
[1] FALSE
D573V8, binary
                 cls
clus                0   1
  FNDC4 MUTATED     4   2
  FNDC4 WILD-TYPE 288  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC4 MUTATED      4    2
  FNDC4 WILD-TYPE  288   57
     clus
vv    FNDC4 MUTATED FNDC4 WILD-TYPE
  NO              4             288
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FNDC4 MUTATED                                          0
  FNDC4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FNDC4 MUTATED                                       0
  FNDC4 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FNDC4 MUTATED                                                        3
  FNDC4 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FNDC4 MUTATED                                                   0
  FNDC4 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FNDC4 MUTATED                                                                   3
  FNDC4 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FNDC4 MUTATED                                                    0
  FNDC4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FNDC4 MUTATED                                                  0
  FNDC4 WILD-TYPE                                               61
D573V9, multiclass
                                                                   clus
vv                                                                  FNDC4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  FNDC4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FNDC4 MUTATED     6   0   0   0
  FNDC4 WILD-TYPE 305  14  15  24
D573V10, multiclass
    clus
vv   FNDC4 MUTATED FNDC4 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D573V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FNDC4 MUTATED       0                         1
  FNDC4 WILD-TYPE    87                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FNDC4 MUTATED                                           0     4
  FNDC4 WILD-TYPE                                         1   239
D573V12, multiclass
                                           clus
vv                                          FNDC4 MUTATED FNDC4 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D573V13, binary
                 cls
clus                0   1
  FNDC4 MUTATED     0   4
  FNDC4 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC4 MUTATED      0    4
  FNDC4 WILD-TYPE    4  306
                        clus
vv                       FNDC4 MUTATED FNDC4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(574) Variable = LIPH MUTATION ANALYSIS
D574V1, survival
                sevent
clus2              0   1
  LIPH MUTATED     5   2
  LIPH WILD-TYPE 225 137
  LIPH MUTATED LIPH WILD-TYPE 
             7            362 
  LIPH MUTATED LIPH WILD-TYPE 
             2            137 
$`LIPH MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-8363 TCGA-F1-6874 TCGA-HU-8602 TCGA-KB-A93J 
       26.70        19.56         0.26        14.47        22.32        36.95 
TCGA-VQ-AA6K 
       12.43 

$`LIPH WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        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-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-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-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-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-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-ZA-A8F6 
       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          14.12 
[1] "0.3 - 37.0 (19.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D574V2, 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       2       15       38       29        37        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LIPH MUTATED           0          0          0          2        0
  LIPH WILD-TYPE         3         70         53         30       38
D574V3, multiclass
            clus
vv           LIPH MUTATED LIPH WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             0             37
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LIPH MUTATED     0   3   0   4
  LIPH WILD-TYPE  22  89 173  93
D574V4, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  T1            0             22
  T2            3             89
  T3            0            173
  T4            4             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
  LIPH MUTATED     4   1   0   2
  LIPH WILD-TYPE 114 103  77  75
D574V5, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  N0            4            114
  N1            1            103
  N2            0             77
  N3            2             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"
D574V6, binary
                cls
clus               0   1
  LIPH MUTATED     7   0
  LIPH WILD-TYPE 339  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      7    0
  LIPH WILD-TYPE  339   29
   clus
vv  LIPH MUTATED LIPH WILD-TYPE
  0            7            339
  1            0             29
[1] 2 2
[1] FALSE
D574V7, binary
                cls
clus               0   1
  LIPH MUTATED     3   4
  LIPH WILD-TYPE 142 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      3    4
  LIPH WILD-TYPE  142  244
        clus
vv       LIPH MUTATED LIPH WILD-TYPE
  FEMALE            3            142
  MALE              4            244
[1] 2 2
[1] FALSE
D574V8, binary
                cls
clus               0   1
  LIPH MUTATED     5   2
  LIPH WILD-TYPE 287  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      5    2
  LIPH WILD-TYPE  287   57
     clus
vv    LIPH MUTATED LIPH WILD-TYPE
  NO             5            287
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LIPH MUTATED                                          1
  LIPH WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LIPH MUTATED                                       4
  LIPH WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LIPH MUTATED                                                        1
  LIPH WILD-TYPE                                                    157
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LIPH MUTATED                                                   0
  LIPH WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LIPH MUTATED                                                                   1
  LIPH WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LIPH MUTATED                                                    0
  LIPH WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LIPH MUTATED                                                  0
  LIPH WILD-TYPE                                               61
D574V9, multiclass
                                                                   clus
vv                                                                  LIPH MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  LIPH WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LIPH MUTATED     5   1   0   0
  LIPH WILD-TYPE 306  13  15  24
D574V10, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  R0            5            306
  R1            1             13
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D574V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  LIPH MUTATED       1                         0
  LIPH WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LIPH MUTATED                                           0     6
  LIPH WILD-TYPE                                         1   237
D574V12, multiclass
                                           clus
vv                                          LIPH MUTATED LIPH WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D574V13, binary
                cls
clus               0   1
  LIPH MUTATED     0   5
  LIPH WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      0    5
  LIPH WILD-TYPE    4  305
                        clus
vv                       LIPH MUTATED LIPH WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(575) Variable = FBXO43 MUTATION ANALYSIS
D575V1, survival
                  sevent
clus2                0   1
  FBXO43 MUTATED     7   3
  FBXO43 WILD-TYPE 223 136
  FBXO43 MUTATED FBXO43 WILD-TYPE 
              10              359 
  FBXO43 MUTATED FBXO43 WILD-TYPE 
               3              136 
$`FBXO43 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-8484 TCGA-BR-A4QL TCGA-CG-4305 
        6.97        34.68         4.31        25.18        16.14        15.95 
TCGA-CG-5721 TCGA-HU-8602 TCGA-HU-A4H8 TCGA-MX-A5UJ 
        6.02        22.32        14.07        19.73 

$`FBXO43 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  FBXO43 MUTATED FBXO43 WILD-TYPE 
            4.31             0.00 
  FBXO43 MUTATED FBXO43 WILD-TYPE 
           34.68           122.30 
  FBXO43 MUTATED FBXO43 WILD-TYPE 
          16.045           14.170 
[1] "4.3 - 34.7 (16.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D575V2, 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       2       15       38       29        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO43 MUTATED           0          3          1          0        1
  FBXO43 WILD-TYPE         3         67         52         32       37
D575V3, multiclass
            clus
vv           FBXO43 MUTATED FBXO43 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO43 MUTATED     1   2   4   3
  FBXO43 WILD-TYPE  21  90 169  94
D575V4, multiclass
    clus
vv   FBXO43 MUTATED FBXO43 WILD-TYPE
  T1              1               21
  T2              2               90
  T3              4              169
  T4              3               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
  FBXO43 MUTATED     3   5   1   1
  FBXO43 WILD-TYPE 115  99  76  76
D575V5, multiclass
    clus
vv   FBXO43 MUTATED FBXO43 WILD-TYPE
  N0              3              115
  N1              5               99
  N2              1               76
  N3              1               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"
D575V6, binary
                  cls
clus                 0   1
  FBXO43 MUTATED     9   0
  FBXO43 WILD-TYPE 337  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO43 MUTATED      9    0
  FBXO43 WILD-TYPE  337   29
   clus
vv  FBXO43 MUTATED FBXO43 WILD-TYPE
  0              9              337
  1              0               29
[1] 2 2
[1] FALSE
D575V7, binary
                  cls
clus                 0   1
  FBXO43 MUTATED     5   5
  FBXO43 WILD-TYPE 140 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO43 MUTATED      5    5
  FBXO43 WILD-TYPE  140  243
        clus
vv       FBXO43 MUTATED FBXO43 WILD-TYPE
  FEMALE              5              140
  MALE                5              243
[1] 2 2
[1] FALSE
D575V8, binary
                  cls
clus                 0   1
  FBXO43 MUTATED    10   0
  FBXO43 WILD-TYPE 282  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO43 MUTATED     10    0
  FBXO43 WILD-TYPE  282   59
     clus
vv    FBXO43 MUTATED FBXO43 WILD-TYPE
  NO              10              282
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FBXO43 MUTATED                                          0
  FBXO43 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FBXO43 MUTATED                                       1
  FBXO43 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBXO43 MUTATED                                                        6
  FBXO43 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FBXO43 MUTATED                                                   0
  FBXO43 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBXO43 MUTATED                                                                   1
  FBXO43 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FBXO43 MUTATED                                                    0
  FBXO43 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FBXO43 MUTATED                                                  2
  FBXO43 WILD-TYPE                                               59
D575V9, multiclass
                                                                   clus
vv                                                                  FBXO43 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  FBXO43 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FBXO43 MUTATED     9   0   0   1
  FBXO43 WILD-TYPE 302  14  15  23
D575V10, multiclass
    clus
vv   FBXO43 MUTATED FBXO43 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D575V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FBXO43 MUTATED       2                         0
  FBXO43 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXO43 MUTATED                                           0     6
  FBXO43 WILD-TYPE                                         1   237
D575V12, multiclass
                                           clus
vv                                          FBXO43 MUTATED FBXO43 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D575V13, binary
                  cls
clus                 0   1
  FBXO43 MUTATED     0   8
  FBXO43 WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO43 MUTATED      0    8
  FBXO43 WILD-TYPE    4  302
                        clus
vv                       FBXO43 MUTATED FBXO43 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(576) Variable = HOXB7 MUTATION ANALYSIS
D576V1, survival
                 sevent
clus2               0   1
  HOXB7 MUTATED     4   2
  HOXB7 WILD-TYPE 226 137
  HOXB7 MUTATED HOXB7 WILD-TYPE 
              6             363 
  HOXB7 MUTATED HOXB7 WILD-TYPE 
              2             137 
$`HOXB7 MUTATED`
TCGA-BR-8081 TCGA-HU-A4GT TCGA-MX-A5UJ TCGA-VQ-A8P2 TCGA-VQ-AA6I TCGA-VQ-AA6K 
       32.25         6.51        19.73        38.14        16.14        12.43 

$`HOXB7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-AA6J TCGA-ZA-A8F6 
       26.04        27.55        17.26 

  HOXB7 MUTATED HOXB7 WILD-TYPE 
           6.51            0.00 
  HOXB7 MUTATED HOXB7 WILD-TYPE 
          38.14          122.30 
  HOXB7 MUTATED HOXB7 WILD-TYPE 
         17.935          14.170 
[1] "6.5 - 38.1 (17.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D576V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HOXB7 MUTATED         0        0        0        0         1         1
  HOXB7 WILD-TYPE       2       15       40       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HOXB7 MUTATED           0          2          1          1        0
  HOXB7 WILD-TYPE         3         68         52         31       38
D576V3, multiclass
            clus
vv           HOXB7 MUTATED HOXB7 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HOXB7 MUTATED     0   0   3   3
  HOXB7 WILD-TYPE  22  92 170  94
D576V4, multiclass
    clus
vv   HOXB7 MUTATED HOXB7 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             3             170
  T4             3              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
  HOXB7 MUTATED     2   1   1   2
  HOXB7 WILD-TYPE 116 103  76  75
D576V5, multiclass
    clus
vv   HOXB7 MUTATED HOXB7 WILD-TYPE
  N0             2             116
  N1             1             103
  N2             1              76
  N3             2              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"
D576V6, binary
                 cls
clus                0   1
  HOXB7 MUTATED     6   0
  HOXB7 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXB7 MUTATED      6    0
  HOXB7 WILD-TYPE  340   29
   clus
vv  HOXB7 MUTATED HOXB7 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D576V7, binary
                 cls
clus                0   1
  HOXB7 MUTATED     3   3
  HOXB7 WILD-TYPE 142 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXB7 MUTATED      3    3
  HOXB7 WILD-TYPE  142  245
        clus
vv       HOXB7 MUTATED HOXB7 WILD-TYPE
  FEMALE             3             142
  MALE               3             245
[1] 2 2
[1] FALSE
D576V8, binary
                 cls
clus                0   1
  HOXB7 MUTATED     4   2
  HOXB7 WILD-TYPE 288  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXB7 MUTATED      4    2
  HOXB7 WILD-TYPE  288   57
     clus
vv    HOXB7 MUTATED HOXB7 WILD-TYPE
  NO              4             288
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HOXB7 MUTATED                                          1
  HOXB7 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HOXB7 MUTATED                                       0
  HOXB7 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HOXB7 MUTATED                                                        1
  HOXB7 WILD-TYPE                                                    157
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HOXB7 MUTATED                                                   1
  HOXB7 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HOXB7 MUTATED                                                                   1
  HOXB7 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HOXB7 MUTATED                                                    0
  HOXB7 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HOXB7 MUTATED                                                  2
  HOXB7 WILD-TYPE                                               59
D576V9, multiclass
                                                                   clus
vv                                                                  HOXB7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  HOXB7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HOXB7 MUTATED     5   1   0   0
  HOXB7 WILD-TYPE 306  13  15  24
D576V10, multiclass
    clus
vv   HOXB7 MUTATED HOXB7 WILD-TYPE
  R0             5             306
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D576V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HOXB7 MUTATED       1                         0
  HOXB7 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HOXB7 MUTATED                                           0     5
  HOXB7 WILD-TYPE                                         1   238
D576V12, multiclass
                                           clus
vv                                          HOXB7 MUTATED HOXB7 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D576V13, binary
                 cls
clus                0   1
  HOXB7 MUTATED     0   3
  HOXB7 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXB7 MUTATED      0    3
  HOXB7 WILD-TYPE    4  307
                        clus
vv                       HOXB7 MUTATED HOXB7 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(577) Variable = AGAP6 MUTATION ANALYSIS
D577V1, survival
                 sevent
clus2               0   1
  AGAP6 MUTATED     6   4
  AGAP6 WILD-TYPE 224 135
  AGAP6 MUTATED AGAP6 WILD-TYPE 
             10             359 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              4             135 
$`AGAP6 MUTATED`
TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8360 TCGA-BR-8487 TCGA-BR-A4QL 
        6.18        34.68        35.84         6.18         1.12        16.14 
TCGA-CD-8527 TCGA-CG-5726 TCGA-F1-A448 TCGA-R5-A7ZI 
        7.17        28.96        21.27        74.53 

$`AGAP6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  AGAP6 MUTATED AGAP6 WILD-TYPE 
           1.12            0.00 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
          74.53          122.30 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
         18.705          14.170 
[1] "1.1 - 74.5 (18.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D577V2, 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       2       14       38       29        34        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AGAP6 MUTATED           0          0          2          0        1
  AGAP6 WILD-TYPE         3         70         51         32       37
D577V3, multiclass
            clus
vv           AGAP6 MUTATED AGAP6 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             2              51
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AGAP6 MUTATED     1   3   5   1
  AGAP6 WILD-TYPE  21  89 168  96
D577V4, multiclass
    clus
vv   AGAP6 MUTATED AGAP6 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             5             168
  T4             1              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
  AGAP6 MUTATED     6   2   0   2
  AGAP6 WILD-TYPE 112 102  77  75
D577V5, multiclass
    clus
vv   AGAP6 MUTATED AGAP6 WILD-TYPE
  N0             6             112
  N1             2             102
  N2             0              77
  N3             2              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"
D577V6, binary
                 cls
clus                0   1
  AGAP6 MUTATED     9   1
  AGAP6 WILD-TYPE 337  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      9    1
  AGAP6 WILD-TYPE  337   28
   clus
vv  AGAP6 MUTATED AGAP6 WILD-TYPE
  0             9             337
  1             1              28
[1] 2 2
[1] FALSE
D577V7, binary
                 cls
clus                0   1
  AGAP6 MUTATED     6   4
  AGAP6 WILD-TYPE 139 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      6    4
  AGAP6 WILD-TYPE  139  244
        clus
vv       AGAP6 MUTATED AGAP6 WILD-TYPE
  FEMALE             6             139
  MALE               4             244
[1] 2 2
[1] FALSE
D577V8, binary
                 cls
clus                0   1
  AGAP6 MUTATED     8   1
  AGAP6 WILD-TYPE 284  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      8    1
  AGAP6 WILD-TYPE  284   58
     clus
vv    AGAP6 MUTATED AGAP6 WILD-TYPE
  NO              8             284
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AGAP6 MUTATED                                          0
  AGAP6 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AGAP6 MUTATED                                       1
  AGAP6 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AGAP6 MUTATED                                                        5
  AGAP6 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AGAP6 MUTATED                                                   1
  AGAP6 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AGAP6 MUTATED                                                                   3
  AGAP6 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AGAP6 MUTATED                                                    0
  AGAP6 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AGAP6 MUTATED                                                  0
  AGAP6 WILD-TYPE                                               61
D577V9, multiclass
                                                                   clus
vv                                                                  AGAP6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  AGAP6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AGAP6 MUTATED     9   0   0   1
  AGAP6 WILD-TYPE 302  14  15  23
D577V10, multiclass
    clus
vv   AGAP6 MUTATED AGAP6 WILD-TYPE
  R0             9             302
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D577V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AGAP6 MUTATED       1                         0
  AGAP6 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AGAP6 MUTATED                                           0     8
  AGAP6 WILD-TYPE                                         1   235
D577V12, multiclass
                                           clus
vv                                          AGAP6 MUTATED AGAP6 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D577V13, binary
                 cls
clus                0   1
  AGAP6 MUTATED     2   7
  AGAP6 WILD-TYPE   2 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      2    7
  AGAP6 WILD-TYPE    2  303
                        clus
vv                       AGAP6 MUTATED AGAP6 WILD-TYPE
  HISPANIC OR LATINO                 2               2
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(578) Variable = GPR160 MUTATION ANALYSIS
D578V1, survival
                  sevent
clus2                0   1
  GPR160 MUTATED     4   2
  GPR160 WILD-TYPE 226 137
  GPR160 MUTATED GPR160 WILD-TYPE 
               6              363 
  GPR160 MUTATED GPR160 WILD-TYPE 
               2              137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  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           14.170 
[1] "7.0 - 65.1 (26.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.5"
D578V2, 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       2       15       39       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR160 MUTATED           0          1          0          1        1
  GPR160 WILD-TYPE         3         69         53         31       37
D578V3, multiclass
            clus
vv           GPR160 MUTATED GPR160 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR160 MUTATED     1   2   2   2
  GPR160 WILD-TYPE  21  90 171  95
D578V4, multiclass
    clus
vv   GPR160 MUTATED GPR160 WILD-TYPE
  T1              1               21
  T2              2               90
  T3              2              171
  T4              2               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
  GPR160 MUTATED     2   1   3   0
  GPR160 WILD-TYPE 116 103  74  77
D578V5, multiclass
    clus
vv   GPR160 MUTATED GPR160 WILD-TYPE
  N0              2              116
  N1              1              103
  N2              3               74
  N3              0               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"
D578V6, binary
                  cls
clus                 0   1
  GPR160 MUTATED     6   1
  GPR160 WILD-TYPE 340  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      6    1
  GPR160 WILD-TYPE  340   28
   clus
vv  GPR160 MUTATED GPR160 WILD-TYPE
  0              6              340
  1              1               28
[1] 2 2
[1] FALSE
D578V7, binary
                  cls
clus                 0   1
  GPR160 MUTATED     6   2
  GPR160 WILD-TYPE 139 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      6    2
  GPR160 WILD-TYPE  139  246
        clus
vv       GPR160 MUTATED GPR160 WILD-TYPE
  FEMALE              6              139
  MALE                2              246
[1] 2 2
[1] FALSE
D578V8, binary
                  cls
clus                 0   1
  GPR160 MUTATED     5   0
  GPR160 WILD-TYPE 287  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      5    0
  GPR160 WILD-TYPE  287   59
     clus
vv    GPR160 MUTATED GPR160 WILD-TYPE
  NO               5              287
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GPR160 MUTATED                                          0
  GPR160 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GPR160 MUTATED                                       1
  GPR160 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR160 MUTATED                                                        5
  GPR160 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GPR160 MUTATED                                                   0
  GPR160 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR160 MUTATED                                                                   1
  GPR160 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GPR160 MUTATED                                                    0
  GPR160 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GPR160 MUTATED                                                  1
  GPR160 WILD-TYPE                                               60
D578V9, multiclass
                                                                   clus
vv                                                                  GPR160 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  GPR160 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR160 MUTATED     5   0   0   3
  GPR160 WILD-TYPE 306  14  15  21
D578V10, multiclass
    clus
vv   GPR160 MUTATED GPR160 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D578V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GPR160 MUTATED       2                         0
  GPR160 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR160 MUTATED                                           0     5
  GPR160 WILD-TYPE                                         1   238
D578V12, multiclass
                                           clus
vv                                          GPR160 MUTATED GPR160 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D578V13, binary
                  cls
clus                 0   1
  GPR160 MUTATED     0   7
  GPR160 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      0    7
  GPR160 WILD-TYPE    4  303
                        clus
vv                       GPR160 MUTATED GPR160 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(579) Variable = FAM46D MUTATION ANALYSIS
D579V1, survival
                  sevent
clus2                0   1
  FAM46D MUTATED     8   2
  FAM46D WILD-TYPE 222 137
  FAM46D MUTATED FAM46D WILD-TYPE 
              10              359 
  FAM46D MUTATED FAM46D WILD-TYPE 
               2              137 
$`FAM46D MUTATED`
TCGA-BR-6453 TCGA-BR-6563 TCGA-BR-8369 TCGA-BR-8485 TCGA-CD-A4MG TCGA-CG-5723 
       15.95        39.12        14.04         9.21         6.58       105.07 
TCGA-CG-5733 TCGA-D7-6822 TCGA-F1-6874 TCGA-VQ-A8P2 
       21.07        12.33        14.47        38.14 

$`FAM46D WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-F1-6875 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-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 

  FAM46D MUTATED FAM46D WILD-TYPE 
            6.58             0.00 
  FAM46D MUTATED FAM46D WILD-TYPE 
          105.07           122.30 
  FAM46D MUTATED FAM46D WILD-TYPE 
           15.21            14.17 
[1] "6.6 - 105.1 (15.2)" "0.0 - 122.3 (14.2)"
[1] "hr=" "2.4"
D579V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM46D MUTATED         0        0        2        1         2         1
  FAM46D WILD-TYPE       2       15       38       29        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM46D MUTATED           0          2          1          1        0
  FAM46D WILD-TYPE         3         68         52         31       38
D579V3, multiclass
            clus
vv           FAM46D MUTATED FAM46D WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM46D MUTATED     0   5   3   2
  FAM46D WILD-TYPE  22  87 170  95
D579V4, multiclass
    clus
vv   FAM46D MUTATED FAM46D WILD-TYPE
  T1              0               22
  T2              5               87
  T3              3              170
  T4              2               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
  FAM46D MUTATED     3   4   1   2
  FAM46D WILD-TYPE 115 100  76  75
D579V5, multiclass
    clus
vv   FAM46D MUTATED FAM46D WILD-TYPE
  N0              3              115
  N1              4              100
  N2              1               76
  N3              2               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"
D579V6, binary
                  cls
clus                 0   1
  FAM46D MUTATED    10   0
  FAM46D WILD-TYPE 336  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM46D MUTATED     10    0
  FAM46D WILD-TYPE  336   29
   clus
vv  FAM46D MUTATED FAM46D WILD-TYPE
  0             10              336
  1              0               29
[1] 2 2
[1] FALSE
D579V7, binary
                  cls
clus                 0   1
  FAM46D MUTATED     3   7
  FAM46D WILD-TYPE 142 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM46D MUTATED      3    7
  FAM46D WILD-TYPE  142  241
        clus
vv       FAM46D MUTATED FAM46D WILD-TYPE
  FEMALE              3              142
  MALE                7              241
[1] 2 2
[1] FALSE
D579V8, binary
                  cls
clus                 0   1
  FAM46D MUTATED     9   1
  FAM46D WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM46D MUTATED      9    1
  FAM46D WILD-TYPE  283   58
     clus
vv    FAM46D MUTATED FAM46D WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM46D MUTATED                                          0
  FAM46D WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM46D MUTATED                                       1
  FAM46D WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM46D MUTATED                                                        5
  FAM46D WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM46D MUTATED                                                   1
  FAM46D WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM46D MUTATED                                                                   2
  FAM46D WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM46D MUTATED                                                    0
  FAM46D WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM46D MUTATED                                                  1
  FAM46D WILD-TYPE                                               60
D579V9, multiclass
                                                                   clus
vv                                                                  FAM46D MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  FAM46D WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAM46D MUTATED     9   0   0   0
  FAM46D WILD-TYPE 302  14  15  24
D579V10, multiclass
    clus
vv   FAM46D MUTATED FAM46D WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D579V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAM46D MUTATED       1                         0
  FAM46D WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM46D MUTATED                                           0     7
  FAM46D WILD-TYPE                                         1   236
D579V12, multiclass
                                           clus
vv                                          FAM46D MUTATED FAM46D WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D579V13, binary
                  cls
clus                 0   1
  FAM46D MUTATED     0   7
  FAM46D WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM46D MUTATED      0    7
  FAM46D WILD-TYPE    4  303
                        clus
vv                       FAM46D MUTATED FAM46D WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(580) Variable = CSF3R MUTATION ANALYSIS
D580V1, survival
                 sevent
clus2               0   1
  CSF3R MUTATED     9   2
  CSF3R WILD-TYPE 221 137
  CSF3R MUTATED CSF3R WILD-TYPE 
             11             358 
  CSF3R MUTATED CSF3R WILD-TYPE 
              2             137 
$`CSF3R MUTATED`
TCGA-BR-6452 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8368 TCGA-CD-A4MG TCGA-CG-4305 
       34.68        33.21        29.59         4.31         6.58        15.95 
TCGA-CG-4437 TCGA-D7-A4YV TCGA-F1-6874 TCGA-HF-7134 TCGA-HF-A5NB 
        8.05         5.92        14.47        52.21        30.51 

$`CSF3R WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
          15.95           14.12 
[1] "4.3 - 52.2 (15.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.3"
D580V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CSF3R MUTATED         0        1        3        2         2         2
  CSF3R WILD-TYPE       2       14       37       28        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSF3R MUTATED           0          1          0          1        0
  CSF3R WILD-TYPE         3         69         53         31       38
D580V3, multiclass
            clus
vv           CSF3R MUTATED CSF3R WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               2              28
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CSF3R MUTATED     1   5   3   3
  CSF3R WILD-TYPE  21  87 170  94
D580V4, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  T1             1              21
  T2             5              87
  T3             3             170
  T4             3              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
  CSF3R MUTATED     7   4   0   1
  CSF3R WILD-TYPE 111 100  77  76
D580V5, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  N0             7             111
  N1             4             100
  N2             0              77
  N3             1              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"
D580V6, binary
                 cls
clus                0   1
  CSF3R MUTATED    12   0
  CSF3R WILD-TYPE 334  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED     12    0
  CSF3R WILD-TYPE  334   29
   clus
vv  CSF3R MUTATED CSF3R WILD-TYPE
  0            12             334
  1             0              29
[1] 2 2
[1] FALSE
D580V7, binary
                 cls
clus                0   1
  CSF3R MUTATED     5   7
  CSF3R WILD-TYPE 140 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED      5    7
  CSF3R WILD-TYPE  140  241
        clus
vv       CSF3R MUTATED CSF3R WILD-TYPE
  FEMALE             5             140
  MALE               7             241
[1] 2 2
[1] FALSE
D580V8, binary
                 cls
clus                0   1
  CSF3R MUTATED    10   1
  CSF3R WILD-TYPE 282  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED     10    1
  CSF3R WILD-TYPE  282   58
     clus
vv    CSF3R MUTATED CSF3R WILD-TYPE
  NO             10             282
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CSF3R MUTATED                                          0
  CSF3R WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CSF3R MUTATED                                       1
  CSF3R WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CSF3R MUTATED                                                        4
  CSF3R WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CSF3R MUTATED                                                   2
  CSF3R WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CSF3R MUTATED                                                                   4
  CSF3R WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CSF3R MUTATED                                                    0
  CSF3R WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CSF3R MUTATED                                                  1
  CSF3R WILD-TYPE                                               60
D580V9, multiclass
                                                                   clus
vv                                                                  CSF3R MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  CSF3R WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CSF3R MUTATED    10   1   0   0
  CSF3R WILD-TYPE 301  13  15  24
D580V10, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  R0            10             301
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D580V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CSF3R MUTATED       1                         0
  CSF3R WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CSF3R MUTATED                                           0     6
  CSF3R WILD-TYPE                                         1   237
D580V12, multiclass
                                           clus
vv                                          CSF3R MUTATED CSF3R WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D580V13, binary
                 cls
clus                0   1
  CSF3R MUTATED     0   7
  CSF3R WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED      0    7
  CSF3R WILD-TYPE    4  303
                        clus
vv                       CSF3R MUTATED CSF3R WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(581) Variable = PRMT3 MUTATION ANALYSIS
D581V1, survival
                 sevent
clus2               0   1
  PRMT3 MUTATED     3   5
  PRMT3 WILD-TYPE 227 134
  PRMT3 MUTATED PRMT3 WILD-TYPE 
              8             361 
  PRMT3 MUTATED PRMT3 WILD-TYPE 
              5             134 
$`PRMT3 MUTATED`
TCGA-B7-A5TI TCGA-BR-8382 TCGA-CD-5801 TCGA-D7-A6EY TCGA-F1-6874 TCGA-HJ-7597 
       19.56        25.05        13.18        11.44        14.47        26.47 
TCGA-HU-A4GN TCGA-VQ-A8DL 
       29.98         0.92 

$`PRMT3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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 

  PRMT3 MUTATED PRMT3 WILD-TYPE 
           0.92            0.00 
  PRMT3 MUTATED PRMT3 WILD-TYPE 
          29.98          122.30 
  PRMT3 MUTATED PRMT3 WILD-TYPE 
         17.015          14.170 
[1] "0.9 - 30.0 (17.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D581V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRMT3 MUTATED         0        0        2        0         2         0
  PRMT3 WILD-TYPE       2       15       38       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRMT3 MUTATED           0          1          1          2        0
  PRMT3 WILD-TYPE         3         69         52         30       38
D581V3, multiclass
            clus
vv           PRMT3 MUTATED PRMT3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRMT3 MUTATED     0   3   3   2
  PRMT3 WILD-TYPE  22  89 170  95
D581V4, multiclass
    clus
vv   PRMT3 MUTATED PRMT3 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             3             170
  T4             2              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
  PRMT3 MUTATED     3   3   0   3
  PRMT3 WILD-TYPE 115 101  77  74
D581V5, multiclass
    clus
vv   PRMT3 MUTATED PRMT3 WILD-TYPE
  N0             3             115
  N1             3             101
  N2             0              77
  N3             3              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"
D581V6, binary
                 cls
clus                0   1
  PRMT3 MUTATED     8   0
  PRMT3 WILD-TYPE 338  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT3 MUTATED      8    0
  PRMT3 WILD-TYPE  338   29
   clus
vv  PRMT3 MUTATED PRMT3 WILD-TYPE
  0             8             338
  1             0              29
[1] 2 2
[1] FALSE
D581V7, binary
                 cls
clus                0   1
  PRMT3 MUTATED     5   4
  PRMT3 WILD-TYPE 140 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT3 MUTATED      5    4
  PRMT3 WILD-TYPE  140  244
        clus
vv       PRMT3 MUTATED PRMT3 WILD-TYPE
  FEMALE             5             140
  MALE               4             244
[1] 2 2
[1] FALSE
D581V8, binary
                 cls
clus                0   1
  PRMT3 MUTATED     8   0
  PRMT3 WILD-TYPE 284  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT3 MUTATED      8    0
  PRMT3 WILD-TYPE  284   59
     clus
vv    PRMT3 MUTATED PRMT3 WILD-TYPE
  NO              8             284
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PRMT3 MUTATED                                          1
  PRMT3 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PRMT3 MUTATED                                       1
  PRMT3 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRMT3 MUTATED                                                        3
  PRMT3 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PRMT3 MUTATED                                                   0
  PRMT3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRMT3 MUTATED                                                                   1
  PRMT3 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PRMT3 MUTATED                                                    0
  PRMT3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PRMT3 MUTATED                                                  3
  PRMT3 WILD-TYPE                                               58
D581V9, multiclass
                                                                   clus
vv                                                                  PRMT3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  PRMT3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRMT3 MUTATED     7   0   0   1
  PRMT3 WILD-TYPE 304  14  15  23
D581V10, multiclass
    clus
vv   PRMT3 MUTATED PRMT3 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D581V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PRMT3 MUTATED       2                         0
  PRMT3 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRMT3 MUTATED                                           0     7
  PRMT3 WILD-TYPE                                         1   236
D581V12, multiclass
                                           clus
vv                                          PRMT3 MUTATED PRMT3 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D581V13, binary
                 cls
clus                0   1
  PRMT3 MUTATED     0   8
  PRMT3 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT3 MUTATED      0    8
  PRMT3 WILD-TYPE    4  302
                        clus
vv                       PRMT3 MUTATED PRMT3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(582) Variable = FGF7 MUTATION ANALYSIS
D582V1, survival
                sevent
clus2              0   1
  FGF7 MUTATED     4   1
  FGF7 WILD-TYPE 226 138
  FGF7 MUTATED FGF7 WILD-TYPE 
             5            364 
  FGF7 MUTATED FGF7 WILD-TYPE 
             1            138 
$`FGF7 MUTATED`
TCGA-CG-4460 TCGA-BR-6802 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8680 
       21.99        30.90        29.59         4.31        31.96 

$`FGF7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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 

  FGF7 MUTATED FGF7 WILD-TYPE 
          4.31           0.00 
  FGF7 MUTATED FGF7 WILD-TYPE 
         31.96         122.30 
  FGF7 MUTATED FGF7 WILD-TYPE 
         29.59          14.12 
[1] "4.3 - 32.0 (29.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.6"
D582V2, 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       2       15       39       30        37        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FGF7 MUTATED           0          1          0          0        2
  FGF7 WILD-TYPE         3         69         53         32       36
D582V3, multiclass
            clus
vv           FGF7 MUTATED FGF7 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FGF7 MUTATED     0   1   1   3
  FGF7 WILD-TYPE  22  91 172  94
D582V4, multiclass
    clus
vv   FGF7 MUTATED FGF7 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            1            172
  T4            3             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
  FGF7 MUTATED     2   1   2   0
  FGF7 WILD-TYPE 116 103  75  77
D582V5, multiclass
    clus
vv   FGF7 MUTATED FGF7 WILD-TYPE
  N0            2            116
  N1            1            103
  N2            2             75
  N3            0             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"
D582V6, binary
                cls
clus               0   1
  FGF7 MUTATED     3   2
  FGF7 WILD-TYPE 343  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF7 MUTATED      3    2
  FGF7 WILD-TYPE  343   27
   clus
vv  FGF7 MUTATED FGF7 WILD-TYPE
  0            3            343
  1            2             27
[1] 2 2
[1] FALSE
D582V7, binary
                cls
clus               0   1
  FGF7 MUTATED     3   2
  FGF7 WILD-TYPE 142 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF7 MUTATED      3    2
  FGF7 WILD-TYPE  142  246
        clus
vv       FGF7 MUTATED FGF7 WILD-TYPE
  FEMALE            3            142
  MALE              2            246
[1] 2 2
[1] FALSE
D582V8, binary
                cls
clus               0   1
  FGF7 MUTATED     5   0
  FGF7 WILD-TYPE 287  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF7 MUTATED      5    0
  FGF7 WILD-TYPE  287   59
     clus
vv    FGF7 MUTATED FGF7 WILD-TYPE
  NO             5            287
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FGF7 MUTATED                                          0
  FGF7 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FGF7 MUTATED                                       0
  FGF7 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FGF7 MUTATED                                                        3
  FGF7 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FGF7 MUTATED                                                   0
  FGF7 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FGF7 MUTATED                                                                   1
  FGF7 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FGF7 MUTATED                                                    0
  FGF7 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FGF7 MUTATED                                                  1
  FGF7 WILD-TYPE                                               60
D582V9, multiclass
                                                                   clus
vv                                                                  FGF7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  FGF7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FGF7 MUTATED     4   0   1   0
  FGF7 WILD-TYPE 307  14  14  24
D582V10, multiclass
    clus
vv   FGF7 MUTATED FGF7 WILD-TYPE
  R0            4            307
  R1            0             14
  R2            1             14
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D582V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FGF7 MUTATED       1                         0
  FGF7 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FGF7 MUTATED                                           0     3
  FGF7 WILD-TYPE                                         1   240
D582V12, multiclass
                                           clus
vv                                          FGF7 MUTATED FGF7 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D582V13, binary
                cls
clus               0   1
  FGF7 MUTATED     0   4
  FGF7 WILD-TYPE   4 306
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGF7 MUTATED      0    4
  FGF7 WILD-TYPE    4  306
                        clus
vv                       FGF7 MUTATED FGF7 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            4            306
[1] 2 2
[1] FALSE

Clustering(583) Variable = AGAP5 MUTATION ANALYSIS
D583V1, survival
                 sevent
clus2               0   1
  AGAP5 MUTATED     6   2
  AGAP5 WILD-TYPE 224 137
  AGAP5 MUTATED AGAP5 WILD-TYPE 
              8             361 
  AGAP5 MUTATED AGAP5 WILD-TYPE 
              2             137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  AGAP5 MUTATED AGAP5 WILD-TYPE 
           1.12            0.00 
  AGAP5 MUTATED AGAP5 WILD-TYPE 
         122.30          116.38 
  AGAP5 MUTATED AGAP5 WILD-TYPE 
         12.755          14.430 
[1] "1.1 - 122.3 (12.8)" "0.0 - 116.4 (14.4)"
[1] "hr=" "1.8"
D583V2, 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       2       15       39       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AGAP5 MUTATED           0          0          2          1        1
  AGAP5 WILD-TYPE         3         70         51         31       37
D583V3, multiclass
            clus
vv           AGAP5 MUTATED AGAP5 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AGAP5 MUTATED     1   0   4   2
  AGAP5 WILD-TYPE  21  92 169  95
D583V4, multiclass
    clus
vv   AGAP5 MUTATED AGAP5 WILD-TYPE
  T1             1              21
  T2             0              92
  T3             4             169
  T4             2              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
  AGAP5 MUTATED     2   1   2   2
  AGAP5 WILD-TYPE 116 103  75  75
D583V5, multiclass
    clus
vv   AGAP5 MUTATED AGAP5 WILD-TYPE
  N0             2             116
  N1             1             103
  N2             2              75
  N3             2              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"
D583V6, binary
                 cls
clus                0   1
  AGAP5 MUTATED     7   1
  AGAP5 WILD-TYPE 339  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP5 MUTATED      7    1
  AGAP5 WILD-TYPE  339   28
   clus
vv  AGAP5 MUTATED AGAP5 WILD-TYPE
  0             7             339
  1             1              28
[1] 2 2
[1] FALSE
D583V7, binary
                 cls
clus                0   1
  AGAP5 MUTATED     3   5
  AGAP5 WILD-TYPE 142 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP5 MUTATED      3    5
  AGAP5 WILD-TYPE  142  243
        clus
vv       AGAP5 MUTATED AGAP5 WILD-TYPE
  FEMALE             3             142
  MALE               5             243
[1] 2 2
[1] FALSE
D583V8, binary
                 cls
clus                0   1
  AGAP5 MUTATED     6   2
  AGAP5 WILD-TYPE 286  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP5 MUTATED      6    2
  AGAP5 WILD-TYPE  286   57
     clus
vv    AGAP5 MUTATED AGAP5 WILD-TYPE
  NO              6             286
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AGAP5 MUTATED                                          0
  AGAP5 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AGAP5 MUTATED                                       0
  AGAP5 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AGAP5 MUTATED                                                        4
  AGAP5 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AGAP5 MUTATED                                                   0
  AGAP5 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AGAP5 MUTATED                                                                   1
  AGAP5 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AGAP5 MUTATED                                                    0
  AGAP5 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AGAP5 MUTATED                                                  3
  AGAP5 WILD-TYPE                                               58
D583V9, multiclass
                                                                   clus
vv                                                                  AGAP5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  AGAP5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AGAP5 MUTATED     7   0   0   1
  AGAP5 WILD-TYPE 304  14  15  23
D583V10, multiclass
    clus
vv   AGAP5 MUTATED AGAP5 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D583V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AGAP5 MUTATED       2                         1
  AGAP5 WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AGAP5 MUTATED                                           0     5
  AGAP5 WILD-TYPE                                         1   238
D583V12, multiclass
                                           clus
vv                                          AGAP5 MUTATED AGAP5 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D583V13, binary
                 cls
clus                0   1
  AGAP5 MUTATED     0   8
  AGAP5 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP5 MUTATED      0    8
  AGAP5 WILD-TYPE    4  302
                        clus
vv                       AGAP5 MUTATED AGAP5 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(584) Variable = STEAP2 MUTATION ANALYSIS
D584V1, survival
                  sevent
clus2                0   1
  STEAP2 MUTATED     5   0
  STEAP2 WILD-TYPE 225 139
  STEAP2 MUTATED STEAP2 WILD-TYPE 
               5              364 
  STEAP2 MUTATED STEAP2 WILD-TYPE 
               0              139 
$`STEAP2 MUTATED`
TCGA-BR-6452 TCGA-F1-6874 TCGA-FP-7829 TCGA-HU-8602 TCGA-HU-A4GU 
       34.68        14.47        19.53        22.32         6.58 

$`STEAP2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  STEAP2 MUTATED STEAP2 WILD-TYPE 
            6.58             0.00 
  STEAP2 MUTATED STEAP2 WILD-TYPE 
           34.68           122.30 
  STEAP2 MUTATED STEAP2 WILD-TYPE 
           19.53            14.12 
[1] "6.6 - 34.7 (19.5)"  "0.0 - 122.3 (14.1)"
[1] "hr="     "9100000"
D584V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STEAP2 MUTATED         0        0        1        0         1         3
  STEAP2 WILD-TYPE       2       15       39       30        36        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STEAP2 MUTATED           0          0          0          0        0
  STEAP2 WILD-TYPE         3         70         53         32       38
D584V3, multiclass
            clus
vv           STEAP2 MUTATED STEAP2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  STEAP2 MUTATED     0   1   3   1
  STEAP2 WILD-TYPE  22  91 170  96
D584V4, multiclass
    clus
vv   STEAP2 MUTATED STEAP2 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              3              170
  T4              1               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
  STEAP2 MUTATED     3   3   0   0
  STEAP2 WILD-TYPE 115 101  77  77
D584V5, multiclass
    clus
vv   STEAP2 MUTATED STEAP2 WILD-TYPE
  N0              3              115
  N1              3              101
  N2              0               77
  N3              0               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"
D584V6, binary
                  cls
clus                 0   1
  STEAP2 MUTATED     6   0
  STEAP2 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STEAP2 MUTATED      6    0
  STEAP2 WILD-TYPE  340   29
   clus
vv  STEAP2 MUTATED STEAP2 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D584V7, binary
                  cls
clus                 0   1
  STEAP2 MUTATED     3   3
  STEAP2 WILD-TYPE 142 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STEAP2 MUTATED      3    3
  STEAP2 WILD-TYPE  142  245
        clus
vv       STEAP2 MUTATED STEAP2 WILD-TYPE
  FEMALE              3              142
  MALE                3              245
[1] 2 2
[1] FALSE
D584V8, binary
                  cls
clus                 0   1
  STEAP2 MUTATED     4   1
  STEAP2 WILD-TYPE 288  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STEAP2 MUTATED      4    1
  STEAP2 WILD-TYPE  288   58
     clus
vv    STEAP2 MUTATED STEAP2 WILD-TYPE
  NO               4              288
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  STEAP2 MUTATED                                          0
  STEAP2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  STEAP2 MUTATED                                       2
  STEAP2 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  STEAP2 MUTATED                                                        2
  STEAP2 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  STEAP2 MUTATED                                                   1
  STEAP2 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  STEAP2 MUTATED                                                                   1
  STEAP2 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  STEAP2 MUTATED                                                    0
  STEAP2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  STEAP2 MUTATED                                                  0
  STEAP2 WILD-TYPE                                               61
D584V9, multiclass
                                                                   clus
vv                                                                  STEAP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  STEAP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  STEAP2 MUTATED     5   0   0   1
  STEAP2 WILD-TYPE 306  14  15  23
D584V10, multiclass
    clus
vv   STEAP2 MUTATED STEAP2 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D584V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  STEAP2 MUTATED       2                         0
  STEAP2 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  STEAP2 MUTATED                                           0     4
  STEAP2 WILD-TYPE                                         1   239
D584V12, multiclass
                                           clus
vv                                          STEAP2 MUTATED STEAP2 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D584V13, binary
                  cls
clus                 0   1
  STEAP2 MUTATED     0   6
  STEAP2 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STEAP2 MUTATED      0    6
  STEAP2 WILD-TYPE    4  304
                        clus
vv                       STEAP2 MUTATED STEAP2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(585) Variable = CDKL3 MUTATION ANALYSIS
D585V1, survival
                 sevent
clus2               0   1
  CDKL3 MUTATED     5   2
  CDKL3 WILD-TYPE 225 137
  CDKL3 MUTATED CDKL3 WILD-TYPE 
              7             362 
  CDKL3 MUTATED CDKL3 WILD-TYPE 
              2             137 
$`CDKL3 MUTATED`
TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-8589 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A6EY 
        6.97        32.78        27.12         6.02       105.07        11.44 
TCGA-VQ-A8P2 
       38.14 

$`CDKL3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  CDKL3 MUTATED CDKL3 WILD-TYPE 
           6.02            0.00 
  CDKL3 MUTATED CDKL3 WILD-TYPE 
         105.07          122.30 
  CDKL3 MUTATED CDKL3 WILD-TYPE 
          27.12           14.22 
[1] "6.0 - 105.1 (27.1)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.8"
D585V2, 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       2       15       40       29        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDKL3 MUTATED           0          2          2          0        1
  CDKL3 WILD-TYPE         3         68         51         32       37
D585V3, multiclass
            clus
vv           CDKL3 MUTATED CDKL3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDKL3 MUTATED     0   1   3   3
  CDKL3 WILD-TYPE  22  91 170  94
D585V4, multiclass
    clus
vv   CDKL3 MUTATED CDKL3 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             3             170
  T4             3              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
  CDKL3 MUTATED     1   5   0   1
  CDKL3 WILD-TYPE 117  99  77  76
D585V5, multiclass
    clus
vv   CDKL3 MUTATED CDKL3 WILD-TYPE
  N0             1             117
  N1             5              99
  N2             0              77
  N3             1              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"
D585V6, binary
                 cls
clus                0   1
  CDKL3 MUTATED     6   0
  CDKL3 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL3 MUTATED      6    0
  CDKL3 WILD-TYPE  340   29
   clus
vv  CDKL3 MUTATED CDKL3 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D585V7, binary
                 cls
clus                0   1
  CDKL3 MUTATED     2   5
  CDKL3 WILD-TYPE 143 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL3 MUTATED      2    5
  CDKL3 WILD-TYPE  143  243
        clus
vv       CDKL3 MUTATED CDKL3 WILD-TYPE
  FEMALE             2             143
  MALE               5             243
[1] 2 2
[1] FALSE
D585V8, binary
                 cls
clus                0   1
  CDKL3 MUTATED     6   1
  CDKL3 WILD-TYPE 286  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL3 MUTATED      6    1
  CDKL3 WILD-TYPE  286   58
     clus
vv    CDKL3 MUTATED CDKL3 WILD-TYPE
  NO              6             286
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CDKL3 MUTATED                                          0
  CDKL3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CDKL3 MUTATED                                       0
  CDKL3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDKL3 MUTATED                                                        4
  CDKL3 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CDKL3 MUTATED                                                   1
  CDKL3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDKL3 MUTATED                                                                   1
  CDKL3 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CDKL3 MUTATED                                                    0
  CDKL3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CDKL3 MUTATED                                                  1
  CDKL3 WILD-TYPE                                               60
D585V9, multiclass
                                                                   clus
vv                                                                  CDKL3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  CDKL3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDKL3 MUTATED     6   0   0   1
  CDKL3 WILD-TYPE 305  14  15  23
D585V10, multiclass
    clus
vv   CDKL3 MUTATED CDKL3 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D585V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CDKL3 MUTATED       0                         0
  CDKL3 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDKL3 MUTATED                                           0     5
  CDKL3 WILD-TYPE                                         1   238
D585V12, multiclass
                                           clus
vv                                          CDKL3 MUTATED CDKL3 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D585V13, binary
                 cls
clus                0   1
  CDKL3 MUTATED     0   4
  CDKL3 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL3 MUTATED      0    4
  CDKL3 WILD-TYPE    4  306
                        clus
vv                       CDKL3 MUTATED CDKL3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(586) Variable = FAM113A MUTATION ANALYSIS
D586V1, survival
                   sevent
clus2                 0   1
  FAM113A MUTATED     4   4
  FAM113A WILD-TYPE 226 135
  FAM113A MUTATED FAM113A WILD-TYPE 
                8               361 
  FAM113A MUTATED FAM113A WILD-TYPE 
                4               135 
$`FAM113A MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6457 TCGA-BR-8363 
       21.99         6.97        30.90        34.68        13.68         0.26 
TCGA-CG-5721 TCGA-HU-A4H8 
        6.02        14.07 

$`FAM113A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.87        17.29        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-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-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 

  FAM113A MUTATED FAM113A WILD-TYPE 
             0.26              0.00 
  FAM113A MUTATED FAM113A WILD-TYPE 
            34.68            122.30 
  FAM113A MUTATED FAM113A WILD-TYPE 
           13.875            14.430 
[1] "0.3 - 34.7 (13.9)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.5"
D586V2, 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       2       15       38       30        35        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM113A MUTATED           0          1          0          0        2
  FAM113A WILD-TYPE         3         69         53         32       36
D586V3, multiclass
            clus
vv           FAM113A MUTATED FAM113A WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM113A MUTATED     1   2   4   2
  FAM113A WILD-TYPE  21  90 169  95
D586V4, multiclass
    clus
vv   FAM113A MUTATED FAM113A WILD-TYPE
  T1               1                21
  T2               2                90
  T3               4               169
  T4               2                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
  FAM113A MUTATED     3   4   0   0
  FAM113A WILD-TYPE 115 100  77  77
D586V5, multiclass
    clus
vv   FAM113A MUTATED FAM113A WILD-TYPE
  N0               3               115
  N1               4               100
  N2               0                77
  N3               0                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"
D586V6, binary
                   cls
clus                  0   1
  FAM113A MUTATED     6   1
  FAM113A WILD-TYPE 340  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113A MUTATED      6    1
  FAM113A WILD-TYPE  340   28
   clus
vv  FAM113A MUTATED FAM113A WILD-TYPE
  0               6               340
  1               1                28
[1] 2 2
[1] FALSE
D586V7, binary
                   cls
clus                  0   1
  FAM113A MUTATED     5   4
  FAM113A WILD-TYPE 140 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113A MUTATED      5    4
  FAM113A WILD-TYPE  140  244
        clus
vv       FAM113A MUTATED FAM113A WILD-TYPE
  FEMALE               5               140
  MALE                 4               244
[1] 2 2
[1] FALSE
D586V8, binary
                   cls
clus                  0   1
  FAM113A MUTATED     8   0
  FAM113A WILD-TYPE 284  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113A MUTATED      8    0
  FAM113A WILD-TYPE  284   59
     clus
vv    FAM113A MUTATED FAM113A WILD-TYPE
  NO                8               284
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM113A MUTATED                                          0
  FAM113A WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM113A MUTATED                                       0
  FAM113A WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM113A MUTATED                                                        6
  FAM113A WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM113A MUTATED                                                   0
  FAM113A WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM113A MUTATED                                                                   2
  FAM113A WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM113A MUTATED                                                    0
  FAM113A WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM113A MUTATED                                                  1
  FAM113A WILD-TYPE                                               60
D586V9, multiclass
                                                                   clus
vv                                                                  FAM113A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  FAM113A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM113A MUTATED     5   0   1   3
  FAM113A WILD-TYPE 306  14  14  21
D586V10, multiclass
    clus
vv   FAM113A MUTATED FAM113A WILD-TYPE
  R0               5               306
  R1               0                14
  R2               1                14
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D586V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM113A MUTATED       1                         0
  FAM113A WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM113A MUTATED                                           0     6
  FAM113A WILD-TYPE                                         1   237
D586V12, multiclass
                                           clus
vv                                          FAM113A MUTATED FAM113A WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D586V13, binary
                   cls
clus                  0   1
  FAM113A MUTATED     0   7
  FAM113A WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM113A MUTATED      0    7
  FAM113A WILD-TYPE    4  303
                        clus
vv                       FAM113A MUTATED FAM113A WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(587) Variable = ZNF207 MUTATION ANALYSIS
D587V1, survival
                  sevent
clus2                0   1
  ZNF207 MUTATED     6   2
  ZNF207 WILD-TYPE 224 137
  ZNF207 MUTATED ZNF207 WILD-TYPE 
               8              361 
  ZNF207 MUTATED ZNF207 WILD-TYPE 
               2              137 
$`ZNF207 MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8680 TCGA-BR-A4QL 
       34.68        36.16        14.43        29.59        31.96        16.14 
TCGA-CD-A4MJ TCGA-HF-A5NB 
       12.62        30.51 

$`ZNF207 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  ZNF207 MUTATED ZNF207 WILD-TYPE 
           12.62             0.00 
  ZNF207 MUTATED ZNF207 WILD-TYPE 
           36.16           122.30 
  ZNF207 MUTATED ZNF207 WILD-TYPE 
           30.05            14.07 
[1] "12.6 - 36.2 (30.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.2"
D587V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF207 MUTATED         0        1        1        0         1         1
  ZNF207 WILD-TYPE       2       14       39       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF207 MUTATED           1          0          1          1        1
  ZNF207 WILD-TYPE         2         70         52         31       37
D587V3, multiclass
            clus
vv           ZNF207 MUTATED ZNF207 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               1                2
  STAGE IIIA              0               70
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF207 MUTATED     1   1   2   4
  ZNF207 WILD-TYPE  21  91 171  93
D587V4, multiclass
    clus
vv   ZNF207 MUTATED ZNF207 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              2              171
  T4              4               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
  ZNF207 MUTATED     4   1   1   2
  ZNF207 WILD-TYPE 114 103  76  75
D587V5, multiclass
    clus
vv   ZNF207 MUTATED ZNF207 WILD-TYPE
  N0              4              114
  N1              1              103
  N2              1               76
  N3              2               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"
D587V6, binary
                  cls
clus                 0   1
  ZNF207 MUTATED     7   1
  ZNF207 WILD-TYPE 339  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF207 MUTATED      7    1
  ZNF207 WILD-TYPE  339   28
   clus
vv  ZNF207 MUTATED ZNF207 WILD-TYPE
  0              7              339
  1              1               28
[1] 2 2
[1] FALSE
D587V7, binary
                  cls
clus                 0   1
  ZNF207 MUTATED     4   4
  ZNF207 WILD-TYPE 141 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF207 MUTATED      4    4
  ZNF207 WILD-TYPE  141  244
        clus
vv       ZNF207 MUTATED ZNF207 WILD-TYPE
  FEMALE              4              141
  MALE                4              244
[1] 2 2
[1] FALSE
D587V8, binary
                  cls
clus                 0   1
  ZNF207 MUTATED     7   1
  ZNF207 WILD-TYPE 285  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF207 MUTATED      7    1
  ZNF207 WILD-TYPE  285   58
     clus
vv    ZNF207 MUTATED ZNF207 WILD-TYPE
  NO               7              285
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF207 MUTATED                                          0
  ZNF207 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF207 MUTATED                                       0
  ZNF207 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF207 MUTATED                                                        4
  ZNF207 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF207 MUTATED                                                   1
  ZNF207 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF207 MUTATED                                                                   1
  ZNF207 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF207 MUTATED                                                    1
  ZNF207 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF207 MUTATED                                                  1
  ZNF207 WILD-TYPE                                               60
D587V9, multiclass
                                                                   clus
vv                                                                  ZNF207 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ZNF207 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF207 MUTATED     6   1   0   0
  ZNF207 WILD-TYPE 305  13  15  24
D587V10, multiclass
    clus
vv   ZNF207 MUTATED ZNF207 WILD-TYPE
  R0              6              305
  R1              1               13
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D587V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF207 MUTATED       2                         0
  ZNF207 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF207 MUTATED                                           0     5
  ZNF207 WILD-TYPE                                         1   238
D587V12, multiclass
                                           clus
vv                                          ZNF207 MUTATED ZNF207 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D587V13, binary
                  cls
clus                 0   1
  ZNF207 MUTATED     0   7
  ZNF207 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF207 MUTATED      0    7
  ZNF207 WILD-TYPE    4  303
                        clus
vv                       ZNF207 MUTATED ZNF207 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(588) Variable = ICAM3 MUTATION ANALYSIS
D588V1, survival
                 sevent
clus2               0   1
  ICAM3 MUTATED     1   2
  ICAM3 WILD-TYPE 229 137
  ICAM3 MUTATED ICAM3 WILD-TYPE 
              3             366 
  ICAM3 MUTATED ICAM3 WILD-TYPE 
              2             137 
$`ICAM3 MUTATED`
TCGA-CG-4460 TCGA-BR-4191 TCGA-HF-A5NB 
       21.99        18.35        30.51 

$`ICAM3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  ICAM3 MUTATED ICAM3 WILD-TYPE 
          18.35            0.00 
  ICAM3 MUTATED ICAM3 WILD-TYPE 
          30.51          122.30 
  ICAM3 MUTATED ICAM3 WILD-TYPE 
          21.99           14.12 
[1] "18.4 - 30.5 (22.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D588V2, 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       2       15       40       30        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ICAM3 MUTATED           0          0          0          1        2
  ICAM3 WILD-TYPE         3         70         53         31       36
D588V3, multiclass
            clus
vv           ICAM3 MUTATED ICAM3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ICAM3 MUTATED     0   0   0   3
  ICAM3 WILD-TYPE  22  92 173  94
D588V4, multiclass
    clus
vv   ICAM3 MUTATED ICAM3 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             0             173
  T4             3              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
  ICAM3 MUTATED     0   2   1   1
  ICAM3 WILD-TYPE 118 102  76  76
D588V5, multiclass
    clus
vv   ICAM3 MUTATED ICAM3 WILD-TYPE
  N0             0             118
  N1             2             102
  N2             1              76
  N3             1              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"
D588V6, binary
                 cls
clus                0   1
  ICAM3 MUTATED     3   1
  ICAM3 WILD-TYPE 343  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM3 MUTATED      3    1
  ICAM3 WILD-TYPE  343   28
   clus
vv  ICAM3 MUTATED ICAM3 WILD-TYPE
  0             3             343
  1             1              28
[1] 2 2
[1] FALSE
D588V7, binary
                 cls
clus                0   1
  ICAM3 MUTATED     3   1
  ICAM3 WILD-TYPE 142 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM3 MUTATED      3    1
  ICAM3 WILD-TYPE  142  247
        clus
vv       ICAM3 MUTATED ICAM3 WILD-TYPE
  FEMALE             3             142
  MALE               1             247
[1] 2 2
[1] FALSE
D588V8, binary
                 cls
clus                0   1
  ICAM3 MUTATED     2   1
  ICAM3 WILD-TYPE 290  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM3 MUTATED      2    1
  ICAM3 WILD-TYPE  290   58
     clus
vv    ICAM3 MUTATED ICAM3 WILD-TYPE
  NO              2             290
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ICAM3 MUTATED                                          0
  ICAM3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ICAM3 MUTATED                                       0
  ICAM3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ICAM3 MUTATED                                                        2
  ICAM3 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ICAM3 MUTATED                                                   1
  ICAM3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ICAM3 MUTATED                                                                   1
  ICAM3 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ICAM3 MUTATED                                                    0
  ICAM3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ICAM3 MUTATED                                                  0
  ICAM3 WILD-TYPE                                               61
D588V9, multiclass
                                                                   clus
vv                                                                  ICAM3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  ICAM3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ICAM3 MUTATED     0   1   1   2
  ICAM3 WILD-TYPE 311  13  14  22
D588V10, multiclass
    clus
vv   ICAM3 MUTATED ICAM3 WILD-TYPE
  R0             0             311
  R1             1              13
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D588V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ICAM3 MUTATED       0                         0
  ICAM3 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ICAM3 MUTATED                                           0     2
  ICAM3 WILD-TYPE                                         1   241
D588V12, multiclass
[1] "Remove cluster labels:" "ICAM3 MUTATED"         
clus
  ICAM3 MUTATED ICAM3 WILD-TYPE 
              2             338 
     TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-FP-A8CX      TCGA-KB-A93G 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-MX-A663      TCGA-B7-5816      TCGA-B7-5818      TCGA-B7-A5TI 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-B7-A5TJ      TCGA-B7-A5TK      TCGA-B7-A5TN      TCGA-BR-4183 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-4184      TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4201 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4362 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4369      TCGA-BR-4370 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453      TCGA-BR-6454 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457      TCGA-BR-6458 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565      TCGA-BR-6566 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707      TCGA-BR-6709 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-7704      TCGA-BR-7707      TCGA-BR-7715      TCGA-BR-7716 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-7717      TCGA-BR-7722      TCGA-BR-7723      TCGA-BR-7851 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-7901      TCGA-BR-7957      TCGA-BR-7958      TCGA-BR-7959 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-8058      TCGA-BR-8059      TCGA-BR-8060      TCGA-BR-8077 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-8078      TCGA-BR-8080      TCGA-BR-8081      TCGA-BR-8284 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-8285      TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-8295      TCGA-BR-8297      TCGA-BR-8360      TCGA-BR-8361 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373      TCGA-BR-8380 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-A4J4      TCGA-BR-A4J5      TCGA-BR-A4J6      TCGA-BR-A4J7 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-BR-A4QI      TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5798 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-CD-5799      TCGA-CD-5800      TCGA-CD-5801      TCGA-CD-5802 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-CD-5803      TCGA-CD-5804      TCGA-CD-5813      TCGA-CD-8524 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-CD-8525      TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-CD-8529      TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-CD-8533      TCGA-CD-8534      TCGA-CD-8535      TCGA-CD-8536 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-CD-A486      TCGA-CD-A487      TCGA-CD-A489      TCGA-CD-A48A 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-CD-A48C      TCGA-CD-A4MG      TCGA-CD-A4MH      TCGA-CD-A4MI 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-CD-A4MJ      TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-D7-6518      TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-D7-8572      TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-D7-8576      TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-D7-A4YU      TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-D7-A4Z0      TCGA-D7-A6ET      TCGA-D7-A6EV      TCGA-D7-A6EX 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-D7-A6EY      TCGA-D7-A6EZ      TCGA-D7-A6F0      TCGA-D7-A6F2 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-D7-A747      TCGA-D7-A748      TCGA-D7-A74A      TCGA-D7-A74B 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-EQ-5647      TCGA-EQ-8122      TCGA-F1-6874      TCGA-F1-6875 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-F1-A448      TCGA-F1-A72C      TCGA-FP-7735      TCGA-FP-7829 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BE 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-FP-A4BF      TCGA-FP-A9TM      TCGA-HJ-7597      TCGA-HU-8238 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-HU-8243      TCGA-HU-8244      TCGA-HU-8249      TCGA-HU-8602 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610      TCGA-HU-A4G2 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8      TCGA-HU-A4G9 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF      TCGA-HU-A4GH 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-HU-A4GJ      TCGA-HU-A4GN      TCGA-HU-A4GP      TCGA-HU-A4GQ 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX      TCGA-HU-A4GY 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3      TCGA-HU-A4H4 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8      TCGA-HU-A4HB 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-IN-8663      TCGA-IN-A6RI      TCGA-IN-A6RJ      TCGA-IN-A6RL 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-IN-A6RN      TCGA-IN-A6RO      TCGA-IN-A6RP      TCGA-IN-A6RR 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-IN-A6RS      TCGA-IN-A7NR      TCGA-IN-A7NT      TCGA-IN-A7NU 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-IN-AB1V      TCGA-IN-AB1X      TCGA-IP-7968      TCGA-KB-A93J 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-MX-A5UG      TCGA-MX-A5UJ      TCGA-MX-A666      TCGA-R5-A7O7 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-R5-A7ZE      TCGA-R5-A7ZF      TCGA-R5-A7ZI      TCGA-R5-A7ZR 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-R5-A804      TCGA-R5-A805      TCGA-RD-A7BS      TCGA-RD-A7BT 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-RD-A7BW      TCGA-RD-A7C1      TCGA-RD-A8MV      TCGA-RD-A8MW 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-RD-A8N0      TCGA-RD-A8N1      TCGA-RD-A8N2      TCGA-RD-A8N4 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-RD-A8N5      TCGA-RD-A8N6      TCGA-RD-A8N9      TCGA-SW-A7EA 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-SW-A7EB      TCGA-VQ-A8DL      TCGA-VQ-A8DU      TCGA-VQ-A8DV 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-VQ-A8DZ      TCGA-VQ-A8E2      TCGA-VQ-A8E7      TCGA-VQ-A8P2 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-VQ-A8P3      TCGA-VQ-A8PE      TCGA-VQ-A8PK      TCGA-VQ-A8PM 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-VQ-A8PQ      TCGA-VQ-A91U      TCGA-VQ-A92D      TCGA-VQ-AA64 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-VQ-AA68      TCGA-VQ-AA69      TCGA-VQ-AA6A      TCGA-VQ-AA6B 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-VQ-AA6F      TCGA-VQ-AA6G      TCGA-VQ-AA6I      TCGA-VQ-AA6J 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
     TCGA-VQ-AA6K      TCGA-ZA-A8F6 
"ICAM3 WILD-TYPE" "ICAM3 WILD-TYPE" 
D588V13, binary
                 cls
clus                0   1
  ICAM3 MUTATED     0   2
  ICAM3 WILD-TYPE   4 308
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM3 MUTATED      0    2
  ICAM3 WILD-TYPE    4  308
                        clus
vv                       ICAM3 MUTATED ICAM3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             2             308
[1] 2 2
[1] FALSE

Clustering(589) Variable = MKL1 MUTATION ANALYSIS
D589V1, survival
                sevent
clus2              0   1
  MKL1 MUTATED    10   2
  MKL1 WILD-TYPE 220 137
  MKL1 MUTATED MKL1 WILD-TYPE 
            12            357 
  MKL1 MUTATED MKL1 WILD-TYPE 
             2            137 
$`MKL1 MUTATED`
TCGA-B7-A5TI TCGA-BR-8680 TCGA-CD-8525 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 
       19.56        31.96        12.59       105.07        65.10        21.07 
TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GQ TCGA-HU-A4H8 
       30.51        22.32        22.68         3.25         0.10        14.07 

$`MKL1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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 

  MKL1 MUTATED MKL1 WILD-TYPE 
           0.1            0.0 
  MKL1 MUTATED MKL1 WILD-TYPE 
        105.07         122.30 
  MKL1 MUTATED MKL1 WILD-TYPE 
        21.695         14.070 
[1] "0.1 - 105.1 (21.7)" "0.0 - 122.3 (14.1)"
[1] "hr=" "3.1"
D589V2, 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       2       15       38       29        37        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MKL1 MUTATED           0          3          1          3        1
  MKL1 WILD-TYPE         3         67         52         29       37
D589V3, multiclass
            clus
vv           MKL1 MUTATED MKL1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             0             37
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            1             52
  STAGE IIIC            3             29
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MKL1 MUTATED     1   3   2   7
  MKL1 WILD-TYPE  21  89 171  90
D589V4, multiclass
    clus
vv   MKL1 MUTATED MKL1 WILD-TYPE
  T1            1             21
  T2            3             89
  T3            2            171
  T4            7             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
  MKL1 MUTATED     3   5   4   2
  MKL1 WILD-TYPE 115  99  73  75
D589V5, multiclass
    clus
vv   MKL1 MUTATED MKL1 WILD-TYPE
  N0            3            115
  N1            5             99
  N2            4             73
  N3            2             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"
D589V6, binary
                cls
clus               0   1
  MKL1 MUTATED    14   1
  MKL1 WILD-TYPE 332  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED     14    1
  MKL1 WILD-TYPE  332   28
   clus
vv  MKL1 MUTATED MKL1 WILD-TYPE
  0           14            332
  1            1             28
[1] 2 2
[1] FALSE
D589V7, binary
                cls
clus               0   1
  MKL1 MUTATED     8   7
  MKL1 WILD-TYPE 137 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED      8    7
  MKL1 WILD-TYPE  137  241
        clus
vv       MKL1 MUTATED MKL1 WILD-TYPE
  FEMALE            8            137
  MALE              7            241
[1] 2 2
[1] FALSE
D589V8, binary
                cls
clus               0   1
  MKL1 MUTATED     9   2
  MKL1 WILD-TYPE 283  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED      9    2
  MKL1 WILD-TYPE  283   57
     clus
vv    MKL1 MUTATED MKL1 WILD-TYPE
  NO             9            283
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MKL1 MUTATED                                          0
  MKL1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MKL1 MUTATED                                       4
  MKL1 WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MKL1 MUTATED                                                        4
  MKL1 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MKL1 MUTATED                                                   2
  MKL1 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MKL1 MUTATED                                                                   2
  MKL1 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MKL1 MUTATED                                                    0
  MKL1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MKL1 MUTATED                                                  3
  MKL1 WILD-TYPE                                               58
D589V9, multiclass
                                                                   clus
vv                                                                  MKL1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  MKL1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MKL1 MUTATED     9   1   0   3
  MKL1 WILD-TYPE 302  13  15  21
D589V10, multiclass
    clus
vv   MKL1 MUTATED MKL1 WILD-TYPE
  R0            9            302
  R1            1             13
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D589V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MKL1 MUTATED       7                         0
  MKL1 WILD-TYPE    80                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MKL1 MUTATED                                           0     4
  MKL1 WILD-TYPE                                         1   239
D589V12, multiclass
                                           clus
vv                                          MKL1 MUTATED MKL1 WILD-TYPE
  ASIAN                                                7             80
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D589V13, binary
                cls
clus               0   1
  MKL1 MUTATED     0  11
  MKL1 WILD-TYPE   4 299
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED      0   11
  MKL1 WILD-TYPE    4  299
                        clus
vv                       MKL1 MUTATED MKL1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           11            299
[1] 2 2
[1] FALSE

Clustering(590) Variable = HSP90AA1 MUTATION ANALYSIS
D590V1, survival
                    sevent
clus2                  0   1
  HSP90AA1 MUTATED     9   2
  HSP90AA1 WILD-TYPE 221 137
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                11                358 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                 2                137 
$`HSP90AA1 MUTATED`
TCGA-BR-7196 TCGA-BR-7716 TCGA-BR-8078 TCGA-CG-5733 TCGA-D7-A4YU TCGA-D7-A4YY 
       21.90        39.78        29.59        21.07        16.44        13.78 
TCGA-F1-6874 TCGA-FP-A4BF TCGA-HU-A4H3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       14.47         5.52        29.00        38.14        37.22 

$`HSP90AA1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-7197 TCGA-BR-7703 
       40.21        30.90        31.20        44.94         9.21        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       35.24        35.84        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-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-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91        14.27         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-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB 
       11.08         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-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-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 

  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
              5.52               0.00 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
             39.78             122.30 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
            21.900             14.055 
[1] "5.5 - 39.8 (21.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.9"
D590V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HSP90AA1 MUTATED         1        0        1        0         0         2
  HSP90AA1 WILD-TYPE       1       15       39       30        37        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSP90AA1 MUTATED           0          4          2          1        1
  HSP90AA1 WILD-TYPE         3         66         51         31       37
D590V3, multiclass
            clus
vv           HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 0                 37
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                4                 66
  STAGE IIIB                2                 51
  STAGE IIIC                1                 31
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HSP90AA1 MUTATED     1   2   5   4
  HSP90AA1 WILD-TYPE  21  90 168  93
D590V4, multiclass
    clus
vv   HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  T1                1                 21
  T2                2                 90
  T3                5                168
  T4                4                 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
  HSP90AA1 MUTATED     2   4   2   4
  HSP90AA1 WILD-TYPE 116 100  75  73
D590V5, multiclass
    clus
vv   HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  N0                2                116
  N1                4                100
  N2                2                 75
  N3                4                 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"
D590V6, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED    10   1
  HSP90AA1 WILD-TYPE 336  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED     10    1
  HSP90AA1 WILD-TYPE  336   28
   clus
vv  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  0               10                336
  1                1                 28
[1] 2 2
[1] FALSE
D590V7, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED     4   8
  HSP90AA1 WILD-TYPE 141 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      4    8
  HSP90AA1 WILD-TYPE  141  240
        clus
vv       HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  FEMALE                4                141
  MALE                  8                240
[1] 2 2
[1] FALSE
D590V8, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED     8   3
  HSP90AA1 WILD-TYPE 284  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      8    3
  HSP90AA1 WILD-TYPE  284   56
     clus
vv    HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  NO                 8                284
  YES                3                 56
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HSP90AA1 MUTATED                                          1
  HSP90AA1 WILD-TYPE                                        7
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HSP90AA1 MUTATED                                       1
  HSP90AA1 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HSP90AA1 MUTATED                                                        5
  HSP90AA1 WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HSP90AA1 MUTATED                                                   1
  HSP90AA1 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HSP90AA1 MUTATED                                                                   2
  HSP90AA1 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HSP90AA1 MUTATED                                                    0
  HSP90AA1 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HSP90AA1 MUTATED                                                  2
  HSP90AA1 WILD-TYPE                                               59
D590V9, multiclass
                                                                   clus
vv                                                                  HSP90AA1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  HSP90AA1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HSP90AA1 MUTATED    11   1   0   0
  HSP90AA1 WILD-TYPE 300  13  15  24
D590V10, multiclass
    clus
vv   HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  R0               11                300
  R1                1                 13
  R2                0                 15
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D590V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  HSP90AA1 MUTATED       1                         1
  HSP90AA1 WILD-TYPE    86                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HSP90AA1 MUTATED                                           0     9
  HSP90AA1 WILD-TYPE                                         1   234
D590V12, multiclass
                                           clus
vv                                          HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    9                234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D590V13, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED     0   9
  HSP90AA1 WILD-TYPE   4 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      0    9
  HSP90AA1 WILD-TYPE    4  301
                        clus
vv                       HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                9                301
[1] 2 2
[1] FALSE

Clustering(591) Variable = PRPF4B MUTATION ANALYSIS
D591V1, survival
                  sevent
clus2                0   1
  PRPF4B MUTATED     6   1
  PRPF4B WILD-TYPE 224 138
  PRPF4B MUTATED PRPF4B WILD-TYPE 
               7              362 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
               1              138 
$`PRPF4B MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8368 TCGA-BR-8678 TCGA-BR-A4QL 
       34.68        44.94        36.16         4.31        24.79        16.14 
TCGA-CG-5728 
       65.10 

$`PRPF4B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53        26.73        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-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 

  PRPF4B MUTATED PRPF4B WILD-TYPE 
            4.31             0.00 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
            65.1            122.3 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
           34.68            14.07 
[1] "4.3 - 65.1 (34.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "4.1"
D591V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRPF4B MUTATED         0        1        3        0         2         0
  PRPF4B WILD-TYPE       2       14       37       30        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRPF4B MUTATED           0          1          1          0        1
  PRPF4B WILD-TYPE         3         69         52         32       37
D591V3, multiclass
            clus
vv           PRPF4B MUTATED PRPF4B WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                3               37
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PRPF4B MUTATED     1   3   3   2
  PRPF4B WILD-TYPE  21  89 170  95
D591V4, multiclass
    clus
vv   PRPF4B MUTATED PRPF4B WILD-TYPE
  T1              1               21
  T2              3               89
  T3              3              170
  T4              2               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
  PRPF4B MUTATED     7   1   1   1
  PRPF4B WILD-TYPE 111 103  76  76
D591V5, multiclass
    clus
vv   PRPF4B MUTATED PRPF4B WILD-TYPE
  N0              7              111
  N1              1              103
  N2              1               76
  N3              1               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"
D591V6, binary
                  cls
clus                 0   1
  PRPF4B MUTATED    10   0
  PRPF4B WILD-TYPE 336  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED     10    0
  PRPF4B WILD-TYPE  336   29
   clus
vv  PRPF4B MUTATED PRPF4B WILD-TYPE
  0             10              336
  1              0               29
[1] 2 2
[1] FALSE
D591V7, binary
                  cls
clus                 0   1
  PRPF4B MUTATED     8   2
  PRPF4B WILD-TYPE 137 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED      8    2
  PRPF4B WILD-TYPE  137  246
        clus
vv       PRPF4B MUTATED PRPF4B WILD-TYPE
  FEMALE              8              137
  MALE                2              246
[1] 2 2
[1] FALSE
D591V8, binary
                  cls
clus                 0   1
  PRPF4B MUTATED     6   0
  PRPF4B WILD-TYPE 286  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED      6    0
  PRPF4B WILD-TYPE  286   59
     clus
vv    PRPF4B MUTATED PRPF4B WILD-TYPE
  NO               6              286
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PRPF4B MUTATED                                          0
  PRPF4B WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PRPF4B MUTATED                                       0
  PRPF4B WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRPF4B MUTATED                                                        8
  PRPF4B WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PRPF4B MUTATED                                                   0
  PRPF4B WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRPF4B MUTATED                                                                   1
  PRPF4B WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PRPF4B MUTATED                                                    1
  PRPF4B WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PRPF4B MUTATED                                                  0
  PRPF4B WILD-TYPE                                               61
D591V9, multiclass
                                                                   clus
vv                                                                  PRPF4B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  PRPF4B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PRPF4B MUTATED     7   0   0   3
  PRPF4B WILD-TYPE 304  14  15  21
D591V10, multiclass
    clus
vv   PRPF4B MUTATED PRPF4B WILD-TYPE
  R0              7              304
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D591V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PRPF4B MUTATED       0                         0
  PRPF4B WILD-TYPE    87                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRPF4B MUTATED                                           0     9
  PRPF4B WILD-TYPE                                         1   234
D591V12, multiclass
                                           clus
vv                                          PRPF4B MUTATED PRPF4B WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D591V13, binary
                  cls
clus                 0   1
  PRPF4B MUTATED     0   9
  PRPF4B WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED      0    9
  PRPF4B WILD-TYPE    4  301
                        clus
vv                       PRPF4B MUTATED PRPF4B WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(592) Variable = BRCA2 MUTATION ANALYSIS
D592V1, survival
                 sevent
clus2               0   1
  BRCA2 MUTATED    22   7
  BRCA2 WILD-TYPE 208 132
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             29             340 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              7             132 
$`BRCA2 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8361 
        6.97        34.68        44.94        29.59         6.18        31.10 
TCGA-BR-8368 TCGA-BR-8384 TCGA-BR-8680 TCGA-CD-8529 TCGA-CD-A48C TCGA-CD-A4MG 
        4.31         3.72        31.96        12.30        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5733 
       11.77        12.62        15.95         6.02        65.10        21.07 
TCGA-D7-6520 TCGA-D7-A4YT TCGA-D7-A6EZ TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4G8 
       18.84        14.27        20.32        77.29        22.32        22.68 
TCGA-HU-A4GN TCGA-HU-A4GU TCGA-IN-A6RL TCGA-IN-A6RP TCGA-VQ-A8P2 
       29.98         6.58        13.35         6.44        38.14 

$`BRCA2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-A4MH TCGA-CG-4300 TCGA-CG-4301 
       12.30        11.31        12.43        12.20        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-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-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        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-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-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-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-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 

  BRCA2 MUTATED BRCA2 WILD-TYPE 
           3.72            0.00 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
          77.29          122.30 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
          15.95           14.12 
[1] "3.7 - 77.3 (15.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D592V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRCA2 MUTATED         0        1        3        2         5         5
  BRCA2 WILD-TYPE       2       14       37       28        32        47
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BRCA2 MUTATED           0          9          0          3        4
  BRCA2 WILD-TYPE         3         61         53         29       34
D592V3, multiclass
            clus
vv           BRCA2 MUTATED BRCA2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               2              28
  STAGE IIA              5              32
  STAGE IIB              5              47
  STAGE III              0               3
  STAGE IIIA             9              61
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BRCA2 MUTATED     2  10  10  10
  BRCA2 WILD-TYPE  20  82 163  87
D592V4, multiclass
    clus
vv   BRCA2 MUTATED BRCA2 WILD-TYPE
  T1             2              20
  T2            10              82
  T3            10             163
  T4            10              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
  BRCA2 MUTATED    12  12   7   2
  BRCA2 WILD-TYPE 106  92  70  75
D592V5, multiclass
    clus
vv   BRCA2 MUTATED BRCA2 WILD-TYPE
  N0            12             106
  N1            12              92
  N2             7              70
  N3             2              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"
D592V6, binary
                 cls
clus                0   1
  BRCA2 MUTATED    30   2
  BRCA2 WILD-TYPE 316  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     30    2
  BRCA2 WILD-TYPE  316   27
   clus
vv  BRCA2 MUTATED BRCA2 WILD-TYPE
  0            30             316
  1             2              27
[1] 2 2
[1] FALSE
D592V7, binary
                 cls
clus                0   1
  BRCA2 MUTATED    13  20
  BRCA2 WILD-TYPE 132 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     13   20
  BRCA2 WILD-TYPE  132  228
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  FEMALE            13             132
  MALE              20             228
[1] 2 2
[1] FALSE
D592V8, binary
                 cls
clus                0   1
  BRCA2 MUTATED    24   5
  BRCA2 WILD-TYPE 268  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     24    5
  BRCA2 WILD-TYPE  268   54
     clus
vv    BRCA2 MUTATED BRCA2 WILD-TYPE
  NO             24             268
  YES             5              54
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BRCA2 MUTATED                                          0
  BRCA2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BRCA2 MUTATED                                       4
  BRCA2 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BRCA2 MUTATED                                                       17
  BRCA2 WILD-TYPE                                                    141
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BRCA2 MUTATED                                                   3
  BRCA2 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BRCA2 MUTATED                                                                   5
  BRCA2 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BRCA2 MUTATED                                                    0
  BRCA2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BRCA2 MUTATED                                                  4
  BRCA2 WILD-TYPE                                               57
D592V9, multiclass
                                                                   clus
vv                                                                  BRCA2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       17
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  BRCA2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        141
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BRCA2 MUTATED    24   0   0   4
  BRCA2 WILD-TYPE 287  14  15  20
D592V10, multiclass
    clus
vv   BRCA2 MUTATED BRCA2 WILD-TYPE
  R0            24             287
  R1             0              14
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D592V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BRCA2 MUTATED      11                         0
  BRCA2 WILD-TYPE    76                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRCA2 MUTATED                                           0    17
  BRCA2 WILD-TYPE                                         1   226
D592V12, multiclass
                                           clus
vv                                          BRCA2 MUTATED BRCA2 WILD-TYPE
  ASIAN                                                11              76
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D592V13, binary
                 cls
clus                0   1
  BRCA2 MUTATED     0  27
  BRCA2 WILD-TYPE   4 283
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED      0   27
  BRCA2 WILD-TYPE    4  283
                        clus
vv                       BRCA2 MUTATED BRCA2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            27             283
[1] 2 2
[1] FALSE

Clustering(593) Variable = MAP3K1 MUTATION ANALYSIS
D593V1, survival
                  sevent
clus2                0   1
  MAP3K1 MUTATED     6   8
  MAP3K1 WILD-TYPE 224 131
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
              14              355 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
               8              131 
$`MAP3K1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6852 TCGA-BR-8360 TCGA-BR-8680 
        6.97        30.90         6.61        44.94         6.18        31.96 
TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5733 TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77         6.02        28.96        21.07         0.10         6.51 
TCGA-HU-A4H8 TCGA-VQ-A8PQ 
       14.07        15.65 

$`MAP3K1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-5734 TCGA-D7-5577 
       15.02        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-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-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-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 

  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
             0.1              0.0 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
           44.94           122.30 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
           12.92            14.43 
[1] "0.1 - 44.9 (12.9)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.7"
D593V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP3K1 MUTATED         0        1        1        0         3         1
  MAP3K1 WILD-TYPE       2       14       39       30        34        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP3K1 MUTATED           1          3          0          1        3
  MAP3K1 WILD-TYPE         2         67         53         31       35
D593V3, multiclass
            clus
vv           MAP3K1 MUTATED MAP3K1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               1               51
  STAGE III               1                2
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP3K1 MUTATED     2   3   5   5
  MAP3K1 WILD-TYPE  20  89 168  92
D593V4, multiclass
    clus
vv   MAP3K1 MUTATED MAP3K1 WILD-TYPE
  T1              2               20
  T2              3               89
  T3              5              168
  T4              5               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
  MAP3K1 MUTATED     5   6   3   0
  MAP3K1 WILD-TYPE 113  98  74  77
D593V5, multiclass
    clus
vv   MAP3K1 MUTATED MAP3K1 WILD-TYPE
  N0              5              113
  N1              6               98
  N2              3               74
  N3              0               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"
D593V6, binary
                  cls
clus                 0   1
  MAP3K1 MUTATED    12   2
  MAP3K1 WILD-TYPE 334  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K1 MUTATED     12    2
  MAP3K1 WILD-TYPE  334   27
   clus
vv  MAP3K1 MUTATED MAP3K1 WILD-TYPE
  0             12              334
  1              2               27
[1] 2 2
[1] FALSE
D593V7, binary
                  cls
clus                 0   1
  MAP3K1 MUTATED     6   9
  MAP3K1 WILD-TYPE 139 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K1 MUTATED      6    9
  MAP3K1 WILD-TYPE  139  239
        clus
vv       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  FEMALE              6              139
  MALE                9              239
[1] 2 2
[1] FALSE
D593V8, binary
                  cls
clus                 0   1
  MAP3K1 MUTATED    14   0
  MAP3K1 WILD-TYPE 278  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K1 MUTATED     14    0
  MAP3K1 WILD-TYPE  278   59
     clus
vv    MAP3K1 MUTATED MAP3K1 WILD-TYPE
  NO              14              278
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MAP3K1 MUTATED                                          0
  MAP3K1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MAP3K1 MUTATED                                       0
  MAP3K1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP3K1 MUTATED                                                        5
  MAP3K1 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MAP3K1 MUTATED                                                   0
  MAP3K1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP3K1 MUTATED                                                                   5
  MAP3K1 WILD-TYPE                                                                63
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MAP3K1 MUTATED                                                    0
  MAP3K1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MAP3K1 MUTATED                                                  5
  MAP3K1 WILD-TYPE                                               56
D593V9, multiclass
                                                                   clus
vv                                                                  MAP3K1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               5
                                                                   clus
vv                                                                  MAP3K1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP3K1 MUTATED    10   0   1   3
  MAP3K1 WILD-TYPE 301  14  14  21
D593V10, multiclass
    clus
vv   MAP3K1 MUTATED MAP3K1 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              1               14
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAP3K1 MUTATED       5                         0
  MAP3K1 WILD-TYPE    82                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP3K1 MUTATED                                           0     7
  MAP3K1 WILD-TYPE                                         1   236
D593V12, multiclass
                                           clus
vv                                          MAP3K1 MUTATED MAP3K1 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V13, binary
                  cls
clus                 0   1
  MAP3K1 MUTATED     0  11
  MAP3K1 WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K1 MUTATED      0   11
  MAP3K1 WILD-TYPE    4  299
                        clus
vv                       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(594) Variable = ASPN MUTATION ANALYSIS
D594V1, survival
                sevent
clus2              0   1
  ASPN MUTATED     4   2
  ASPN WILD-TYPE 226 137
  ASPN MUTATED ASPN WILD-TYPE 
             6            363 
  ASPN MUTATED ASPN WILD-TYPE 
             2            137 
$`ASPN MUTATED`
TCGA-BR-7703 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8680 TCGA-CG-4306 
       36.16        32.25         0.26        31.27        31.96         1.02 

$`ASPN WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  ASPN MUTATED ASPN WILD-TYPE 
          0.26           0.00 
  ASPN MUTATED ASPN WILD-TYPE 
         36.16         122.30 
  ASPN MUTATED ASPN WILD-TYPE 
        31.615         14.170 
[1] "0.3 - 36.2 (31.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D594V2, 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       2       14       39       30        37        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ASPN MUTATED           0          0          0          1        2
  ASPN WILD-TYPE         3         70         53         31       36
D594V3, multiclass
            clus
vv           ASPN MUTATED ASPN WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ASPN MUTATED     1   1   1   3
  ASPN WILD-TYPE  21  91 172  94
D594V4, multiclass
    clus
vv   ASPN MUTATED ASPN WILD-TYPE
  T1            1             21
  T2            1             91
  T3            1            172
  T4            3             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
  ASPN MUTATED     3   0   2   1
  ASPN WILD-TYPE 115 104  75  76
D594V5, multiclass
    clus
vv   ASPN MUTATED ASPN WILD-TYPE
  N0            3            115
  N1            0            104
  N2            2             75
  N3            1             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"
D594V6, binary
                cls
clus               0   1
  ASPN MUTATED     4   2
  ASPN WILD-TYPE 342  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      4    2
  ASPN WILD-TYPE  342   27
   clus
vv  ASPN MUTATED ASPN WILD-TYPE
  0            4            342
  1            2             27
[1] 2 2
[1] FALSE
D594V7, binary
                cls
clus               0   1
  ASPN MUTATED     2   4
  ASPN WILD-TYPE 143 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      2    4
  ASPN WILD-TYPE  143  244
        clus
vv       ASPN MUTATED ASPN WILD-TYPE
  FEMALE            2            143
  MALE              4            244
[1] 2 2
[1] FALSE
D594V8, binary
                cls
clus               0   1
  ASPN MUTATED     5   0
  ASPN WILD-TYPE 287  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      5    0
  ASPN WILD-TYPE  287   59
     clus
vv    ASPN MUTATED ASPN WILD-TYPE
  NO             5            287
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ASPN MUTATED                                          0
  ASPN WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ASPN MUTATED                                       0
  ASPN WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ASPN MUTATED                                                        4
  ASPN WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ASPN MUTATED                                                   0
  ASPN WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ASPN MUTATED                                                                   0
  ASPN WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ASPN MUTATED                                                    1
  ASPN WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ASPN MUTATED                                                  1
  ASPN WILD-TYPE                                               60
D594V9, multiclass
                                                                   clus
vv                                                                  ASPN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  ASPN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ASPN MUTATED     5   0   1   0
  ASPN WILD-TYPE 306  14  14  24
D594V10, multiclass
    clus
vv   ASPN MUTATED ASPN WILD-TYPE
  R0            5            306
  R1            0             14
  R2            1             14
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D594V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ASPN MUTATED       1                         0
  ASPN WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ASPN MUTATED                                           0     4
  ASPN WILD-TYPE                                         1   239
D594V12, multiclass
                                           clus
vv                                          ASPN MUTATED ASPN WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D594V13, binary
                cls
clus               0   1
  ASPN MUTATED     0   5
  ASPN WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPN MUTATED      0    5
  ASPN WILD-TYPE    4  305
                        clus
vv                       ASPN MUTATED ASPN WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(595) Variable = PHACTR1 MUTATION ANALYSIS
D595V1, survival
                   sevent
clus2                 0   1
  PHACTR1 MUTATED     2   5
  PHACTR1 WILD-TYPE 228 134
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                7               362 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                5               134 
$`PHACTR1 MUTATED`
TCGA-BR-4280 TCGA-BR-8059 TCGA-BR-A4QL TCGA-CG-4305 TCGA-D7-A6EY TCGA-HU-A4GQ 
        6.61        14.43        16.14        15.95        11.44         0.10 
TCGA-VQ-A8P2 
       38.14 

$`PHACTR1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
              0.1               0.0 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
            38.14            122.30 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
            14.43             14.22 
[1] "0.1 - 38.1 (14.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.4"
D595V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHACTR1 MUTATED         1        0        0        1         0         0
  PHACTR1 WILD-TYPE       1       15       40       29        37        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHACTR1 MUTATED           2          2          2          1        0
  PHACTR1 WILD-TYPE         1         68         51         31       38
D595V3, multiclass
            clus
vv           PHACTR1 MUTATED PHACTR1 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 1                29
  STAGE IIA                0                37
  STAGE IIB                0                52
  STAGE III                2                 1
  STAGE IIIA               2                68
  STAGE IIIB               2                51
  STAGE IIIC               1                31
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PHACTR1 MUTATED     1   2   2   4
  PHACTR1 WILD-TYPE  21  90 171  93
D595V4, multiclass
    clus
vv   PHACTR1 MUTATED PHACTR1 WILD-TYPE
  T1               1                21
  T2               2                90
  T3               2               171
  T4               4                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
  PHACTR1 MUTATED     1   5   1   2
  PHACTR1 WILD-TYPE 117  99  76  75
D595V5, multiclass
    clus
vv   PHACTR1 MUTATED PHACTR1 WILD-TYPE
  N0               1               117
  N1               5                99
  N2               1                76
  N3               2                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"
D595V6, binary
                   cls
clus                  0   1
  PHACTR1 MUTATED     9   0
  PHACTR1 WILD-TYPE 337  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR1 MUTATED      9    0
  PHACTR1 WILD-TYPE  337   29
   clus
vv  PHACTR1 MUTATED PHACTR1 WILD-TYPE
  0               9               337
  1               0                29
[1] 2 2
[1] FALSE
D595V7, binary
                   cls
clus                  0   1
  PHACTR1 MUTATED     5   5
  PHACTR1 WILD-TYPE 140 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR1 MUTATED      5    5
  PHACTR1 WILD-TYPE  140  243
        clus
vv       PHACTR1 MUTATED PHACTR1 WILD-TYPE
  FEMALE               5               140
  MALE                 5               243
[1] 2 2
[1] FALSE
D595V8, binary
                   cls
clus                  0   1
  PHACTR1 MUTATED     7   1
  PHACTR1 WILD-TYPE 285  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR1 MUTATED      7    1
  PHACTR1 WILD-TYPE  285   58
     clus
vv    PHACTR1 MUTATED PHACTR1 WILD-TYPE
  NO                7               285
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PHACTR1 MUTATED                                          0
  PHACTR1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PHACTR1 MUTATED                                       0
  PHACTR1 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PHACTR1 MUTATED                                                        6
  PHACTR1 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PHACTR1 MUTATED                                                   1
  PHACTR1 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PHACTR1 MUTATED                                                                   1
  PHACTR1 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PHACTR1 MUTATED                                                    0
  PHACTR1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PHACTR1 MUTATED                                                  2
  PHACTR1 WILD-TYPE                                               59
D595V9, multiclass
                                                                   clus
vv                                                                  PHACTR1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  PHACTR1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PHACTR1 MUTATED     7   0   0   3
  PHACTR1 WILD-TYPE 304  14  15  21
D595V10, multiclass
    clus
vv   PHACTR1 MUTATED PHACTR1 WILD-TYPE
  R0               7               304
  R1               0                14
  R2               0                15
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D595V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PHACTR1 MUTATED       1                         1
  PHACTR1 WILD-TYPE    86                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PHACTR1 MUTATED                                           0     7
  PHACTR1 WILD-TYPE                                         1   236
D595V12, multiclass
                                           clus
vv                                          PHACTR1 MUTATED PHACTR1 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D595V13, binary
                   cls
clus                  0   1
  PHACTR1 MUTATED     0   8
  PHACTR1 WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR1 MUTATED      0    8
  PHACTR1 WILD-TYPE    4  302
                        clus
vv                       PHACTR1 MUTATED PHACTR1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(596) Variable = DNAJB13 MUTATION ANALYSIS
D596V1, survival
                   sevent
clus2                 0   1
  DNAJB13 MUTATED     2   2
  DNAJB13 WILD-TYPE 228 137
  DNAJB13 MUTATED DNAJB13 WILD-TYPE 
                4               365 
  DNAJB13 MUTATED DNAJB13 WILD-TYPE 
                2               137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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            14.430 
[1] "5.9 - 38.1 (6.7)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.9"
D596V2, 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       2       15       40       29        36        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJB13 MUTATED           0          1          0          0        0
  DNAJB13 WILD-TYPE         3         69         53         32       38
D596V3, multiclass
            clus
vv           DNAJB13 MUTATED DNAJB13 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DNAJB13 MUTATED     0   1   2   2
  DNAJB13 WILD-TYPE  22  91 171  95
D596V4, multiclass
    clus
vv   DNAJB13 MUTATED DNAJB13 WILD-TYPE
  T1               0                22
  T2               1                91
  T3               2               171
  T4               2                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
  DNAJB13 MUTATED     2   4   0   0
  DNAJB13 WILD-TYPE 116 100  77  77
D596V5, multiclass
    clus
vv   DNAJB13 MUTATED DNAJB13 WILD-TYPE
  N0               2               116
  N1               4               100
  N2               0                77
  N3               0                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"
D596V6, binary
                   cls
clus                  0   1
  DNAJB13 MUTATED     6   0
  DNAJB13 WILD-TYPE 340  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB13 MUTATED      6    0
  DNAJB13 WILD-TYPE  340   29
   clus
vv  DNAJB13 MUTATED DNAJB13 WILD-TYPE
  0               6               340
  1               0                29
[1] 2 2
[1] FALSE
D596V7, binary
                   cls
clus                  0   1
  DNAJB13 MUTATED     3   3
  DNAJB13 WILD-TYPE 142 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB13 MUTATED      3    3
  DNAJB13 WILD-TYPE  142  245
        clus
vv       DNAJB13 MUTATED DNAJB13 WILD-TYPE
  FEMALE               3               142
  MALE                 3               245
[1] 2 2
[1] FALSE
D596V8, binary
                   cls
clus                  0   1
  DNAJB13 MUTATED     4   1
  DNAJB13 WILD-TYPE 288  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB13 MUTATED      4    1
  DNAJB13 WILD-TYPE  288   58
     clus
vv    DNAJB13 MUTATED DNAJB13 WILD-TYPE
  NO                4               288
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DNAJB13 MUTATED                                          0
  DNAJB13 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DNAJB13 MUTATED                                       0
  DNAJB13 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DNAJB13 MUTATED                                                        1
  DNAJB13 WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DNAJB13 MUTATED                                                   1
  DNAJB13 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DNAJB13 MUTATED                                                                   3
  DNAJB13 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DNAJB13 MUTATED                                                    0
  DNAJB13 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DNAJB13 MUTATED                                                  1
  DNAJB13 WILD-TYPE                                               60
D596V9, multiclass
                                                                   clus
vv                                                                  DNAJB13 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  DNAJB13 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DNAJB13 MUTATED     5   0   0   1
  DNAJB13 WILD-TYPE 306  14  15  23
D596V10, multiclass
    clus
vv   DNAJB13 MUTATED DNAJB13 WILD-TYPE
  R0               5               306
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D596V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  DNAJB13 MUTATED       1                         0
  DNAJB13 WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DNAJB13 MUTATED                                           0     5
  DNAJB13 WILD-TYPE                                         1   238
D596V12, multiclass
                                           clus
vv                                          DNAJB13 MUTATED DNAJB13 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D596V13, binary
                   cls
clus                  0   1
  DNAJB13 MUTATED     0   5
  DNAJB13 WILD-TYPE   4 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB13 MUTATED      0    5
  DNAJB13 WILD-TYPE    4  305
                        clus
vv                       DNAJB13 MUTATED DNAJB13 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(597) Variable = KDM3B MUTATION ANALYSIS
D597V1, survival
                 sevent
clus2               0   1
  KDM3B MUTATED    15   4
  KDM3B WILD-TYPE 215 135
  KDM3B MUTATED KDM3B WILD-TYPE 
             19             350 
  KDM3B MUTATED KDM3B WILD-TYPE 
              4             135 
$`KDM3B MUTATED`
TCGA-CG-4460 TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-8361 
       21.99        11.01         6.97        34.68        15.95        31.10 
TCGA-BR-8680 TCGA-BR-A4PE TCGA-CD-5803 TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-5721 
       31.96        20.42        11.21        12.62        15.95         6.02 
TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-A4YY TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-R5-A7ZI 
      105.07        65.10        13.78        11.77         0.10        74.53 
TCGA-VQ-A8P2 
       38.14 

$`KDM3B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        26.70        11.70        19.56         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-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-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-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-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.15        13.18        13.35        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-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-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-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-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-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-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 

  KDM3B MUTATED KDM3B WILD-TYPE 
            0.1             0.0 
  KDM3B MUTATED KDM3B WILD-TYPE 
         105.07          122.30 
  KDM3B MUTATED KDM3B WILD-TYPE 
          15.95           14.12 
[1] "0.1 - 105.1 (15.9)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.4"
D597V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KDM3B MUTATED         0        1        3        3         2         1
  KDM3B WILD-TYPE       2       14       37       27        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KDM3B MUTATED           0          2          1          2        4
  KDM3B WILD-TYPE         3         68         52         30       34
D597V3, multiclass
            clus
vv           KDM3B MUTATED KDM3B WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               3              27
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KDM3B MUTATED     1   6   4   8
  KDM3B WILD-TYPE  21  86 169  89
D597V4, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  T1             1              21
  T2             6              86
  T3             4             169
  T4             8              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
  KDM3B MUTATED     6   8   3   1
  KDM3B WILD-TYPE 112  96  74  76
D597V5, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  N0             6             112
  N1             8              96
  N2             3              74
  N3             1              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"
D597V6, binary
                 cls
clus                0   1
  KDM3B MUTATED    16   3
  KDM3B WILD-TYPE 330  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     16    3
  KDM3B WILD-TYPE  330   26
   clus
vv  KDM3B MUTATED KDM3B WILD-TYPE
  0            16             330
  1             3              26
[1] 2 2
[1] FALSE
D597V7, binary
                 cls
clus                0   1
  KDM3B MUTATED     8  12
  KDM3B WILD-TYPE 137 236
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED      8   12
  KDM3B WILD-TYPE  137  236
        clus
vv       KDM3B MUTATED KDM3B WILD-TYPE
  FEMALE             8             137
  MALE              12             236
[1] 2 2
[1] FALSE
D597V8, binary
                 cls
clus                0   1
  KDM3B MUTATED    16   2
  KDM3B WILD-TYPE 276  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     16    2
  KDM3B WILD-TYPE  276   57
     clus
vv    KDM3B MUTATED KDM3B WILD-TYPE
  NO             16             276
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KDM3B MUTATED                                          0
  KDM3B WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KDM3B MUTATED                                       1
  KDM3B WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KDM3B MUTATED                                                       11
  KDM3B WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KDM3B MUTATED                                                   1
  KDM3B WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KDM3B MUTATED                                                                   4
  KDM3B WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KDM3B MUTATED                                                    0
  KDM3B WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KDM3B MUTATED                                                  3
  KDM3B WILD-TYPE                                               58
D597V9, multiclass
                                                                   clus
vv                                                                  KDM3B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  KDM3B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KDM3B MUTATED    14   0   1   2
  KDM3B WILD-TYPE 297  14  14  22
D597V10, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  R0            14             297
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D597V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KDM3B MUTATED       5                         0
  KDM3B WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KDM3B MUTATED                                           0    10
  KDM3B WILD-TYPE                                         1   233
D597V12, multiclass
                                           clus
vv                                          KDM3B MUTATED KDM3B WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D597V13, binary
                 cls
clus                0   1
  KDM3B MUTATED     1  13
  KDM3B WILD-TYPE   3 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED      1   13
  KDM3B WILD-TYPE    3  297
                        clus
vv                       KDM3B MUTATED KDM3B WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(598) Variable = PDCD1 MUTATION ANALYSIS
D598V1, survival
                 sevent
clus2               0   1
  PDCD1 MUTATED     3   1
  PDCD1 WILD-TYPE 227 138
  PDCD1 MUTATED PDCD1 WILD-TYPE 
              4             365 
  PDCD1 MUTATED PDCD1 WILD-TYPE 
              1             138 
$`PDCD1 MUTATED`
TCGA-BR-8487 TCGA-D7-A6EY TCGA-FP-A4BE TCGA-VQ-A8P3 
        1.12        11.44        11.08        37.22 

$`PDCD1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  PDCD1 MUTATED PDCD1 WILD-TYPE 
           1.12            0.00 
  PDCD1 MUTATED PDCD1 WILD-TYPE 
          37.22          122.30 
  PDCD1 MUTATED PDCD1 WILD-TYPE 
          11.26           14.43 
[1] "1.1 - 37.2 (11.3)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D598V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PDCD1 MUTATED         0        0        0        0         2         0
  PDCD1 WILD-TYPE       2       15       40       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PDCD1 MUTATED           0          2          1          0        0
  PDCD1 WILD-TYPE         3         68         52         32       38
D598V3, multiclass
            clus
vv           PDCD1 MUTATED PDCD1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PDCD1 MUTATED     0   0   3   2
  PDCD1 WILD-TYPE  22  92 170  95
D598V4, multiclass
    clus
vv   PDCD1 MUTATED PDCD1 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             3             170
  T4             2              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
  PDCD1 MUTATED     3   1   0   1
  PDCD1 WILD-TYPE 115 103  77  76
D598V5, multiclass
    clus
vv   PDCD1 MUTATED PDCD1 WILD-TYPE
  N0             3             115
  N1             1             103
  N2             0              77
  N3             1              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"
D598V6, binary
                 cls
clus                0   1
  PDCD1 MUTATED     5   0
  PDCD1 WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD1 MUTATED      5    0
  PDCD1 WILD-TYPE  341   29
   clus
vv  PDCD1 MUTATED PDCD1 WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D598V7, binary
                 cls
clus                0   1
  PDCD1 MUTATED     3   2
  PDCD1 WILD-TYPE 142 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD1 MUTATED      3    2
  PDCD1 WILD-TYPE  142  246
        clus
vv       PDCD1 MUTATED PDCD1 WILD-TYPE
  FEMALE             3             142
  MALE               2             246
[1] 2 2
[1] FALSE
D598V8, binary
                 cls
clus                0   1
  PDCD1 MUTATED     2   2
  PDCD1 WILD-TYPE 290  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD1 MUTATED      2    2
  PDCD1 WILD-TYPE  290   57
     clus
vv    PDCD1 MUTATED PDCD1 WILD-TYPE
  NO              2             290
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PDCD1 MUTATED                                          0
  PDCD1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PDCD1 MUTATED                                       0
  PDCD1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PDCD1 MUTATED                                                        3
  PDCD1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PDCD1 MUTATED                                                   0
  PDCD1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PDCD1 MUTATED                                                                   0
  PDCD1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PDCD1 MUTATED                                                    0
  PDCD1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PDCD1 MUTATED                                                  2
  PDCD1 WILD-TYPE                                               59
D598V9, multiclass
                                                                   clus
vv                                                                  PDCD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  PDCD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PDCD1 MUTATED     4   0   0   1
  PDCD1 WILD-TYPE 307  14  15  23
D598V10, multiclass
    clus
vv   PDCD1 MUTATED PDCD1 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D598V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PDCD1 MUTATED       0                         1
  PDCD1 WILD-TYPE    87                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PDCD1 MUTATED                                           0     4
  PDCD1 WILD-TYPE                                         1   239
D598V12, multiclass
                                           clus
vv                                          PDCD1 MUTATED PDCD1 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D598V13, binary
                 cls
clus                0   1
  PDCD1 MUTATED     0   4
  PDCD1 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD1 MUTATED      0    4
  PDCD1 WILD-TYPE    4  306
                        clus
vv                       PDCD1 MUTATED PDCD1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(599) Variable = SYCP2L MUTATION ANALYSIS
D599V1, survival
                  sevent
clus2                0   1
  SYCP2L MUTATED     9   3
  SYCP2L WILD-TYPE 221 136
  SYCP2L MUTATED SYCP2L WILD-TYPE 
              12              357 
  SYCP2L MUTATED SYCP2L WILD-TYPE 
               3              136 
$`SYCP2L MUTATED`
TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-8382 TCGA-BR-8588 TCGA-BR-A4J5 TCGA-BR-A4QL 
       11.70        34.68        25.05        12.79        28.34        16.14 
TCGA-CD-8529 TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-4306 TCGA-HU-A4G8 TCGA-MX-A666 
       12.30        12.43        15.95         1.02        22.68        14.04 

$`SYCP2L WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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-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 

  SYCP2L MUTATED SYCP2L WILD-TYPE 
            1.02             0.00 
  SYCP2L MUTATED SYCP2L WILD-TYPE 
           34.68           122.30 
  SYCP2L MUTATED SYCP2L WILD-TYPE 
          14.995           14.270 
[1] "1.0 - 34.7 (15.0)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D599V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SYCP2L MUTATED         0        0        1        2         2         2
  SYCP2L WILD-TYPE       2       15       39       28        35        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYCP2L MUTATED           0          1          1          1        2
  SYCP2L WILD-TYPE         3         69         52         31       36
D599V3, multiclass
            clus
vv           SYCP2L MUTATED SYCP2L WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               2               35
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SYCP2L MUTATED     0   3   5   4
  SYCP2L WILD-TYPE  22  89 168  93
D599V4, multiclass
    clus
vv   SYCP2L MUTATED SYCP2L WILD-TYPE
  T1              0               22
  T2              3               89
  T3              5              168
  T4              4               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
  SYCP2L MUTATED     5   4   1   2
  SYCP2L WILD-TYPE 113 100  76  75
D599V5, multiclass
    clus
vv   SYCP2L MUTATED SYCP2L WILD-TYPE
  N0              5              113
  N1              4              100
  N2              1               76
  N3              2               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"
D599V6, binary
                  cls
clus                 0   1
  SYCP2L MUTATED    10   2
  SYCP2L WILD-TYPE 336  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYCP2L MUTATED     10    2
  SYCP2L WILD-TYPE  336   27
   clus
vv  SYCP2L MUTATED SYCP2L WILD-TYPE
  0             10              336
  1              2               27
[1] 2 2
[1] FALSE
D599V7, binary
                  cls
clus                 0   1
  SYCP2L MUTATED     6   7
  SYCP2L WILD-TYPE 139 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYCP2L MUTATED      6    7
  SYCP2L WILD-TYPE  139  241
        clus
vv       SYCP2L MUTATED SYCP2L WILD-TYPE
  FEMALE              6              139
  MALE                7              241
[1] 2 2
[1] FALSE
D599V8, binary
                  cls
clus                 0   1
  SYCP2L MUTATED    10   1
  SYCP2L WILD-TYPE 282  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYCP2L MUTATED     10    1
  SYCP2L WILD-TYPE  282   58
     clus
vv    SYCP2L MUTATED SYCP2L WILD-TYPE
  NO              10              282
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SYCP2L MUTATED                                          0
  SYCP2L WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SYCP2L MUTATED                                       2
  SYCP2L WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SYCP2L MUTATED                                                        9
  SYCP2L WILD-TYPE                                                    149
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SYCP2L MUTATED                                                   2
  SYCP2L WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SYCP2L MUTATED                                                                   0
  SYCP2L WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SYCP2L MUTATED                                                    0
  SYCP2L WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SYCP2L MUTATED                                                  0
  SYCP2L WILD-TYPE                                               61
D599V9, multiclass
                                                                   clus
vv                                                                  SYCP2L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  SYCP2L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SYCP2L MUTATED     9   0   1   1
  SYCP2L WILD-TYPE 302  14  14  23
D599V10, multiclass
    clus
vv   SYCP2L MUTATED SYCP2L WILD-TYPE
  R0              9              302
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D599V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SYCP2L MUTATED       4                         0
  SYCP2L WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SYCP2L MUTATED                                           0     7
  SYCP2L WILD-TYPE                                         1   236
D599V12, multiclass
                                           clus
vv                                          SYCP2L MUTATED SYCP2L WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D599V13, binary
                  cls
clus                 0   1
  SYCP2L MUTATED     0  11
  SYCP2L WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYCP2L MUTATED      0   11
  SYCP2L WILD-TYPE    4  299
                        clus
vv                       SYCP2L MUTATED SYCP2L WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(600) Variable = RNF111 MUTATION ANALYSIS
D600V1, survival
                  sevent
clus2                0   1
  RNF111 MUTATED     5   4
  RNF111 WILD-TYPE 225 135
  RNF111 MUTATED RNF111 WILD-TYPE 
               9              360 
  RNF111 MUTATED RNF111 WILD-TYPE 
               4              135 
$`RNF111 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6566 TCGA-BR-8680 TCGA-CG-4465 TCGA-CG-5721 
        6.97         6.61        32.78        31.96         9.01         6.02 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-VQ-A8P2 
       16.44         5.92        38.14 

$`RNF111 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  RNF111 MUTATED RNF111 WILD-TYPE 
            5.92             0.00 
  RNF111 MUTATED RNF111 WILD-TYPE 
           38.14           122.30 
  RNF111 MUTATED RNF111 WILD-TYPE 
            9.01            14.35 
[1] "5.9 - 38.1 (9.0)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D600V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RNF111 MUTATED         0        0        0        0         1         1
  RNF111 WILD-TYPE       2       15       40       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF111 MUTATED           1          2          1          0        3
  RNF111 WILD-TYPE         2         68         52         32       35
D600V3, multiclass
            clus
vv           RNF111 MUTATED RNF111 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               1                2
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF111 MUTATED     0   1   5   4
  RNF111 WILD-TYPE  22  91 168  93
D600V4, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              5              168
  T4              4               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
  RNF111 MUTATED     1   6   1   2
  RNF111 WILD-TYPE 117  98  76  75
D600V5, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  N0              1              117
  N1              6               98
  N2              1               76
  N3              2               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"
D600V6, binary
                  cls
clus                 0   1
  RNF111 MUTATED     7   2
  RNF111 WILD-TYPE 339  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED      7    2
  RNF111 WILD-TYPE  339   27
   clus
vv  RNF111 MUTATED RNF111 WILD-TYPE
  0              7              339
  1              2               27
[1] 2 2
[1] FALSE
D600V7, binary
                  cls
clus                 0   1
  RNF111 MUTATED     6   5
  RNF111 WILD-TYPE 139 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED      6    5
  RNF111 WILD-TYPE  139  243
        clus
vv       RNF111 MUTATED RNF111 WILD-TYPE
  FEMALE              6              139
  MALE                5              243
[1] 2 2
[1] FALSE
D600V8, binary
                  cls
clus                 0   1
  RNF111 MUTATED     7   1
  RNF111 WILD-TYPE 285  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED      7    1
  RNF111 WILD-TYPE  285   58
     clus
vv    RNF111 MUTATED RNF111 WILD-TYPE
  NO               7              285
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RNF111 MUTATED                                          0
  RNF111 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RNF111 MUTATED                                       1
  RNF111 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RNF111 MUTATED                                                        5
  RNF111 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RNF111 MUTATED                                                   1
  RNF111 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RNF111 MUTATED                                                                   1
  RNF111 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RNF111 MUTATED                                                    0
  RNF111 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RNF111 MUTATED                                                  3
  RNF111 WILD-TYPE                                               58
D600V9, multiclass
                                                                   clus
vv                                                                  RNF111 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  RNF111 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RNF111 MUTATED     6   0   1   4
  RNF111 WILD-TYPE 305  14  14  20
D600V10, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              1               14
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D600V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RNF111 MUTATED       1                         0
  RNF111 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RNF111 MUTATED                                           0     8
  RNF111 WILD-TYPE                                         1   235
D600V12, multiclass
                                           clus
vv                                          RNF111 MUTATED RNF111 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D600V13, binary
                  cls
clus                 0   1
  RNF111 MUTATED     0   8
  RNF111 WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED      0    8
  RNF111 WILD-TYPE    4  302
                        clus
vv                       RNF111 MUTATED RNF111 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(601) Variable = OPLAH MUTATION ANALYSIS
D601V1, survival
                 sevent
clus2               0   1
  OPLAH MUTATED    10   8
  OPLAH WILD-TYPE 220 131
  OPLAH MUTATED OPLAH WILD-TYPE 
             18             351 
  OPLAH MUTATED OPLAH WILD-TYPE 
              8             131 
$`OPLAH MUTATED`
TCGA-CG-4460 TCGA-BR-7703 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8368 
       21.99        36.16        33.21        29.59         6.18         4.31 
TCGA-BR-8372 TCGA-BR-A4J1 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 
       31.27         0.72        16.14         6.58         1.02         6.02 
TCGA-D7-A4YY TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-HU-A4GQ TCGA-MX-A5UJ TCGA-VQ-A8P2 
       13.78        11.44        20.32         0.10        19.73        38.14 

$`OPLAH WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        29.56        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-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-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-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-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-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74A 
       11.31        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-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 

  OPLAH MUTATED OPLAH WILD-TYPE 
            0.1             0.0 
  OPLAH MUTATED OPLAH WILD-TYPE 
          38.14          122.30 
  OPLAH MUTATED OPLAH WILD-TYPE 
          14.96           14.27 
[1] "0.1 - 38.1 (15.0)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D601V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OPLAH MUTATED         1        1        2        0         2         2
  OPLAH WILD-TYPE       1       14       38       30        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OPLAH MUTATED           0          6          3          2        3
  OPLAH WILD-TYPE         3         64         50         30       35
D601V3, multiclass
            clus
vv           OPLAH MUTATED OPLAH WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             6              64
  STAGE IIIB             3              50
  STAGE IIIC             2              30
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OPLAH MUTATED     2   2   8  10
  OPLAH WILD-TYPE  20  90 165  87
D601V4, multiclass
    clus
vv   OPLAH MUTATED OPLAH WILD-TYPE
  T1             2              20
  T2             2              90
  T3             8             165
  T4            10              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
  OPLAH MUTATED     8   7   4   4
  OPLAH WILD-TYPE 110  97  73  73
D601V5, multiclass
    clus
vv   OPLAH MUTATED OPLAH WILD-TYPE
  N0             8             110
  N1             7              97
  N2             4              73
  N3             4              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"
D601V6, binary
                 cls
clus                0   1
  OPLAH MUTATED    20   2
  OPLAH WILD-TYPE 326  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED     20    2
  OPLAH WILD-TYPE  326   27
   clus
vv  OPLAH MUTATED OPLAH WILD-TYPE
  0            20             326
  1             2              27
[1] 2 2
[1] FALSE
D601V7, binary
                 cls
clus                0   1
  OPLAH MUTATED     8  15
  OPLAH WILD-TYPE 137 233
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED      8   15
  OPLAH WILD-TYPE  137  233
        clus
vv       OPLAH MUTATED OPLAH WILD-TYPE
  FEMALE             8             137
  MALE              15             233
[1] 2 2
[1] FALSE
D601V8, binary
                 cls
clus                0   1
  OPLAH MUTATED    16   2
  OPLAH WILD-TYPE 276  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED     16    2
  OPLAH WILD-TYPE  276   57
     clus
vv    OPLAH MUTATED OPLAH WILD-TYPE
  NO             16             276
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OPLAH MUTATED                                          0
  OPLAH WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OPLAH MUTATED                                       1
  OPLAH WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OPLAH MUTATED                                                       10
  OPLAH WILD-TYPE                                                    148
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OPLAH MUTATED                                                   2
  OPLAH WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OPLAH MUTATED                                                                   6
  OPLAH WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OPLAH MUTATED                                                    1
  OPLAH WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OPLAH MUTATED                                                  3
  OPLAH WILD-TYPE                                               58
D601V9, multiclass
                                                                   clus
vv                                                                  OPLAH MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  OPLAH WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OPLAH MUTATED    18   0   2   2
  OPLAH WILD-TYPE 293  14  13  22
D601V10, multiclass
    clus
vv   OPLAH MUTATED OPLAH WILD-TYPE
  R0            18             293
  R1             0              14
  R2             2              13
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D601V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OPLAH MUTATED       3                         1
  OPLAH WILD-TYPE    84                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OPLAH MUTATED                                           0    15
  OPLAH WILD-TYPE                                         1   228
D601V12, multiclass
                                           clus
vv                                          OPLAH MUTATED OPLAH WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D601V13, binary
                 cls
clus                0   1
  OPLAH MUTATED     0  18
  OPLAH WILD-TYPE   4 292
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPLAH MUTATED      0   18
  OPLAH WILD-TYPE    4  292
                        clus
vv                       OPLAH MUTATED OPLAH WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            18             292
[1] 2 2
[1] FALSE

Clustering(602) Variable = DYX1C1 MUTATION ANALYSIS
D602V1, survival
                  sevent
clus2                0   1
  DYX1C1 MUTATED     9   2
  DYX1C1 WILD-TYPE 221 137
  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
              11              358 
  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
               2              137 
$`DYX1C1 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8284 TCGA-BR-8369 TCGA-BR-8680 TCGA-BR-A4J8 
        6.97        34.68         8.05        14.04        31.96        13.51 
TCGA-CG-5723 TCGA-D7-A4YY TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GN 
      105.07        13.78        24.20        11.77        29.98 

$`DYX1C1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
            6.97             0.00 
  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
          105.07           122.30 
  DYX1C1 MUTATED DYX1C1 WILD-TYPE 
           14.04            14.35 
[1] "7.0 - 105.1 (14.0)" "0.0 - 122.3 (14.3)"
[1] "hr=" "2.6"
D602V2, 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       2       13       40       29        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DYX1C1 MUTATED           0          1          3          1        1
  DYX1C1 WILD-TYPE         3         69         50         31       37
D602V3, multiclass
            clus
vv           DYX1C1 MUTATED DYX1C1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                2               13
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              3               50
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DYX1C1 MUTATED     3   2   5   2
  DYX1C1 WILD-TYPE  19  90 168  95
D602V4, multiclass
    clus
vv   DYX1C1 MUTATED DYX1C1 WILD-TYPE
  T1              3               19
  T2              2               90
  T3              5              168
  T4              2               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
  DYX1C1 MUTATED     3   3   1   4
  DYX1C1 WILD-TYPE 115 101  76  73
D602V5, multiclass
    clus
vv   DYX1C1 MUTATED DYX1C1 WILD-TYPE
  N0              3              115
  N1              3              101
  N2              1               76
  N3              4               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"
D602V6, binary
                  cls
clus                 0   1
  DYX1C1 MUTATED    10   1
  DYX1C1 WILD-TYPE 336  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYX1C1 MUTATED     10    1
  DYX1C1 WILD-TYPE  336   28
   clus
vv  DYX1C1 MUTATED DYX1C1 WILD-TYPE
  0             10              336
  1              1               28
[1] 2 2
[1] FALSE
D602V7, binary
                  cls
clus                 0   1
  DYX1C1 MUTATED     6   6
  DYX1C1 WILD-TYPE 139 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYX1C1 MUTATED      6    6
  DYX1C1 WILD-TYPE  139  242
        clus
vv       DYX1C1 MUTATED DYX1C1 WILD-TYPE
  FEMALE              6              139
  MALE                6              242
[1] 2 2
[1] FALSE
D602V8, binary
                  cls
clus                 0   1
  DYX1C1 MUTATED    10   1
  DYX1C1 WILD-TYPE 282  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYX1C1 MUTATED     10    1
  DYX1C1 WILD-TYPE  282   58
     clus
vv    DYX1C1 MUTATED DYX1C1 WILD-TYPE
  NO              10              282
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DYX1C1 MUTATED                                          0
  DYX1C1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DYX1C1 MUTATED                                       0
  DYX1C1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DYX1C1 MUTATED                                                        7
  DYX1C1 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DYX1C1 MUTATED                                                   0
  DYX1C1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DYX1C1 MUTATED                                                                   1
  DYX1C1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DYX1C1 MUTATED                                                    0
  DYX1C1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DYX1C1 MUTATED                                                  4
  DYX1C1 WILD-TYPE                                               57
D602V9, multiclass
                                                                   clus
vv                                                                  DYX1C1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  DYX1C1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DYX1C1 MUTATED    10   0   0   2
  DYX1C1 WILD-TYPE 301  14  15  22
D602V10, multiclass
    clus
vv   DYX1C1 MUTATED DYX1C1 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D602V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DYX1C1 MUTATED       4                         0
  DYX1C1 WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DYX1C1 MUTATED                                           0     7
  DYX1C1 WILD-TYPE                                         1   236
D602V12, multiclass
                                           clus
vv                                          DYX1C1 MUTATED DYX1C1 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D602V13, binary
                  cls
clus                 0   1
  DYX1C1 MUTATED     0  11
  DYX1C1 WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYX1C1 MUTATED      0   11
  DYX1C1 WILD-TYPE    4  299
                        clus
vv                       DYX1C1 MUTATED DYX1C1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(603) Variable = RSF1 MUTATION ANALYSIS
D603V1, survival
                sevent
clus2              0   1
  RSF1 MUTATED    10   3
  RSF1 WILD-TYPE 220 136
  RSF1 MUTATED RSF1 WILD-TYPE 
            13            356 
  RSF1 MUTATED RSF1 WILD-TYPE 
             3            136 
$`RSF1 MUTATED`
TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8680 
        7.43        30.90        34.68        44.94        32.25        31.96 
TCGA-CG-4305 TCGA-CG-4437 TCGA-FP-7916 TCGA-HU-A4G3 TCGA-HU-A4GX TCGA-HU-A4HD 
       15.95         8.05        14.07         5.59        20.25        33.40 
TCGA-IP-7968 
        2.53 

$`RSF1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-4191 
        9.47         9.44         6.61         6.97         4.64        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-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-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-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-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-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-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-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       15.68        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-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 

  RSF1 MUTATED RSF1 WILD-TYPE 
          2.53           0.00 
  RSF1 MUTATED RSF1 WILD-TYPE 
         44.94         122.30 
  RSF1 MUTATED RSF1 WILD-TYPE 
         20.25          14.12 
[1] "2.5 - 44.9 (20.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2"  
D603V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RSF1 MUTATED         0        0        1        2         2         2
  RSF1 WILD-TYPE       2       15       39       28        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RSF1 MUTATED           0          1          1          2        1
  RSF1 WILD-TYPE         3         69         52         30       37
D603V3, multiclass
            clus
vv           RSF1 MUTATED RSF1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              2             28
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            2             30
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RSF1 MUTATED     0   5   4   4
  RSF1 WILD-TYPE  22  87 169  93
D603V4, multiclass
    clus
vv   RSF1 MUTATED RSF1 WILD-TYPE
  T1            0             22
  T2            5             87
  T3            4            169
  T4            4             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
  RSF1 MUTATED     4   4   5   1
  RSF1 WILD-TYPE 114 100  72  76
D603V5, multiclass
    clus
vv   RSF1 MUTATED RSF1 WILD-TYPE
  N0            4            114
  N1            4            100
  N2            5             72
  N3            1             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"
D603V6, binary
                cls
clus               0   1
  RSF1 MUTATED    12   1
  RSF1 WILD-TYPE 334  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  RSF1 MUTATED     12    1
  RSF1 WILD-TYPE  334   28
   clus
vv  RSF1 MUTATED RSF1 WILD-TYPE
  0           12            334
  1            1             28
[1] 2 2
[1] FALSE
D603V7, binary
                cls
clus               0   1
  RSF1 MUTATED     7   8
  RSF1 WILD-TYPE 138 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  RSF1 MUTATED      7    8
  RSF1 WILD-TYPE  138  240
        clus
vv       RSF1 MUTATED RSF1 WILD-TYPE
  FEMALE            7            138
  MALE              8            240
[1] 2 2
[1] FALSE
D603V8, binary
                cls
clus               0   1
  RSF1 MUTATED    12   0
  RSF1 WILD-TYPE 280  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  RSF1 MUTATED     12    0
  RSF1 WILD-TYPE  280   59
     clus
vv    RSF1 MUTATED RSF1 WILD-TYPE
  NO            12            280
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RSF1 MUTATED                                          0
  RSF1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RSF1 MUTATED                                       2
  RSF1 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RSF1 MUTATED                                                        8
  RSF1 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RSF1 MUTATED                                                   0
  RSF1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RSF1 MUTATED                                                                   2
  RSF1 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RSF1 MUTATED                                                    0
  RSF1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RSF1 MUTATED                                                  3
  RSF1 WILD-TYPE                                               58
D603V9, multiclass
                                                                   clus
vv                                                                  RSF1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  RSF1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RSF1 MUTATED    11   0   0   3
  RSF1 WILD-TYPE 300  14  15  21
D603V10, multiclass
    clus
vv   RSF1 MUTATED RSF1 WILD-TYPE
  R0           11            300
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RSF1 MUTATED       5                         0
  RSF1 WILD-TYPE    82                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RSF1 MUTATED                                           0     7
  RSF1 WILD-TYPE                                         1   236
D603V12, multiclass
                                           clus
vv                                          RSF1 MUTATED RSF1 WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V13, binary
                cls
clus               0   1
  RSF1 MUTATED     0  12
  RSF1 WILD-TYPE   4 298
[1] "tbl2"
                cls
clus             [,1] [,2]
  RSF1 MUTATED      0   12
  RSF1 WILD-TYPE    4  298
                        clus
vv                       RSF1 MUTATED RSF1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           12            298
[1] 2 2
[1] FALSE

Clustering(604) Variable = PRICKLE4 MUTATION ANALYSIS
D604V1, survival
                    sevent
clus2                  0   1
  PRICKLE4 MUTATED     3   1
  PRICKLE4 WILD-TYPE 227 138
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
                 4                365 
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
                 1                138 
$`PRICKLE4 MUTATED`
TCGA-CG-4305 TCGA-CG-5723 TCGA-CG-5726 TCGA-HU-A4GX 
       15.95       105.07        28.96        20.25 

$`PRICKLE4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
             15.95               0.00 
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
            105.07             122.30 
  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE 
            24.605             14.070 
[1] "15.9 - 105.1 (24.6)" "0.0 - 122.3 (14.1)" 
[1] "hr=" "2.6"
D604V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRICKLE4 MUTATED         0        1        0        2         0         0
  PRICKLE4 WILD-TYPE       2       14       40       28        37        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRICKLE4 MUTATED           0          0          0          1        0
  PRICKLE4 WILD-TYPE         3         70         53         31       38
D604V3, multiclass
            clus
vv           PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  0                 40
  STAGE II                  2                 28
  STAGE IIA                 0                 37
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                0                 53
  STAGE IIIC                1                 31
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PRICKLE4 MUTATED     1   2   1   1
  PRICKLE4 WILD-TYPE  21  90 172  96
D604V4, multiclass
    clus
vv   PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  T1                1                 21
  T2                2                 90
  T3                1                172
  T4                1                 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
  PRICKLE4 MUTATED     1   2   1   0
  PRICKLE4 WILD-TYPE 117 102  76  77
D604V5, multiclass
    clus
vv   PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  N0                1                117
  N1                2                102
  N2                1                 76
  N3                0                 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"
D604V6, binary
                    cls
clus                   0   1
  PRICKLE4 MUTATED     5   0
  PRICKLE4 WILD-TYPE 341  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRICKLE4 MUTATED      5    0
  PRICKLE4 WILD-TYPE  341   29
   clus
vv  PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  0                5                341
  1                0                 29
[1] 2 2
[1] FALSE
D604V7, binary
                    cls
clus                   0   1
  PRICKLE4 MUTATED     3   3
  PRICKLE4 WILD-TYPE 142 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRICKLE4 MUTATED      3    3
  PRICKLE4 WILD-TYPE  142  245
        clus
vv       PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  FEMALE                3                142
  MALE                  3                245
[1] 2 2
[1] FALSE
D604V8, binary
                    cls
clus                   0   1
  PRICKLE4 MUTATED     3   0
  PRICKLE4 WILD-TYPE 289  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRICKLE4 MUTATED      3    0
  PRICKLE4 WILD-TYPE  289   59
     clus
vv    PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  NO                 3                289
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PRICKLE4 MUTATED                                          0
  PRICKLE4 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PRICKLE4 MUTATED                                       1
  PRICKLE4 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRICKLE4 MUTATED                                                        4
  PRICKLE4 WILD-TYPE                                                    154
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PRICKLE4 MUTATED                                                   0
  PRICKLE4 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRICKLE4 MUTATED                                                                   1
  PRICKLE4 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PRICKLE4 MUTATED                                                    0
  PRICKLE4 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PRICKLE4 MUTATED                                                  0
  PRICKLE4 WILD-TYPE                                               61
D604V9, multiclass
                                                                   clus
vv                                                                  PRICKLE4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 0
                                                                   clus
vv                                                                  PRICKLE4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  PRICKLE4 MUTATED     4   0   0   2
  PRICKLE4 WILD-TYPE 307  14  15  22
D604V10, multiclass
    clus
vv   PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  R0                4                307
  R1                0                 14
  R2                0                 15
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D604V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PRICKLE4 MUTATED       1                         0
  PRICKLE4 WILD-TYPE    86                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRICKLE4 MUTATED                                           0     2
  PRICKLE4 WILD-TYPE                                         1   241
D604V12, multiclass
                                           clus
vv                                          PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    2                241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D604V13, binary
                    cls
clus                   0   1
  PRICKLE4 MUTATED     0   3
  PRICKLE4 WILD-TYPE   4 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRICKLE4 MUTATED      0    3
  PRICKLE4 WILD-TYPE    4  307
                        clus
vv                       PRICKLE4 MUTATED PRICKLE4 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                3                307
[1] 2 2
[1] FALSE

Clustering(605) Variable = ANTXR1 MUTATION ANALYSIS
D605V1, survival
                  sevent
clus2                0   1
  ANTXR1 MUTATED     6   4
  ANTXR1 WILD-TYPE 224 135
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              10              359 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
               4              135 
$`ANTXR1 MUTATED`
TCGA-BR-6452 TCGA-BR-8369 TCGA-BR-8680 TCGA-CG-4306 TCGA-CG-5726 TCGA-D7-A6EY 
       34.68        14.04        31.96         1.02        28.96        11.44 
TCGA-F1-A448 TCGA-HU-A4GU TCGA-R5-A7ZI TCGA-RD-A8N6 
       21.27         6.58        74.53         8.94 

$`ANTXR1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  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           14.270 
[1] "1.0 - 74.5 (17.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D605V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANTXR1 MUTATED         0        1        0        0         1         1
  ANTXR1 WILD-TYPE       2       14       40       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANTXR1 MUTATED           0          1          3          0        3
  ANTXR1 WILD-TYPE         3         69         50         32       35
D605V3, multiclass
            clus
vv           ANTXR1 MUTATED ANTXR1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              3               50
  STAGE IIIC              0               32
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ANTXR1 MUTATED     1   1   6   2
  ANTXR1 WILD-TYPE  21  91 167  95
D605V4, multiclass
    clus
vv   ANTXR1 MUTATED ANTXR1 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              6              167
  T4              2               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
  ANTXR1 MUTATED     2   2   3   3
  ANTXR1 WILD-TYPE 116 102  74  74
D605V5, multiclass
    clus
vv   ANTXR1 MUTATED ANTXR1 WILD-TYPE
  N0              2              116
  N1              2              102
  N2              3               74
  N3              3               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"
D605V6, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED     7   3
  ANTXR1 WILD-TYPE 339  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED      7    3
  ANTXR1 WILD-TYPE  339   26
   clus
vv  ANTXR1 MUTATED ANTXR1 WILD-TYPE
  0              7              339
  1              3               26
[1] 2 2
[1] FALSE
D605V7, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED     5   5
  ANTXR1 WILD-TYPE 140 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED      5    5
  ANTXR1 WILD-TYPE  140  243
        clus
vv       ANTXR1 MUTATED ANTXR1 WILD-TYPE
  FEMALE              5              140
  MALE                5              243
[1] 2 2
[1] FALSE
D605V8, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED     7   1
  ANTXR1 WILD-TYPE 285  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED      7    1
  ANTXR1 WILD-TYPE  285   58
     clus
vv    ANTXR1 MUTATED ANTXR1 WILD-TYPE
  NO               7              285
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ANTXR1 MUTATED                                          0
  ANTXR1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ANTXR1 MUTATED                                       2
  ANTXR1 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANTXR1 MUTATED                                                        3
  ANTXR1 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ANTXR1 MUTATED                                                   1
  ANTXR1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANTXR1 MUTATED                                                                   2
  ANTXR1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ANTXR1 MUTATED                                                    0
  ANTXR1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ANTXR1 MUTATED                                                  2
  ANTXR1 WILD-TYPE                                               59
D605V9, multiclass
                                                                   clus
vv                                                                  ANTXR1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  ANTXR1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ANTXR1 MUTATED     9   0   1   0
  ANTXR1 WILD-TYPE 302  14  14  24
D605V10, multiclass
    clus
vv   ANTXR1 MUTATED ANTXR1 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              1               14
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D605V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ANTXR1 MUTATED       2                         0
  ANTXR1 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANTXR1 MUTATED                                           0     6
  ANTXR1 WILD-TYPE                                         1   237
D605V12, multiclass
                                           clus
vv                                          ANTXR1 MUTATED ANTXR1 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D605V13, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED     2   6
  ANTXR1 WILD-TYPE   2 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED      2    6
  ANTXR1 WILD-TYPE    2  304
                        clus
vv                       ANTXR1 MUTATED ANTXR1 WILD-TYPE
  HISPANIC OR LATINO                  2                2
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(606) Variable = DNAJA1 MUTATION ANALYSIS
D606V1, survival
                  sevent
clus2                0   1
  DNAJA1 MUTATED     5   2
  DNAJA1 WILD-TYPE 225 137
  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
               7              362 
  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
               2              137 
$`DNAJA1 MUTATED`
TCGA-BR-8591 TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 TCGA-HF-A5NB TCGA-HU-A4H8 
       28.14         1.02         6.02        28.96        30.51        14.07 
TCGA-VQ-A8P2 
       38.14 

$`DNAJA1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
            1.02             0.00 
  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
           38.14           122.30 
  DNAJA1 MUTATED DNAJA1 WILD-TYPE 
           28.14            14.22 
[1] "1.0 - 38.1 (28.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D606V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DNAJA1 MUTATED         1        1        1        0         0         0
  DNAJA1 WILD-TYPE       1       14       39       30        37        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJA1 MUTATED           0          2          0          2        2
  DNAJA1 WILD-TYPE         3         68         53         30       36
D606V3, multiclass
            clus
vv           DNAJA1 MUTATED DNAJA1 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DNAJA1 MUTATED     3   0   1   5
  DNAJA1 WILD-TYPE  19  92 172  92
D606V4, multiclass
    clus
vv   DNAJA1 MUTATED DNAJA1 WILD-TYPE
  T1              3               19
  T2              0               92
  T3              1              172
  T4              5               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
  DNAJA1 MUTATED     2   4   1   2
  DNAJA1 WILD-TYPE 116 100  76  75
D606V5, multiclass
    clus
vv   DNAJA1 MUTATED DNAJA1 WILD-TYPE
  N0              2              116
  N1              4              100
  N2              1               76
  N3              2               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"
D606V6, binary
                  cls
clus                 0   1
  DNAJA1 MUTATED     7   1
  DNAJA1 WILD-TYPE 339  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJA1 MUTATED      7    1
  DNAJA1 WILD-TYPE  339   28
   clus
vv  DNAJA1 MUTATED DNAJA1 WILD-TYPE
  0              7              339
  1              1               28
[1] 2 2
[1] FALSE
D606V7, binary
                  cls
clus                 0   1
  DNAJA1 MUTATED     2   7
  DNAJA1 WILD-TYPE 143 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJA1 MUTATED      2    7
  DNAJA1 WILD-TYPE  143  241
        clus
vv       DNAJA1 MUTATED DNAJA1 WILD-TYPE
  FEMALE              2              143
  MALE                7              241
[1] 2 2
[1] FALSE
D606V8, binary
                  cls
clus                 0   1
  DNAJA1 MUTATED     4   2
  DNAJA1 WILD-TYPE 288  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJA1 MUTATED      4    2
  DNAJA1 WILD-TYPE  288   57
     clus
vv    DNAJA1 MUTATED DNAJA1 WILD-TYPE
  NO               4              288
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DNAJA1 MUTATED                                          0
  DNAJA1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DNAJA1 MUTATED                                       0
  DNAJA1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DNAJA1 MUTATED                                                        4
  DNAJA1 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DNAJA1 MUTATED                                                   2
  DNAJA1 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DNAJA1 MUTATED                                                                   2
  DNAJA1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DNAJA1 MUTATED                                                    0
  DNAJA1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DNAJA1 MUTATED                                                  1
  DNAJA1 WILD-TYPE                                               60
D606V9, multiclass
                                                                   clus
vv                                                                  DNAJA1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  DNAJA1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DNAJA1 MUTATED     6   1   1   1
  DNAJA1 WILD-TYPE 305  13  14  23
D606V10, multiclass
    clus
vv   DNAJA1 MUTATED DNAJA1 WILD-TYPE
  R0              6              305
  R1              1               13
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D606V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DNAJA1 MUTATED       1                         1
  DNAJA1 WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DNAJA1 MUTATED                                           0     3
  DNAJA1 WILD-TYPE                                         1   240
D606V12, multiclass
                                           clus
vv                                          DNAJA1 MUTATED DNAJA1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D606V13, binary
                  cls
clus                 0   1
  DNAJA1 MUTATED     0   4
  DNAJA1 WILD-TYPE   4 306
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJA1 MUTATED      0    4
  DNAJA1 WILD-TYPE    4  306
                        clus
vv                       DNAJA1 MUTATED DNAJA1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              306
[1] 2 2
[1] FALSE

Clustering(607) Variable = C11ORF80 MUTATION ANALYSIS
D607V1, survival
                    sevent
clus2                  0   1
  C11ORF80 MUTATED     5   0
  C11ORF80 WILD-TYPE 225 139
  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
                 5                364 
  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
                 0                139 
$`C11ORF80 MUTATED`
TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8591 TCGA-BR-A4PF TCGA-HU-A4GT 
       35.84        31.10        28.14         1.15         6.51 

$`C11ORF80 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4QI 
        0.66        32.52        13.51        20.65        20.42        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-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 

  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
              1.15               0.00 
  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
             35.84             122.30 
  C11ORF80 MUTATED C11ORF80 WILD-TYPE 
             28.14              14.22 
[1] "1.1 - 35.8 (28.1)"  "0.0 - 122.3 (14.2)"
[1] "hr="     "9200000"
D607V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C11ORF80 MUTATED         0        0        2        0         1         0
  C11ORF80 WILD-TYPE       2       15       38       30        36        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C11ORF80 MUTATED           0          0          1          2        0
  C11ORF80 WILD-TYPE         3         70         52         30       38
D607V3, multiclass
            clus
vv           C11ORF80 MUTATED C11ORF80 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  2                 38
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                1                 52
  STAGE IIIC                2                 30
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C11ORF80 MUTATED     0   2   1   3
  C11ORF80 WILD-TYPE  22  90 172  94
D607V4, multiclass
    clus
vv   C11ORF80 MUTATED C11ORF80 WILD-TYPE
  T1                0                 22
  T2                2                 90
  T3                1                172
  T4                3                 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
  C11ORF80 MUTATED     3   0   2   1
  C11ORF80 WILD-TYPE 115 104  75  76
D607V5, multiclass
    clus
vv   C11ORF80 MUTATED C11ORF80 WILD-TYPE
  N0                3                115
  N1                0                104
  N2                2                 75
  N3                1                 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"
D607V6, binary
                    cls
clus                   0   1
  C11ORF80 MUTATED     6   0
  C11ORF80 WILD-TYPE 340  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF80 MUTATED      6    0
  C11ORF80 WILD-TYPE  340   29
   clus
vv  C11ORF80 MUTATED C11ORF80 WILD-TYPE
  0                6                340
  1                0                 29
[1] 2 2
[1] FALSE
D607V7, binary
                    cls
clus                   0   1
  C11ORF80 MUTATED     3   3
  C11ORF80 WILD-TYPE 142 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF80 MUTATED      3    3
  C11ORF80 WILD-TYPE  142  245
        clus
vv       C11ORF80 MUTATED C11ORF80 WILD-TYPE
  FEMALE                3                142
  MALE                  3                245
[1] 2 2
[1] FALSE
D607V8, binary
                    cls
clus                   0   1
  C11ORF80 MUTATED     5   0
  C11ORF80 WILD-TYPE 287  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF80 MUTATED      5    0
  C11ORF80 WILD-TYPE  287   59
     clus
vv    C11ORF80 MUTATED C11ORF80 WILD-TYPE
  NO                 5                287
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C11ORF80 MUTATED                                          0
  C11ORF80 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C11ORF80 MUTATED                                       0
  C11ORF80 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C11ORF80 MUTATED                                                        4
  C11ORF80 WILD-TYPE                                                    154
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C11ORF80 MUTATED                                                   0
  C11ORF80 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C11ORF80 MUTATED                                                                   1
  C11ORF80 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C11ORF80 MUTATED                                                    0
  C11ORF80 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C11ORF80 MUTATED                                                  1
  C11ORF80 WILD-TYPE                                               60
D607V9, multiclass
                                                                   clus
vv                                                                  C11ORF80 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  C11ORF80 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C11ORF80 MUTATED     6   0   0   0
  C11ORF80 WILD-TYPE 305  14  15  24
D607V10, multiclass
    clus
vv   C11ORF80 MUTATED C11ORF80 WILD-TYPE
  R0                6                305
  R1                0                 14
  R2                0                 15
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D607V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C11ORF80 MUTATED       1                         0
  C11ORF80 WILD-TYPE    86                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C11ORF80 MUTATED                                           0     4
  C11ORF80 WILD-TYPE                                         1   239
D607V12, multiclass
                                           clus
vv                                          C11ORF80 MUTATED C11ORF80 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D607V13, binary
                    cls
clus                   0   1
  C11ORF80 MUTATED     0   5
  C11ORF80 WILD-TYPE   4 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF80 MUTATED      0    5
  C11ORF80 WILD-TYPE    4  305
                        clus
vv                       C11ORF80 MUTATED C11ORF80 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                5                305
[1] 2 2
[1] FALSE

Clustering(608) Variable = CLCA4 MUTATION ANALYSIS
D608V1, survival
                 sevent
clus2               0   1
  CLCA4 MUTATED     8   8
  CLCA4 WILD-TYPE 222 131
  CLCA4 MUTATED CLCA4 WILD-TYPE 
             16             353 
  CLCA4 MUTATED CLCA4 WILD-TYPE 
              8             131 
$`CLCA4 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7704 TCGA-BR-8361 
       26.70        30.90         6.61        34.68        35.24        31.10 
TCGA-BR-8363 TCGA-BR-8382 TCGA-CD-8528 TCGA-CG-5717 TCGA-CG-5723 TCGA-D7-A4YV 
        0.26        25.05        12.33         6.97       105.07         5.92 
TCGA-D7-A6EY TCGA-FP-A4BE TCGA-VQ-A8P2 TCGA-VQ-A8PE 
       11.44        11.08        38.14        22.19 

$`CLCA4 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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-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-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 

  CLCA4 MUTATED CLCA4 WILD-TYPE 
           0.26            0.00 
  CLCA4 MUTATED CLCA4 WILD-TYPE 
         105.07          122.30 
  CLCA4 MUTATED CLCA4 WILD-TYPE 
          23.62           14.17 
[1] "0.3 - 105.1 (23.6)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D608V2, 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       2       15       39       27        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLCA4 MUTATED           1          2          2          2        0
  CLCA4 WILD-TYPE         2         68         51         30       38
D608V3, multiclass
            clus
vv           CLCA4 MUTATED CLCA4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               3              27
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              1               2
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CLCA4 MUTATED     0   5   6   5
  CLCA4 WILD-TYPE  22  87 167  92
D608V4, multiclass
    clus
vv   CLCA4 MUTATED CLCA4 WILD-TYPE
  T1             0              22
  T2             5              87
  T3             6             167
  T4             5              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
  CLCA4 MUTATED     6   6   1   3
  CLCA4 WILD-TYPE 112  98  76  74
D608V5, multiclass
    clus
vv   CLCA4 MUTATED CLCA4 WILD-TYPE
  N0             6             112
  N1             6              98
  N2             1              76
  N3             3              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"
D608V6, binary
                 cls
clus                0   1
  CLCA4 MUTATED    17   0
  CLCA4 WILD-TYPE 329  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCA4 MUTATED     17    0
  CLCA4 WILD-TYPE  329   29
   clus
vv  CLCA4 MUTATED CLCA4 WILD-TYPE
  0            17             329
  1             0              29
[1] 2 2
[1] FALSE
D608V7, binary
                 cls
clus                0   1
  CLCA4 MUTATED    12   5
  CLCA4 WILD-TYPE 133 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCA4 MUTATED     12    5
  CLCA4 WILD-TYPE  133  243
        clus
vv       CLCA4 MUTATED CLCA4 WILD-TYPE
  FEMALE            12             133
  MALE               5             243
[1] 2 2
[1] FALSE
D608V8, binary
                 cls
clus                0   1
  CLCA4 MUTATED    13   3
  CLCA4 WILD-TYPE 279  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCA4 MUTATED     13    3
  CLCA4 WILD-TYPE  279   56
     clus
vv    CLCA4 MUTATED CLCA4 WILD-TYPE
  NO             13             279
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CLCA4 MUTATED                                          0
  CLCA4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CLCA4 MUTATED                                       1
  CLCA4 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CLCA4 MUTATED                                                       11
  CLCA4 WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CLCA4 MUTATED                                                   1
  CLCA4 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CLCA4 MUTATED                                                                   1
  CLCA4 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CLCA4 MUTATED                                                    0
  CLCA4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CLCA4 MUTATED                                                  3
  CLCA4 WILD-TYPE                                               58
D608V9, multiclass
                                                                   clus
vv                                                                  CLCA4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  CLCA4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CLCA4 MUTATED    14   0   0   3
  CLCA4 WILD-TYPE 297  14  15  21
D608V10, multiclass
    clus
vv   CLCA4 MUTATED CLCA4 WILD-TYPE
  R0            14             297
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D608V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CLCA4 MUTATED       1                         1
  CLCA4 WILD-TYPE    86                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CLCA4 MUTATED                                           0    13
  CLCA4 WILD-TYPE                                         1   230
D608V12, multiclass
                                           clus
vv                                          CLCA4 MUTATED CLCA4 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D608V13, binary
                 cls
clus                0   1
  CLCA4 MUTATED     0  13
  CLCA4 WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCA4 MUTATED      0   13
  CLCA4 WILD-TYPE    4  297
                        clus
vv                       CLCA4 MUTATED CLCA4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(609) Variable = ANAPC1 MUTATION ANALYSIS
D609V1, survival
                  sevent
clus2                0   1
  ANAPC1 MUTATED    10   3
  ANAPC1 WILD-TYPE 220 136
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
              13              356 
  ANAPC1 MUTATED ANAPC1 WILD-TYPE 
               3              136 
$`ANAPC1 MUTATED`
TCGA-CG-4460 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8381 TCGA-BR-8382 
       21.99        29.59         6.18         0.26         7.36        25.05 
TCGA-BR-8680 TCGA-CG-5723 TCGA-CG-5728 TCGA-HF-A5NB TCGA-HU-A4GU TCGA-SW-A7EA 
       31.96       105.07        65.10        30.51         6.58        19.04 
TCGA-VQ-A8P2 
       38.14 

$`ANAPC1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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 
           25.05            14.07 
[1] "0.3 - 105.1 (25.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.3"
D609V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANAPC1 MUTATED         1        0        4        1         1         3
  ANAPC1 WILD-TYPE       1       15       36       29        36        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANAPC1 MUTATED           0          2          0          2        2
  ANAPC1 WILD-TYPE         3         68         53         30       36
D609V3, multiclass
            clus
vv           ANAPC1 MUTATED ANAPC1 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                4               36
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ANAPC1 MUTATED     1   5   3   7
  ANAPC1 WILD-TYPE  21  87 170  90
D609V4, multiclass
    clus
vv   ANAPC1 MUTATED ANAPC1 WILD-TYPE
  T1              1               21
  T2              5               87
  T3              3              170
  T4              7               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
  ANAPC1 MUTATED     7   6   1   2
  ANAPC1 WILD-TYPE 111  98  76  75
D609V5, multiclass
    clus
vv   ANAPC1 MUTATED ANAPC1 WILD-TYPE
  N0              7              111
  N1              6               98
  N2              1               76
  N3              2               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"
D609V6, binary
                  cls
clus                 0   1
  ANAPC1 MUTATED    13   2
  ANAPC1 WILD-TYPE 333  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC1 MUTATED     13    2
  ANAPC1 WILD-TYPE  333   27
   clus
vv  ANAPC1 MUTATED ANAPC1 WILD-TYPE
  0             13              333
  1              2               27
[1] 2 2
[1] FALSE
D609V7, binary
                  cls
clus                 0   1
  ANAPC1 MUTATED     8   8
  ANAPC1 WILD-TYPE 137 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC1 MUTATED      8    8
  ANAPC1 WILD-TYPE  137  240
        clus
vv       ANAPC1 MUTATED ANAPC1 WILD-TYPE
  FEMALE              8              137
  MALE                8              240
[1] 2 2
[1] FALSE
D609V8, binary
                  cls
clus                 0   1
  ANAPC1 MUTATED    11   2
  ANAPC1 WILD-TYPE 281  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC1 MUTATED     11    2
  ANAPC1 WILD-TYPE  281   57
     clus
vv    ANAPC1 MUTATED ANAPC1 WILD-TYPE
  NO              11              281
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ANAPC1 MUTATED                                          0
  ANAPC1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ANAPC1 MUTATED                                       2
  ANAPC1 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANAPC1 MUTATED                                                        7
  ANAPC1 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ANAPC1 MUTATED                                                   2
  ANAPC1 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANAPC1 MUTATED                                                                   4
  ANAPC1 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ANAPC1 MUTATED                                                    0
  ANAPC1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ANAPC1 MUTATED                                                  1
  ANAPC1 WILD-TYPE                                               60
D609V9, multiclass
                                                                   clus
vv                                                                  ANAPC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ANAPC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ANAPC1 MUTATED    13   1   1   1
  ANAPC1 WILD-TYPE 298  13  14  23
D609V10, multiclass
    clus
vv   ANAPC1 MUTATED ANAPC1 WILD-TYPE
  R0             13              298
  R1              1               13
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D609V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ANAPC1 MUTATED       2                         1
  ANAPC1 WILD-TYPE    85                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANAPC1 MUTATED                                           0     8
  ANAPC1 WILD-TYPE                                         1   235
D609V12, multiclass
                                           clus
vv                                          ANAPC1 MUTATED ANAPC1 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D609V13, binary
                  cls
clus                 0   1
  ANAPC1 MUTATED     0  10
  ANAPC1 WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC1 MUTATED      0   10
  ANAPC1 WILD-TYPE    4  300
                        clus
vv                       ANAPC1 MUTATED ANAPC1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(610) Variable = SYT4 MUTATION ANALYSIS
D610V1, survival
                sevent
clus2              0   1
  SYT4 MUTATED     6   6
  SYT4 WILD-TYPE 224 133
  SYT4 MUTATED SYT4 WILD-TYPE 
            12            357 
  SYT4 MUTATED SYT4 WILD-TYPE 
             6            133 
$`SYT4 MUTATED`
TCGA-MX-A663 TCGA-BR-4253 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8363 TCGA-BR-A4QL 
        9.86         4.08        29.59         9.60         0.26        16.14 
TCGA-CG-5721 TCGA-D7-A4YU TCGA-HU-8602 TCGA-HU-A4GX TCGA-IN-A6RR TCGA-IN-A7NU 
        6.02        16.44        22.32        20.25         6.74        11.70 

$`SYT4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15        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-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         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-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       11.44         0.69        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-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-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-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-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-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51        10.62        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 

  SYT4 MUTATED SYT4 WILD-TYPE 
          0.26           0.00 
  SYT4 MUTATED SYT4 WILD-TYPE 
         29.59         122.30 
  SYT4 MUTATED SYT4 WILD-TYPE 
         10.78          14.43 
[1] "0.3 - 29.6 (10.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.8"
D610V2, 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       2       15       39       30        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYT4 MUTATED           0          2          3          2        2
  SYT4 WILD-TYPE         3         68         50         30       36
D610V3, multiclass
            clus
vv           SYT4 MUTATED SYT4 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            3             50
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SYT4 MUTATED     0   1   6   6
  SYT4 WILD-TYPE  22  91 167  91
D610V4, multiclass
    clus
vv   SYT4 MUTATED SYT4 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            6            167
  T4            6             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
  SYT4 MUTATED     4   3   2   4
  SYT4 WILD-TYPE 114 101  75  73
D610V5, multiclass
    clus
vv   SYT4 MUTATED SYT4 WILD-TYPE
  N0            4            114
  N1            3            101
  N2            2             75
  N3            4             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"
D610V6, binary
                cls
clus               0   1
  SYT4 MUTATED    14   0
  SYT4 WILD-TYPE 332  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT4 MUTATED     14    0
  SYT4 WILD-TYPE  332   29
   clus
vv  SYT4 MUTATED SYT4 WILD-TYPE
  0           14            332
  1            0             29
[1] 2 2
[1] FALSE
D610V7, binary
                cls
clus               0   1
  SYT4 MUTATED     9   5
  SYT4 WILD-TYPE 136 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT4 MUTATED      9    5
  SYT4 WILD-TYPE  136  243
        clus
vv       SYT4 MUTATED SYT4 WILD-TYPE
  FEMALE            9            136
  MALE              5            243
[1] 2 2
[1] FALSE
D610V8, binary
                cls
clus               0   1
  SYT4 MUTATED    12   0
  SYT4 WILD-TYPE 280  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT4 MUTATED     12    0
  SYT4 WILD-TYPE  280   59
     clus
vv    SYT4 MUTATED SYT4 WILD-TYPE
  NO            12            280
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SYT4 MUTATED                                          0
  SYT4 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SYT4 MUTATED                                       2
  SYT4 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SYT4 MUTATED                                                        9
  SYT4 WILD-TYPE                                                    149
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SYT4 MUTATED                                                   1
  SYT4 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SYT4 MUTATED                                                                   1
  SYT4 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SYT4 MUTATED                                                    0
  SYT4 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SYT4 MUTATED                                                  1
  SYT4 WILD-TYPE                                               60
D610V9, multiclass
                                                                   clus
vv                                                                  SYT4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  SYT4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SYT4 MUTATED    11   0   0   3
  SYT4 WILD-TYPE 300  14  15  21
D610V10, multiclass
    clus
vv   SYT4 MUTATED SYT4 WILD-TYPE
  R0           11            300
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D610V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SYT4 MUTATED       2                         0
  SYT4 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SYT4 MUTATED                                           0    11
  SYT4 WILD-TYPE                                         1   232
D610V12, multiclass
                                           clus
vv                                          SYT4 MUTATED SYT4 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D610V13, binary
                cls
clus               0   1
  SYT4 MUTATED     0  13
  SYT4 WILD-TYPE   4 297
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT4 MUTATED      0   13
  SYT4 WILD-TYPE    4  297
                        clus
vv                       SYT4 MUTATED SYT4 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           13            297
[1] 2 2
[1] FALSE

Clustering(611) Variable = TAF6 MUTATION ANALYSIS
D611V1, survival
                sevent
clus2              0   1
  TAF6 MUTATED     7   4
  TAF6 WILD-TYPE 223 135
  TAF6 MUTATED TAF6 WILD-TYPE 
            11            358 
  TAF6 MUTATED TAF6 WILD-TYPE 
             4            135 
$`TAF6 MUTATED`
TCGA-B7-5816 TCGA-BR-8683 TCGA-BR-A4J1 TCGA-CD-8536 TCGA-CG-5721 TCGA-D7-A4YV 
       26.70         9.86         0.72        12.43         6.02         5.92 
TCGA-D7-A4YY TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4G9 TCGA-VQ-A8P2 
       13.78        11.44        22.32        24.20        38.14 

$`TAF6 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58        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-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        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-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       14.27        16.44        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-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-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 

  TAF6 MUTATED TAF6 WILD-TYPE 
          0.72           0.00 
  TAF6 MUTATED TAF6 WILD-TYPE 
         38.14         122.30 
  TAF6 MUTATED TAF6 WILD-TYPE 
         12.43          14.45 
[1] "0.7 - 38.1 (12.4)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D611V2, 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       2       14       40       29        37        48
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAF6 MUTATED           0          3          3          0        1
  TAF6 WILD-TYPE         3         67         50         32       37
D611V3, multiclass
            clus
vv           TAF6 MUTATED TAF6 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             0             37
  STAGE IIB             4             48
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            3             50
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TAF6 MUTATED     1   0   4   8
  TAF6 WILD-TYPE  21  92 169  89
D611V4, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  T1            1             21
  T2            0             92
  T3            4            169
  T4            8             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
  TAF6 MUTATED     6   5   1   2
  TAF6 WILD-TYPE 112  99  76  75
D611V5, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  N0            6            112
  N1            5             99
  N2            1             76
  N3            2             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"
D611V6, binary
                cls
clus               0   1
  TAF6 MUTATED    14   0
  TAF6 WILD-TYPE 332  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED     14    0
  TAF6 WILD-TYPE  332   29
   clus
vv  TAF6 MUTATED TAF6 WILD-TYPE
  0           14            332
  1            0             29
[1] 2 2
[1] FALSE
D611V7, binary
                cls
clus               0   1
  TAF6 MUTATED     7   7
  TAF6 WILD-TYPE 138 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      7    7
  TAF6 WILD-TYPE  138  241
        clus
vv       TAF6 MUTATED TAF6 WILD-TYPE
  FEMALE            7            138
  MALE              7            241
[1] 2 2
[1] FALSE
D611V8, binary
                cls
clus               0   1
  TAF6 MUTATED     9   2
  TAF6 WILD-TYPE 283  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      9    2
  TAF6 WILD-TYPE  283   57
     clus
vv    TAF6 MUTATED TAF6 WILD-TYPE
  NO             9            283
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TAF6 MUTATED                                          0
  TAF6 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TAF6 MUTATED                                       2
  TAF6 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TAF6 MUTATED                                                        5
  TAF6 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TAF6 MUTATED                                                   1
  TAF6 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TAF6 MUTATED                                                                   2
  TAF6 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TAF6 MUTATED                                                    0
  TAF6 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TAF6 MUTATED                                                  4
  TAF6 WILD-TYPE                                               57
D611V9, multiclass
                                                                   clus
vv                                                                  TAF6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  TAF6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TAF6 MUTATED    12   0   0   2
  TAF6 WILD-TYPE 299  14  15  22
D611V10, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  R0           12            299
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D611V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TAF6 MUTATED       5                         0
  TAF6 WILD-TYPE    82                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAF6 MUTATED                                           0     8
  TAF6 WILD-TYPE                                         1   235
D611V12, multiclass
                                           clus
vv                                          TAF6 MUTATED TAF6 WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D611V13, binary
                cls
clus               0   1
  TAF6 MUTATED     0  12
  TAF6 WILD-TYPE   4 298
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      0   12
  TAF6 WILD-TYPE    4  298
                        clus
vv                       TAF6 MUTATED TAF6 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           12            298
[1] 2 2
[1] FALSE

Clustering(612) Variable = C9ORF41 MUTATION ANALYSIS
D612V1, survival
                   sevent
clus2                 0   1
  C9ORF41 MUTATED     3   1
  C9ORF41 WILD-TYPE 227 138
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
                4               365 
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
                1               138 
$`C9ORF41 MUTATED`
TCGA-BR-8078 TCGA-D7-A6EY TCGA-F1-A448 TCGA-HF-A5NB 
       29.59        11.44        21.27        30.51 

$`C9ORF41 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
            11.44              0.00 
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
            30.51            122.30 
  C9ORF41 MUTATED C9ORF41 WILD-TYPE 
            25.43             14.17 
[1] "11.4 - 30.5 (25.4)" "0.0 - 122.3 (14.2)"
[1] "hr=" "2.1"
D612V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C9ORF41 MUTATED         0        0        0        0         0         1
  C9ORF41 WILD-TYPE       2       15       40       30        37        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF41 MUTATED           0          0          2          1        0
  C9ORF41 WILD-TYPE         3         70         51         31       38
D612V3, multiclass
            clus
vv           C9ORF41 MUTATED C9ORF41 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                0                37
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               2                51
  STAGE IIIC               1                31
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C9ORF41 MUTATED     1   0   2   2
  C9ORF41 WILD-TYPE  21  92 171  95
D612V4, multiclass
    clus
vv   C9ORF41 MUTATED C9ORF41 WILD-TYPE
  T1               1                21
  T2               0                92
  T3               2               171
  T4               2                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
  C9ORF41 MUTATED     1   0   0   3
  C9ORF41 WILD-TYPE 117 104  77  74
D612V5, multiclass
    clus
vv   C9ORF41 MUTATED C9ORF41 WILD-TYPE
  N0               1               117
  N1               0               104
  N2               0                77
  N3               3                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"
D612V6, binary
                   cls
clus                  0   1
  C9ORF41 MUTATED     5   0
  C9ORF41 WILD-TYPE 341  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF41 MUTATED      5    0
  C9ORF41 WILD-TYPE  341   29
   clus
vv  C9ORF41 MUTATED C9ORF41 WILD-TYPE
  0               5               341
  1               0                29
[1] 2 2
[1] FALSE
D612V7, binary
                   cls
clus                  0   1
  C9ORF41 MUTATED     4   1
  C9ORF41 WILD-TYPE 141 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF41 MUTATED      4    1
  C9ORF41 WILD-TYPE  141  247
        clus
vv       C9ORF41 MUTATED C9ORF41 WILD-TYPE
  FEMALE               4               141
  MALE                 1               247
[1] 2 2
[1] FALSE
D612V8, binary
                   cls
clus                  0   1
  C9ORF41 MUTATED     2   2
  C9ORF41 WILD-TYPE 290  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF41 MUTATED      2    2
  C9ORF41 WILD-TYPE  290   57
     clus
vv    C9ORF41 MUTATED C9ORF41 WILD-TYPE
  NO                2               290
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C9ORF41 MUTATED                                          0
  C9ORF41 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C9ORF41 MUTATED                                       0
  C9ORF41 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C9ORF41 MUTATED                                                        2
  C9ORF41 WILD-TYPE                                                    156
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C9ORF41 MUTATED                                                   2
  C9ORF41 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C9ORF41 MUTATED                                                                   0
  C9ORF41 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C9ORF41 MUTATED                                                    0
  C9ORF41 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C9ORF41 MUTATED                                                  1
  C9ORF41 WILD-TYPE                                               60
D612V9, multiclass
                                                                   clus
vv                                                                  C9ORF41 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  C9ORF41 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C9ORF41 MUTATED     3   1   0   1
  C9ORF41 WILD-TYPE 308  13  15  23
D612V10, multiclass
    clus
vv   C9ORF41 MUTATED C9ORF41 WILD-TYPE
  R0               3               308
  R1               1                13
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D612V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C9ORF41 MUTATED       0                         0
  C9ORF41 WILD-TYPE    87                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C9ORF41 MUTATED                                           0     4
  C9ORF41 WILD-TYPE                                         1   239
D612V12, multiclass
                                           clus
vv                                          C9ORF41 MUTATED C9ORF41 WILD-TYPE
  ASIAN                                                   0                87
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D612V13, binary
                   cls
clus                  0   1
  C9ORF41 MUTATED     1   3
  C9ORF41 WILD-TYPE   3 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF41 MUTATED      1    3
  C9ORF41 WILD-TYPE    3  307
                        clus
vv                       C9ORF41 MUTATED C9ORF41 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               3               307
[1] 2 2
[1] FALSE

Clustering(613) Variable = MARCH7 MUTATION ANALYSIS
D613V1, survival
                  sevent
clus2                0   1
  MARCH7 MUTATED     4   2
  MARCH7 WILD-TYPE 226 137
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               6              363 
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               2              137 
$`MARCH7 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-8368 TCGA-CG-5728 TCGA-HU-A4G8 
       21.99         6.97        44.94         4.31        65.10        22.68 

$`MARCH7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  MARCH7 MUTATED MARCH7 WILD-TYPE 
            4.31             0.00 
  MARCH7 MUTATED MARCH7 WILD-TYPE 
            65.1            122.3 
  MARCH7 MUTATED MARCH7 WILD-TYPE 
          22.335           14.170 
[1] "4.3 - 65.1 (22.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D613V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MARCH7 MUTATED         0        0        2        0         1         1
  MARCH7 WILD-TYPE       2       15       38       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MARCH7 MUTATED           0          1          0          0        1
  MARCH7 WILD-TYPE         3         69         53         32       37
D613V3, multiclass
            clus
vv           MARCH7 MUTATED MARCH7 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MARCH7 MUTATED     0   2   3   1
  MARCH7 WILD-TYPE  22  90 170  96
D613V4, multiclass
    clus
vv   MARCH7 MUTATED MARCH7 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              3              170
  T4              1               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
  MARCH7 MUTATED     3   3   0   0
  MARCH7 WILD-TYPE 115 101  77  77
D613V5, multiclass
    clus
vv   MARCH7 MUTATED MARCH7 WILD-TYPE
  N0              3              115
  N1              3              101
  N2              0               77
  N3              0               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"
D613V6, binary
                  cls
clus                 0   1
  MARCH7 MUTATED     4   1
  MARCH7 WILD-TYPE 342  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH7 MUTATED      4    1
  MARCH7 WILD-TYPE  342   28
   clus
vv  MARCH7 MUTATED MARCH7 WILD-TYPE
  0              4              342
  1              1               28
[1] 2 2
[1] FALSE
D613V7, binary
                  cls
clus                 0   1
  MARCH7 MUTATED     5   1
  MARCH7 WILD-TYPE 140 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH7 MUTATED      5    1
  MARCH7 WILD-TYPE  140  247
        clus
vv       MARCH7 MUTATED MARCH7 WILD-TYPE
  FEMALE              5              140
  MALE                1              247
[1] 2 2
[1] FALSE
D613V8, binary
                  cls
clus                 0   1
  MARCH7 MUTATED     5   0
  MARCH7 WILD-TYPE 287  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH7 MUTATED      5    0
  MARCH7 WILD-TYPE  287   59
     clus
vv    MARCH7 MUTATED MARCH7 WILD-TYPE
  NO               5              287
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MARCH7 MUTATED                                          0
  MARCH7 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MARCH7 MUTATED                                       1
  MARCH7 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MARCH7 MUTATED                                                        3
  MARCH7 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MARCH7 MUTATED                                                   0
  MARCH7 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MARCH7 MUTATED                                                                   2
  MARCH7 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MARCH7 MUTATED                                                    0
  MARCH7 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MARCH7 MUTATED                                                  0
  MARCH7 WILD-TYPE                                               61
D613V9, multiclass
                                                                   clus
vv                                                                  MARCH7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  MARCH7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MARCH7 MUTATED     3   0   1   1
  MARCH7 WILD-TYPE 308  14  14  23
D613V10, multiclass
    clus
vv   MARCH7 MUTATED MARCH7 WILD-TYPE
  R0              3              308
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D613V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MARCH7 MUTATED       1                         0
  MARCH7 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MARCH7 MUTATED                                           0     3
  MARCH7 WILD-TYPE                                         1   240
D613V12, multiclass
                                           clus
vv                                          MARCH7 MUTATED MARCH7 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D613V13, binary
                  cls
clus                 0   1
  MARCH7 MUTATED     0   4
  MARCH7 WILD-TYPE   4 306
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH7 MUTATED      0    4
  MARCH7 WILD-TYPE    4  306
                        clus
vv                       MARCH7 MUTATED MARCH7 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              306
[1] 2 2
[1] FALSE

Clustering(614) Variable = TAPT1 MUTATION ANALYSIS
D614V1, survival
                 sevent
clus2               0   1
  TAPT1 MUTATED     2   3
  TAPT1 WILD-TYPE 228 136
  TAPT1 MUTATED TAPT1 WILD-TYPE 
              5             364 
  TAPT1 MUTATED TAPT1 WILD-TYPE 
              3             136 
$`TAPT1 MUTATED`
TCGA-BR-6452 TCGA-BR-8295 TCGA-CD-A4MG TCGA-CG-5721 TCGA-IN-A6RR 
       34.68         2.20         6.58         6.02         6.74 

$`TAPT1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8297 
        8.05         0.56        29.42         2.66        19.96         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-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-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 

  TAPT1 MUTATED TAPT1 WILD-TYPE 
            2.2             0.0 
  TAPT1 MUTATED TAPT1 WILD-TYPE 
          34.68          122.30 
  TAPT1 MUTATED TAPT1 WILD-TYPE 
           6.58           14.45 
[1] "2.2 - 34.7 (6.6)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "2.9"
D614V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TAPT1 MUTATED         0        0        0        0         2         1
  TAPT1 WILD-TYPE       2       15       40       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAPT1 MUTATED           0          2          0          0        1
  TAPT1 WILD-TYPE         3         68         53         32       37
D614V3, multiclass
            clus
vv           TAPT1 MUTATED TAPT1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TAPT1 MUTATED     0   0   3   3
  TAPT1 WILD-TYPE  22  92 170  94
D614V4, multiclass
    clus
vv   TAPT1 MUTATED TAPT1 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             3             170
  T4             3              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
  TAPT1 MUTATED     4   2   0   0
  TAPT1 WILD-TYPE 114 102  77  77
D614V5, multiclass
    clus
vv   TAPT1 MUTATED TAPT1 WILD-TYPE
  N0             4             114
  N1             2             102
  N2             0              77
  N3             0              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"
D614V6, binary
                 cls
clus                0   1
  TAPT1 MUTATED     6   0
  TAPT1 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPT1 MUTATED      6    0
  TAPT1 WILD-TYPE  340   29
   clus
vv  TAPT1 MUTATED TAPT1 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D614V7, binary
                 cls
clus                0   1
  TAPT1 MUTATED     3   3
  TAPT1 WILD-TYPE 142 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPT1 MUTATED      3    3
  TAPT1 WILD-TYPE  142  245
        clus
vv       TAPT1 MUTATED TAPT1 WILD-TYPE
  FEMALE             3             142
  MALE               3             245
[1] 2 2
[1] FALSE
D614V8, binary
                 cls
clus                0   1
  TAPT1 MUTATED     5   0
  TAPT1 WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPT1 MUTATED      5    0
  TAPT1 WILD-TYPE  287   59
     clus
vv    TAPT1 MUTATED TAPT1 WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TAPT1 MUTATED                                          0
  TAPT1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TAPT1 MUTATED                                       1
  TAPT1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TAPT1 MUTATED                                                        4
  TAPT1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TAPT1 MUTATED                                                   0
  TAPT1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TAPT1 MUTATED                                                                   1
  TAPT1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TAPT1 MUTATED                                                    0
  TAPT1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TAPT1 MUTATED                                                  0
  TAPT1 WILD-TYPE                                               61
D614V9, multiclass
                                                                   clus
vv                                                                  TAPT1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  TAPT1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TAPT1 MUTATED     4   0   0   1
  TAPT1 WILD-TYPE 307  14  15  23
D614V10, multiclass
    clus
vv   TAPT1 MUTATED TAPT1 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D614V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TAPT1 MUTATED       1                         0
  TAPT1 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAPT1 MUTATED                                           0     4
  TAPT1 WILD-TYPE                                         1   239
D614V12, multiclass
                                           clus
vv                                          TAPT1 MUTATED TAPT1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D614V13, binary
                 cls
clus                0   1
  TAPT1 MUTATED     0   5
  TAPT1 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPT1 MUTATED      0    5
  TAPT1 WILD-TYPE    4  305
                        clus
vv                       TAPT1 MUTATED TAPT1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(615) Variable = SDAD1 MUTATION ANALYSIS
D615V1, survival
                 sevent
clus2               0   1
  SDAD1 MUTATED     2   3
  SDAD1 WILD-TYPE 228 136
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              5             364 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              3             136 
$`SDAD1 MUTATED`
TCGA-BR-8372 TCGA-CD-A4MJ TCGA-CG-5733 TCGA-D7-A6EY TCGA-FP-7916 
       31.27        12.62        21.07        11.44        14.07 

$`SDAD1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  SDAD1 MUTATED SDAD1 WILD-TYPE 
          11.44            0.00 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
          31.27          122.30 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
          14.07           14.35 
[1] "11.4 - 31.3 (14.1)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D615V2, 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       2       15       39       30        37        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SDAD1 MUTATED           0          1          1          2        0
  SDAD1 WILD-TYPE         3         69         52         30       38
D615V3, multiclass
            clus
vv           SDAD1 MUTATED SDAD1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SDAD1 MUTATED     1   2   1   3
  SDAD1 WILD-TYPE  21  90 172  94
D615V4, multiclass
    clus
vv   SDAD1 MUTATED SDAD1 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             1             172
  T4             3              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
  SDAD1 MUTATED     2   1   1   3
  SDAD1 WILD-TYPE 116 103  76  74
D615V5, multiclass
    clus
vv   SDAD1 MUTATED SDAD1 WILD-TYPE
  N0             2             116
  N1             1             103
  N2             1              76
  N3             3              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"
D615V6, binary
                 cls
clus                0   1
  SDAD1 MUTATED     7   0
  SDAD1 WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      7    0
  SDAD1 WILD-TYPE  339   29
   clus
vv  SDAD1 MUTATED SDAD1 WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D615V7, binary
                 cls
clus                0   1
  SDAD1 MUTATED     4   4
  SDAD1 WILD-TYPE 141 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      4    4
  SDAD1 WILD-TYPE  141  244
        clus
vv       SDAD1 MUTATED SDAD1 WILD-TYPE
  FEMALE             4             141
  MALE               4             244
[1] 2 2
[1] FALSE
D615V8, binary
                 cls
clus                0   1
  SDAD1 MUTATED     6   0
  SDAD1 WILD-TYPE 286  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      6    0
  SDAD1 WILD-TYPE  286   59
     clus
vv    SDAD1 MUTATED SDAD1 WILD-TYPE
  NO              6             286
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SDAD1 MUTATED                                          0
  SDAD1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SDAD1 MUTATED                                       1
  SDAD1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SDAD1 MUTATED                                                        4
  SDAD1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SDAD1 MUTATED                                                   0
  SDAD1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SDAD1 MUTATED                                                                   2
  SDAD1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SDAD1 MUTATED                                                    0
  SDAD1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SDAD1 MUTATED                                                  1
  SDAD1 WILD-TYPE                                               60
D615V9, multiclass
                                                                   clus
vv                                                                  SDAD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  SDAD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SDAD1 MUTATED     4   0   0   2
  SDAD1 WILD-TYPE 307  14  15  22
D615V10, multiclass
    clus
vv   SDAD1 MUTATED SDAD1 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D615V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SDAD1 MUTATED       2                         0
  SDAD1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SDAD1 MUTATED                                           0     5
  SDAD1 WILD-TYPE                                         1   238
D615V12, multiclass
                                           clus
vv                                          SDAD1 MUTATED SDAD1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D615V13, binary
                 cls
clus                0   1
  SDAD1 MUTATED     0   7
  SDAD1 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      0    7
  SDAD1 WILD-TYPE    4  303
                        clus
vv                       SDAD1 MUTATED SDAD1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(616) Variable = PPIAL4A MUTATION ANALYSIS
D616V1, survival
                   sevent
clus2                 0   1
  PPIAL4A MUTATED     2   1
  PPIAL4A WILD-TYPE 228 138
  PPIAL4A MUTATED PPIAL4A WILD-TYPE 
                3               366 
  PPIAL4A MUTATED PPIAL4A WILD-TYPE 
                1               138 
$`PPIAL4A MUTATED`
TCGA-BR-7958 TCGA-BR-8370 TCGA-CD-A4MG 
       29.56         3.32         6.58 

$`PPIAL4A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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             14.35 
[1] "3.3 - 29.6 (6.6)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D616V2, 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       2       15       40       30        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPIAL4A MUTATED           0          0          2          0        0
  PPIAL4A WILD-TYPE         3         70         51         32       38
D616V3, multiclass
            clus
vv           PPIAL4A MUTATED PPIAL4A WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               2                51
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PPIAL4A MUTATED     0   0   2   1
  PPIAL4A WILD-TYPE  22  92 171  96
D616V4, multiclass
    clus
vv   PPIAL4A MUTATED PPIAL4A WILD-TYPE
  T1               0                22
  T2               0                92
  T3               2               171
  T4               1                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
  PPIAL4A MUTATED     2   0   0   1
  PPIAL4A WILD-TYPE 116 104  77  76
D616V5, multiclass
    clus
vv   PPIAL4A MUTATED PPIAL4A WILD-TYPE
  N0               2               116
  N1               0               104
  N2               0                77
  N3               1                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"
D616V6, binary
                   cls
clus                  0   1
  PPIAL4A MUTATED     3   0
  PPIAL4A WILD-TYPE 343  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIAL4A MUTATED      3    0
  PPIAL4A WILD-TYPE  343   29
   clus
vv  PPIAL4A MUTATED PPIAL4A WILD-TYPE
  0               3               343
  1               0                29
[1] 2 2
[1] FALSE
D616V7, binary
                   cls
clus                  0   1
  PPIAL4A MUTATED     0   3
  PPIAL4A WILD-TYPE 145 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIAL4A MUTATED      0    3
  PPIAL4A WILD-TYPE  145  245
        clus
vv       PPIAL4A MUTATED PPIAL4A WILD-TYPE
  FEMALE               0               145
  MALE                 3               245
[1] 2 2
[1] FALSE
D616V8, binary
                   cls
clus                  0   1
  PPIAL4A MUTATED     3   0
  PPIAL4A WILD-TYPE 289  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIAL4A MUTATED      3    0
  PPIAL4A WILD-TYPE  289   59
     clus
vv    PPIAL4A MUTATED PPIAL4A WILD-TYPE
  NO                3               289
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PPIAL4A MUTATED                                          0
  PPIAL4A WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PPIAL4A MUTATED                                       2
  PPIAL4A WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPIAL4A MUTATED                                                        1
  PPIAL4A WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PPIAL4A MUTATED                                                   0
  PPIAL4A WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPIAL4A MUTATED                                                                   0
  PPIAL4A WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PPIAL4A MUTATED                                                    0
  PPIAL4A WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PPIAL4A MUTATED                                                  0
  PPIAL4A WILD-TYPE                                               61
D616V9, multiclass
                                                                   clus
vv                                                                  PPIAL4A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  PPIAL4A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PPIAL4A MUTATED     2   0   0   0
  PPIAL4A WILD-TYPE 309  14  15  24
D616V10, multiclass
[1] "Remove cluster labels:" "PPIAL4A MUTATED"       
clus
  PPIAL4A MUTATED PPIAL4A WILD-TYPE 
                2               362 
       TCGA-CG-4444        TCGA-CG-4460        TCGA-CG-4475        TCGA-CG-4476 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5727        TCGA-EQ-A4SO        TCGA-F1-6177 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-FP-A8CX        TCGA-HF-7131        TCGA-KB-A93G        TCGA-MX-A663 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4368        TCGA-BR-4369 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452        TCGA-BR-6453 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7959 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8058        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8297        TCGA-BR-8360        TCGA-BR-8361 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8363        TCGA-BR-8364        TCGA-BR-8365        TCGA-BR-8366 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8367        TCGA-BR-8368        TCGA-BR-8369        TCGA-BR-8371 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8372        TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8382        TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8484 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8485        TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8589        TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8676        TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8680        TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8687        TCGA-BR-8690        TCGA-BR-A44T        TCGA-BR-A44U 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-A452        TCGA-BR-A453        TCGA-BR-A4CQ        TCGA-BR-A4CR 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-A4CS        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J7        TCGA-BR-A4J8 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-A4PD        TCGA-BR-A4PE        TCGA-BR-A4PF        TCGA-BR-A4QI 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-A4QL        TCGA-BR-A4QM        TCGA-CD-5800        TCGA-CD-5801 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CD-5804        TCGA-CD-8524        TCGA-CD-8525        TCGA-CD-8526 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CD-8527        TCGA-CD-8528        TCGA-CD-8529        TCGA-CD-8530 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CD-8531        TCGA-CD-8532        TCGA-CD-8533        TCGA-CD-8534 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CD-8535        TCGA-CD-8536        TCGA-CD-A487        TCGA-CG-4300 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4449 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-4455        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5717 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-8570        TCGA-D7-8572        TCGA-D7-8573        TCGA-D7-8574 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-8575        TCGA-D7-8576        TCGA-D7-8578        TCGA-D7-8579 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-A4YT        TCGA-D7-A4YU        TCGA-D7-A4YV        TCGA-D7-A4YX 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-A4YY        TCGA-D7-A4Z0        TCGA-D7-A6ET        TCGA-D7-A6EV 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-A6EX        TCGA-D7-A6EY        TCGA-D7-A6EZ        TCGA-D7-A6F0 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-A6F2        TCGA-D7-A747        TCGA-D7-A748        TCGA-D7-A74A 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-A74B        TCGA-EQ-5647        TCGA-F1-6874        TCGA-F1-6875 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-F1-A448        TCGA-F1-A72C        TCGA-FP-7735        TCGA-FP-7829 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8211 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-FP-8631        TCGA-FP-A4BE        TCGA-FP-A4BF        TCGA-FP-A9TM 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HF-A5NB        TCGA-HJ-7597        TCGA-HU-8238        TCGA-HU-8243 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-8244        TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-8608        TCGA-HU-8610        TCGA-HU-A4G2        TCGA-HU-A4G3 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-A4G6        TCGA-HU-A4G9        TCGA-HU-A4GC        TCGA-HU-A4GD 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-A4GF        TCGA-HU-A4GH        TCGA-HU-A4GJ        TCGA-HU-A4GN 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-A4GP        TCGA-HU-A4GQ        TCGA-HU-A4GT        TCGA-HU-A4GU 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-A4GX        TCGA-HU-A4GY        TCGA-HU-A4H0        TCGA-HU-A4H2 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-A4H3        TCGA-HU-A4H4        TCGA-HU-A4H5        TCGA-HU-A4H6 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-A4H8        TCGA-HU-A4HB        TCGA-HU-A4HD        TCGA-IN-7806 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-IN-8462        TCGA-IN-8663        TCGA-IN-A6RI        TCGA-IN-A6RJ 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-IN-A6RL        TCGA-IN-A6RN        TCGA-IN-A6RO        TCGA-IN-A6RP 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-IN-A6RR        TCGA-IN-A6RS        TCGA-IN-A7NR        TCGA-IN-A7NT 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-IN-A7NU        TCGA-IN-AB1V        TCGA-IN-AB1X        TCGA-IP-7968 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-KB-A6F5        TCGA-KB-A6F7        TCGA-KB-A93J        TCGA-MX-A5UG 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-MX-A5UJ        TCGA-R5-A7ZI        TCGA-RD-A7BS        TCGA-RD-A7BT 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-RD-A7BW        TCGA-RD-A7C1        TCGA-RD-A8MV        TCGA-RD-A8MW 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-RD-A8N0        TCGA-RD-A8N1        TCGA-RD-A8N2        TCGA-RD-A8N4 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-RD-A8N5        TCGA-RD-A8N6        TCGA-RD-A8N9        TCGA-SW-A7EA 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-SW-A7EB        TCGA-VQ-A8DL        TCGA-VQ-A8DT        TCGA-VQ-A8DU 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-VQ-A8DV        TCGA-VQ-A8DZ        TCGA-VQ-A8E2        TCGA-VQ-A8E7 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-VQ-A8P2        TCGA-VQ-A8P3        TCGA-VQ-A8PE        TCGA-VQ-A8PK 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-VQ-A8PM        TCGA-VQ-A8PQ        TCGA-VQ-A91Q        TCGA-VQ-A91U 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-VQ-A91V        TCGA-VQ-A92D        TCGA-VQ-A94T        TCGA-VQ-AA64 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-VQ-AA68        TCGA-VQ-AA69        TCGA-VQ-AA6A        TCGA-VQ-AA6B 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-VQ-AA6F        TCGA-VQ-AA6G        TCGA-VQ-AA6I        TCGA-VQ-AA6J 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-VQ-AA6K        TCGA-ZA-A8F6 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
D616V11, continuous
[1] "Remove cluster labels:" "PPIAL4A MUTATED"       
clus
  PPIAL4A MUTATED PPIAL4A WILD-TYPE 
                2               341 
       TCGA-CG-4444        TCGA-CG-4460        TCGA-CG-4475        TCGA-CG-4476 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-5727        TCGA-EQ-A4SO        TCGA-F1-6177        TCGA-FP-A8CX 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HF-7131        TCGA-KB-A93G        TCGA-MX-A663        TCGA-B7-5816 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-B7-A5TI        TCGA-BR-4183        TCGA-BR-4184        TCGA-BR-4188 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-4191        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4361 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-4362        TCGA-BR-4368        TCGA-BR-6452        TCGA-BR-6453 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7959 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8058        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8297        TCGA-BR-8360        TCGA-BR-8361 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8363        TCGA-BR-8364        TCGA-BR-8365        TCGA-BR-8366 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8367        TCGA-BR-8368        TCGA-BR-8369        TCGA-BR-8371 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8372        TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8382        TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8484 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8485        TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8589        TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8676        TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8680        TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-8687        TCGA-BR-8690        TCGA-BR-A44T        TCGA-BR-A44U 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-A452        TCGA-BR-A453        TCGA-BR-A4CQ        TCGA-BR-A4CR 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-A4CS        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4PD 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-A4PE        TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-BR-A4QM        TCGA-CD-5804        TCGA-CD-8525        TCGA-CD-8526 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CD-8531        TCGA-CD-8535        TCGA-CD-A487        TCGA-CG-4301 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4436        TCGA-CG-4437 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4462 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4474 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5728 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-D7-8570        TCGA-D7-8572 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-8573        TCGA-D7-8574        TCGA-D7-8575        TCGA-D7-8576 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-8578        TCGA-D7-8579        TCGA-D7-A4YT        TCGA-D7-A4YU 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-A4YV        TCGA-D7-A4YX        TCGA-D7-A4YY        TCGA-D7-A4Z0 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-A6ET        TCGA-D7-A6EV        TCGA-D7-A6EX        TCGA-D7-A6EY 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-A6EZ        TCGA-D7-A6F0        TCGA-D7-A6F2        TCGA-D7-A747 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-D7-A748        TCGA-D7-A74A        TCGA-D7-A74B        TCGA-EQ-5647 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6874        TCGA-F1-6875        TCGA-F1-A448 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-F1-A72C        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8210 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-FP-8211        TCGA-FP-8631        TCGA-FP-A4BE        TCGA-FP-A4BF 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-FP-A9TM        TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HF-7136        TCGA-HF-A5NB        TCGA-HJ-7597        TCGA-HU-8238 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-8243        TCGA-HU-8244        TCGA-HU-8249        TCGA-HU-8602 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-8604        TCGA-HU-8608        TCGA-HU-8610        TCGA-HU-A4G2 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-A4G3        TCGA-HU-A4G6        TCGA-HU-A4G8        TCGA-HU-A4G9 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-A4GC        TCGA-HU-A4GD        TCGA-HU-A4GF        TCGA-HU-A4GH 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-A4GJ        TCGA-HU-A4GN        TCGA-HU-A4GP        TCGA-HU-A4GQ 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-A4GT        TCGA-HU-A4GU        TCGA-HU-A4GX        TCGA-HU-A4GY 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-A4H0        TCGA-HU-A4H2        TCGA-HU-A4H3        TCGA-HU-A4H4 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-A4H5        TCGA-HU-A4H6        TCGA-HU-A4H8        TCGA-HU-A4HB 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-HU-A4HD        TCGA-IN-7806        TCGA-IN-7808        TCGA-IN-8462 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-IN-8663        TCGA-IN-A6RI        TCGA-IN-A6RJ        TCGA-IN-A6RL 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-IN-A6RN        TCGA-IN-A6RO        TCGA-IN-A6RP        TCGA-IN-A6RR 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-IN-A6RS        TCGA-IN-A7NR        TCGA-IN-A7NT        TCGA-IN-A7NU 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-IN-AB1V        TCGA-IN-AB1X        TCGA-IP-7968        TCGA-KB-A6F5 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-KB-A6F7        TCGA-KB-A93J        TCGA-MX-A5UG        TCGA-MX-A5UJ 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-R5-A7ZI        TCGA-RD-A7BS        TCGA-RD-A7BT        TCGA-RD-A7BW 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-RD-A7C1        TCGA-RD-A8MV        TCGA-RD-A8MW        TCGA-RD-A8N0 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-RD-A8N1        TCGA-RD-A8N2        TCGA-RD-A8N4        TCGA-RD-A8N5 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-RD-A8N6        TCGA-RD-A8N9        TCGA-SW-A7EA        TCGA-SW-A7EB 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-VQ-A8DL        TCGA-VQ-A8DT        TCGA-VQ-A8DU        TCGA-VQ-A8DV 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-VQ-A8DZ        TCGA-VQ-A8E2        TCGA-VQ-A8E7        TCGA-VQ-A8P2 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-VQ-A8P3        TCGA-VQ-A8PE        TCGA-VQ-A8PK        TCGA-VQ-A8PM 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-VQ-A8PQ        TCGA-VQ-A91Q        TCGA-VQ-A91U        TCGA-VQ-A91V 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-VQ-A92D        TCGA-VQ-A94T        TCGA-VQ-AA64        TCGA-VQ-AA68 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-VQ-AA69        TCGA-VQ-AA6A        TCGA-VQ-AA6B        TCGA-VQ-AA6F 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-VQ-AA6G        TCGA-VQ-AA6I        TCGA-VQ-AA6J        TCGA-VQ-AA6K 
"PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" "PPIAL4A WILD-TYPE" 
       TCGA-ZA-A8F6 
"PPIAL4A WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PPIAL4A MUTATED       1                         0
  PPIAL4A WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPIAL4A MUTATED                                           0     2
  PPIAL4A WILD-TYPE                                         1   241
D616V12, multiclass
                                           clus
vv                                          PPIAL4A MUTATED PPIAL4A WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D616V13, binary
                   cls
clus                  0   1
  PPIAL4A MUTATED     0   3
  PPIAL4A WILD-TYPE   4 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIAL4A MUTATED      0    3
  PPIAL4A WILD-TYPE    4  307
                        clus
vv                       PPIAL4A MUTATED PPIAL4A WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               3               307
[1] 2 2
[1] FALSE

Clustering(617) Variable = SCN10A MUTATION ANALYSIS
D617V1, survival
                  sevent
clus2                0   1
  SCN10A MUTATED    25  11
  SCN10A WILD-TYPE 205 128
  SCN10A MUTATED SCN10A WILD-TYPE 
              36              333 
  SCN10A MUTATED SCN10A WILD-TYPE 
              11              128 
$`SCN10A MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6801 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8285 
       34.68        32.78        40.21        44.94        29.59         0.56 
TCGA-BR-8363 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        0.26        26.33         4.31        27.12         9.34        28.14 
TCGA-BR-8678 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-5721 
       24.79        12.43         6.58         1.02         4.01         6.02 
TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-FP-8631 TCGA-HU-A4GN 
      105.07        65.10        14.76        11.24         0.56        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-IN-8663 TCGA-IN-A6RR TCGA-IN-AB1X 
        0.10        20.25        23.84         3.39         6.74        13.51 
TCGA-VQ-A8DT TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-AA64 TCGA-VQ-AA68 
       48.79        43.36        38.14        37.22        18.41        43.66 

$`SCN10A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-6802 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        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-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-8364 TCGA-BR-8365 
        2.20         7.40         6.18        31.10        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        0.95        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-8592 TCGA-BR-8676 TCGA-BR-8677 
       20.22         1.12        12.79         6.28         7.53        26.73 
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-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-4441 TCGA-CG-4443 
       15.95         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-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-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       36.43        13.78        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-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-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-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-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-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-A8DU 
        8.94        35.61        19.04         5.79         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       13.25        13.02        37.41        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-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 

  SCN10A MUTATED SCN10A WILD-TYPE 
             0.1              0.0 
  SCN10A MUTATED SCN10A WILD-TYPE 
          105.07           122.30 
  SCN10A MUTATED SCN10A WILD-TYPE 
          22.045           14.070 
[1] "0.1 - 105.1 (22.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D617V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCN10A MUTATED         0        0        4        1         8         5
  SCN10A WILD-TYPE       2       15       36       29        29        47
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SCN10A MUTATED           0          5          5          7        4
  SCN10A WILD-TYPE         3         65         48         25       34
D617V3, multiclass
            clus
vv           SCN10A MUTATED SCN10A WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                4               36
  STAGE II                1               29
  STAGE IIA               8               29
  STAGE IIB               5               47
  STAGE III               0                3
  STAGE IIIA              5               65
  STAGE IIIB              5               48
  STAGE IIIC              7               25
  STAGE IV                4               34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SCN10A MUTATED     0  10  15  14
  SCN10A WILD-TYPE  22  82 158  83
D617V4, multiclass
    clus
vv   SCN10A MUTATED SCN10A WILD-TYPE
  T1              0               22
  T2             10               82
  T3             15              158
  T4             14               83
[1] 4 2
[1] TRUE
[1] "dimension of 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    13   7  12   7
  SCN10A WILD-TYPE 105  97  65  70
D617V5, multiclass
    clus
vv   SCN10A MUTATED SCN10A WILD-TYPE
  N0             13              105
  N1              7               97
  N2             12               65
  N3              7               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"
D617V6, binary
                  cls
clus                 0   1
  SCN10A MUTATED    36   2
  SCN10A WILD-TYPE 310  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCN10A MUTATED     36    2
  SCN10A WILD-TYPE  310   27
   clus
vv  SCN10A MUTATED SCN10A WILD-TYPE
  0             36              310
  1              2               27
[1] 2 2
[1] FALSE
D617V7, binary
                  cls
clus                 0   1
  SCN10A MUTATED    18  21
  SCN10A WILD-TYPE 127 227
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCN10A MUTATED     18   21
  SCN10A WILD-TYPE  127  227
        clus
vv       SCN10A MUTATED SCN10A WILD-TYPE
  FEMALE             18              127
  MALE               21              227
[1] 2 2
[1] FALSE
D617V8, binary
                  cls
clus                 0   1
  SCN10A MUTATED    25   8
  SCN10A WILD-TYPE 267  51
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCN10A MUTATED     25    8
  SCN10A WILD-TYPE  267   51
     clus
vv    SCN10A MUTATED SCN10A WILD-TYPE
  NO              25              267
  YES              8               51
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SCN10A MUTATED                                          0
  SCN10A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SCN10A MUTATED                                       2
  SCN10A WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SCN10A MUTATED                                                       22
  SCN10A WILD-TYPE                                                    136
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SCN10A MUTATED                                                   2
  SCN10A WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SCN10A MUTATED                                                                   7
  SCN10A WILD-TYPE                                                                61
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SCN10A MUTATED                                                    0
  SCN10A WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SCN10A MUTATED                                                  6
  SCN10A WILD-TYPE                                               55
D617V9, multiclass
                                                                   clus
vv                                                                  SCN10A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              7
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               6
                                                                   clus
vv                                                                  SCN10A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         136
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               61
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SCN10A MUTATED    33   0   2   2
  SCN10A WILD-TYPE 278  14  13  22
D617V10, multiclass
    clus
vv   SCN10A MUTATED SCN10A WILD-TYPE
  R0             33              278
  R1              0               14
  R2              2               13
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D617V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SCN10A MUTATED       7                         0
  SCN10A WILD-TYPE    80                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SCN10A MUTATED                                           0    26
  SCN10A WILD-TYPE                                         1   217
D617V12, multiclass
                                           clus
vv                                          SCN10A MUTATED SCN10A WILD-TYPE
  ASIAN                                                  7               80
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 26              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D617V13, binary
                  cls
clus                 0   1
  SCN10A MUTATED     0  28
  SCN10A WILD-TYPE   4 282
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCN10A MUTATED      0   28
  SCN10A WILD-TYPE    4  282
                        clus
vv                       SCN10A MUTATED SCN10A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             28              282
[1] 2 2
[1] FALSE

Clustering(618) Variable = PSD MUTATION ANALYSIS
D618V1, survival
               sevent
clus2             0   1
  PSD MUTATED    12   5
  PSD WILD-TYPE 218 134
  PSD MUTATED PSD WILD-TYPE 
           17           352 
  PSD MUTATED PSD WILD-TYPE 
            5           134 
$`PSD MUTATED`
TCGA-BR-4257 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8487 
        9.67        36.16        35.84        29.59         0.26         1.12 
TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5726 TCGA-D7-A6EX TCGA-HF-7132 
       27.12        31.96         6.58        28.96        11.31        77.29 
TCGA-HJ-7597 TCGA-HU-A4G9 TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H3 
       26.47        24.20         6.58         2.10        29.00 

$`PSD WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-A4GX 
       21.37        29.98         8.98         0.10         6.51        20.25 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        0.26        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 

  PSD MUTATED PSD WILD-TYPE 
         0.26          0.00 
  PSD MUTATED PSD WILD-TYPE 
        77.29        122.30 
  PSD MUTATED PSD WILD-TYPE 
        26.47         14.12 
[1] "0.3 - 77.3 (26.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D618V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PSD MUTATED         1        3        3        1         2         2
  PSD WILD-TYPE       1       12       37       29        35        50
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PSD MUTATED           0          1          1          2        1
  PSD WILD-TYPE         3         69         52         30       37
D618V3, multiclass
            clus
vv           PSD MUTATED PSD WILD-TYPE
  STAGE I              1             1
  STAGE IA             3            12
  STAGE IB             3            37
  STAGE II             1            29
  STAGE IIA            2            35
  STAGE IIB            2            50
  STAGE III            0             3
  STAGE IIIA           1            69
  STAGE IIIB           1            52
  STAGE IIIC           2            30
  STAGE IV             1            37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  PSD MUTATED     4   4   4   5
  PSD WILD-TYPE  18  88 169  92
D618V4, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  T1           4            18
  T2           4            88
  T3           4           169
  T4           5            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
  PSD MUTATED     9   4   2   2
  PSD WILD-TYPE 109 100  75  75
D618V5, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  N0           9           109
  N1           4           100
  N2           2            75
  N3           2            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"
D618V6, binary
               cls
clus              0   1
  PSD MUTATED    15   1
  PSD WILD-TYPE 331  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     15    1
  PSD WILD-TYPE  331   28
   clus
vv  PSD MUTATED PSD WILD-TYPE
  0          15           331
  1           1            28
[1] 2 2
[1] FALSE
D618V7, binary
               cls
clus              0   1
  PSD MUTATED     9   9
  PSD WILD-TYPE 136 239
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED      9    9
  PSD WILD-TYPE  136  239
        clus
vv       PSD MUTATED PSD WILD-TYPE
  FEMALE           9           136
  MALE             9           239
[1] 2 2
[1] FALSE
D618V8, binary
               cls
clus              0   1
  PSD MUTATED    15   1
  PSD WILD-TYPE 277  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     15    1
  PSD WILD-TYPE  277   58
     clus
vv    PSD MUTATED PSD WILD-TYPE
  NO           15           277
  YES           1            58
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PSD MUTATED                                          1
  PSD WILD-TYPE                                        7
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PSD MUTATED                                       4
  PSD WILD-TYPE                                    66
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PSD MUTATED                                                        7
  PSD WILD-TYPE                                                    151
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PSD MUTATED                                                   1
  PSD WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PSD MUTATED                                                                   1
  PSD WILD-TYPE                                                                67
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PSD MUTATED                                                    1
  PSD WILD-TYPE                                                  4
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PSD MUTATED                                                  3
  PSD WILD-TYPE                                               58
D618V9, multiclass
                                                                   clus
vv                                                                  PSD MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            3
                                                                   clus
vv                                                                  PSD WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  PSD MUTATED    16   0   0   1
  PSD WILD-TYPE 295  14  15  23
D618V10, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  R0          16           295
  R1           0            14
  R2           0            15
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D618V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  PSD MUTATED       6                         1
  PSD WILD-TYPE    81                         8
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PSD MUTATED                                           0     9
  PSD WILD-TYPE                                         1   234
D618V12, multiclass
                                           clus
vv                                          PSD MUTATED PSD WILD-TYPE
  ASIAN                                               6            81
  BLACK OR AFRICAN AMERICAN                           1             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               9           234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D618V13, binary
               cls
clus              0   1
  PSD MUTATED     0  16
  PSD WILD-TYPE   4 294
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED      0   16
  PSD WILD-TYPE    4  294
                        clus
vv                       PSD MUTATED PSD WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          16           294
[1] 2 2
[1] FALSE

Clustering(619) Variable = PODN MUTATION ANALYSIS
D619V1, survival
                sevent
clus2              0   1
  PODN MUTATED     6   4
  PODN WILD-TYPE 224 135
  PODN MUTATED PODN WILD-TYPE 
            10            359 
  PODN MUTATED PODN WILD-TYPE 
             4            135 
$`PODN MUTATED`
TCGA-BR-4253 TCGA-BR-7715 TCGA-BR-8363 TCGA-BR-8591 TCGA-CD-8529 TCGA-CG-5726 
        4.08        33.63         0.26        28.14        12.30        28.96 
TCGA-CG-5728 TCGA-D7-A74B TCGA-FP-A4BE TCGA-HU-A4GX 
       65.10         7.13        11.08        20.25 

$`PODN WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-D7-6815 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-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34        19.96         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-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 

  PODN MUTATED PODN WILD-TYPE 
          0.26           0.00 
  PODN MUTATED PODN WILD-TYPE 
          65.1          122.3 
  PODN MUTATED PODN WILD-TYPE 
        16.275         14.270 
[1] "0.3 - 65.1 (16.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D619V2, 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       2       14       38       30        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PODN MUTATED           0          1          1          2        2
  PODN WILD-TYPE         3         69         52         30       36
D619V3, multiclass
            clus
vv           PODN MUTATED PODN WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PODN MUTATED     1   2   4   4
  PODN WILD-TYPE  21  90 169  93
D619V4, multiclass
    clus
vv   PODN MUTATED PODN WILD-TYPE
  T1            1             21
  T2            2             90
  T3            4            169
  T4            4             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
  PODN MUTATED     6   2   2   2
  PODN WILD-TYPE 112 102  75  75
D619V5, multiclass
    clus
vv   PODN MUTATED PODN WILD-TYPE
  N0            6            112
  N1            2            102
  N2            2             75
  N3            2             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"
D619V6, binary
                cls
clus               0   1
  PODN MUTATED    11   1
  PODN WILD-TYPE 335  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  PODN MUTATED     11    1
  PODN WILD-TYPE  335   28
   clus
vv  PODN MUTATED PODN WILD-TYPE
  0           11            335
  1            1             28
[1] 2 2
[1] FALSE
D619V7, binary
                cls
clus               0   1
  PODN MUTATED     7   5
  PODN WILD-TYPE 138 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  PODN MUTATED      7    5
  PODN WILD-TYPE  138  243
        clus
vv       PODN MUTATED PODN WILD-TYPE
  FEMALE            7            138
  MALE              5            243
[1] 2 2
[1] FALSE
D619V8, binary
                cls
clus               0   1
  PODN MUTATED     6   2
  PODN WILD-TYPE 286  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  PODN MUTATED      6    2
  PODN WILD-TYPE  286   57
     clus
vv    PODN MUTATED PODN WILD-TYPE
  NO             6            286
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PODN MUTATED                                          0
  PODN WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PODN MUTATED                                       2
  PODN WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PODN MUTATED                                                        7
  PODN WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PODN MUTATED                                                   1
  PODN WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PODN MUTATED                                                                   2
  PODN WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PODN MUTATED                                                    0
  PODN WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PODN MUTATED                                                  0
  PODN WILD-TYPE                                               61
D619V9, multiclass
                                                                   clus
vv                                                                  PODN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  PODN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PODN MUTATED     9   0   0   3
  PODN WILD-TYPE 302  14  15  21
D619V10, multiclass
    clus
vv   PODN MUTATED PODN WILD-TYPE
  R0            9            302
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D619V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PODN MUTATED       2                         1
  PODN WILD-TYPE    85                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PODN MUTATED                                           0     7
  PODN WILD-TYPE                                         1   236
D619V12, multiclass
                                           clus
vv                                          PODN MUTATED PODN WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D619V13, binary
                cls
clus               0   1
  PODN MUTATED     0  10
  PODN WILD-TYPE   4 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  PODN MUTATED      0   10
  PODN WILD-TYPE    4  300
                        clus
vv                       PODN MUTATED PODN WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           10            300
[1] 2 2
[1] FALSE

Clustering(620) Variable = NUFIP2 MUTATION ANALYSIS
D620V1, survival
                  sevent
clus2                0   1
  NUFIP2 MUTATED     4   3
  NUFIP2 WILD-TYPE 226 136
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
               7              362 
  NUFIP2 MUTATED NUFIP2 WILD-TYPE 
               3              136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-5733 
       15.02        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-D7-8572 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-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 

  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            14.35 
[1] "0.1 - 77.3 (12.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D620V2, 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       2       15       40       29        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUFIP2 MUTATED           0          1          1          2        0
  NUFIP2 WILD-TYPE         3         69         52         30       38
D620V3, multiclass
            clus
vv           NUFIP2 MUTATED NUFIP2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              2               30
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUFIP2 MUTATED     0   2   3   2
  NUFIP2 WILD-TYPE  22  90 170  95
D620V4, multiclass
    clus
vv   NUFIP2 MUTATED NUFIP2 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              3              170
  T4              2               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
  NUFIP2 MUTATED     0   2   2   2
  NUFIP2 WILD-TYPE 118 102  75  75
D620V5, multiclass
    clus
vv   NUFIP2 MUTATED NUFIP2 WILD-TYPE
  N0              0              118
  N1              2              102
  N2              2               75
  N3              2               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"
D620V6, binary
                  cls
clus                 0   1
  NUFIP2 MUTATED     8   0
  NUFIP2 WILD-TYPE 338  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP2 MUTATED      8    0
  NUFIP2 WILD-TYPE  338   29
   clus
vv  NUFIP2 MUTATED NUFIP2 WILD-TYPE
  0              8              338
  1              0               29
[1] 2 2
[1] FALSE
D620V7, binary
                  cls
clus                 0   1
  NUFIP2 MUTATED     3   5
  NUFIP2 WILD-TYPE 142 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP2 MUTATED      3    5
  NUFIP2 WILD-TYPE  142  243
        clus
vv       NUFIP2 MUTATED NUFIP2 WILD-TYPE
  FEMALE              3              142
  MALE                5              243
[1] 2 2
[1] FALSE
D620V8, binary
                  cls
clus                 0   1
  NUFIP2 MUTATED     6   1
  NUFIP2 WILD-TYPE 286  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP2 MUTATED      6    1
  NUFIP2 WILD-TYPE  286   58
     clus
vv    NUFIP2 MUTATED NUFIP2 WILD-TYPE
  NO               6              286
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NUFIP2 MUTATED                                          0
  NUFIP2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NUFIP2 MUTATED                                       0
  NUFIP2 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NUFIP2 MUTATED                                                        3
  NUFIP2 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NUFIP2 MUTATED                                                   1
  NUFIP2 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NUFIP2 MUTATED                                                                   0
  NUFIP2 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NUFIP2 MUTATED                                                    0
  NUFIP2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NUFIP2 MUTATED                                                  4
  NUFIP2 WILD-TYPE                                               57
D620V9, multiclass
                                                                   clus
vv                                                                  NUFIP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  NUFIP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NUFIP2 MUTATED     6   0   0   2
  NUFIP2 WILD-TYPE 305  14  15  22
D620V10, multiclass
    clus
vv   NUFIP2 MUTATED NUFIP2 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D620V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NUFIP2 MUTATED       1                         0
  NUFIP2 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NUFIP2 MUTATED                                           0     6
  NUFIP2 WILD-TYPE                                         1   237
D620V12, multiclass
                                           clus
vv                                          NUFIP2 MUTATED NUFIP2 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D620V13, binary
                  cls
clus                 0   1
  NUFIP2 MUTATED     0   7
  NUFIP2 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP2 MUTATED      0    7
  NUFIP2 WILD-TYPE    4  303
                        clus
vv                       NUFIP2 MUTATED NUFIP2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(621) Variable = FRYL MUTATION ANALYSIS
D621V1, survival
                sevent
clus2              0   1
  FRYL MUTATED    13   6
  FRYL WILD-TYPE 217 133
  FRYL MUTATED FRYL WILD-TYPE 
            19            350 
  FRYL MUTATED FRYL WILD-TYPE 
             6            133 
$`FRYL MUTATED`
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7959 TCGA-BR-8059 
        9.34         9.67        34.68        30.90        33.21        14.43 
TCGA-BR-8285 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 TCGA-CG-5730 
        0.56         4.31         1.12        31.96         6.02         4.01 
TCGA-CG-5733 TCGA-D7-6526 TCGA-HF-7132 TCGA-HU-A4GT TCGA-IN-A6RL TCGA-IN-A7NT 
       21.07        17.19        77.29         6.51        13.35        10.62 
TCGA-VQ-A8P2 
       38.14 

$`FRYL WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
         77.29         122.30 
  FRYL MUTATED FRYL WILD-TYPE 
         13.35          14.37 
[1] "0.6 - 77.3 (13.3)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D621V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FRYL MUTATED         0        0        2        1         3         1
  FRYL WILD-TYPE       2       15       38       29        34        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FRYL MUTATED           1          7          0          1        3
  FRYL WILD-TYPE         2         63         53         31       35
D621V3, multiclass
            clus
vv           FRYL MUTATED FRYL WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             3             34
  STAGE IIB             1             51
  STAGE III             1              2
  STAGE IIIA            7             63
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FRYL MUTATED     1   6   6   7
  FRYL WILD-TYPE  21  86 167  90
D621V4, multiclass
    clus
vv   FRYL MUTATED FRYL WILD-TYPE
  T1            1             21
  T2            6             86
  T3            6            167
  T4            7             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
  FRYL MUTATED     6  10   4   1
  FRYL WILD-TYPE 112  94  73  76
D621V5, multiclass
    clus
vv   FRYL MUTATED FRYL WILD-TYPE
  N0            6            112
  N1           10             94
  N2            4             73
  N3            1             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"
D621V6, binary
                cls
clus               0   1
  FRYL MUTATED    22   2
  FRYL WILD-TYPE 324  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRYL MUTATED     22    2
  FRYL WILD-TYPE  324   27
   clus
vv  FRYL MUTATED FRYL WILD-TYPE
  0           22            324
  1            2             27
[1] 2 2
[1] FALSE
D621V7, binary
                cls
clus               0   1
  FRYL MUTATED    14  10
  FRYL WILD-TYPE 131 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRYL MUTATED     14   10
  FRYL WILD-TYPE  131  238
        clus
vv       FRYL MUTATED FRYL WILD-TYPE
  FEMALE           14            131
  MALE             10            238
[1] 2 2
[1] FALSE
D621V8, binary
                cls
clus               0   1
  FRYL MUTATED    16   2
  FRYL WILD-TYPE 276  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRYL MUTATED     16    2
  FRYL WILD-TYPE  276   57
     clus
vv    FRYL MUTATED FRYL WILD-TYPE
  NO            16            276
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FRYL MUTATED                                          0
  FRYL WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FRYL MUTATED                                       0
  FRYL WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FRYL MUTATED                                                       12
  FRYL WILD-TYPE                                                    146
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FRYL MUTATED                                                   3
  FRYL WILD-TYPE                                                18
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FRYL MUTATED                                                                   6
  FRYL WILD-TYPE                                                                62
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FRYL MUTATED                                                    0
  FRYL WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FRYL MUTATED                                                  3
  FRYL WILD-TYPE                                               58
D621V9, multiclass
                                                                   clus
vv                                                                  FRYL MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  FRYL WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FRYL MUTATED    17   0   1   6
  FRYL WILD-TYPE 294  14  14  18
D621V10, multiclass
    clus
vv   FRYL MUTATED FRYL WILD-TYPE
  R0           17            294
  R1            0             14
  R2            1             14
  RX            6             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D621V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FRYL MUTATED       2                         0
  FRYL WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FRYL MUTATED                                           0    17
  FRYL WILD-TYPE                                         1   226
D621V12, multiclass
                                           clus
vv                                          FRYL MUTATED FRYL WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               17            226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D621V13, binary
                cls
clus               0   1
  FRYL MUTATED     0  18
  FRYL WILD-TYPE   4 292
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRYL MUTATED      0   18
  FRYL WILD-TYPE    4  292
                        clus
vv                       FRYL MUTATED FRYL WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           18            292
[1] 2 2
[1] FALSE

Clustering(622) Variable = MYCN MUTATION ANALYSIS
D622V1, survival
                sevent
clus2              0   1
  MYCN MUTATED     4   2
  MYCN WILD-TYPE 226 137
  MYCN MUTATED MYCN WILD-TYPE 
             6            363 
  MYCN MUTATED MYCN WILD-TYPE 
             2            137 
$`MYCN MUTATED`
TCGA-BR-7703 TCGA-BR-8363 TCGA-BR-A4QL TCGA-CG-5723 TCGA-HU-A4GT TCGA-VQ-A91V 
       36.16         0.26        16.14       105.07         6.51        42.64 

$`MYCN WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       20.81         1.71        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 

  MYCN MUTATED MYCN WILD-TYPE 
          0.26           0.00 
  MYCN MUTATED MYCN WILD-TYPE 
        105.07         122.30 
  MYCN MUTATED MYCN WILD-TYPE 
         26.15          14.17 
[1] "0.3 - 105.1 (26.1)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.5"
D622V2, 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       1       14       39       29        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MYCN MUTATED           0          1          1          0        0
  MYCN WILD-TYPE         3         69         52         32       38
D622V3, multiclass
            clus
vv           MYCN MUTATED MYCN WILD-TYPE
  STAGE I               1              1
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MYCN MUTATED     2   2   3   0
  MYCN WILD-TYPE  20  90 170  97
D622V4, multiclass
    clus
vv   MYCN MUTATED MYCN WILD-TYPE
  T1            2             20
  T2            2             90
  T3            3            170
  T4            0             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
  MYCN MUTATED     3   2   1   1
  MYCN WILD-TYPE 115 102  76  76
D622V5, multiclass
    clus
vv   MYCN MUTATED MYCN WILD-TYPE
  N0            3            115
  N1            2            102
  N2            1             76
  N3            1             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"
D622V6, binary
                cls
clus               0   1
  MYCN MUTATED     6   0
  MYCN WILD-TYPE 340  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYCN MUTATED      6    0
  MYCN WILD-TYPE  340   29
   clus
vv  MYCN MUTATED MYCN WILD-TYPE
  0            6            340
  1            0             29
[1] 2 2
[1] FALSE
D622V7, binary
                cls
clus               0   1
  MYCN MUTATED     3   4
  MYCN WILD-TYPE 142 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYCN MUTATED      3    4
  MYCN WILD-TYPE  142  244
        clus
vv       MYCN MUTATED MYCN WILD-TYPE
  FEMALE            3            142
  MALE              4            244
[1] 2 2
[1] FALSE
D622V8, binary
                cls
clus               0   1
  MYCN MUTATED     6   1
  MYCN WILD-TYPE 286  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYCN MUTATED      6    1
  MYCN WILD-TYPE  286   58
     clus
vv    MYCN MUTATED MYCN WILD-TYPE
  NO             6            286
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MYCN MUTATED                                          0
  MYCN WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MYCN MUTATED                                       0
  MYCN WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MYCN MUTATED                                                        4
  MYCN WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MYCN MUTATED                                                   0
  MYCN WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MYCN MUTATED                                                                   0
  MYCN WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MYCN MUTATED                                                    1
  MYCN WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MYCN MUTATED                                                  2
  MYCN WILD-TYPE                                               59
D622V9, multiclass
                                                                   clus
vv                                                                  MYCN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  MYCN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MYCN MUTATED     7   0   0   0
  MYCN WILD-TYPE 304  14  15  24
D622V10, multiclass
    clus
vv   MYCN MUTATED MYCN WILD-TYPE
  R0            7            304
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D622V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MYCN MUTATED       1                         1
  MYCN WILD-TYPE    86                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MYCN MUTATED                                           0     3
  MYCN WILD-TYPE                                         1   240
D622V12, multiclass
                                           clus
vv                                          MYCN MUTATED MYCN WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D622V13, binary
                cls
clus               0   1
  MYCN MUTATED     0   5
  MYCN WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYCN MUTATED      0    5
  MYCN WILD-TYPE    4  305
                        clus
vv                       MYCN MUTATED MYCN WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(623) Variable = TNK2 MUTATION ANALYSIS
D623V1, survival
                sevent
clus2              0   1
  TNK2 MUTATED    13   4
  TNK2 WILD-TYPE 217 135
  TNK2 MUTATED TNK2 WILD-TYPE 
            17            352 
  TNK2 MUTATED TNK2 WILD-TYPE 
             4            135 
$`TNK2 MUTATED`
TCGA-CG-4460 TCGA-BR-8078 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-A4PE 
       21.99        29.59        31.27        25.05        31.96        20.42 
TCGA-CG-5728 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4G8 
       65.10        14.27         5.92        26.47        22.32        22.68 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-MX-A5UJ TCGA-SW-A7EA TCGA-VQ-A8P2 
       20.25        29.00        19.73        19.04        38.14 

$`TNK2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-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-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-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-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 

  TNK2 MUTATED TNK2 WILD-TYPE 
          5.92           0.00 
  TNK2 MUTATED TNK2 WILD-TYPE 
          65.1          122.3 
  TNK2 MUTATED TNK2 WILD-TYPE 
         22.68          13.87 
[1] "5.9 - 65.1 (22.7)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "2.4"
D623V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNK2 MUTATED         0        0        4        0         0         4
  TNK2 WILD-TYPE       2       15       36       30        37        48
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNK2 MUTATED           0          3          0          4        2
  TNK2 WILD-TYPE         3         67         53         28       36
D623V3, multiclass
            clus
vv           TNK2 MUTATED TNK2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              4             36
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             4             48
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            0             53
  STAGE IIIC            4             28
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TNK2 MUTATED     1   5   3   9
  TNK2 WILD-TYPE  21  87 170  88
D623V4, multiclass
    clus
vv   TNK2 MUTATED TNK2 WILD-TYPE
  T1            1             21
  T2            5             87
  T3            3            170
  T4            9             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
  TNK2 MUTATED     6   4   3   4
  TNK2 WILD-TYPE 112 100  74  73
D623V5, multiclass
    clus
vv   TNK2 MUTATED TNK2 WILD-TYPE
  N0            6            112
  N1            4            100
  N2            3             74
  N3            4             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"
D623V6, binary
                cls
clus               0   1
  TNK2 MUTATED    15   2
  TNK2 WILD-TYPE 331  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNK2 MUTATED     15    2
  TNK2 WILD-TYPE  331   27
   clus
vv  TNK2 MUTATED TNK2 WILD-TYPE
  0           15            331
  1            2             27
[1] 2 2
[1] FALSE
D623V7, binary
                cls
clus               0   1
  TNK2 MUTATED    14   4
  TNK2 WILD-TYPE 131 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNK2 MUTATED     14    4
  TNK2 WILD-TYPE  131  244
        clus
vv       TNK2 MUTATED TNK2 WILD-TYPE
  FEMALE           14            131
  MALE              4            244
[1] 2 2
[1] FALSE
D623V8, binary
                cls
clus               0   1
  TNK2 MUTATED    14   1
  TNK2 WILD-TYPE 278  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNK2 MUTATED     14    1
  TNK2 WILD-TYPE  278   58
     clus
vv    TNK2 MUTATED TNK2 WILD-TYPE
  NO            14            278
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TNK2 MUTATED                                          1
  TNK2 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TNK2 MUTATED                                       5
  TNK2 WILD-TYPE                                    65
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNK2 MUTATED                                                        5
  TNK2 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TNK2 MUTATED                                                   1
  TNK2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNK2 MUTATED                                                                   2
  TNK2 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TNK2 MUTATED                                                    0
  TNK2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TNK2 MUTATED                                                  4
  TNK2 WILD-TYPE                                               57
D623V9, multiclass
                                                                   clus
vv                                                                  TNK2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  TNK2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TNK2 MUTATED    15   0   1   1
  TNK2 WILD-TYPE 296  14  14  23
D623V10, multiclass
    clus
vv   TNK2 MUTATED TNK2 WILD-TYPE
  R0           15            296
  R1            0             14
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D623V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TNK2 MUTATED       5                         0
  TNK2 WILD-TYPE    82                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNK2 MUTATED                                           0    11
  TNK2 WILD-TYPE                                         1   232
D623V12, multiclass
                                           clus
vv                                          TNK2 MUTATED TNK2 WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D623V13, binary
                cls
clus               0   1
  TNK2 MUTATED     0  15
  TNK2 WILD-TYPE   4 295
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNK2 MUTATED      0   15
  TNK2 WILD-TYPE    4  295
                        clus
vv                       TNK2 MUTATED TNK2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           15            295
[1] 2 2
[1] FALSE

Clustering(624) Variable = C2ORF42 MUTATION ANALYSIS
D624V1, survival
                   sevent
clus2                 0   1
  C2ORF42 MUTATED     7   3
  C2ORF42 WILD-TYPE 223 136
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
               10               359 
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
                3               136 
$`C2ORF42 MUTATED`
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7901 TCGA-BR-8081 TCGA-BR-8361 TCGA-CD-A4MI 
        9.67        34.68         3.45        32.25        31.10        11.77 
TCGA-CG-4477 TCGA-FP-A4BE TCGA-HU-A4H3 TCGA-IN-7806 
       30.97        11.08        29.00        36.36 

$`C2ORF42 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-D7-6525 
       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-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-7808 TCGA-IN-8462 
       21.17        14.07        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-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 

  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
             3.45              0.00 
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
            36.36            122.30 
  C2ORF42 MUTATED C2ORF42 WILD-TYPE 
           29.985            14.170 
[1] "3.5 - 36.4 (30.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D624V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C2ORF42 MUTATED         0        0        1        0         2         3
  C2ORF42 WILD-TYPE       2       15       39       30        35        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C2ORF42 MUTATED           0          1          0          2        1
  C2ORF42 WILD-TYPE         3         69         53         30       37
D624V3, multiclass
            clus
vv           C2ORF42 MUTATED C2ORF42 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                3                49
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               2                30
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C2ORF42 MUTATED     0   1   6   4
  C2ORF42 WILD-TYPE  22  91 167  93
D624V4, multiclass
    clus
vv   C2ORF42 MUTATED C2ORF42 WILD-TYPE
  T1               0                22
  T2               1                91
  T3               6               167
  T4               4                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
  C2ORF42 MUTATED     4   3   2   1
  C2ORF42 WILD-TYPE 114 101  75  76
D624V5, multiclass
    clus
vv   C2ORF42 MUTATED C2ORF42 WILD-TYPE
  N0               4               114
  N1               3               101
  N2               2                75
  N3               1                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"
D624V6, binary
                   cls
clus                  0   1
  C2ORF42 MUTATED    11   0
  C2ORF42 WILD-TYPE 335  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF42 MUTATED     11    0
  C2ORF42 WILD-TYPE  335   29
   clus
vv  C2ORF42 MUTATED C2ORF42 WILD-TYPE
  0              11               335
  1               0                29
[1] 2 2
[1] FALSE
D624V7, binary
                   cls
clus                  0   1
  C2ORF42 MUTATED     8   4
  C2ORF42 WILD-TYPE 137 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF42 MUTATED      8    4
  C2ORF42 WILD-TYPE  137  244
        clus
vv       C2ORF42 MUTATED C2ORF42 WILD-TYPE
  FEMALE               8               137
  MALE                 4               244
[1] 2 2
[1] FALSE
D624V8, binary
                   cls
clus                  0   1
  C2ORF42 MUTATED     7   2
  C2ORF42 WILD-TYPE 285  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF42 MUTATED      7    2
  C2ORF42 WILD-TYPE  285   57
     clus
vv    C2ORF42 MUTATED C2ORF42 WILD-TYPE
  NO                7               285
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C2ORF42 MUTATED                                          0
  C2ORF42 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C2ORF42 MUTATED                                       2
  C2ORF42 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C2ORF42 MUTATED                                                        9
  C2ORF42 WILD-TYPE                                                    149
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C2ORF42 MUTATED                                                   0
  C2ORF42 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C2ORF42 MUTATED                                                                   1
  C2ORF42 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C2ORF42 MUTATED                                                    0
  C2ORF42 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C2ORF42 MUTATED                                                  0
  C2ORF42 WILD-TYPE                                               61
D624V9, multiclass
                                                                   clus
vv                                                                  C2ORF42 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  C2ORF42 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C2ORF42 MUTATED     8   0   0   3
  C2ORF42 WILD-TYPE 303  14  15  21
D624V10, multiclass
    clus
vv   C2ORF42 MUTATED C2ORF42 WILD-TYPE
  R0               8               303
  R1               0                14
  R2               0                15
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D624V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C2ORF42 MUTATED       2                         1
  C2ORF42 WILD-TYPE    85                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C2ORF42 MUTATED                                           0     8
  C2ORF42 WILD-TYPE                                         1   235
D624V12, multiclass
                                           clus
vv                                          C2ORF42 MUTATED C2ORF42 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D624V13, binary
                   cls
clus                  0   1
  C2ORF42 MUTATED     0  11
  C2ORF42 WILD-TYPE   4 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF42 MUTATED      0   11
  C2ORF42 WILD-TYPE    4  299
                        clus
vv                       C2ORF42 MUTATED C2ORF42 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              11               299
[1] 2 2
[1] FALSE

Clustering(625) Variable = ADCY10 MUTATION ANALYSIS
D625V1, survival
                  sevent
clus2                0   1
  ADCY10 MUTATED    10   6
  ADCY10 WILD-TYPE 220 133
  ADCY10 MUTATED ADCY10 WILD-TYPE 
              16              353 
  ADCY10 MUTATED ADCY10 WILD-TYPE 
               6              133 
$`ADCY10 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-8382 TCGA-BR-A44T TCGA-BR-A4QL TCGA-CD-8524 
       21.99        34.68        25.05        34.13        16.14        12.76 
TCGA-CD-8536 TCGA-D7-5577 TCGA-FP-8211 TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4GT 
       12.43        25.71        13.58        11.77         0.10         6.51 
TCGA-HU-A4H3 TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-VQ-A8DL 
       29.00        19.73        45.67         0.92 

$`ADCY10 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-A44U TCGA-BR-A452 
        9.86        20.88         8.22        10.68        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-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-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-D7-5578 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-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-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-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-A7ZE TCGA-R5-A7ZF 
       63.62        36.95         3.72        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-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 

  ADCY10 MUTATED ADCY10 WILD-TYPE 
             0.1              0.0 
  ADCY10 MUTATED ADCY10 WILD-TYPE 
           45.67           122.30 
  ADCY10 MUTATED ADCY10 WILD-TYPE 
          17.935           14.170 
[1] "0.1 - 45.7 (17.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D625V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADCY10 MUTATED         0        1        2        2         4         1
  ADCY10 WILD-TYPE       2       14       38       28        33        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADCY10 MUTATED           0          3          1          3        2
  ADCY10 WILD-TYPE         3         67         52         29       36
D625V3, multiclass
            clus
vv           ADCY10 MUTATED ADCY10 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                2               28
  STAGE IIA               4               33
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              3               29
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADCY10 MUTATED     2   3  10   5
  ADCY10 WILD-TYPE  20  89 163  92
D625V4, multiclass
    clus
vv   ADCY10 MUTATED ADCY10 WILD-TYPE
  T1              2               20
  T2              3               89
  T3             10              163
  T4              5               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
  ADCY10 MUTATED    10   3   2   4
  ADCY10 WILD-TYPE 108 101  75  73
D625V5, multiclass
    clus
vv   ADCY10 MUTATED ADCY10 WILD-TYPE
  N0             10              108
  N1              3              101
  N2              2               75
  N3              4               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"
D625V6, binary
                  cls
clus                 0   1
  ADCY10 MUTATED    16   2
  ADCY10 WILD-TYPE 330  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADCY10 MUTATED     16    2
  ADCY10 WILD-TYPE  330   27
   clus
vv  ADCY10 MUTATED ADCY10 WILD-TYPE
  0             16              330
  1              2               27
[1] 2 2
[1] FALSE
D625V7, binary
                  cls
clus                 0   1
  ADCY10 MUTATED    14   6
  ADCY10 WILD-TYPE 131 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADCY10 MUTATED     14    6
  ADCY10 WILD-TYPE  131  242
        clus
vv       ADCY10 MUTATED ADCY10 WILD-TYPE
  FEMALE             14              131
  MALE                6              242
[1] 2 2
[1] FALSE
D625V8, binary
                  cls
clus                 0   1
  ADCY10 MUTATED    14   2
  ADCY10 WILD-TYPE 278  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADCY10 MUTATED     14    2
  ADCY10 WILD-TYPE  278   57
     clus
vv    ADCY10 MUTATED ADCY10 WILD-TYPE
  NO              14              278
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ADCY10 MUTATED                                          0
  ADCY10 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ADCY10 MUTATED                                       2
  ADCY10 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ADCY10 MUTATED                                                        8
  ADCY10 WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ADCY10 MUTATED                                                   0
  ADCY10 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ADCY10 MUTATED                                                                   3
  ADCY10 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ADCY10 MUTATED                                                    0
  ADCY10 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ADCY10 MUTATED                                                  7
  ADCY10 WILD-TYPE                                               54
D625V9, multiclass
                                                                   clus
vv                                                                  ADCY10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               7
                                                                   clus
vv                                                                  ADCY10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ADCY10 MUTATED    15   1   1   2
  ADCY10 WILD-TYPE 296  13  14  22
D625V10, multiclass
    clus
vv   ADCY10 MUTATED ADCY10 WILD-TYPE
  R0             15              296
  R1              1               13
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D625V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ADCY10 MUTATED       6                         0
  ADCY10 WILD-TYPE    81                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ADCY10 MUTATED                                           0    11
  ADCY10 WILD-TYPE                                         1   232
D625V12, multiclass
                                           clus
vv                                          ADCY10 MUTATED ADCY10 WILD-TYPE
  ASIAN                                                  6               81
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D625V13, binary
                  cls
clus                 0   1
  ADCY10 MUTATED     1  15
  ADCY10 WILD-TYPE   3 295
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADCY10 MUTATED      1   15
  ADCY10 WILD-TYPE    3  295
                        clus
vv                       ADCY10 MUTATED ADCY10 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             15              295
[1] 2 2
[1] FALSE

Clustering(626) Variable = QRFPR MUTATION ANALYSIS
D626V1, survival
                 sevent
clus2               0   1
  QRFPR MUTATED     5   6
  QRFPR WILD-TYPE 225 133
  QRFPR MUTATED QRFPR WILD-TYPE 
             11             358 
  QRFPR MUTATED QRFPR WILD-TYPE 
              6             133 
$`QRFPR MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8368 
       19.56         6.97         9.67        34.68         0.26         4.31 
TCGA-CG-4465 TCGA-D7-6822 TCGA-HU-A4H8 TCGA-RD-A7C1 TCGA-VQ-A91U 
        9.01        12.33        14.07        16.67         1.71 

$`QRFPR WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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 
          34.68          122.30 
  QRFPR MUTATED QRFPR WILD-TYPE 
          9.670          14.565 
[1] "0.3 - 34.7 (9.7)"   "0.0 - 122.3 (14.6)"
[1] "hr=" "2.3"
D626V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  QRFPR MUTATED         0        0        5        0         1         0
  QRFPR WILD-TYPE       2       15       35       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  QRFPR MUTATED           0          2          0          1        1
  QRFPR WILD-TYPE         3         68         53         31       37
D626V3, multiclass
            clus
vv           QRFPR MUTATED QRFPR WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               5              35
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  QRFPR MUTATED     1   4   4   2
  QRFPR WILD-TYPE  21  88 169  95
D626V4, multiclass
    clus
vv   QRFPR MUTATED QRFPR WILD-TYPE
  T1             1              21
  T2             4              88
  T3             4             169
  T4             2              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
  QRFPR MUTATED     5   3   0   2
  QRFPR WILD-TYPE 113 101  77  75
D626V5, multiclass
    clus
vv   QRFPR MUTATED QRFPR WILD-TYPE
  N0             5             113
  N1             3             101
  N2             0              77
  N3             2              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"
D626V6, binary
                 cls
clus                0   1
  QRFPR MUTATED     9   1
  QRFPR WILD-TYPE 337  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  QRFPR MUTATED      9    1
  QRFPR WILD-TYPE  337   28
   clus
vv  QRFPR MUTATED QRFPR WILD-TYPE
  0             9             337
  1             1              28
[1] 2 2
[1] FALSE
D626V7, binary
                 cls
clus                0   1
  QRFPR MUTATED     6   6
  QRFPR WILD-TYPE 139 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  QRFPR MUTATED      6    6
  QRFPR WILD-TYPE  139  242
        clus
vv       QRFPR MUTATED QRFPR WILD-TYPE
  FEMALE             6             139
  MALE               6             242
[1] 2 2
[1] FALSE
D626V8, binary
                 cls
clus                0   1
  QRFPR MUTATED    10   0
  QRFPR WILD-TYPE 282  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  QRFPR MUTATED     10    0
  QRFPR WILD-TYPE  282   59
     clus
vv    QRFPR MUTATED QRFPR WILD-TYPE
  NO             10             282
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  QRFPR MUTATED                                          0
  QRFPR WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  QRFPR MUTATED                                       3
  QRFPR WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  QRFPR MUTATED                                                        6
  QRFPR WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  QRFPR MUTATED                                                   0
  QRFPR WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  QRFPR MUTATED                                                                   1
  QRFPR WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  QRFPR MUTATED                                                    0
  QRFPR WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  QRFPR MUTATED                                                  2
  QRFPR WILD-TYPE                                               59
D626V9, multiclass
                                                                   clus
vv                                                                  QRFPR MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  QRFPR WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  QRFPR MUTATED     7   0   1   3
  QRFPR WILD-TYPE 304  14  14  21
D626V10, multiclass
    clus
vv   QRFPR MUTATED QRFPR WILD-TYPE
  R0             7             304
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D626V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  QRFPR MUTATED       2                         0
  QRFPR WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  QRFPR MUTATED                                           0     9
  QRFPR WILD-TYPE                                         1   234
D626V12, multiclass
                                           clus
vv                                          QRFPR MUTATED QRFPR WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D626V13, binary
                 cls
clus                0   1
  QRFPR MUTATED     0  10
  QRFPR WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  QRFPR MUTATED      0   10
  QRFPR WILD-TYPE    4  300
                        clus
vv                       QRFPR MUTATED QRFPR WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(627) Variable = C19ORF26 MUTATION ANALYSIS
D627V1, survival
                    sevent
clus2                  0   1
  C19ORF26 MUTATED     3   3
  C19ORF26 WILD-TYPE 227 136
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
                 6                363 
  C19ORF26 MUTATED C19ORF26 WILD-TYPE 
                 3                136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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              14.17 
[1] "6.0 - 34.7 (16.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D627V2, 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       1       15       38       30        36        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C19ORF26 MUTATED           1          3          0          0        1
  C19ORF26 WILD-TYPE         2         67         53         32       37
D627V3, multiclass
            clus
vv           C19ORF26 MUTATED C19ORF26 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  0                 15
  STAGE IB                  2                 38
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 0                 52
  STAGE III                 1                  2
  STAGE IIIA                3                 67
  STAGE IIIB                0                 53
  STAGE IIIC                0                 32
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C19ORF26 MUTATED     1   2   4   2
  C19ORF26 WILD-TYPE  21  90 169  95
D627V4, multiclass
    clus
vv   C19ORF26 MUTATED C19ORF26 WILD-TYPE
  T1                1                 21
  T2                2                 90
  T3                4                169
  T4                2                 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
  C19ORF26 MUTATED     3   4   2   0
  C19ORF26 WILD-TYPE 115 100  75  77
D627V5, multiclass
    clus
vv   C19ORF26 MUTATED C19ORF26 WILD-TYPE
  N0                3                115
  N1                4                100
  N2                2                 75
  N3                0                 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"
D627V6, binary
                    cls
clus                   0   1
  C19ORF26 MUTATED     9   0
  C19ORF26 WILD-TYPE 337  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF26 MUTATED      9    0
  C19ORF26 WILD-TYPE  337   29
   clus
vv  C19ORF26 MUTATED C19ORF26 WILD-TYPE
  0                9                337
  1                0                 29
[1] 2 2
[1] FALSE
D627V7, binary
                    cls
clus                   0   1
  C19ORF26 MUTATED     5   5
  C19ORF26 WILD-TYPE 140 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF26 MUTATED      5    5
  C19ORF26 WILD-TYPE  140  243
        clus
vv       C19ORF26 MUTATED C19ORF26 WILD-TYPE
  FEMALE                5                140
  MALE                  5                243
[1] 2 2
[1] FALSE
D627V8, binary
                    cls
clus                   0   1
  C19ORF26 MUTATED     8   0
  C19ORF26 WILD-TYPE 284  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF26 MUTATED      8    0
  C19ORF26 WILD-TYPE  284   59
     clus
vv    C19ORF26 MUTATED C19ORF26 WILD-TYPE
  NO                 8                284
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C19ORF26 MUTATED                                          0
  C19ORF26 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C19ORF26 MUTATED                                       0
  C19ORF26 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C19ORF26 MUTATED                                                        5
  C19ORF26 WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C19ORF26 MUTATED                                                   0
  C19ORF26 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C19ORF26 MUTATED                                                                   3
  C19ORF26 WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C19ORF26 MUTATED                                                    0
  C19ORF26 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C19ORF26 MUTATED                                                  2
  C19ORF26 WILD-TYPE                                               59
D627V9, multiclass
                                                                   clus
vv                                                                  C19ORF26 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  C19ORF26 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C19ORF26 MUTATED     7   0   0   1
  C19ORF26 WILD-TYPE 304  14  15  23
D627V10, multiclass
    clus
vv   C19ORF26 MUTATED C19ORF26 WILD-TYPE
  R0                7                304
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D627V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C19ORF26 MUTATED       1                         1
  C19ORF26 WILD-TYPE    86                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C19ORF26 MUTATED                                           0     6
  C19ORF26 WILD-TYPE                                         1   237
D627V12, multiclass
                                           clus
vv                                          C19ORF26 MUTATED C19ORF26 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D627V13, binary
                    cls
clus                   0   1
  C19ORF26 MUTATED     0   8
  C19ORF26 WILD-TYPE   4 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF26 MUTATED      0    8
  C19ORF26 WILD-TYPE    4  302
                        clus
vv                       C19ORF26 MUTATED C19ORF26 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                8                302
[1] 2 2
[1] FALSE

Clustering(628) Variable = SPANXC MUTATION ANALYSIS
D628V1, survival
                  sevent
clus2                0   1
  SPANXC MUTATED     5   1
  SPANXC WILD-TYPE 225 138
  SPANXC MUTATED SPANXC WILD-TYPE 
               6              363 
  SPANXC MUTATED SPANXC WILD-TYPE 
               1              138 
$`SPANXC MUTATED`
TCGA-BR-8078 TCGA-CD-A4MG TCGA-CG-4436 TCGA-HF-A5NB TCGA-HU-A4GN TCGA-HU-A4H3 
       29.59         6.58         7.99        30.51        29.98        29.00 

$`SPANXC WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  SPANXC MUTATED SPANXC WILD-TYPE 
            6.58             0.00 
  SPANXC MUTATED SPANXC WILD-TYPE 
           30.51           122.30 
  SPANXC MUTATED SPANXC WILD-TYPE 
          29.295           14.170 
[1] "6.6 - 30.5 (29.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3"  
D628V2, 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       2       15       38       30        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPANXC MUTATED           0          0          0          2        0
  SPANXC WILD-TYPE         3         70         53         30       38
D628V3, multiclass
            clus
vv           SPANXC MUTATED SPANXC WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SPANXC MUTATED     1   3   1   3
  SPANXC WILD-TYPE  21  89 172  94
D628V4, multiclass
    clus
vv   SPANXC MUTATED SPANXC WILD-TYPE
  T1              1               21
  T2              3               89
  T3              1              172
  T4              3               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
  SPANXC MUTATED     4   1   0   2
  SPANXC WILD-TYPE 114 103  77  75
D628V5, multiclass
    clus
vv   SPANXC MUTATED SPANXC WILD-TYPE
  N0              4              114
  N1              1              103
  N2              0               77
  N3              2               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"
D628V6, binary
                  cls
clus                 0   1
  SPANXC MUTATED     8   0
  SPANXC WILD-TYPE 338  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      8    0
  SPANXC WILD-TYPE  338   29
   clus
vv  SPANXC MUTATED SPANXC WILD-TYPE
  0              8              338
  1              0               29
[1] 2 2
[1] FALSE
D628V7, binary
                  cls
clus                 0   1
  SPANXC MUTATED     4   4
  SPANXC WILD-TYPE 141 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      4    4
  SPANXC WILD-TYPE  141  244
        clus
vv       SPANXC MUTATED SPANXC WILD-TYPE
  FEMALE              4              141
  MALE                4              244
[1] 2 2
[1] FALSE
D628V8, binary
                  cls
clus                 0   1
  SPANXC MUTATED     4   1
  SPANXC WILD-TYPE 288  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      4    1
  SPANXC WILD-TYPE  288   58
     clus
vv    SPANXC MUTATED SPANXC WILD-TYPE
  NO               4              288
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SPANXC MUTATED                                          0
  SPANXC WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SPANXC MUTATED                                       2
  SPANXC WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPANXC MUTATED                                                        2
  SPANXC WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SPANXC MUTATED                                                   1
  SPANXC WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPANXC MUTATED                                                                   2
  SPANXC WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SPANXC MUTATED                                                    0
  SPANXC WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SPANXC MUTATED                                                  1
  SPANXC WILD-TYPE                                               60
D628V9, multiclass
                                                                   clus
vv                                                                  SPANXC MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  SPANXC WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SPANXC MUTATED     5   1   0   1
  SPANXC WILD-TYPE 306  13  15  23
D628V10, multiclass
    clus
vv   SPANXC MUTATED SPANXC WILD-TYPE
  R0              5              306
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D628V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SPANXC MUTATED       3                         0
  SPANXC WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPANXC MUTATED                                           0     2
  SPANXC WILD-TYPE                                         1   241
D628V12, multiclass
                                           clus
vv                                          SPANXC MUTATED SPANXC WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D628V13, binary
                  cls
clus                 0   1
  SPANXC MUTATED     0   5
  SPANXC WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      0    5
  SPANXC WILD-TYPE    4  305
                        clus
vv                       SPANXC MUTATED SPANXC WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(629) Variable = XRN1 MUTATION ANALYSIS
D629V1, survival
                sevent
clus2              0   1
  XRN1 MUTATED    13   7
  XRN1 WILD-TYPE 217 132
  XRN1 MUTATED XRN1 WILD-TYPE 
            20            349 
  XRN1 MUTATED XRN1 WILD-TYPE 
             7            132 
$`XRN1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-8589 
        6.97        30.90         9.67        34.68        18.05        27.12 
TCGA-BR-8591 TCGA-BR-8690 TCGA-CD-8529 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5721 
       28.14        10.68        12.30        15.95         1.02         6.02 
TCGA-CG-5726 TCGA-D7-A6EY TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4G9 TCGA-HU-A4H5 
       28.96        11.44        77.29        30.51        24.20        23.80 
TCGA-HU-A4H8 TCGA-IN-8462 
       14.07        18.81 

$`XRN1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A44T 
       31.96        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-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-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-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-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-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-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        29.00        23.84        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-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 

  XRN1 MUTATED XRN1 WILD-TYPE 
          1.02           0.00 
  XRN1 MUTATED XRN1 WILD-TYPE 
         77.29         122.30 
  XRN1 MUTATED XRN1 WILD-TYPE 
         18.43          14.07 
[1] "1.0 - 77.3 (18.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D629V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XRN1 MUTATED         1        2        2        2         1         1
  XRN1 WILD-TYPE       1       13       38       28        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XRN1 MUTATED           0          3          3          2        3
  XRN1 WILD-TYPE         3         67         50         30       35
D629V3, multiclass
            clus
vv           XRN1 MUTATED XRN1 WILD-TYPE
  STAGE I               1              1
  STAGE IA              2             13
  STAGE IB              2             38
  STAGE II              2             28
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            3             50
  STAGE IIIC            2             30
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  XRN1 MUTATED     5   5   7   6
  XRN1 WILD-TYPE  17  87 166  91
D629V4, multiclass
    clus
vv   XRN1 MUTATED XRN1 WILD-TYPE
  T1            5             17
  T2            5             87
  T3            7            166
  T4            6             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
  XRN1 MUTATED     6   9   1   4
  XRN1 WILD-TYPE 112  95  76  73
D629V5, multiclass
    clus
vv   XRN1 MUTATED XRN1 WILD-TYPE
  N0            6            112
  N1            9             95
  N2            1             76
  N3            4             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"
D629V6, binary
                cls
clus               0   1
  XRN1 MUTATED    19   2
  XRN1 WILD-TYPE 327  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  XRN1 MUTATED     19    2
  XRN1 WILD-TYPE  327   27
   clus
vv  XRN1 MUTATED XRN1 WILD-TYPE
  0           19            327
  1            2             27
[1] 2 2
[1] FALSE
D629V7, binary
                cls
clus               0   1
  XRN1 MUTATED     9  15
  XRN1 WILD-TYPE 136 233
[1] "tbl2"
                cls
clus             [,1] [,2]
  XRN1 MUTATED      9   15
  XRN1 WILD-TYPE  136  233
        clus
vv       XRN1 MUTATED XRN1 WILD-TYPE
  FEMALE            9            136
  MALE             15            233
[1] 2 2
[1] FALSE
D629V8, binary
                cls
clus               0   1
  XRN1 MUTATED    16   3
  XRN1 WILD-TYPE 276  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  XRN1 MUTATED     16    3
  XRN1 WILD-TYPE  276   56
     clus
vv    XRN1 MUTATED XRN1 WILD-TYPE
  NO            16            276
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  XRN1 MUTATED                                          0
  XRN1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  XRN1 MUTATED                                       0
  XRN1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XRN1 MUTATED                                                       15
  XRN1 WILD-TYPE                                                    143
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  XRN1 MUTATED                                                   3
  XRN1 WILD-TYPE                                                18
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XRN1 MUTATED                                                                   2
  XRN1 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  XRN1 MUTATED                                                    1
  XRN1 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  XRN1 MUTATED                                                  3
  XRN1 WILD-TYPE                                               58
D629V9, multiclass
                                                                   clus
vv                                                                  XRN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  XRN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  XRN1 MUTATED    16   1   1   6
  XRN1 WILD-TYPE 295  13  14  18
D629V10, multiclass
    clus
vv   XRN1 MUTATED XRN1 WILD-TYPE
  R0           16            295
  R1            1             13
  R2            1             14
  RX            6             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D629V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  XRN1 MUTATED       4                         1
  XRN1 WILD-TYPE    83                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XRN1 MUTATED                                           0    13
  XRN1 WILD-TYPE                                         1   230
D629V12, multiclass
                                           clus
vv                                          XRN1 MUTATED XRN1 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D629V13, binary
                cls
clus               0   1
  XRN1 MUTATED     0  18
  XRN1 WILD-TYPE   4 292
[1] "tbl2"
                cls
clus             [,1] [,2]
  XRN1 MUTATED      0   18
  XRN1 WILD-TYPE    4  292
                        clus
vv                       XRN1 MUTATED XRN1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           18            292
[1] 2 2
[1] FALSE

Clustering(630) Variable = SORBS2 MUTATION ANALYSIS
D630V1, survival
                  sevent
clus2                0   1
  SORBS2 MUTATED    16   3
  SORBS2 WILD-TYPE 214 136
  SORBS2 MUTATED SORBS2 WILD-TYPE 
              19              350 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               3              136 
$`SORBS2 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 
       21.99        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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
        5.92        36.43        14.76        26.43        11.24        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-F1-6875 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-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-A5UJ TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
        3.72        19.73        14.04        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-A8P3 
       48.79         5.46        13.25        13.02        43.36        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 

  SORBS2 MUTATED SORBS2 WILD-TYPE 
            1.12             0.00 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
           74.53           122.30 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
          22.320           14.055 
[1] "1.1 - 74.5 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.3"
D630V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SORBS2 MUTATED         0        2        1        0         2         3
  SORBS2 WILD-TYPE       2       13       39       30        35        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SORBS2 MUTATED           0          2          1          2        7
  SORBS2 WILD-TYPE         3         68         52         30       31
D630V3, multiclass
            clus
vv           SORBS2 MUTATED SORBS2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                2               13
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              2               30
  STAGE IV                7               31
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SORBS2 MUTATED     2   1   8   9
  SORBS2 WILD-TYPE  20  91 165  88
D630V4, multiclass
    clus
vv   SORBS2 MUTATED SORBS2 WILD-TYPE
  T1              2               20
  T2              1               91
  T3              8              165
  T4              9               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
  SORBS2 MUTATED     6   8   4   2
  SORBS2 WILD-TYPE 112  96  73  75
D630V5, multiclass
    clus
vv   SORBS2 MUTATED SORBS2 WILD-TYPE
  N0              6              112
  N1              8               96
  N2              4               73
  N3              2               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"
D630V6, binary
                  cls
clus                 0   1
  SORBS2 MUTATED    16   5
  SORBS2 WILD-TYPE 330  24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED     16    5
  SORBS2 WILD-TYPE  330   24
   clus
vv  SORBS2 MUTATED SORBS2 WILD-TYPE
  0             16              330
  1              5               24
[1] 2 2
[1] FALSE
D630V7, binary
                  cls
clus                 0   1
  SORBS2 MUTATED    10  11
  SORBS2 WILD-TYPE 135 237
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED     10   11
  SORBS2 WILD-TYPE  135  237
        clus
vv       SORBS2 MUTATED SORBS2 WILD-TYPE
  FEMALE             10              135
  MALE               11              237
[1] 2 2
[1] FALSE
D630V8, binary
                  cls
clus                 0   1
  SORBS2 MUTATED    16   2
  SORBS2 WILD-TYPE 276  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED     16    2
  SORBS2 WILD-TYPE  276   57
     clus
vv    SORBS2 MUTATED SORBS2 WILD-TYPE
  NO              16              276
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SORBS2 MUTATED                                          0
  SORBS2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SORBS2 MUTATED                                       5
  SORBS2 WILD-TYPE                                    65
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SORBS2 MUTATED                                                        6
  SORBS2 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SORBS2 MUTATED                                                   1
  SORBS2 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SORBS2 MUTATED                                                                   4
  SORBS2 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SORBS2 MUTATED                                                    0
  SORBS2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SORBS2 MUTATED                                                  5
  SORBS2 WILD-TYPE                                               56
D630V9, multiclass
                                                                   clus
vv                                                                  SORBS2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               5
                                                                   clus
vv                                                                  SORBS2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SORBS2 MUTATED    17   0   1   2
  SORBS2 WILD-TYPE 294  14  14  22
D630V10, multiclass
    clus
vv   SORBS2 MUTATED SORBS2 WILD-TYPE
  R0             17              294
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D630V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SORBS2 MUTATED       5                         0
  SORBS2 WILD-TYPE    82                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SORBS2 MUTATED                                           0    13
  SORBS2 WILD-TYPE                                         1   230
D630V12, multiclass
                                           clus
vv                                          SORBS2 MUTATED SORBS2 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D630V13, binary
                  cls
clus                 0   1
  SORBS2 MUTATED     2  14
  SORBS2 WILD-TYPE   2 296
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      2   14
  SORBS2 WILD-TYPE    2  296
                        clus
vv                       SORBS2 MUTATED SORBS2 WILD-TYPE
  HISPANIC OR LATINO                  2                2
  NOT HISPANIC OR LATINO             14              296
[1] 2 2
[1] FALSE

Clustering(631) Variable = LRP12 MUTATION ANALYSIS
D631V1, survival
                 sevent
clus2               0   1
  LRP12 MUTATED    17   9
  LRP12 WILD-TYPE 213 130
  LRP12 MUTATED LRP12 WILD-TYPE 
             26             343 
  LRP12 MUTATED LRP12 WILD-TYPE 
              9             130 
$`LRP12 MUTATED`
TCGA-CG-5727 TCGA-FP-A8CX TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6453 
       79.07         0.23        19.56         6.97        34.68        15.95 
TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG 
       32.25         6.18        25.05        31.96        16.14         6.58 
TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-5721 TCGA-D7-A4YV TCGA-D7-A747 TCGA-HF-7134 
       12.62         1.02         6.02         5.92         8.38        52.21 
TCGA-HU-8243 TCGA-HU-8604 TCGA-HU-A4H2 TCGA-HU-A4H8 TCGA-IN-A6RI TCGA-MX-A5UJ 
        5.92        22.82        12.95        14.07        18.38        19.73 
TCGA-VQ-A8P2 TCGA-VQ-AA64 
       38.14        18.41 

$`LRP12 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 
       47.05        21.99        22.98        16.24        20.15         9.86 
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-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-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-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-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-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-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-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-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-F1-6874 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-8244 TCGA-HU-8249 
       63.06        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-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-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-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-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-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 

  LRP12 MUTATED LRP12 WILD-TYPE 
           0.23            0.00 
  LRP12 MUTATED LRP12 WILD-TYPE 
          79.07          122.30 
  LRP12 MUTATED LRP12 WILD-TYPE 
         16.045          14.170 
[1] "0.2 - 79.1 (16.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D631V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRP12 MUTATED         2        2        2        1         5         3
  LRP12 WILD-TYPE       0       13       38       29        32        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRP12 MUTATED           0          4          3          4        4
  LRP12 WILD-TYPE         3         66         50         28       34
D631V3, multiclass
            clus
vv           LRP12 MUTATED LRP12 WILD-TYPE
  STAGE I                2               0
  STAGE IA               2              13
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              5              32
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             3              50
  STAGE IIIC             4              28
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LRP12 MUTATED     5   2  13  10
  LRP12 WILD-TYPE  17  90 160  87
D631V4, multiclass
    clus
vv   LRP12 MUTATED LRP12 WILD-TYPE
  T1             5              17
  T2             2              90
  T3            13             160
  T4            10              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
  LRP12 MUTATED    11   8   5   6
  LRP12 WILD-TYPE 107  96  72  71
D631V5, multiclass
    clus
vv   LRP12 MUTATED LRP12 WILD-TYPE
  N0            11             107
  N1             8              96
  N2             5              72
  N3             6              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"
D631V6, binary
                 cls
clus                0   1
  LRP12 MUTATED    25   2
  LRP12 WILD-TYPE 321  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP12 MUTATED     25    2
  LRP12 WILD-TYPE  321   27
   clus
vv  LRP12 MUTATED LRP12 WILD-TYPE
  0            25             321
  1             2              27
[1] 2 2
[1] FALSE
D631V7, binary
                 cls
clus                0   1
  LRP12 MUTATED    10  20
  LRP12 WILD-TYPE 135 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP12 MUTATED     10   20
  LRP12 WILD-TYPE  135  228
        clus
vv       LRP12 MUTATED LRP12 WILD-TYPE
  FEMALE            10             135
  MALE              20             228
[1] 2 2
[1] FALSE
D631V8, binary
                 cls
clus                0   1
  LRP12 MUTATED    23   3
  LRP12 WILD-TYPE 269  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP12 MUTATED     23    3
  LRP12 WILD-TYPE  269   56
     clus
vv    LRP12 MUTATED LRP12 WILD-TYPE
  NO             23             269
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LRP12 MUTATED                                          1
  LRP12 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LRP12 MUTATED                                       3
  LRP12 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LRP12 MUTATED                                                       13
  LRP12 WILD-TYPE                                                    145
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LRP12 MUTATED                                                   1
  LRP12 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LRP12 MUTATED                                                                   5
  LRP12 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LRP12 MUTATED                                                    0
  LRP12 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LRP12 MUTATED                                                  7
  LRP12 WILD-TYPE                                               54
D631V9, multiclass
                                                                   clus
vv                                                                  LRP12 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              7
                                                                   clus
vv                                                                  LRP12 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LRP12 MUTATED    23   0   1   3
  LRP12 WILD-TYPE 288  14  14  21
D631V10, multiclass
    clus
vv   LRP12 MUTATED LRP12 WILD-TYPE
  R0            23             288
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D631V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LRP12 MUTATED       8                         1
  LRP12 WILD-TYPE    79                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LRP12 MUTATED                                           0    17
  LRP12 WILD-TYPE                                         1   226
D631V12, multiclass
                                           clus
vv                                          LRP12 MUTATED LRP12 WILD-TYPE
  ASIAN                                                 8              79
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D631V13, binary
                 cls
clus                0   1
  LRP12 MUTATED     0  24
  LRP12 WILD-TYPE   4 286
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP12 MUTATED      0   24
  LRP12 WILD-TYPE    4  286
                        clus
vv                       LRP12 MUTATED LRP12 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            24             286
[1] 2 2
[1] FALSE

Clustering(632) Variable = KIF13A MUTATION ANALYSIS
D632V1, survival
                  sevent
clus2                0   1
  KIF13A MUTATED    11   7
  KIF13A WILD-TYPE 219 132
  KIF13A MUTATED KIF13A WILD-TYPE 
              18              351 
  KIF13A MUTATED KIF13A WILD-TYPE 
               7              132 
$`KIF13A MUTATED`
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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       11.61        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-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-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-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-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-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 

  KIF13A MUTATED KIF13A WILD-TYPE 
             0.1              0.0 
  KIF13A MUTATED KIF13A WILD-TYPE 
           34.68           122.30 
  KIF13A MUTATED KIF13A WILD-TYPE 
           12.03            14.43 
[1] "0.1 - 34.7 (12.0)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D632V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIF13A MUTATED         0        0        3        1         4         2
  KIF13A WILD-TYPE       2       15       37       29        33        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF13A MUTATED           0          0          2          3        2
  KIF13A WILD-TYPE         3         70         51         29       36
D632V3, multiclass
            clus
vv           KIF13A MUTATED KIF13A WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                1               29
  STAGE IIA               4               33
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              2               51
  STAGE IIIC              3               29
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIF13A MUTATED     0   5   5   8
  KIF13A WILD-TYPE  22  87 168  89
D632V4, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  T1              0               22
  T2              5               87
  T3              5              168
  T4              8               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
  KIF13A MUTATED     9   4   1   4
  KIF13A WILD-TYPE 109 100  76  73
D632V5, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  N0              9              109
  N1              4              100
  N2              1               76
  N3              4               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"
D632V6, binary
                  cls
clus                 0   1
  KIF13A MUTATED    18   1
  KIF13A WILD-TYPE 328  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED     18    1
  KIF13A WILD-TYPE  328   28
   clus
vv  KIF13A MUTATED KIF13A WILD-TYPE
  0             18              328
  1              1               28
[1] 2 2
[1] FALSE
D632V7, binary
                  cls
clus                 0   1
  KIF13A MUTATED     9  10
  KIF13A WILD-TYPE 136 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED      9   10
  KIF13A WILD-TYPE  136  238
        clus
vv       KIF13A MUTATED KIF13A WILD-TYPE
  FEMALE              9              136
  MALE               10              238
[1] 2 2
[1] FALSE
D632V8, binary
                  cls
clus                 0   1
  KIF13A MUTATED    15   2
  KIF13A WILD-TYPE 277  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED     15    2
  KIF13A WILD-TYPE  277   57
     clus
vv    KIF13A MUTATED KIF13A WILD-TYPE
  NO              15              277
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIF13A MUTATED                                          0
  KIF13A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIF13A MUTATED                                       4
  KIF13A WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIF13A MUTATED                                                        9
  KIF13A WILD-TYPE                                                    149
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIF13A MUTATED                                                   1
  KIF13A WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIF13A MUTATED                                                                   2
  KIF13A WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIF13A MUTATED                                                    0
  KIF13A WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIF13A MUTATED                                                  3
  KIF13A WILD-TYPE                                               58
D632V9, multiclass
                                                                   clus
vv                                                                  KIF13A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  KIF13A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KIF13A MUTATED    13   1   1   2
  KIF13A WILD-TYPE 298  13  14  22
D632V10, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  R0             13              298
  R1              1               13
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D632V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KIF13A MUTATED       5                         1
  KIF13A WILD-TYPE    82                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIF13A MUTATED                                           0     8
  KIF13A WILD-TYPE                                         1   235
D632V12, multiclass
                                           clus
vv                                          KIF13A MUTATED KIF13A WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D632V13, binary
                  cls
clus                 0   1
  KIF13A MUTATED     0  14
  KIF13A WILD-TYPE   4 296
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED      0   14
  KIF13A WILD-TYPE    4  296
                        clus
vv                       KIF13A MUTATED KIF13A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             14              296
[1] 2 2
[1] FALSE

Clustering(633) Variable = C6 MUTATION ANALYSIS
D633V1, survival
              sevent
clus2            0   1
  C6 MUTATED     7   1
  C6 WILD-TYPE 223 138
  C6 MUTATED C6 WILD-TYPE 
           8          361 
  C6 MUTATED C6 WILD-TYPE 
           1          138 
$`C6 MUTATED`
TCGA-B7-5816 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7901 TCGA-BR-8680 
       26.70        44.94        35.24        35.84         3.45        31.96 
TCGA-CD-8529 TCGA-HU-A4GT 
       12.30         6.51 

$`C6 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-7715 
       30.90        31.20        21.90         9.21        36.16        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-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-F1-6874 
        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 

  C6 MUTATED C6 WILD-TYPE 
        3.45         0.00 
  C6 MUTATED C6 WILD-TYPE 
       44.94       122.30 
  C6 MUTATED C6 WILD-TYPE 
       29.33        14.17 
[1] "3.5 - 44.9 (29.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3.9"
D633V2, continuous
              vv
clus           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  C6 MUTATED         0        1        1        1         2         2         0
  C6 WILD-TYPE       2       14       39       29        35        50         3
              vv
clus           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6 MUTATED            0          0          0        2
  C6 WILD-TYPE         70         53         32       36
D633V3, multiclass
            clus
vv           C6 MUTATED C6 WILD-TYPE
  STAGE I             0            2
  STAGE IA            1           14
  STAGE IB            1           39
  STAGE II            1           29
  STAGE IIA           2           35
  STAGE IIB           2           50
  STAGE III           0            3
  STAGE IIIA          0           70
  STAGE IIIB          0           53
  STAGE IIIC          0           32
  STAGE IV            2           36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            T1  T2  T3  T4
  C6 MUTATED     2   1   4   3
  C6 WILD-TYPE  20  91 169  94
D633V4, multiclass
    clus
vv   C6 MUTATED C6 WILD-TYPE
  T1          2           20
  T2          1           91
  T3          4          169
  T4          3           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
  C6 MUTATED     7   2   1   0
  C6 WILD-TYPE 111 102  76  77
D633V5, multiclass
    clus
vv   C6 MUTATED C6 WILD-TYPE
  N0          7          111
  N1          2          102
  N2          1           76
  N3          0           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"
D633V6, binary
              cls
clus             0   1
  C6 MUTATED     9   2
  C6 WILD-TYPE 337  27
[1] "tbl2"
              cls
clus           [,1] [,2]
  C6 MUTATED      9    2
  C6 WILD-TYPE  337   27
   clus
vv  C6 MUTATED C6 WILD-TYPE
  0          9          337
  1          2           27
[1] 2 2
[1] FALSE
D633V7, binary
              cls
clus             0   1
  C6 MUTATED     7   4
  C6 WILD-TYPE 138 244
[1] "tbl2"
              cls
clus           [,1] [,2]
  C6 MUTATED      7    4
  C6 WILD-TYPE  138  244
        clus
vv       C6 MUTATED C6 WILD-TYPE
  FEMALE          7          138
  MALE            4          244
[1] 2 2
[1] FALSE
D633V8, binary
              cls
clus             0   1
  C6 MUTATED     7   2
  C6 WILD-TYPE 285  57
[1] "tbl2"
              cls
clus           [,1] [,2]
  C6 MUTATED      7    2
  C6 WILD-TYPE  285   57
     clus
vv    C6 MUTATED C6 WILD-TYPE
  NO           7          285
  YES          2           57
[1] 2 2
[1] FALSE
              vv
clus           STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C6 MUTATED                                          0
  C6 WILD-TYPE                                        8
              vv
clus           STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C6 MUTATED                                       1
  C6 WILD-TYPE                                    69
              vv
clus           STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C6 MUTATED                                                        6
  C6 WILD-TYPE                                                    152
              vv
clus           STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C6 MUTATED                                                   1
  C6 WILD-TYPE                                                20
              vv
clus           STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C6 MUTATED                                                                   1
  C6 WILD-TYPE                                                                67
              vv
clus           STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C6 MUTATED                                                    0
  C6 WILD-TYPE                                                  5
              vv
clus           STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C6 MUTATED                                                  2
  C6 WILD-TYPE                                               59
D633V9, multiclass
                                                                   clus
vv                                                                  C6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                   0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                      1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                     6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)          1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                         0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                           2
                                                                   clus
vv                                                                  C6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                     152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            R0  R1  R2  RX
  C6 MUTATED     9   0   0   2
  C6 WILD-TYPE 302  14  15  22
D633V10, multiclass
    clus
vv   C6 MUTATED C6 WILD-TYPE
  R0          9          302
  R1          0           14
  R2          0           15
  RX          2           22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D633V11, continuous
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN
  C6 MUTATED       4                         0
  C6 WILD-TYPE    83                         9
              vv
clus           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C6 MUTATED                                           0     7
  C6 WILD-TYPE                                         1   236
D633V12, multiclass
                                           clus
vv                                          C6 MUTATED C6 WILD-TYPE
  ASIAN                                              4           83
  BLACK OR AFRICAN AMERICAN                          0            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER          0            1
  WHITE                                              7          236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D633V13, binary
              cls
clus             0   1
  C6 MUTATED     0  11
  C6 WILD-TYPE   4 299
[1] "tbl2"
              cls
clus           [,1] [,2]
  C6 MUTATED      0   11
  C6 WILD-TYPE    4  299
                        clus
vv                       C6 MUTATED C6 WILD-TYPE
  HISPANIC OR LATINO              0            4
  NOT HISPANIC OR LATINO         11          299
[1] 2 2
[1] FALSE

Clustering(634) Variable = HIVEP3 MUTATION ANALYSIS
D634V1, survival
                  sevent
clus2                0   1
  HIVEP3 MUTATED    21   8
  HIVEP3 WILD-TYPE 209 131
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
              29              340 
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
               8              131 
$`HIVEP3 MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-B7-A5TK TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8361 
       21.99        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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
        9.86        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-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-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-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-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-4455 TCGA-CG-4462 TCGA-CG-4465 
        4.01        14.01        29.98        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-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-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-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
        8.98         6.51         6.58        20.25         0.26        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-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-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 

  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
             0.1              0.0 
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
          105.07           122.30 
  HIVEP3 MUTATED HIVEP3 WILD-TYPE 
           13.15            14.45 
[1] "0.1 - 105.1 (13.2)" "0.0 - 122.3 (14.4)"
[1] "hr=" "1.3"
D634V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HIVEP3 MUTATED         0        1        3        3         6         3
  HIVEP3 WILD-TYPE       2       14       37       27        31        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIVEP3 MUTATED           0          2          3          3        5
  HIVEP3 WILD-TYPE         3         68         50         29       33
D634V3, multiclass
            clus
vv           HIVEP3 MUTATED HIVEP3 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                3               37
  STAGE II                3               27
  STAGE IIA               6               31
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              3               50
  STAGE IIIC              3               29
  STAGE IV                5               33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HIVEP3 MUTATED     3   6  10  11
  HIVEP3 WILD-TYPE  19  86 163  86
D634V4, multiclass
    clus
vv   HIVEP3 MUTATED HIVEP3 WILD-TYPE
  T1              3               19
  T2              6               86
  T3             10              163
  T4             11               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
  HIVEP3 MUTATED    10  10   5   4
  HIVEP3 WILD-TYPE 108  94  72  73
D634V5, multiclass
    clus
vv   HIVEP3 MUTATED HIVEP3 WILD-TYPE
  N0             10              108
  N1             10               94
  N2              5               72
  N3              4               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"
D634V6, binary
                  cls
clus                 0   1
  HIVEP3 MUTATED    25   5
  HIVEP3 WILD-TYPE 321  24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP3 MUTATED     25    5
  HIVEP3 WILD-TYPE  321   24
   clus
vv  HIVEP3 MUTATED HIVEP3 WILD-TYPE
  0             25              321
  1              5               24
[1] 2 2
[1] FALSE
D634V7, binary
                  cls
clus                 0   1
  HIVEP3 MUTATED    15  15
  HIVEP3 WILD-TYPE 130 233
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP3 MUTATED     15   15
  HIVEP3 WILD-TYPE  130  233
        clus
vv       HIVEP3 MUTATED HIVEP3 WILD-TYPE
  FEMALE             15              130
  MALE               15              233
[1] 2 2
[1] FALSE
D634V8, binary
                  cls
clus                 0   1
  HIVEP3 MUTATED    27   1
  HIVEP3 WILD-TYPE 265  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP3 MUTATED     27    1
  HIVEP3 WILD-TYPE  265   58
     clus
vv    HIVEP3 MUTATED HIVEP3 WILD-TYPE
  NO              27              265
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HIVEP3 MUTATED                                          0
  HIVEP3 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HIVEP3 MUTATED                                       4
  HIVEP3 WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HIVEP3 MUTATED                                                       10
  HIVEP3 WILD-TYPE                                                    148
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HIVEP3 MUTATED                                                   2
  HIVEP3 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HIVEP3 MUTATED                                                                   5
  HIVEP3 WILD-TYPE                                                                63
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HIVEP3 MUTATED                                                    1
  HIVEP3 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HIVEP3 MUTATED                                                  8
  HIVEP3 WILD-TYPE                                               53
D634V9, multiclass
                                                                   clus
vv                                                                  HIVEP3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               8
                                                                   clus
vv                                                                  HIVEP3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                53
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HIVEP3 MUTATED    24   0   3   0
  HIVEP3 WILD-TYPE 287  14  12  24
D634V10, multiclass
    clus
vv   HIVEP3 MUTATED HIVEP3 WILD-TYPE
  R0             24              287
  R1              0               14
  R2              3               12
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D634V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  HIVEP3 MUTATED       9                         0
  HIVEP3 WILD-TYPE    78                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HIVEP3 MUTATED                                           0    15
  HIVEP3 WILD-TYPE                                         1   228
D634V12, multiclass
                                           clus
vv                                          HIVEP3 MUTATED HIVEP3 WILD-TYPE
  ASIAN                                                  9               78
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 15              228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D634V13, binary
                  cls
clus                 0   1
  HIVEP3 MUTATED     0  23
  HIVEP3 WILD-TYPE   4 287
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP3 MUTATED      0   23
  HIVEP3 WILD-TYPE    4  287
                        clus
vv                       HIVEP3 MUTATED HIVEP3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             23              287
[1] 2 2
[1] FALSE

Clustering(635) Variable = FAM123C MUTATION ANALYSIS
D635V1, survival
                   sevent
clus2                 0   1
  FAM123C MUTATED    10   3
  FAM123C WILD-TYPE 220 136
  FAM123C MUTATED FAM123C WILD-TYPE 
               13               356 
  FAM123C MUTATED FAM123C WILD-TYPE 
                3               136 
$`FAM123C MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-8360 TCGA-CG-4306 TCGA-CG-4465 
       34.68        44.94        21.90         6.18         1.02         9.01 
TCGA-CG-5721 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-F1-6874 TCGA-HF-7134 TCGA-HF-A5NB 
        6.02         5.92        13.78        14.47        52.21        30.51 
TCGA-HU-A4GX 
       20.25 

$`FAM123C WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       30.90        31.20         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-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-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-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-A4BF TCGA-FP-A9TM 
        5.03        13.58         0.56        11.08         5.52         6.21 
TCGA-HF-7132 TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       77.29        63.06        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 

  FAM123C MUTATED FAM123C WILD-TYPE 
             1.02              0.00 
  FAM123C MUTATED FAM123C WILD-TYPE 
            52.21            122.30 
  FAM123C MUTATED FAM123C WILD-TYPE 
            14.47             14.22 
[1] "1.0 - 52.2 (14.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.7"
D635V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM123C MUTATED         0        1        1        0         3         1
  FAM123C WILD-TYPE       2       14       39       30        34        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM123C MUTATED           0          0          1          2        4
  FAM123C WILD-TYPE         3         70         52         30       34
D635V3, multiclass
            clus
vv           FAM123C MUTATED FAM123C WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                3                34
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               1                52
  STAGE IIIC               2                30
  STAGE IV                 4                34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM123C MUTATED     1   1   7   4
  FAM123C WILD-TYPE  21  91 166  93
D635V4, multiclass
    clus
vv   FAM123C MUTATED FAM123C WILD-TYPE
  T1               1                21
  T2               1                91
  T3               7               166
  T4               4                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
  FAM123C MUTATED     5   2   2   4
  FAM123C WILD-TYPE 113 102  75  73
D635V5, multiclass
    clus
vv   FAM123C MUTATED FAM123C WILD-TYPE
  N0               5               113
  N1               2               102
  N2               2                75
  N3               4                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"
D635V6, binary
                   cls
clus                  0   1
  FAM123C MUTATED    10   3
  FAM123C WILD-TYPE 336  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123C MUTATED     10    3
  FAM123C WILD-TYPE  336   26
   clus
vv  FAM123C MUTATED FAM123C WILD-TYPE
  0              10               336
  1               3                26
[1] 2 2
[1] FALSE
D635V7, binary
                   cls
clus                  0   1
  FAM123C MUTATED     6   7
  FAM123C WILD-TYPE 139 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123C MUTATED      6    7
  FAM123C WILD-TYPE  139  241
        clus
vv       FAM123C MUTATED FAM123C WILD-TYPE
  FEMALE               6               139
  MALE                 7               241
[1] 2 2
[1] FALSE
D635V8, binary
                   cls
clus                  0   1
  FAM123C MUTATED     9   2
  FAM123C WILD-TYPE 283  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123C MUTATED      9    2
  FAM123C WILD-TYPE  283   57
     clus
vv    FAM123C MUTATED FAM123C WILD-TYPE
  NO                9               283
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM123C MUTATED                                          0
  FAM123C WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM123C MUTATED                                       2
  FAM123C WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM123C MUTATED                                                        5
  FAM123C WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM123C MUTATED                                                   1
  FAM123C WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM123C MUTATED                                                                   4
  FAM123C WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM123C MUTATED                                                    0
  FAM123C WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM123C MUTATED                                                  1
  FAM123C WILD-TYPE                                               60
D635V9, multiclass
                                                                   clus
vv                                                                  FAM123C MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  FAM123C WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM123C MUTATED    10   1   2   0
  FAM123C WILD-TYPE 301  13  13  24
D635V10, multiclass
    clus
vv   FAM123C MUTATED FAM123C WILD-TYPE
  R0              10               301
  R1               1                13
  R2               2                13
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D635V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM123C MUTATED       1                         0
  FAM123C WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM123C MUTATED                                           0     7
  FAM123C WILD-TYPE                                         1   236
D635V12, multiclass
                                           clus
vv                                          FAM123C MUTATED FAM123C WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D635V13, binary
                   cls
clus                  0   1
  FAM123C MUTATED     0   8
  FAM123C WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123C MUTATED      0    8
  FAM123C WILD-TYPE    4  302
                        clus
vv                       FAM123C MUTATED FAM123C WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(636) Variable = EPHB6 MUTATION ANALYSIS
D636V1, survival
                 sevent
clus2               0   1
  EPHB6 MUTATED    12   3
  EPHB6 WILD-TYPE 218 136
  EPHB6 MUTATED EPHB6 WILD-TYPE 
             15             354 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
              3             136 
$`EPHB6 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8361 
        6.97        34.68        30.90        35.84        29.59        31.10 
TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5728 TCGA-D7-A6EY TCGA-F1-6874 
       28.14        31.96         6.58        65.10        11.44        14.47 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-VQ-A8P2 
       29.00        23.80        38.14 

$`EPHB6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
           6.58            0.00 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
           65.1           122.3 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
          29.59           14.04 
[1] "6.6 - 65.1 (29.6)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "2.9"
D636V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPHB6 MUTATED         0        1        4        0         2         1
  EPHB6 WILD-TYPE       2       14       36       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPHB6 MUTATED           0          3          1          3        1
  EPHB6 WILD-TYPE         3         67         52         29       37
D636V3, multiclass
            clus
vv           EPHB6 MUTATED EPHB6 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               4              36
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             3              29
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHB6 MUTATED     1   4   5   6
  EPHB6 WILD-TYPE  21  88 168  91
D636V4, multiclass
    clus
vv   EPHB6 MUTATED EPHB6 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             5             168
  T4             6              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
  EPHB6 MUTATED     8   2   3   3
  EPHB6 WILD-TYPE 110 102  74  74
D636V5, multiclass
    clus
vv   EPHB6 MUTATED EPHB6 WILD-TYPE
  N0             8             110
  N1             2             102
  N2             3              74
  N3             3              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"
D636V6, binary
                 cls
clus                0   1
  EPHB6 MUTATED    15   1
  EPHB6 WILD-TYPE 331  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED     15    1
  EPHB6 WILD-TYPE  331   28
   clus
vv  EPHB6 MUTATED EPHB6 WILD-TYPE
  0            15             331
  1             1              28
[1] 2 2
[1] FALSE
D636V7, binary
                 cls
clus                0   1
  EPHB6 MUTATED     8   9
  EPHB6 WILD-TYPE 137 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED      8    9
  EPHB6 WILD-TYPE  137  239
        clus
vv       EPHB6 MUTATED EPHB6 WILD-TYPE
  FEMALE             8             137
  MALE               9             239
[1] 2 2
[1] FALSE
D636V8, binary
                 cls
clus                0   1
  EPHB6 MUTATED    12   2
  EPHB6 WILD-TYPE 280  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED     12    2
  EPHB6 WILD-TYPE  280   57
     clus
vv    EPHB6 MUTATED EPHB6 WILD-TYPE
  NO             12             280
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EPHB6 MUTATED                                          0
  EPHB6 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EPHB6 MUTATED                                       2
  EPHB6 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPHB6 MUTATED                                                        9
  EPHB6 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EPHB6 MUTATED                                                   1
  EPHB6 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPHB6 MUTATED                                                                   2
  EPHB6 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EPHB6 MUTATED                                                    1
  EPHB6 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EPHB6 MUTATED                                                  2
  EPHB6 WILD-TYPE                                               59
D636V9, multiclass
                                                                   clus
vv                                                                  EPHB6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  EPHB6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EPHB6 MUTATED    14   0   0   2
  EPHB6 WILD-TYPE 297  14  15  22
D636V10, multiclass
    clus
vv   EPHB6 MUTATED EPHB6 WILD-TYPE
  R0            14             297
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D636V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EPHB6 MUTATED       5                         0
  EPHB6 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPHB6 MUTATED                                           0    11
  EPHB6 WILD-TYPE                                         1   232
D636V12, multiclass
                                           clus
vv                                          EPHB6 MUTATED EPHB6 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D636V13, binary
                 cls
clus                0   1
  EPHB6 MUTATED     0  15
  EPHB6 WILD-TYPE   4 295
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED      0   15
  EPHB6 WILD-TYPE    4  295
                        clus
vv                       EPHB6 MUTATED EPHB6 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            15             295
[1] 2 2
[1] FALSE

Clustering(637) Variable = PTPN13 MUTATION ANALYSIS
D637V1, survival
                  sevent
clus2                0   1
  PTPN13 MUTATED    20   9
  PTPN13 WILD-TYPE 210 130
  PTPN13 MUTATED PTPN13 WILD-TYPE 
              29              340 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
               9              130 
$`PTPN13 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8297 
        6.97        34.68        30.90        44.94        32.25         7.40 
TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QM TCGA-CD-5801 
        6.18         0.26         1.12        31.96         5.13        13.18 
TCGA-CD-8535 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
       12.82         8.05        14.01         6.02       105.07        28.96 
TCGA-D7-6527 TCGA-EQ-5647 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GT TCGA-HU-A4H8 
       10.26         0.62        26.47        22.32         6.51        14.07 
TCGA-R5-A7ZI TCGA-RD-A7C1 TCGA-RD-A8N9 TCGA-VQ-A8P2 TCGA-VQ-A91V 
       74.53        16.67        35.61        38.14        42.64 

$`PTPN13 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.96         2.20        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-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-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
       16.14        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-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-4438 
        3.02        27.02        15.95         1.02         7.99        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-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99         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-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        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-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34        19.96         7.13         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-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-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-SW-A7EA 
      115.69       116.38        71.38        57.44         8.94        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 

  PTPN13 MUTATED PTPN13 WILD-TYPE 
            0.26             0.00 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
          105.07           122.30 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
           14.07            14.35 
[1] "0.3 - 105.1 (14.1)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D637V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPN13 MUTATED         0        1        4        4         5         2
  PTPN13 WILD-TYPE       2       14       36       26        32        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN13 MUTATED           0          8          0          1        4
  PTPN13 WILD-TYPE         3         62         53         31       34
D637V3, multiclass
            clus
vv           PTPN13 MUTATED PTPN13 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                4               36
  STAGE II                4               26
  STAGE IIA               5               32
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              8               62
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                4               34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTPN13 MUTATED     2   8  11   8
  PTPN13 WILD-TYPE  20  84 162  89
D637V4, multiclass
    clus
vv   PTPN13 MUTATED PTPN13 WILD-TYPE
  T1              2               20
  T2              8               84
  T3             11              162
  T4              8               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
  PTPN13 MUTATED    11  11   5   2
  PTPN13 WILD-TYPE 107  93  72  75
D637V5, multiclass
    clus
vv   PTPN13 MUTATED PTPN13 WILD-TYPE
  N0             11              107
  N1             11               93
  N2              5               72
  N3              2               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"
D637V6, binary
                  cls
clus                 0   1
  PTPN13 MUTATED    24   3
  PTPN13 WILD-TYPE 322  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN13 MUTATED     24    3
  PTPN13 WILD-TYPE  322   26
   clus
vv  PTPN13 MUTATED PTPN13 WILD-TYPE
  0             24              322
  1              3               26
[1] 2 2
[1] FALSE
D637V7, binary
                  cls
clus                 0   1
  PTPN13 MUTATED    11  18
  PTPN13 WILD-TYPE 134 230
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN13 MUTATED     11   18
  PTPN13 WILD-TYPE  134  230
        clus
vv       PTPN13 MUTATED PTPN13 WILD-TYPE
  FEMALE             11              134
  MALE               18              230
[1] 2 2
[1] FALSE
D637V8, binary
                  cls
clus                 0   1
  PTPN13 MUTATED    23   4
  PTPN13 WILD-TYPE 269  55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN13 MUTATED     23    4
  PTPN13 WILD-TYPE  269   55
     clus
vv    PTPN13 MUTATED PTPN13 WILD-TYPE
  NO              23              269
  YES              4               55
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PTPN13 MUTATED                                          1
  PTPN13 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PTPN13 MUTATED                                       5
  PTPN13 WILD-TYPE                                    65
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTPN13 MUTATED                                                       12
  PTPN13 WILD-TYPE                                                    146
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PTPN13 MUTATED                                                   1
  PTPN13 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTPN13 MUTATED                                                                   5
  PTPN13 WILD-TYPE                                                                63
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PTPN13 MUTATED                                                    1
  PTPN13 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PTPN13 MUTATED                                                  4
  PTPN13 WILD-TYPE                                               57
D637V9, multiclass
                                                                   clus
vv                                                                  PTPN13 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  PTPN13 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PTPN13 MUTATED    27   0   1   1
  PTPN13 WILD-TYPE 284  14  14  23
D637V10, multiclass
    clus
vv   PTPN13 MUTATED PTPN13 WILD-TYPE
  R0             27              284
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D637V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PTPN13 MUTATED       7                         0
  PTPN13 WILD-TYPE    80                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPN13 MUTATED                                           0    16
  PTPN13 WILD-TYPE                                         1   227
D637V12, multiclass
                                           clus
vv                                          PTPN13 MUTATED PTPN13 WILD-TYPE
  ASIAN                                                  7               80
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 16              227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D637V13, binary
                  cls
clus                 0   1
  PTPN13 MUTATED     1  21
  PTPN13 WILD-TYPE   3 289
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN13 MUTATED      1   21
  PTPN13 WILD-TYPE    3  289
                        clus
vv                       PTPN13 MUTATED PTPN13 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             21              289
[1] 2 2
[1] FALSE

Clustering(638) Variable = CALCRL MUTATION ANALYSIS
D638V1, survival
                  sevent
clus2                0   1
  CALCRL MUTATED     6   3
  CALCRL WILD-TYPE 224 136
  CALCRL MUTATED CALCRL WILD-TYPE 
               9              360 
  CALCRL MUTATED CALCRL WILD-TYPE 
               3              136 
$`CALCRL MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8683 TCGA-CG-4305 
       26.70         6.97        31.10        14.04         9.86        15.95 
TCGA-CG-5724 TCGA-D7-A6EX TCGA-D7-A74A 
       12.03        11.31        19.96 

$`CALCRL WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-A6ET TCGA-D7-A6EV 
        5.92        36.43        13.78        14.76        26.43        11.24 
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-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 

  CALCRL MUTATED CALCRL WILD-TYPE 
            6.97             0.00 
  CALCRL MUTATED CALCRL WILD-TYPE 
            31.1            122.3 
  CALCRL MUTATED CALCRL WILD-TYPE 
           14.04            14.35 
[1] "7.0 - 31.1 (14.0)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D638V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CALCRL MUTATED         0        0        0        1         0         1
  CALCRL WILD-TYPE       2       15       40       29        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CALCRL MUTATED           0          3          2          1        1
  CALCRL WILD-TYPE         3         67         51         31       37
D638V3, multiclass
            clus
vv           CALCRL MUTATED CALCRL WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              2               51
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CALCRL MUTATED     0   1   6   3
  CALCRL WILD-TYPE  22  91 167  94
D638V4, multiclass
    clus
vv   CALCRL MUTATED CALCRL WILD-TYPE
  T1              0               22
  T2              1               91
  T3              6              167
  T4              3               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
  CALCRL MUTATED     1   2   4   2
  CALCRL WILD-TYPE 117 102  73  75
D638V5, multiclass
    clus
vv   CALCRL MUTATED CALCRL WILD-TYPE
  N0              1              117
  N1              2              102
  N2              4               73
  N3              2               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"
D638V6, binary
                  cls
clus                 0   1
  CALCRL MUTATED     7   1
  CALCRL WILD-TYPE 339  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CALCRL MUTATED      7    1
  CALCRL WILD-TYPE  339   28
   clus
vv  CALCRL MUTATED CALCRL WILD-TYPE
  0              7              339
  1              1               28
[1] 2 2
[1] FALSE
D638V7, binary
                  cls
clus                 0   1
  CALCRL MUTATED     6   4
  CALCRL WILD-TYPE 139 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CALCRL MUTATED      6    4
  CALCRL WILD-TYPE  139  244
        clus
vv       CALCRL MUTATED CALCRL WILD-TYPE
  FEMALE              6              139
  MALE                4              244
[1] 2 2
[1] FALSE
D638V8, binary
                  cls
clus                 0   1
  CALCRL MUTATED     9   0
  CALCRL WILD-TYPE 283  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CALCRL MUTATED      9    0
  CALCRL WILD-TYPE  283   59
     clus
vv    CALCRL MUTATED CALCRL WILD-TYPE
  NO               9              283
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CALCRL MUTATED                                          0
  CALCRL WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CALCRL MUTATED                                       2
  CALCRL WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CALCRL MUTATED                                                        5
  CALCRL WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CALCRL MUTATED                                                   0
  CALCRL WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CALCRL MUTATED                                                                   0
  CALCRL WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CALCRL MUTATED                                                    0
  CALCRL WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CALCRL MUTATED                                                  3
  CALCRL WILD-TYPE                                               58
D638V9, multiclass
                                                                   clus
vv                                                                  CALCRL MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  CALCRL WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CALCRL MUTATED     7   0   1   2
  CALCRL WILD-TYPE 304  14  14  22
D638V10, multiclass
    clus
vv   CALCRL MUTATED CALCRL WILD-TYPE
  R0              7              304
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D638V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CALCRL MUTATED       1                         0
  CALCRL WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CALCRL MUTATED                                           0     7
  CALCRL WILD-TYPE                                         1   236
D638V12, multiclass
                                           clus
vv                                          CALCRL MUTATED CALCRL WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D638V13, binary
                  cls
clus                 0   1
  CALCRL MUTATED     0   8
  CALCRL WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CALCRL MUTATED      0    8
  CALCRL WILD-TYPE    4  302
                        clus
vv                       CALCRL MUTATED CALCRL WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(639) Variable = AZGP1 MUTATION ANALYSIS
D639V1, survival
                 sevent
clus2               0   1
  AZGP1 MUTATED     2   2
  AZGP1 WILD-TYPE 228 137
  AZGP1 MUTATED AZGP1 WILD-TYPE 
              4             365 
  AZGP1 MUTATED AZGP1 WILD-TYPE 
              2             137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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          14.270 
[1] "6.6 - 38.1 (19.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D639V2, 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       2       15       40       29        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AZGP1 MUTATED           0          1          0          1        0
  AZGP1 WILD-TYPE         3         69         53         31       38
D639V3, multiclass
            clus
vv           AZGP1 MUTATED AZGP1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AZGP1 MUTATED     0   1   1   2
  AZGP1 WILD-TYPE  22  91 172  95
D639V4, multiclass
    clus
vv   AZGP1 MUTATED AZGP1 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             1             172
  T4             2              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
  AZGP1 MUTATED     1   2   1   0
  AZGP1 WILD-TYPE 117 102  76  77
D639V5, multiclass
    clus
vv   AZGP1 MUTATED AZGP1 WILD-TYPE
  N0             1             117
  N1             2             102
  N2             1              76
  N3             0              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"
D639V6, binary
                 cls
clus                0   1
  AZGP1 MUTATED     4   0
  AZGP1 WILD-TYPE 342  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AZGP1 MUTATED      4    0
  AZGP1 WILD-TYPE  342   29
   clus
vv  AZGP1 MUTATED AZGP1 WILD-TYPE
  0             4             342
  1             0              29
[1] 2 2
[1] FALSE
D639V7, binary
                 cls
clus                0   1
  AZGP1 MUTATED     2   2
  AZGP1 WILD-TYPE 143 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AZGP1 MUTATED      2    2
  AZGP1 WILD-TYPE  143  246
        clus
vv       AZGP1 MUTATED AZGP1 WILD-TYPE
  FEMALE             2             143
  MALE               2             246
[1] 2 2
[1] FALSE
D639V8, binary
                 cls
clus                0   1
  AZGP1 MUTATED     3   1
  AZGP1 WILD-TYPE 289  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AZGP1 MUTATED      3    1
  AZGP1 WILD-TYPE  289   58
     clus
vv    AZGP1 MUTATED AZGP1 WILD-TYPE
  NO              3             289
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AZGP1 MUTATED                                          0
  AZGP1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AZGP1 MUTATED                                       1
  AZGP1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AZGP1 MUTATED                                                        1
  AZGP1 WILD-TYPE                                                    157
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AZGP1 MUTATED                                                   1
  AZGP1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AZGP1 MUTATED                                                                   1
  AZGP1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AZGP1 MUTATED                                                    0
  AZGP1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AZGP1 MUTATED                                                  0
  AZGP1 WILD-TYPE                                               61
D639V9, multiclass
                                                                   clus
vv                                                                  AZGP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  AZGP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AZGP1 MUTATED     3   0   0   0
  AZGP1 WILD-TYPE 308  14  15  24
D639V10, multiclass
    clus
vv   AZGP1 MUTATED AZGP1 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D639V11, continuous
[1] "Remove cluster labels:" "AZGP1 MUTATED"         
clus
  AZGP1 MUTATED AZGP1 WILD-TYPE 
              2             341 
     TCGA-CG-4444      TCGA-CG-4460      TCGA-CG-4475      TCGA-CG-4476 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-CG-5727      TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-FP-A8CX 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-HF-7131      TCGA-KB-A93G      TCGA-MX-A663      TCGA-B7-5816 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-B7-A5TI      TCGA-BR-4183      TCGA-BR-4184      TCGA-BR-4188 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-4191      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4361 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-4362      TCGA-BR-4368      TCGA-BR-6452      TCGA-BR-6453 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-6709      TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-6803      TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-7703      TCGA-BR-7704      TCGA-BR-7707      TCGA-BR-7715 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722      TCGA-BR-7723 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957      TCGA-BR-7958 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059      TCGA-BR-8060 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080      TCGA-BR-8081 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-8284      TCGA-BR-8285      TCGA-BR-8286      TCGA-BR-8289 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-8291      TCGA-BR-8295      TCGA-BR-8297      TCGA-BR-8360 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373      TCGA-BR-8380 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-A4J4      TCGA-BR-A4J5      TCGA-BR-A4J6      TCGA-BR-A4J8 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5804      TCGA-CD-8525 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-CD-8526      TCGA-CD-8531      TCGA-CD-8535      TCGA-CD-A487 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4436 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-CG-4437      TCGA-CG-4438      TCGA-CG-4440      TCGA-CG-4441 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-CG-4442      TCGA-CG-4443      TCGA-CG-4449      TCGA-CG-4455 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-CG-4462      TCGA-CG-4465      TCGA-CG-4466      TCGA-CG-4469 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-CG-4474      TCGA-CG-4477      TCGA-CG-5717      TCGA-CG-5718 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-CG-5719      TCGA-CG-5720      TCGA-CG-5721      TCGA-CG-5722 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-CG-5723      TCGA-CG-5724      TCGA-CG-5725      TCGA-CG-5726 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-CG-5728      TCGA-CG-5730      TCGA-CG-5732      TCGA-CG-5733 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-CG-5734      TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-D7-6518      TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-D7-8572      TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-D7-8576      TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-D7-A4YU      TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-D7-A4Z0      TCGA-D7-A6ET      TCGA-D7-A6EV      TCGA-D7-A6EX 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-D7-A6EY      TCGA-D7-A6EZ      TCGA-D7-A6F0      TCGA-D7-A6F2 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-D7-A747      TCGA-D7-A748      TCGA-D7-A74A      TCGA-D7-A74B 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-EQ-5647      TCGA-EQ-8122      TCGA-F1-6874      TCGA-F1-6875 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-F1-A448      TCGA-F1-A72C      TCGA-FP-7735      TCGA-FP-7829 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BE 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-FP-A4BF      TCGA-FP-A9TM      TCGA-HF-7132      TCGA-HF-7133 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-HF-7134      TCGA-HF-7136      TCGA-HF-A5NB      TCGA-HJ-7597 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-HU-8238      TCGA-HU-8243      TCGA-HU-8244      TCGA-HU-8249 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-HU-A4GH      TCGA-HU-A4GJ      TCGA-HU-A4GN      TCGA-HU-A4GP 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-HU-A4HB      TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-IN-8462      TCGA-IN-8663      TCGA-IN-A6RI      TCGA-IN-A6RJ 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-IN-A6RL      TCGA-IN-A6RN      TCGA-IN-A6RO      TCGA-IN-A6RP 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-IN-A6RR      TCGA-IN-A6RS      TCGA-IN-A7NR      TCGA-IN-A7NT 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-IN-A7NU      TCGA-IN-AB1V      TCGA-IN-AB1X      TCGA-IP-7968 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-KB-A6F5      TCGA-KB-A6F7      TCGA-KB-A93J      TCGA-MX-A5UG 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-MX-A5UJ      TCGA-R5-A7ZI      TCGA-RD-A7BS      TCGA-RD-A7BT 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-RD-A7BW      TCGA-RD-A7C1      TCGA-RD-A8MV      TCGA-RD-A8MW 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-RD-A8N0      TCGA-RD-A8N1      TCGA-RD-A8N2      TCGA-RD-A8N4 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-RD-A8N5      TCGA-RD-A8N6      TCGA-RD-A8N9      TCGA-SW-A7EA 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-SW-A7EB      TCGA-VQ-A8DL      TCGA-VQ-A8DT      TCGA-VQ-A8DU 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-VQ-A8DV      TCGA-VQ-A8DZ      TCGA-VQ-A8E2      TCGA-VQ-A8E7 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-VQ-A8P3      TCGA-VQ-A8PE      TCGA-VQ-A8PK      TCGA-VQ-A8PM 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-VQ-A8PQ      TCGA-VQ-A91Q      TCGA-VQ-A91U      TCGA-VQ-A91V 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-VQ-A92D      TCGA-VQ-A94T      TCGA-VQ-AA64      TCGA-VQ-AA68 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-VQ-AA69      TCGA-VQ-AA6A      TCGA-VQ-AA6B      TCGA-VQ-AA6F 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-VQ-AA6G      TCGA-VQ-AA6I      TCGA-VQ-AA6J      TCGA-VQ-AA6K 
"AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" "AZGP1 WILD-TYPE" 
     TCGA-ZA-A8F6 
"AZGP1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AZGP1 MUTATED       2                         0
  AZGP1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AZGP1 MUTATED                                           0     2
  AZGP1 WILD-TYPE                                         1   241
D639V12, multiclass
                                           clus
vv                                          AZGP1 MUTATED AZGP1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D639V13, binary
                 cls
clus                0   1
  AZGP1 MUTATED     0   3
  AZGP1 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AZGP1 MUTATED      0    3
  AZGP1 WILD-TYPE    4  307
                        clus
vv                       AZGP1 MUTATED AZGP1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(640) Variable = DOK1 MUTATION ANALYSIS
D640V1, survival
                sevent
clus2              0   1
  DOK1 MUTATED     3   1
  DOK1 WILD-TYPE 227 138
  DOK1 MUTATED DOK1 WILD-TYPE 
             4            365 
  DOK1 MUTATED DOK1 WILD-TYPE 
             1            138 
$`DOK1 MUTATED`
TCGA-BR-6452 TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-VQ-A8DT 
       34.68        16.14        12.62        48.79 

$`DOK1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  DOK1 MUTATED DOK1 WILD-TYPE 
         12.62           0.00 
  DOK1 MUTATED DOK1 WILD-TYPE 
         48.79         122.30 
  DOK1 MUTATED DOK1 WILD-TYPE 
         25.41          14.17 
[1] "12.6 - 48.8 (25.4)" "0.0 - 122.3 (14.2)"
[1] "hr=" "2.1"
D640V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DOK1 MUTATED         0        0        1        0         1         0
  DOK1 WILD-TYPE       2       15       39       30        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DOK1 MUTATED           0          0          2          0        0
  DOK1 WILD-TYPE         3         70         51         32       38
D640V3, multiclass
            clus
vv           DOK1 MUTATED DOK1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            2             51
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DOK1 MUTATED     0   1   3   0
  DOK1 WILD-TYPE  22  91 170  97
D640V4, multiclass
    clus
vv   DOK1 MUTATED DOK1 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            3            170
  T4            0             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
  DOK1 MUTATED     2   1   0   2
  DOK1 WILD-TYPE 116 103  77  75
D640V5, multiclass
    clus
vv   DOK1 MUTATED DOK1 WILD-TYPE
  N0            2            116
  N1            1            103
  N2            0             77
  N3            2             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"
D640V6, binary
                cls
clus               0   1
  DOK1 MUTATED     5   0
  DOK1 WILD-TYPE 341  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  DOK1 MUTATED      5    0
  DOK1 WILD-TYPE  341   29
   clus
vv  DOK1 MUTATED DOK1 WILD-TYPE
  0            5            341
  1            0             29
[1] 2 2
[1] FALSE
D640V7, binary
                cls
clus               0   1
  DOK1 MUTATED     3   2
  DOK1 WILD-TYPE 142 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  DOK1 MUTATED      3    2
  DOK1 WILD-TYPE  142  246
        clus
vv       DOK1 MUTATED DOK1 WILD-TYPE
  FEMALE            3            142
  MALE              2            246
[1] 2 2
[1] FALSE
D640V8, binary
                cls
clus               0   1
  DOK1 MUTATED     3   1
  DOK1 WILD-TYPE 289  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  DOK1 MUTATED      3    1
  DOK1 WILD-TYPE  289   58
     clus
vv    DOK1 MUTATED DOK1 WILD-TYPE
  NO             3            289
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DOK1 MUTATED                                          0
  DOK1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DOK1 MUTATED                                       0
  DOK1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DOK1 MUTATED                                                        4
  DOK1 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DOK1 MUTATED                                                   0
  DOK1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DOK1 MUTATED                                                                   1
  DOK1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DOK1 MUTATED                                                    0
  DOK1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DOK1 MUTATED                                                  0
  DOK1 WILD-TYPE                                               61
D640V9, multiclass
                                                                   clus
vv                                                                  DOK1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  DOK1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DOK1 MUTATED     3   0   0   1
  DOK1 WILD-TYPE 308  14  15  23
D640V10, multiclass
    clus
vv   DOK1 MUTATED DOK1 WILD-TYPE
  R0            3            308
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D640V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DOK1 MUTATED       1                         0
  DOK1 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DOK1 MUTATED                                           0     3
  DOK1 WILD-TYPE                                         1   240
D640V12, multiclass
                                           clus
vv                                          DOK1 MUTATED DOK1 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D640V13, binary
                cls
clus               0   1
  DOK1 MUTATED     0   4
  DOK1 WILD-TYPE   4 306
[1] "tbl2"
                cls
clus             [,1] [,2]
  DOK1 MUTATED      0    4
  DOK1 WILD-TYPE    4  306
                        clus
vv                       DOK1 MUTATED DOK1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            4            306
[1] 2 2
[1] FALSE

Clustering(641) Variable = CDC5L MUTATION ANALYSIS
D641V1, survival
                 sevent
clus2               0   1
  CDC5L MUTATED     9   4
  CDC5L WILD-TYPE 221 135
  CDC5L MUTATED CDC5L WILD-TYPE 
             13             356 
  CDC5L MUTATED CDC5L WILD-TYPE 
              4             135 
$`CDC5L MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6801 TCGA-BR-7707 
       26.70         6.97        30.90        34.68        40.21        35.84 
TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A4MI TCGA-FP-A4BE TCGA-HU-A4H8 TCGA-IN-7808 
        1.12        31.96        11.77        11.08        14.07         3.45 
TCGA-MX-A666 
       14.04 

$`CDC5L WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        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-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-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-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-R5-A7O7 
        5.56        63.62        36.95         3.72        19.73        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 

  CDC5L MUTATED CDC5L WILD-TYPE 
           1.12            0.00 
  CDC5L MUTATED CDC5L WILD-TYPE 
          40.21          122.30 
  CDC5L MUTATED CDC5L WILD-TYPE 
          14.07           14.35 
[1] "1.1 - 40.2 (14.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D641V2, 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       2       15       38       30        32        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC5L MUTATED           0          2          0          0        1
  CDC5L WILD-TYPE         3         68         53         32       37
D641V3, multiclass
            clus
vv           CDC5L MUTATED CDC5L WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              5              32
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDC5L MUTATED     1   3   8   3
  CDC5L WILD-TYPE  21  89 165  94
D641V4, multiclass
    clus
vv   CDC5L MUTATED CDC5L WILD-TYPE
  T1             1              21
  T2             3              89
  T3             8             165
  T4             3              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
  CDC5L MUTATED     7   4   1   1
  CDC5L WILD-TYPE 111 100  76  76
D641V5, multiclass
    clus
vv   CDC5L MUTATED CDC5L WILD-TYPE
  N0             7             111
  N1             4             100
  N2             1              76
  N3             1              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"
D641V6, binary
                 cls
clus                0   1
  CDC5L MUTATED    11   2
  CDC5L WILD-TYPE 335  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED     11    2
  CDC5L WILD-TYPE  335   27
   clus
vv  CDC5L MUTATED CDC5L WILD-TYPE
  0            11             335
  1             2              27
[1] 2 2
[1] FALSE
D641V7, binary
                 cls
clus                0   1
  CDC5L MUTATED     6  10
  CDC5L WILD-TYPE 139 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED      6   10
  CDC5L WILD-TYPE  139  238
        clus
vv       CDC5L MUTATED CDC5L WILD-TYPE
  FEMALE             6             139
  MALE              10             238
[1] 2 2
[1] FALSE
D641V8, binary
                 cls
clus                0   1
  CDC5L MUTATED    13   1
  CDC5L WILD-TYPE 279  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED     13    1
  CDC5L WILD-TYPE  279   58
     clus
vv    CDC5L MUTATED CDC5L WILD-TYPE
  NO             13             279
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CDC5L MUTATED                                          0
  CDC5L WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CDC5L MUTATED                                       2
  CDC5L WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDC5L MUTATED                                                       11
  CDC5L WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CDC5L MUTATED                                                   0
  CDC5L WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDC5L MUTATED                                                                   1
  CDC5L WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CDC5L MUTATED                                                    0
  CDC5L WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CDC5L MUTATED                                                  2
  CDC5L WILD-TYPE                                               59
D641V9, multiclass
                                                                   clus
vv                                                                  CDC5L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  CDC5L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDC5L MUTATED     9   0   0   4
  CDC5L WILD-TYPE 302  14  15  20
D641V10, multiclass
    clus
vv   CDC5L MUTATED CDC5L WILD-TYPE
  R0             9             302
  R1             0              14
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D641V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CDC5L MUTATED       3                         1
  CDC5L WILD-TYPE    84                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDC5L MUTATED                                           0    12
  CDC5L WILD-TYPE                                         1   231
D641V12, multiclass
                                           clus
vv                                          CDC5L MUTATED CDC5L WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D641V13, binary
                 cls
clus                0   1
  CDC5L MUTATED     0  16
  CDC5L WILD-TYPE   4 294
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED      0   16
  CDC5L WILD-TYPE    4  294
                        clus
vv                       CDC5L MUTATED CDC5L WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            16             294
[1] 2 2
[1] FALSE

Clustering(642) Variable = KIF2B MUTATION ANALYSIS
D642V1, survival
                 sevent
clus2               0   1
  KIF2B MUTATED    22   8
  KIF2B WILD-TYPE 208 131
  KIF2B MUTATED KIF2B WILD-TYPE 
             30             339 
  KIF2B MUTATED KIF2B WILD-TYPE 
              8             131 
$`KIF2B MUTATED`
TCGA-EQ-A4SO TCGA-B7-5816 TCGA-BR-6453 TCGA-BR-6563 TCGA-BR-7707 TCGA-BR-7722 
       16.24        26.70        15.95        39.12        35.84        15.32 
TCGA-BR-7723 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8589 
       28.73         7.40        31.10         9.21         1.12        27.12 
TCGA-BR-8687 TCGA-CD-A4MG TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-5721 TCGA-CG-5728 
        8.22         6.58         7.99        54.08         6.02        65.10 
TCGA-D7-6817 TCGA-D7-8576 TCGA-D7-A4Z0 TCGA-D7-A747 TCGA-FP-7829 TCGA-HF-7132 
       12.79        14.66        14.76         8.38        19.53        77.29 
TCGA-HJ-7597 TCGA-HU-A4H5 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-AB1V TCGA-VQ-AA6J 
       26.47        23.80        18.38        13.35        15.75        27.55 

$`KIF2B WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        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-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-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       18.15         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-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-8486 
        7.36        25.05         3.72         5.39        25.18        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-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-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-4440 TCGA-CG-4441 
       27.02        15.95         1.02         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-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-D7-6818 
       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-D7-8578 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-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-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-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-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-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-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP 
        3.45        18.81         3.39        12.46        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-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-AA6K TCGA-ZA-A8F6 
       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 
         16.095          14.040 
[1] "1.1 - 77.3 (16.1)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.7"
D642V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIF2B MUTATED         1        1        5        1         4         7
  KIF2B WILD-TYPE       1       14       35       29        33        45
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF2B MUTATED           0          2          5          4        2
  KIF2B WILD-TYPE         3         68         48         28       36
D642V3, multiclass
            clus
vv           KIF2B MUTATED KIF2B WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               5              35
  STAGE II               1              29
  STAGE IIA              4              33
  STAGE IIB              7              45
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             5              48
  STAGE IIIC             4              28
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KIF2B MUTATED     2  10   9  11
  KIF2B WILD-TYPE  20  82 164  86
D642V4, multiclass
    clus
vv   KIF2B MUTATED KIF2B WILD-TYPE
  T1             2              20
  T2            10              82
  T3             9             164
  T4            11              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
  KIF2B MUTATED    12  10   5   5
  KIF2B WILD-TYPE 106  94  72  72
D642V5, multiclass
    clus
vv   KIF2B MUTATED KIF2B WILD-TYPE
  N0            12             106
  N1            10              94
  N2             5              72
  N3             5              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"
D642V6, binary
                 cls
clus                0   1
  KIF2B MUTATED    30   0
  KIF2B WILD-TYPE 316  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF2B MUTATED     30    0
  KIF2B WILD-TYPE  316   29
   clus
vv  KIF2B MUTATED KIF2B WILD-TYPE
  0            30             316
  1             0              29
[1] 2 2
[1] FALSE
D642V7, binary
                 cls
clus                0   1
  KIF2B MUTATED    10  22
  KIF2B WILD-TYPE 135 226
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF2B MUTATED     10   22
  KIF2B WILD-TYPE  135  226
        clus
vv       KIF2B MUTATED KIF2B WILD-TYPE
  FEMALE            10             135
  MALE              22             226
[1] 2 2
[1] FALSE
D642V8, binary
                 cls
clus                0   1
  KIF2B MUTATED    24   5
  KIF2B WILD-TYPE 268  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF2B MUTATED     24    5
  KIF2B WILD-TYPE  268   54
     clus
vv    KIF2B MUTATED KIF2B WILD-TYPE
  NO             24             268
  YES             5              54
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIF2B MUTATED                                          1
  KIF2B WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIF2B MUTATED                                       4
  KIF2B WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIF2B MUTATED                                                       14
  KIF2B WILD-TYPE                                                    144
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIF2B MUTATED                                                   3
  KIF2B WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIF2B MUTATED                                                                   6
  KIF2B WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIF2B MUTATED                                                    1
  KIF2B WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIF2B MUTATED                                                  2
  KIF2B WILD-TYPE                                               59
D642V9, multiclass
                                                                   clus
vv                                                                  KIF2B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  KIF2B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KIF2B MUTATED    30   1   0   0
  KIF2B WILD-TYPE 281  13  15  24
D642V10, multiclass
    clus
vv   KIF2B MUTATED KIF2B WILD-TYPE
  R0            30             281
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D642V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KIF2B MUTATED       2                         1
  KIF2B WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIF2B MUTATED                                           0    24
  KIF2B WILD-TYPE                                         1   219
D642V12, multiclass
                                           clus
vv                                          KIF2B MUTATED KIF2B WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                24             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D642V13, binary
                 cls
clus                0   1
  KIF2B MUTATED     0  26
  KIF2B WILD-TYPE   4 284
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF2B MUTATED      0   26
  KIF2B WILD-TYPE    4  284
                        clus
vv                       KIF2B MUTATED KIF2B WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            26             284
[1] 2 2
[1] FALSE

Clustering(643) Variable = NOBOX MUTATION ANALYSIS
D643V1, survival
                 sevent
clus2               0   1
  NOBOX MUTATED     4   3
  NOBOX WILD-TYPE 226 136
  NOBOX MUTATED NOBOX WILD-TYPE 
              7             362 
  NOBOX MUTATED NOBOX WILD-TYPE 
              3             136 
$`NOBOX MUTATED`
TCGA-BR-7958 TCGA-BR-8360 TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-4306 TCGA-D7-A6EZ 
       29.56         6.18        31.96        11.77         1.02        20.32 
TCGA-VQ-A8P2 
       38.14 

$`NOBOX WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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           14.22 
[1] "1.0 - 38.1 (20.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1"  
D643V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOBOX MUTATED         0        0        1        0         1         0
  NOBOX WILD-TYPE       2       15       39       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOBOX MUTATED           0          3          1          0        3
  NOBOX WILD-TYPE         3         67         52         32       35
D643V3, multiclass
            clus
vv           NOBOX MUTATED NOBOX WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NOBOX MUTATED     0   1   4   4
  NOBOX WILD-TYPE  22  91 169  93
D643V4, multiclass
    clus
vv   NOBOX MUTATED NOBOX WILD-TYPE
  T1             0              22
  T2             1              91
  T3             4             169
  T4             4              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
  NOBOX MUTATED     3   2   4   0
  NOBOX WILD-TYPE 115 102  73  77
D643V5, multiclass
    clus
vv   NOBOX MUTATED NOBOX WILD-TYPE
  N0             3             115
  N1             2             102
  N2             4              73
  N3             0              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"
D643V6, binary
                 cls
clus                0   1
  NOBOX MUTATED     8   2
  NOBOX WILD-TYPE 338  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOBOX MUTATED      8    2
  NOBOX WILD-TYPE  338   27
   clus
vv  NOBOX MUTATED NOBOX WILD-TYPE
  0             8             338
  1             2              27
[1] 2 2
[1] FALSE
D643V7, binary
                 cls
clus                0   1
  NOBOX MUTATED     2   8
  NOBOX WILD-TYPE 143 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOBOX MUTATED      2    8
  NOBOX WILD-TYPE  143  240
        clus
vv       NOBOX MUTATED NOBOX WILD-TYPE
  FEMALE             2             143
  MALE               8             240
[1] 2 2
[1] FALSE
D643V8, binary
                 cls
clus                0   1
  NOBOX MUTATED     5   1
  NOBOX WILD-TYPE 287  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOBOX MUTATED      5    1
  NOBOX WILD-TYPE  287   58
     clus
vv    NOBOX MUTATED NOBOX WILD-TYPE
  NO              5             287
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NOBOX MUTATED                                          0
  NOBOX WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NOBOX MUTATED                                       0
  NOBOX WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NOBOX MUTATED                                                        5
  NOBOX WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NOBOX MUTATED                                                   1
  NOBOX WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NOBOX MUTATED                                                                   3
  NOBOX WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NOBOX MUTATED                                                    0
  NOBOX WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NOBOX MUTATED                                                  1
  NOBOX WILD-TYPE                                               60
D643V9, multiclass
                                                                   clus
vv                                                                  NOBOX MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  NOBOX WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NOBOX MUTATED     6   0   1   2
  NOBOX WILD-TYPE 305  14  14  22
D643V10, multiclass
    clus
vv   NOBOX MUTATED NOBOX WILD-TYPE
  R0             6             305
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D643V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NOBOX MUTATED       2                         0
  NOBOX WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOBOX MUTATED                                           0     6
  NOBOX WILD-TYPE                                         1   237
D643V12, multiclass
                                           clus
vv                                          NOBOX MUTATED NOBOX WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D643V13, binary
                 cls
clus                0   1
  NOBOX MUTATED     0   7
  NOBOX WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOBOX MUTATED      0    7
  NOBOX WILD-TYPE    4  303
                        clus
vv                       NOBOX MUTATED NOBOX WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(644) Variable = GPR45 MUTATION ANALYSIS
D644V1, survival
                 sevent
clus2               0   1
  GPR45 MUTATED    11   5
  GPR45 WILD-TYPE 219 134
  GPR45 MUTATED GPR45 WILD-TYPE 
             16             353 
  GPR45 MUTATED GPR45 WILD-TYPE 
              5             134 
$`GPR45 MUTATED`
TCGA-CG-4460 TCGA-MX-A663 TCGA-BR-4184 TCGA-BR-6802 TCGA-BR-8284 TCGA-BR-8360 
       21.99         9.86         6.97        30.90         8.05         6.18 
TCGA-BR-8361 TCGA-CG-4305 TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4GU 
       31.10        15.95        22.68        11.77         6.51         6.58 
TCGA-HU-A4H4 TCGA-IN-A6RP TCGA-R5-A7ZI TCGA-RD-A8N6 
       23.84         6.44        74.53         8.94 

$`GPR45 WILD-TYPE`
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-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-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-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-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-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-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-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-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-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 

  GPR45 MUTATED GPR45 WILD-TYPE 
           6.18            0.00 
  GPR45 MUTATED GPR45 WILD-TYPE 
          74.53          122.30 
  GPR45 MUTATED GPR45 WILD-TYPE 
         10.815          14.430 
[1] "6.2 - 74.5 (10.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D644V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR45 MUTATED         0        1        0        1         3         3
  GPR45 WILD-TYPE       2       14       40       29        34        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR45 MUTATED           0          3          0          3        2
  GPR45 WILD-TYPE         3         67         53         29       36
D644V3, multiclass
            clus
vv           GPR45 MUTATED GPR45 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPR45 MUTATED     2   3   7   4
  GPR45 WILD-TYPE  20  89 166  93
D644V4, multiclass
    clus
vv   GPR45 MUTATED GPR45 WILD-TYPE
  T1             2              20
  T2             3              89
  T3             7             166
  T4             4              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
  GPR45 MUTATED     4   6   4   2
  GPR45 WILD-TYPE 114  98  73  75
D644V5, multiclass
    clus
vv   GPR45 MUTATED GPR45 WILD-TYPE
  N0             4             114
  N1             6              98
  N2             4              73
  N3             2              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"
D644V6, binary
                 cls
clus                0   1
  GPR45 MUTATED    13   2
  GPR45 WILD-TYPE 333  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR45 MUTATED     13    2
  GPR45 WILD-TYPE  333   27
   clus
vv  GPR45 MUTATED GPR45 WILD-TYPE
  0            13             333
  1             2              27
[1] 2 2
[1] FALSE
D644V7, binary
                 cls
clus                0   1
  GPR45 MUTATED     8   8
  GPR45 WILD-TYPE 137 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR45 MUTATED      8    8
  GPR45 WILD-TYPE  137  240
        clus
vv       GPR45 MUTATED GPR45 WILD-TYPE
  FEMALE             8             137
  MALE               8             240
[1] 2 2
[1] FALSE
D644V8, binary
                 cls
clus                0   1
  GPR45 MUTATED    15   1
  GPR45 WILD-TYPE 277  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR45 MUTATED     15    1
  GPR45 WILD-TYPE  277   58
     clus
vv    GPR45 MUTATED GPR45 WILD-TYPE
  NO             15             277
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GPR45 MUTATED                                          0
  GPR45 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GPR45 MUTATED                                       3
  GPR45 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR45 MUTATED                                                        6
  GPR45 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GPR45 MUTATED                                                   0
  GPR45 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR45 MUTATED                                                                   4
  GPR45 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GPR45 MUTATED                                                    0
  GPR45 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GPR45 MUTATED                                                  3
  GPR45 WILD-TYPE                                               58
D644V9, multiclass
                                                                   clus
vv                                                                  GPR45 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  GPR45 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GPR45 MUTATED    13   0   1   1
  GPR45 WILD-TYPE 298  14  14  23
D644V10, multiclass
    clus
vv   GPR45 MUTATED GPR45 WILD-TYPE
  R0            13             298
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D644V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GPR45 MUTATED       5                         0
  GPR45 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR45 MUTATED                                           0     9
  GPR45 WILD-TYPE                                         1   234
D644V12, multiclass
                                           clus
vv                                          GPR45 MUTATED GPR45 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D644V13, binary
                 cls
clus                0   1
  GPR45 MUTATED     1  13
  GPR45 WILD-TYPE   3 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR45 MUTATED      1   13
  GPR45 WILD-TYPE    3  297
                        clus
vv                       GPR45 MUTATED GPR45 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(645) Variable = ACTR8 MUTATION ANALYSIS
D645V1, survival
                 sevent
clus2               0   1
  ACTR8 MUTATED     7   2
  ACTR8 WILD-TYPE 223 137
  ACTR8 MUTATED ACTR8 WILD-TYPE 
              9             360 
  ACTR8 MUTATED ACTR8 WILD-TYPE 
              2             137 
$`ACTR8 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7901 TCGA-BR-8680 TCGA-BR-A4IU 
        6.97        34.68        32.78         3.45        31.96        27.55 
TCGA-FP-A4BE TCGA-HF-A5NB TCGA-VQ-A8P2 
       11.08        30.51        38.14 

$`ACTR8 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       34.98         1.48        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-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 

  ACTR8 MUTATED ACTR8 WILD-TYPE 
           3.45            0.00 
  ACTR8 MUTATED ACTR8 WILD-TYPE 
          38.14          122.30 
  ACTR8 MUTATED ACTR8 WILD-TYPE 
          30.51           14.12 
[1] "3.5 - 38.1 (30.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.3"
D645V2, 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       2       15       40       30        34        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACTR8 MUTATED           0          4          0          1        1
  ACTR8 WILD-TYPE         3         66         53         31       37
D645V3, multiclass
            clus
vv           ACTR8 MUTATED ACTR8 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACTR8 MUTATED     0   0   5   6
  ACTR8 WILD-TYPE  22  92 168  91
D645V4, multiclass
    clus
vv   ACTR8 MUTATED ACTR8 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             5             168
  T4             6              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
  ACTR8 MUTATED     5   4   1   1
  ACTR8 WILD-TYPE 113 100  76  76
D645V5, multiclass
    clus
vv   ACTR8 MUTATED ACTR8 WILD-TYPE
  N0             5             113
  N1             4             100
  N2             1              76
  N3             1              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"
D645V6, binary
                 cls
clus                0   1
  ACTR8 MUTATED     9   1
  ACTR8 WILD-TYPE 337  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTR8 MUTATED      9    1
  ACTR8 WILD-TYPE  337   28
   clus
vv  ACTR8 MUTATED ACTR8 WILD-TYPE
  0             9             337
  1             1              28
[1] 2 2
[1] FALSE
D645V7, binary
                 cls
clus                0   1
  ACTR8 MUTATED     5   6
  ACTR8 WILD-TYPE 140 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTR8 MUTATED      5    6
  ACTR8 WILD-TYPE  140  242
        clus
vv       ACTR8 MUTATED ACTR8 WILD-TYPE
  FEMALE             5             140
  MALE               6             242
[1] 2 2
[1] FALSE
D645V8, binary
                 cls
clus                0   1
  ACTR8 MUTATED     7   3
  ACTR8 WILD-TYPE 285  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTR8 MUTATED      7    3
  ACTR8 WILD-TYPE  285   56
     clus
vv    ACTR8 MUTATED ACTR8 WILD-TYPE
  NO              7             285
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ACTR8 MUTATED                                          0
  ACTR8 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ACTR8 MUTATED                                       1
  ACTR8 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ACTR8 MUTATED                                                        6
  ACTR8 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ACTR8 MUTATED                                                   2
  ACTR8 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ACTR8 MUTATED                                                                   1
  ACTR8 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ACTR8 MUTATED                                                    0
  ACTR8 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ACTR8 MUTATED                                                  1
  ACTR8 WILD-TYPE                                               60
D645V9, multiclass
                                                                   clus
vv                                                                  ACTR8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  ACTR8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ACTR8 MUTATED     8   1   0   2
  ACTR8 WILD-TYPE 303  13  15  22
D645V10, multiclass
    clus
vv   ACTR8 MUTATED ACTR8 WILD-TYPE
  R0             8             303
  R1             1              13
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D645V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ACTR8 MUTATED       2                         1
  ACTR8 WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ACTR8 MUTATED                                           0     7
  ACTR8 WILD-TYPE                                         1   236
D645V12, multiclass
                                           clus
vv                                          ACTR8 MUTATED ACTR8 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D645V13, binary
                 cls
clus                0   1
  ACTR8 MUTATED     0   9
  ACTR8 WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTR8 MUTATED      0    9
  ACTR8 WILD-TYPE    4  301
                        clus
vv                       ACTR8 MUTATED ACTR8 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(646) Variable = SCAMP2 MUTATION ANALYSIS
D646V1, survival
                  sevent
clus2                0   1
  SCAMP2 MUTATED     4   1
  SCAMP2 WILD-TYPE 226 138
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
               5              364 
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
               1              138 
$`SCAMP2 MUTATED`
TCGA-BR-8382 TCGA-CD-8534 TCGA-CG-4305 TCGA-HU-A4GT TCGA-R5-A7ZI 
       25.05        12.07        15.95         6.51        74.53 

$`SCAMP2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8535 
       12.30        12.39        12.59        11.64        15.39        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-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-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 

  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
            6.51             0.00 
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
           74.53           122.30 
  SCAMP2 MUTATED SCAMP2 WILD-TYPE 
           15.95            14.22 
[1] "6.5 - 74.5 (15.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.4"
D646V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCAMP2 MUTATED         0        0        0        2         1         1
  SCAMP2 WILD-TYPE       2       15       40       28        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SCAMP2 MUTATED           0          0          0          1        1
  SCAMP2 WILD-TYPE         3         70         53         31       37
D646V3, multiclass
            clus
vv           SCAMP2 MUTATED SCAMP2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                2               28
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SCAMP2 MUTATED     0   1   2   3
  SCAMP2 WILD-TYPE  22  91 171  94
D646V4, multiclass
    clus
vv   SCAMP2 MUTATED SCAMP2 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              2              171
  T4              3               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
  SCAMP2 MUTATED     3   3   0   1
  SCAMP2 WILD-TYPE 115 101  77  76
D646V5, multiclass
    clus
vv   SCAMP2 MUTATED SCAMP2 WILD-TYPE
  N0              3              115
  N1              3              101
  N2              0               77
  N3              1               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"
D646V6, binary
                  cls
clus                 0   1
  SCAMP2 MUTATED     6   1
  SCAMP2 WILD-TYPE 340  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAMP2 MUTATED      6    1
  SCAMP2 WILD-TYPE  340   28
   clus
vv  SCAMP2 MUTATED SCAMP2 WILD-TYPE
  0              6              340
  1              1               28
[1] 2 2
[1] FALSE
D646V7, binary
                  cls
clus                 0   1
  SCAMP2 MUTATED     4   3
  SCAMP2 WILD-TYPE 141 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAMP2 MUTATED      4    3
  SCAMP2 WILD-TYPE  141  245
        clus
vv       SCAMP2 MUTATED SCAMP2 WILD-TYPE
  FEMALE              4              141
  MALE                3              245
[1] 2 2
[1] FALSE
D646V8, binary
                  cls
clus                 0   1
  SCAMP2 MUTATED     6   0
  SCAMP2 WILD-TYPE 286  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAMP2 MUTATED      6    0
  SCAMP2 WILD-TYPE  286   59
     clus
vv    SCAMP2 MUTATED SCAMP2 WILD-TYPE
  NO               6              286
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SCAMP2 MUTATED                                          0
  SCAMP2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SCAMP2 MUTATED                                       2
  SCAMP2 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SCAMP2 MUTATED                                                        3
  SCAMP2 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SCAMP2 MUTATED                                                   0
  SCAMP2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SCAMP2 MUTATED                                                                   1
  SCAMP2 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SCAMP2 MUTATED                                                    0
  SCAMP2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SCAMP2 MUTATED                                                  1
  SCAMP2 WILD-TYPE                                               60
D646V9, multiclass
                                                                   clus
vv                                                                  SCAMP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  SCAMP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SCAMP2 MUTATED     6   0   0   1
  SCAMP2 WILD-TYPE 305  14  15  23
D646V10, multiclass
    clus
vv   SCAMP2 MUTATED SCAMP2 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D646V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SCAMP2 MUTATED       2                         0
  SCAMP2 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SCAMP2 MUTATED                                           0     4
  SCAMP2 WILD-TYPE                                         1   239
D646V12, multiclass
                                           clus
vv                                          SCAMP2 MUTATED SCAMP2 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D646V13, binary
                  cls
clus                 0   1
  SCAMP2 MUTATED     1   5
  SCAMP2 WILD-TYPE   3 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAMP2 MUTATED      1    5
  SCAMP2 WILD-TYPE    3  305
                        clus
vv                       SCAMP2 MUTATED SCAMP2 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(647) Variable = HMGCLL1 MUTATION ANALYSIS
D647V1, survival
                   sevent
clus2                 0   1
  HMGCLL1 MUTATED     7   3
  HMGCLL1 WILD-TYPE 223 136
  HMGCLL1 MUTATED HMGCLL1 WILD-TYPE 
               10               359 
  HMGCLL1 MUTATED HMGCLL1 WILD-TYPE 
                3               136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-D7-6820 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-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-A4H4 
        6.51        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-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.44        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 

  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            14.470 
[1] "6.0 - 29.0 (12.6)"  "0.0 - 122.3 (14.5)"
[1] "hr=" "1"  
D647V2, 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       2       15       39       29        37        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HMGCLL1 MUTATED           0          2          0          1        2
  HMGCLL1 WILD-TYPE         3         68         53         31       36
D647V3, multiclass
            clus
vv           HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                0                37
  STAGE IIB                3                49
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  HMGCLL1 MUTATED     1   2   3   4
  HMGCLL1 WILD-TYPE  21  90 170  93
D647V4, multiclass
    clus
vv   HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  T1               1                21
  T2               2                90
  T3               3               170
  T4               4                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
  HMGCLL1 MUTATED     2   6   0   2
  HMGCLL1 WILD-TYPE 116  98  77  75
D647V5, multiclass
    clus
vv   HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  N0               2               116
  N1               6                98
  N2               0                77
  N3               2                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"
D647V6, binary
                   cls
clus                  0   1
  HMGCLL1 MUTATED     9   1
  HMGCLL1 WILD-TYPE 337  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HMGCLL1 MUTATED      9    1
  HMGCLL1 WILD-TYPE  337   28
   clus
vv  HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  0               9               337
  1               1                28
[1] 2 2
[1] FALSE
D647V7, binary
                   cls
clus                  0   1
  HMGCLL1 MUTATED     3   7
  HMGCLL1 WILD-TYPE 142 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HMGCLL1 MUTATED      3    7
  HMGCLL1 WILD-TYPE  142  241
        clus
vv       HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  FEMALE               3               142
  MALE                 7               241
[1] 2 2
[1] FALSE
D647V8, binary
                   cls
clus                  0   1
  HMGCLL1 MUTATED     7   2
  HMGCLL1 WILD-TYPE 285  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HMGCLL1 MUTATED      7    2
  HMGCLL1 WILD-TYPE  285   57
     clus
vv    HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  NO                7               285
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HMGCLL1 MUTATED                                          0
  HMGCLL1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HMGCLL1 MUTATED                                       3
  HMGCLL1 WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HMGCLL1 MUTATED                                                        4
  HMGCLL1 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HMGCLL1 MUTATED                                                   1
  HMGCLL1 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HMGCLL1 MUTATED                                                                   1
  HMGCLL1 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HMGCLL1 MUTATED                                                    0
  HMGCLL1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HMGCLL1 MUTATED                                                  1
  HMGCLL1 WILD-TYPE                                               60
D647V9, multiclass
                                                                   clus
vv                                                                  HMGCLL1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  HMGCLL1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  HMGCLL1 MUTATED    10   0   0   0
  HMGCLL1 WILD-TYPE 301  14  15  24
D647V10, multiclass
    clus
vv   HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  R0              10               301
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D647V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  HMGCLL1 MUTATED       4                         0
  HMGCLL1 WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HMGCLL1 MUTATED                                           0     4
  HMGCLL1 WILD-TYPE                                         1   239
D647V12, multiclass
                                           clus
vv                                          HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D647V13, binary
                   cls
clus                  0   1
  HMGCLL1 MUTATED     0   8
  HMGCLL1 WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HMGCLL1 MUTATED      0    8
  HMGCLL1 WILD-TYPE    4  302
                        clus
vv                       HMGCLL1 MUTATED HMGCLL1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(648) Variable = COL11A1 MUTATION ANALYSIS
D648V1, survival
                   sevent
clus2                 0   1
  COL11A1 MUTATED    33   6
  COL11A1 WILD-TYPE 197 133
  COL11A1 MUTATED COL11A1 WILD-TYPE 
               39               330 
  COL11A1 MUTATED COL11A1 WILD-TYPE 
                6               133 
$`COL11A1 MUTATED`
TCGA-CG-5727 TCGA-B7-5818 TCGA-B7-A5TN TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-6453 
       79.07        11.70         9.44         4.64        30.90        15.95 
TCGA-BR-7704 TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8372 TCGA-BR-8487 
       35.24        29.42        31.10        14.04        31.27         1.12 
TCGA-BR-8588 TCGA-BR-8680 TCGA-BR-A4J7 TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-4438 
       12.79        31.96        32.52        12.43        15.95        54.08 
TCGA-CG-5723 TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A74A TCGA-EQ-8122 
      105.07        13.78        14.76        11.44        19.96         7.99 
TCGA-FP-A4BE TCGA-HF-7133 TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GU 
       11.08        63.06        22.32        29.98         8.98         6.58 
TCGA-HU-A4GX TCGA-IN-A6RP TCGA-IP-7968 TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-VQ-A8DT 
       20.25         6.44         2.53        45.67        74.53        48.79 
TCGA-VQ-A8P2 TCGA-VQ-A8PE TCGA-VQ-AA6I 
       38.14        22.19        16.14 

$`COL11A1 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 
        9.86        26.70        19.56        11.01         9.47         6.61 
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        6.97         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-6455 
        9.67         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-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-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        8.05         0.56         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-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        4.31         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-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-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-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-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99         8.05         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-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
        5.92        36.43        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-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-7134 TCGA-HF-A5NB 
        0.56         5.52         6.21        77.29        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-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-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-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-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
        3.72        19.73        14.04        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-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-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-VQ-AA6K TCGA-ZA-A8F6 
       32.94        54.12        26.04        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 
           19.960            14.025 
[1] "1.1 - 105.1 (20.0)" "0.0 - 122.3 (14.0)"
[1] "hr=" "3.5"
D648V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  COL11A1 MUTATED         0        0        1        6         5         8
  COL11A1 WILD-TYPE       2       15       39       24        32        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL11A1 MUTATED           0          3          7          4        5
  COL11A1 WILD-TYPE         3         67         46         28       33
D648V3, multiclass
            clus
vv           COL11A1 MUTATED COL11A1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 6                24
  STAGE IIA                5                32
  STAGE IIB                8                44
  STAGE III                0                 3
  STAGE IIIA               3                67
  STAGE IIIB               7                46
  STAGE IIIC               4                28
  STAGE IV                 5                33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  COL11A1 MUTATED     1   9  17  13
  COL11A1 WILD-TYPE  21  83 156  84
D648V4, multiclass
    clus
vv   COL11A1 MUTATED COL11A1 WILD-TYPE
  T1               1                21
  T2               9                83
  T3              17               156
  T4              13                84
[1] 4 2
[1] TRUE
[1] "dimension of 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    11  10   7   9
  COL11A1 WILD-TYPE 107  94  70  68
D648V5, multiclass
    clus
vv   COL11A1 MUTATED COL11A1 WILD-TYPE
  N0              11               107
  N1              10                94
  N2               7                70
  N3               9                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"
D648V6, binary
                   cls
clus                  0   1
  COL11A1 MUTATED    36   3
  COL11A1 WILD-TYPE 310  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED     36    3
  COL11A1 WILD-TYPE  310   26
   clus
vv  COL11A1 MUTATED COL11A1 WILD-TYPE
  0              36               310
  1               3                26
[1] 2 2
[1] FALSE
D648V7, binary
                   cls
clus                  0   1
  COL11A1 MUTATED    16  25
  COL11A1 WILD-TYPE 129 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED     16   25
  COL11A1 WILD-TYPE  129  223
        clus
vv       COL11A1 MUTATED COL11A1 WILD-TYPE
  FEMALE              16               129
  MALE                25               223
[1] 2 2
[1] FALSE
D648V8, binary
                   cls
clus                  0   1
  COL11A1 MUTATED    30   8
  COL11A1 WILD-TYPE 262  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED     30    8
  COL11A1 WILD-TYPE  262   51
     clus
vv    COL11A1 MUTATED COL11A1 WILD-TYPE
  NO               30               262
  YES               8                51
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  COL11A1 MUTATED                                          0
  COL11A1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  COL11A1 MUTATED                                       6
  COL11A1 WILD-TYPE                                    64
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  COL11A1 MUTATED                                                       18
  COL11A1 WILD-TYPE                                                    140
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  COL11A1 MUTATED                                                   4
  COL11A1 WILD-TYPE                                                17
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  COL11A1 MUTATED                                                                   7
  COL11A1 WILD-TYPE                                                                61
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  COL11A1 MUTATED                                                    0
  COL11A1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  COL11A1 MUTATED                                                  6
  COL11A1 WILD-TYPE                                               55
D648V9, multiclass
                                                                   clus
vv                                                                  COL11A1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         18
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               7
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                6
                                                                   clus
vv                                                                  COL11A1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          140
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                61
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  COL11A1 MUTATED    34   1   0   3
  COL11A1 WILD-TYPE 277  13  15  21
D648V10, multiclass
    clus
vv   COL11A1 MUTATED COL11A1 WILD-TYPE
  R0              34               277
  R1               1                13
  R2               0                15
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D648V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  COL11A1 MUTATED       8                         1
  COL11A1 WILD-TYPE    79                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  COL11A1 MUTATED                                           0    26
  COL11A1 WILD-TYPE                                         1   217
D648V12, multiclass
                                           clus
vv                                          COL11A1 MUTATED COL11A1 WILD-TYPE
  ASIAN                                                   8                79
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  26               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D648V13, binary
                   cls
clus                  0   1
  COL11A1 MUTATED     2  30
  COL11A1 WILD-TYPE   2 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED      2   30
  COL11A1 WILD-TYPE    2  280
                        clus
vv                       COL11A1 MUTATED COL11A1 WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              30               280
[1] 2 2
[1] FALSE

Clustering(649) Variable = BIN3 MUTATION ANALYSIS
D649V1, survival
                sevent
clus2              0   1
  BIN3 MUTATED     3   1
  BIN3 WILD-TYPE 227 138
  BIN3 MUTATED BIN3 WILD-TYPE 
             4            365 
  BIN3 MUTATED BIN3 WILD-TYPE 
             1            138 
$`BIN3 MUTATED`
TCGA-BR-8487 TCGA-CG-5733 TCGA-HF-A5NB TCGA-MX-A5UJ 
        1.12        21.07        30.51        19.73 

$`BIN3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  BIN3 MUTATED BIN3 WILD-TYPE 
          1.12           0.00 
  BIN3 MUTATED BIN3 WILD-TYPE 
         30.51         122.30 
  BIN3 MUTATED BIN3 WILD-TYPE 
         20.40          14.17 
[1] "1.1 - 30.5 (20.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D649V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BIN3 MUTATED         0        0        0        0         1         0
  BIN3 WILD-TYPE       2       15       40       30        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BIN3 MUTATED           0          2          0          1        0
  BIN3 WILD-TYPE         3         68         53         31       38
D649V3, multiclass
            clus
vv           BIN3 MUTATED BIN3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BIN3 MUTATED     0   1   2   1
  BIN3 WILD-TYPE  22  91 171  96
D649V4, multiclass
    clus
vv   BIN3 MUTATED BIN3 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            2            171
  T4            1             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
  BIN3 MUTATED     1   0   2   1
  BIN3 WILD-TYPE 117 104  75  76
D649V5, multiclass
    clus
vv   BIN3 MUTATED BIN3 WILD-TYPE
  N0            1            117
  N1            0            104
  N2            2             75
  N3            1             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"
D649V6, binary
                cls
clus               0   1
  BIN3 MUTATED     4   0
  BIN3 WILD-TYPE 342  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  BIN3 MUTATED      4    0
  BIN3 WILD-TYPE  342   29
   clus
vv  BIN3 MUTATED BIN3 WILD-TYPE
  0            4            342
  1            0             29
[1] 2 2
[1] FALSE
D649V7, binary
                cls
clus               0   1
  BIN3 MUTATED     4   0
  BIN3 WILD-TYPE 141 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  BIN3 MUTATED      4    0
  BIN3 WILD-TYPE  141  248
        clus
vv       BIN3 MUTATED BIN3 WILD-TYPE
  FEMALE            4            141
  MALE              0            248
[1] 2 2
[1] FALSE
D649V8, binary
                cls
clus               0   1
  BIN3 MUTATED     3   1
  BIN3 WILD-TYPE 289  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  BIN3 MUTATED      3    1
  BIN3 WILD-TYPE  289   58
     clus
vv    BIN3 MUTATED BIN3 WILD-TYPE
  NO             3            289
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BIN3 MUTATED                                          0
  BIN3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BIN3 MUTATED                                       0
  BIN3 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BIN3 MUTATED                                                        1
  BIN3 WILD-TYPE                                                    157
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BIN3 MUTATED                                                   1
  BIN3 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BIN3 MUTATED                                                                   1
  BIN3 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BIN3 MUTATED                                                    0
  BIN3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BIN3 MUTATED                                                  1
  BIN3 WILD-TYPE                                               60
D649V9, multiclass
                                                                   clus
vv                                                                  BIN3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  BIN3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BIN3 MUTATED     3   1   0   0
  BIN3 WILD-TYPE 308  13  15  24
D649V10, multiclass
    clus
vv   BIN3 MUTATED BIN3 WILD-TYPE
  R0            3            308
  R1            1             13
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D649V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BIN3 MUTATED       0                         0
  BIN3 WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BIN3 MUTATED                                           0     2
  BIN3 WILD-TYPE                                         1   241
D649V12, multiclass
[1] "Remove cluster labels:" "BIN3 MUTATED"          
clus
  BIN3 MUTATED BIN3 WILD-TYPE 
             2            338 
    TCGA-EQ-A4SO     TCGA-F1-6177     TCGA-FP-A8CX     TCGA-KB-A93G 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-MX-A663     TCGA-B7-5816     TCGA-B7-5818     TCGA-B7-A5TI 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-B7-A5TJ     TCGA-B7-A5TK     TCGA-B7-A5TN     TCGA-BR-4183 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-4184     TCGA-BR-4187     TCGA-BR-4188     TCGA-BR-4191 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-4201     TCGA-BR-4253     TCGA-BR-4255     TCGA-BR-4256 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-4257     TCGA-BR-4267     TCGA-BR-4279     TCGA-BR-4280 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-4292     TCGA-BR-4294     TCGA-BR-4357     TCGA-BR-4361 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-4362     TCGA-BR-4363     TCGA-BR-4366     TCGA-BR-4368 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-4369     TCGA-BR-4370     TCGA-BR-4371     TCGA-BR-6452 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-6453     TCGA-BR-6454     TCGA-BR-6455     TCGA-BR-6456 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-6457     TCGA-BR-6458     TCGA-BR-6563     TCGA-BR-6564 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-6565     TCGA-BR-6566     TCGA-BR-6705     TCGA-BR-6706 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-6707     TCGA-BR-6709     TCGA-BR-6710     TCGA-BR-6801 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-6802     TCGA-BR-6803     TCGA-BR-6852     TCGA-BR-7196 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-7197     TCGA-BR-7703     TCGA-BR-7704     TCGA-BR-7707 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-7715     TCGA-BR-7716     TCGA-BR-7717     TCGA-BR-7722 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-7723     TCGA-BR-7851     TCGA-BR-7901     TCGA-BR-7957 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-7958     TCGA-BR-7959     TCGA-BR-8058     TCGA-BR-8059 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-8060     TCGA-BR-8077     TCGA-BR-8078     TCGA-BR-8080 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-8081     TCGA-BR-8284     TCGA-BR-8285     TCGA-BR-8286 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-8289     TCGA-BR-8291     TCGA-BR-8295     TCGA-BR-8297 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-8360     TCGA-BR-8361     TCGA-BR-8363     TCGA-BR-8364 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-8365     TCGA-BR-8366     TCGA-BR-8367     TCGA-BR-8368 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-8369     TCGA-BR-8370     TCGA-BR-8371     TCGA-BR-8372 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-8373     TCGA-BR-8380     TCGA-BR-8381     TCGA-BR-8382 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-8384     TCGA-BR-8483     TCGA-BR-8484     TCGA-BR-8485 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-8486     TCGA-BR-8588     TCGA-BR-8589     TCGA-BR-8590 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-8591     TCGA-BR-8592     TCGA-BR-8676     TCGA-BR-8677 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-8678     TCGA-BR-8679     TCGA-BR-8680     TCGA-BR-8682 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-8683     TCGA-BR-8686     TCGA-BR-8687     TCGA-BR-8690 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-A44T     TCGA-BR-A44U     TCGA-BR-A452     TCGA-BR-A453 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-A4CQ     TCGA-BR-A4CR     TCGA-BR-A4CS     TCGA-BR-A4IU 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-A4IV     TCGA-BR-A4IY     TCGA-BR-A4IZ     TCGA-BR-A4J1 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-A4J2     TCGA-BR-A4J4     TCGA-BR-A4J5     TCGA-BR-A4J6 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-A4J7     TCGA-BR-A4J8     TCGA-BR-A4PD     TCGA-BR-A4PE 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-BR-A4PF     TCGA-BR-A4QI     TCGA-BR-A4QL     TCGA-BR-A4QM 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-CD-5798     TCGA-CD-5799     TCGA-CD-5800     TCGA-CD-5801 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-CD-5802     TCGA-CD-5803     TCGA-CD-5804     TCGA-CD-5813 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-CD-8524     TCGA-CD-8525     TCGA-CD-8526     TCGA-CD-8527 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-CD-8528     TCGA-CD-8529     TCGA-CD-8530     TCGA-CD-8531 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-CD-8532     TCGA-CD-8533     TCGA-CD-8534     TCGA-CD-8535 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-CD-8536     TCGA-CD-A486     TCGA-CD-A487     TCGA-CD-A489 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-CD-A48A     TCGA-CD-A48C     TCGA-CD-A4MG     TCGA-CD-A4MH 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-CD-A4MI     TCGA-CD-A4MJ     TCGA-D7-5577     TCGA-D7-5578 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-D7-5579     TCGA-D7-6518     TCGA-D7-6519     TCGA-D7-6520 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-D7-6521     TCGA-D7-6522     TCGA-D7-6524     TCGA-D7-6525 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-D7-6526     TCGA-D7-6527     TCGA-D7-6528     TCGA-D7-6815 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-D7-6817     TCGA-D7-6818     TCGA-D7-6820     TCGA-D7-6822 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-D7-8570     TCGA-D7-8572     TCGA-D7-8573     TCGA-D7-8574 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-D7-8575     TCGA-D7-8576     TCGA-D7-8578     TCGA-D7-8579 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-D7-A4YT     TCGA-D7-A4YU     TCGA-D7-A4YV     TCGA-D7-A4YX 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-D7-A4YY     TCGA-D7-A4Z0     TCGA-D7-A6ET     TCGA-D7-A6EV 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-D7-A6EX     TCGA-D7-A6EY     TCGA-D7-A6EZ     TCGA-D7-A6F0 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-D7-A6F2     TCGA-D7-A747     TCGA-D7-A748     TCGA-D7-A74A 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-D7-A74B     TCGA-EQ-5647     TCGA-EQ-8122     TCGA-F1-6874 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-F1-6875     TCGA-F1-A448     TCGA-F1-A72C     TCGA-FP-7735 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-FP-7829     TCGA-FP-7916     TCGA-FP-7998     TCGA-FP-8099 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-FP-8209     TCGA-FP-8210     TCGA-FP-8211     TCGA-FP-8631 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-FP-A4BE     TCGA-FP-A4BF     TCGA-FP-A9TM     TCGA-HJ-7597 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-HU-8238     TCGA-HU-8243     TCGA-HU-8244     TCGA-HU-8249 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-HU-8602     TCGA-HU-8604     TCGA-HU-8608     TCGA-HU-8610 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-HU-A4G2     TCGA-HU-A4G3     TCGA-HU-A4G6     TCGA-HU-A4G8 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-HU-A4G9     TCGA-HU-A4GC     TCGA-HU-A4GD     TCGA-HU-A4GF 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-HU-A4GH     TCGA-HU-A4GJ     TCGA-HU-A4GN     TCGA-HU-A4GP 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-HU-A4GQ     TCGA-HU-A4GT     TCGA-HU-A4GU     TCGA-HU-A4GX 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-HU-A4GY     TCGA-HU-A4H0     TCGA-HU-A4H2     TCGA-HU-A4H3 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-HU-A4H4     TCGA-HU-A4H5     TCGA-HU-A4H6     TCGA-HU-A4H8 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-HU-A4HB     TCGA-HU-A4HD     TCGA-IN-7806     TCGA-IN-7808 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-IN-8462     TCGA-IN-8663     TCGA-IN-A6RI     TCGA-IN-A6RJ 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-IN-A6RL     TCGA-IN-A6RN     TCGA-IN-A6RO     TCGA-IN-A6RP 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-IN-A6RR     TCGA-IN-A6RS     TCGA-IN-A7NR     TCGA-IN-A7NT 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-IN-A7NU     TCGA-IN-AB1V     TCGA-IN-AB1X     TCGA-IP-7968 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-KB-A93J     TCGA-MX-A5UG     TCGA-MX-A666     TCGA-R5-A7O7 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-R5-A7ZE     TCGA-R5-A7ZF     TCGA-R5-A7ZI     TCGA-R5-A7ZR 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-R5-A804     TCGA-R5-A805     TCGA-RD-A7BS     TCGA-RD-A7BT 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-RD-A7BW     TCGA-RD-A7C1     TCGA-RD-A8MV     TCGA-RD-A8MW 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-RD-A8N0     TCGA-RD-A8N1     TCGA-RD-A8N2     TCGA-RD-A8N4 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-RD-A8N5     TCGA-RD-A8N6     TCGA-RD-A8N9     TCGA-SW-A7EA 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-SW-A7EB     TCGA-VQ-A8DL     TCGA-VQ-A8DU     TCGA-VQ-A8DV 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-VQ-A8DZ     TCGA-VQ-A8E2     TCGA-VQ-A8E7     TCGA-VQ-A8P2 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-VQ-A8P3     TCGA-VQ-A8PE     TCGA-VQ-A8PK     TCGA-VQ-A8PM 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-VQ-A8PQ     TCGA-VQ-A91U     TCGA-VQ-A92D     TCGA-VQ-AA64 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-VQ-AA68     TCGA-VQ-AA69     TCGA-VQ-AA6A     TCGA-VQ-AA6B 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-VQ-AA6F     TCGA-VQ-AA6G     TCGA-VQ-AA6I     TCGA-VQ-AA6J 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
    TCGA-VQ-AA6K     TCGA-ZA-A8F6 
"BIN3 WILD-TYPE" "BIN3 WILD-TYPE" 
D649V13, binary
                cls
clus               0   1
  BIN3 MUTATED     0   2
  BIN3 WILD-TYPE   4 308
[1] "tbl2"
                cls
clus             [,1] [,2]
  BIN3 MUTATED      0    2
  BIN3 WILD-TYPE    4  308
                        clus
vv                       BIN3 MUTATED BIN3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            2            308
[1] 2 2
[1] FALSE

Clustering(650) Variable = SLC25A17 MUTATION ANALYSIS
D650V1, survival
                    sevent
clus2                  0   1
  SLC25A17 MUTATED     0   3
  SLC25A17 WILD-TYPE 230 136
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 3                366 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 3                136 
$`SLC25A17 MUTATED`
TCGA-BR-4257 TCGA-CD-A4MG TCGA-CG-4306 
        9.67         6.58         1.02 

$`SLC25A17 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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              14.45 
[1] "1.0 - 9.7 (6.6)"    "0.0 - 122.3 (14.4)"
[1] "hr=" "9.1"
D650V2, 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       2       15       40       30        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A17 MUTATED           0          0          0          0        1
  SLC25A17 WILD-TYPE         3         70         53         32       37
D650V3, multiclass
            clus
vv           SLC25A17 MUTATED SLC25A17 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                0                 53
  STAGE IIIC                0                 32
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC25A17 MUTATED     0   0   2   1
  SLC25A17 WILD-TYPE  22  92 171  96
D650V4, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  T1                0                 22
  T2                0                 92
  T3                2                171
  T4                1                 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
  SLC25A17 MUTATED     2   0   1   0
  SLC25A17 WILD-TYPE 116 104  76  77
D650V5, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  N0                2                116
  N1                0                104
  N2                1                 76
  N3                0                 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"
D650V6, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     3   1
  SLC25A17 WILD-TYPE 343  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      3    1
  SLC25A17 WILD-TYPE  343   28
   clus
vv  SLC25A17 MUTATED SLC25A17 WILD-TYPE
  0                3                343
  1                1                 28
[1] 2 2
[1] FALSE
D650V7, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     1   3
  SLC25A17 WILD-TYPE 144 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      1    3
  SLC25A17 WILD-TYPE  144  245
        clus
vv       SLC25A17 MUTATED SLC25A17 WILD-TYPE
  FEMALE                1                144
  MALE                  3                245
[1] 2 2
[1] FALSE
D650V8, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     3   0
  SLC25A17 WILD-TYPE 289  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      3    0
  SLC25A17 WILD-TYPE  289   59
     clus
vv    SLC25A17 MUTATED SLC25A17 WILD-TYPE
  NO                 3                289
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC25A17 MUTATED                                          0
  SLC25A17 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC25A17 MUTATED                                       1
  SLC25A17 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC25A17 MUTATED                                                        2
  SLC25A17 WILD-TYPE                                                    156
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC25A17 MUTATED                                                   0
  SLC25A17 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC25A17 MUTATED                                                                   1
  SLC25A17 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC25A17 MUTATED                                                    0
  SLC25A17 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC25A17 MUTATED                                                  0
  SLC25A17 WILD-TYPE                                               61
D650V9, multiclass
                                                                   clus
vv                                                                  SLC25A17 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 0
                                                                   clus
vv                                                                  SLC25A17 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SLC25A17 MUTATED     1   0   1   1
  SLC25A17 WILD-TYPE 310  14  14  23
D650V10, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  R0                1                310
  R1                0                 14
  R2                1                 14
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D650V11, continuous
[1] "Remove cluster labels:" "SLC25A17 MUTATED"      
clus
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 1                342 
        TCGA-CG-4444         TCGA-CG-4460         TCGA-CG-4475 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-5727         TCGA-EQ-A4SO 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-F1-6177         TCGA-FP-A8CX         TCGA-HF-7131 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-KB-A93G         TCGA-MX-A663         TCGA-B7-5816 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-B7-A5TI         TCGA-BR-4183         TCGA-BR-4184 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-4188         TCGA-BR-4191         TCGA-BR-4253 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-4255         TCGA-BR-4256         TCGA-BR-4267 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-4279         TCGA-BR-4280         TCGA-BR-4361 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-4362         TCGA-BR-4368         TCGA-BR-6452 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-6453         TCGA-BR-6454         TCGA-BR-6455 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-6456         TCGA-BR-6457         TCGA-BR-6458 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7901 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-7957         TCGA-BR-7958         TCGA-BR-7959 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8058         TCGA-BR-8059         TCGA-BR-8060 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8297         TCGA-BR-8360 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8361         TCGA-BR-8363         TCGA-BR-8364 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8365         TCGA-BR-8366         TCGA-BR-8367 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8368         TCGA-BR-8369         TCGA-BR-8370 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8371         TCGA-BR-8372         TCGA-BR-8373 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8380         TCGA-BR-8381         TCGA-BR-8382 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8384         TCGA-BR-8483         TCGA-BR-8484 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8485         TCGA-BR-8486         TCGA-BR-8487 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8588         TCGA-BR-8589         TCGA-BR-8590 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8591         TCGA-BR-8592         TCGA-BR-8676 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8677         TCGA-BR-8678         TCGA-BR-8679 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8680         TCGA-BR-8682         TCGA-BR-8683 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-8686         TCGA-BR-8687         TCGA-BR-8690 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A44T         TCGA-BR-A44U         TCGA-BR-A452 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A453         TCGA-BR-A4CQ         TCGA-BR-A4CR 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A4CS         TCGA-BR-A4IU         TCGA-BR-A4IV 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4PD 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A4PE         TCGA-BR-A4PF         TCGA-BR-A4QI 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-BR-A4QL         TCGA-BR-A4QM         TCGA-CD-5804 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CD-8525         TCGA-CD-8526         TCGA-CD-8531 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CD-8535         TCGA-CD-A487         TCGA-CG-4301 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4436 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4442         TCGA-CG-4443 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4462 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5717 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-D7-8570 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-8572         TCGA-D7-8573         TCGA-D7-8574 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-8575         TCGA-D7-8576         TCGA-D7-8578 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-8579         TCGA-D7-A4YT         TCGA-D7-A4YU 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-A4YV         TCGA-D7-A4YX         TCGA-D7-A4YY 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-A4Z0         TCGA-D7-A6ET         TCGA-D7-A6EV 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-A6EX         TCGA-D7-A6EY         TCGA-D7-A6EZ 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-A6F0         TCGA-D7-A6F2         TCGA-D7-A747 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-D7-A748         TCGA-D7-A74A         TCGA-D7-A74B 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6874 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-F1-6875         TCGA-F1-A448         TCGA-F1-A72C 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-FP-8210         TCGA-FP-8211         TCGA-FP-8631 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-FP-A4BE         TCGA-FP-A4BF         TCGA-FP-A9TM 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HF-7132         TCGA-HF-7133         TCGA-HF-7134 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HF-7136         TCGA-HF-A5NB         TCGA-HJ-7597 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-8238         TCGA-HU-8243         TCGA-HU-8244 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-8249         TCGA-HU-8602         TCGA-HU-8604 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-8608         TCGA-HU-8610         TCGA-HU-A4G2 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4G3         TCGA-HU-A4G6         TCGA-HU-A4G8 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4G9         TCGA-HU-A4GC         TCGA-HU-A4GD 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4GF         TCGA-HU-A4GH         TCGA-HU-A4GJ 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4GN         TCGA-HU-A4GP         TCGA-HU-A4GQ 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4GT         TCGA-HU-A4GU         TCGA-HU-A4GX 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4GY         TCGA-HU-A4H0         TCGA-HU-A4H2 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4H3         TCGA-HU-A4H4         TCGA-HU-A4H5 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4H6         TCGA-HU-A4H8         TCGA-HU-A4HB 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-HU-A4HD         TCGA-IN-7806         TCGA-IN-7808 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-IN-8462         TCGA-IN-8663         TCGA-IN-A6RI 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-IN-A6RJ         TCGA-IN-A6RL         TCGA-IN-A6RN 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-IN-A6RO         TCGA-IN-A6RP         TCGA-IN-A6RR 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-IN-A6RS         TCGA-IN-A7NR         TCGA-IN-A7NT 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-IN-A7NU         TCGA-IN-AB1V         TCGA-IN-AB1X 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-IP-7968         TCGA-KB-A6F5         TCGA-KB-A6F7 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-KB-A93J         TCGA-MX-A5UG         TCGA-MX-A5UJ 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-R5-A7ZI         TCGA-RD-A7BS         TCGA-RD-A7BT 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-RD-A7BW         TCGA-RD-A7C1         TCGA-RD-A8MV 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-RD-A8MW         TCGA-RD-A8N0         TCGA-RD-A8N1 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-RD-A8N2         TCGA-RD-A8N4         TCGA-RD-A8N5 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-RD-A8N6         TCGA-RD-A8N9         TCGA-SW-A7EA 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-SW-A7EB         TCGA-VQ-A8DL         TCGA-VQ-A8DT 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-VQ-A8DU         TCGA-VQ-A8DV         TCGA-VQ-A8DZ 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-VQ-A8E2         TCGA-VQ-A8E7         TCGA-VQ-A8P2 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-VQ-A8P3         TCGA-VQ-A8PE         TCGA-VQ-A8PK 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-VQ-A8PM         TCGA-VQ-A8PQ         TCGA-VQ-A91Q 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-VQ-A91U         TCGA-VQ-A91V         TCGA-VQ-A92D 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-VQ-A94T         TCGA-VQ-AA64         TCGA-VQ-AA68 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-VQ-AA69         TCGA-VQ-AA6A         TCGA-VQ-AA6B 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-VQ-AA6F         TCGA-VQ-AA6G         TCGA-VQ-AA6I 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
        TCGA-VQ-AA6J         TCGA-VQ-AA6K         TCGA-ZA-A8F6 
"SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" "SLC25A17 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SLC25A17 MUTATED       1                         0
  SLC25A17 WILD-TYPE    86                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC25A17 MUTATED                                           0     2
  SLC25A17 WILD-TYPE                                         1   241
D650V12, multiclass
                                           clus
vv                                          SLC25A17 MUTATED SLC25A17 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    2                241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D650V13, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     0   3
  SLC25A17 WILD-TYPE   4 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      0    3
  SLC25A17 WILD-TYPE    4  307
                        clus
vv                       SLC25A17 MUTATED SLC25A17 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                3                307
[1] 2 2
[1] FALSE

Clustering(651) Variable = CTSO MUTATION ANALYSIS
D651V1, survival
                sevent
clus2              0   1
  CTSO MUTATED     5   1
  CTSO WILD-TYPE 225 138
  CTSO MUTATED CTSO WILD-TYPE 
             6            363 
  CTSO MUTATED CTSO WILD-TYPE 
             1            138 
$`CTSO MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8680 TCGA-CD-8524 TCGA-HU-8602 TCGA-VQ-AA6A 
        6.61        34.68        31.96        12.76        22.32        38.93 

$`CTSO WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  CTSO MUTATED CTSO WILD-TYPE 
          6.61           0.00 
  CTSO MUTATED CTSO WILD-TYPE 
         38.93         122.30 
  CTSO MUTATED CTSO WILD-TYPE 
         27.14          14.17 
[1] "6.6 - 38.9 (27.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3.1"
D651V2, 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       2       15       40       29        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTSO MUTATED           1          0          0          1        1
  CTSO WILD-TYPE         2         70         53         31       37
D651V3, multiclass
            clus
vv           CTSO MUTATED CTSO WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             1              2
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTSO MUTATED     0   1   2   3
  CTSO WILD-TYPE  22  91 171  94
D651V4, multiclass
    clus
vv   CTSO MUTATED CTSO WILD-TYPE
  T1            0             22
  T2            1             91
  T3            2            171
  T4            3             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
  CTSO MUTATED     3   1   1   1
  CTSO WILD-TYPE 115 103  76  76
D651V5, multiclass
    clus
vv   CTSO MUTATED CTSO WILD-TYPE
  N0            3            115
  N1            1            103
  N2            1             76
  N3            1             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"
D651V6, binary
                cls
clus               0   1
  CTSO MUTATED     5   1
  CTSO WILD-TYPE 341  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSO MUTATED      5    1
  CTSO WILD-TYPE  341   28
   clus
vv  CTSO MUTATED CTSO WILD-TYPE
  0            5            341
  1            1             28
[1] 2 2
[1] FALSE
D651V7, binary
                cls
clus               0   1
  CTSO MUTATED     4   2
  CTSO WILD-TYPE 141 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSO MUTATED      4    2
  CTSO WILD-TYPE  141  246
        clus
vv       CTSO MUTATED CTSO WILD-TYPE
  FEMALE            4            141
  MALE              2            246
[1] 2 2
[1] FALSE
D651V8, binary
                cls
clus               0   1
  CTSO MUTATED     5   1
  CTSO WILD-TYPE 287  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSO MUTATED      5    1
  CTSO WILD-TYPE  287   58
     clus
vv    CTSO MUTATED CTSO WILD-TYPE
  NO             5            287
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CTSO MUTATED                                          0
  CTSO WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CTSO MUTATED                                       1
  CTSO WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTSO MUTATED                                                        2
  CTSO WILD-TYPE                                                    156
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CTSO MUTATED                                                   0
  CTSO WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTSO MUTATED                                                                   2
  CTSO WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CTSO MUTATED                                                    0
  CTSO WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CTSO MUTATED                                                  1
  CTSO WILD-TYPE                                               60
D651V9, multiclass
                                                                   clus
vv                                                                  CTSO MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  CTSO WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CTSO MUTATED     5   0   0   1
  CTSO WILD-TYPE 306  14  15  23
D651V10, multiclass
    clus
vv   CTSO MUTATED CTSO WILD-TYPE
  R0            5            306
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D651V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CTSO MUTATED       3                         0
  CTSO WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTSO MUTATED                                           0     3
  CTSO WILD-TYPE                                         1   240
D651V12, multiclass
                                           clus
vv                                          CTSO MUTATED CTSO WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D651V13, binary
                cls
clus               0   1
  CTSO MUTATED     0   5
  CTSO WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSO MUTATED      0    5
  CTSO WILD-TYPE    4  305
                        clus
vv                       CTSO MUTATED CTSO WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(652) Variable = PAM MUTATION ANALYSIS
D652V1, survival
               sevent
clus2             0   1
  PAM MUTATED     4   4
  PAM WILD-TYPE 226 135
  PAM MUTATED PAM WILD-TYPE 
            8           361 
  PAM MUTATED PAM WILD-TYPE 
            4           135 
$`PAM MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6706 TCGA-BR-8078 TCGA-CG-4465 TCGA-HU-A4G8 
       26.70         6.97        18.05        29.59         9.01        22.68 
TCGA-HU-A4GN TCGA-VQ-A94T 
       29.98        11.24 

$`PAM WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  PAM MUTATED PAM WILD-TYPE 
         6.97          0.00 
  PAM MUTATED PAM WILD-TYPE 
        29.98        122.30 
  PAM MUTATED PAM WILD-TYPE 
       20.365        14.170 
[1] "7.0 - 30.0 (20.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D652V2, 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       2       15       40       30        36        49
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAM MUTATED           0          2          1          0        1
  PAM WILD-TYPE         3         68         52         32       37
D652V3, multiclass
            clus
vv           PAM MUTATED PAM WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             0            40
  STAGE II             0            30
  STAGE IIA            1            36
  STAGE IIB            3            49
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           1            52
  STAGE IIIC           0            32
  STAGE IV             1            37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  PAM MUTATED     0   1   4   3
  PAM WILD-TYPE  22  91 169  94
D652V4, multiclass
    clus
vv   PAM MUTATED PAM WILD-TYPE
  T1           0            22
  T2           1            91
  T3           4           169
  T4           3            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
  PAM MUTATED     2   4   1   1
  PAM WILD-TYPE 116 100  76  76
D652V5, multiclass
    clus
vv   PAM MUTATED PAM WILD-TYPE
  N0           2           116
  N1           4           100
  N2           1            76
  N3           1            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"
D652V6, binary
               cls
clus              0   1
  PAM MUTATED     7   1
  PAM WILD-TYPE 339  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      7    1
  PAM WILD-TYPE  339   28
   clus
vv  PAM MUTATED PAM WILD-TYPE
  0           7           339
  1           1            28
[1] 2 2
[1] FALSE
D652V7, binary
               cls
clus              0   1
  PAM MUTATED     5   4
  PAM WILD-TYPE 140 244
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      5    4
  PAM WILD-TYPE  140  244
        clus
vv       PAM MUTATED PAM WILD-TYPE
  FEMALE           5           140
  MALE             4           244
[1] 2 2
[1] FALSE
D652V8, binary
               cls
clus              0   1
  PAM MUTATED     7   0
  PAM WILD-TYPE 285  59
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      7    0
  PAM WILD-TYPE  285   59
     clus
vv    PAM MUTATED PAM WILD-TYPE
  NO            7           285
  YES           0            59
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PAM MUTATED                                          0
  PAM WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PAM MUTATED                                       4
  PAM WILD-TYPE                                    66
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAM MUTATED                                                        4
  PAM WILD-TYPE                                                    154
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PAM MUTATED                                                   0
  PAM WILD-TYPE                                                21
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAM MUTATED                                                                   0
  PAM WILD-TYPE                                                                68
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PAM MUTATED                                                    0
  PAM WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PAM MUTATED                                                  1
  PAM WILD-TYPE                                               60
D652V9, multiclass
                                                                   clus
vv                                                                  PAM MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            1
                                                                   clus
vv                                                                  PAM WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  PAM MUTATED     5   0   1   2
  PAM WILD-TYPE 306  14  14  22
D652V10, multiclass
    clus
vv   PAM MUTATED PAM WILD-TYPE
  R0           5           306
  R1           0            14
  R2           1            14
  RX           2            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D652V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  PAM MUTATED       2                         0
  PAM WILD-TYPE    85                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAM MUTATED                                           0     5
  PAM WILD-TYPE                                         1   238
D652V12, multiclass
                                           clus
vv                                          PAM MUTATED PAM WILD-TYPE
  ASIAN                                               2            85
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               5           238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D652V13, binary
               cls
clus              0   1
  PAM MUTATED     0   7
  PAM WILD-TYPE   4 303
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      0    7
  PAM WILD-TYPE    4  303
                        clus
vv                       PAM MUTATED PAM WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           7           303
[1] 2 2
[1] FALSE

Clustering(653) Variable = TLE1 MUTATION ANALYSIS
D653V1, survival
                sevent
clus2              0   1
  TLE1 MUTATED     9   2
  TLE1 WILD-TYPE 221 137
  TLE1 MUTATED TLE1 WILD-TYPE 
            11            358 
  TLE1 MUTATED TLE1 WILD-TYPE 
             2            137 
$`TLE1 MUTATED`
TCGA-CG-4460 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8360 TCGA-BR-8372 
       21.99         6.61        34.68        35.84         6.18        31.27 
TCGA-BR-8487 TCGA-BR-8589 TCGA-HF-A5NB TCGA-HU-8602 TCGA-VQ-A8E2 
        1.12        27.12        30.51        22.32        43.36 

$`TLE1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-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-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 

  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          14.07 
[1] "1.1 - 43.4 (27.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.8"
D653V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TLE1 MUTATED         0        0        1        0         3         1
  TLE1 WILD-TYPE       2       15       39       30        34        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TLE1 MUTATED           1          0          2          2        2
  TLE1 WILD-TYPE         2         70         51         30       36
D653V3, multiclass
            clus
vv           TLE1 MUTATED TLE1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             3             34
  STAGE IIB             1             51
  STAGE III             1              2
  STAGE IIIA            0             70
  STAGE IIIB            2             51
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TLE1 MUTATED     0   2   4   6
  TLE1 WILD-TYPE  22  90 169  91
D653V4, multiclass
    clus
vv   TLE1 MUTATED TLE1 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            4            169
  T4            6             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
  TLE1 MUTATED     5   3   2   2
  TLE1 WILD-TYPE 113 101  75  75
D653V5, multiclass
    clus
vv   TLE1 MUTATED TLE1 WILD-TYPE
  N0            5            113
  N1            3            101
  N2            2             75
  N3            2             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"
D653V6, binary
                cls
clus               0   1
  TLE1 MUTATED    11   1
  TLE1 WILD-TYPE 335  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLE1 MUTATED     11    1
  TLE1 WILD-TYPE  335   28
   clus
vv  TLE1 MUTATED TLE1 WILD-TYPE
  0           11            335
  1            1             28
[1] 2 2
[1] FALSE
D653V7, binary
                cls
clus               0   1
  TLE1 MUTATED     8   4
  TLE1 WILD-TYPE 137 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLE1 MUTATED      8    4
  TLE1 WILD-TYPE  137  244
        clus
vv       TLE1 MUTATED TLE1 WILD-TYPE
  FEMALE            8            137
  MALE              4            244
[1] 2 2
[1] FALSE
D653V8, binary
                cls
clus               0   1
  TLE1 MUTATED     9   2
  TLE1 WILD-TYPE 283  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLE1 MUTATED      9    2
  TLE1 WILD-TYPE  283   57
     clus
vv    TLE1 MUTATED TLE1 WILD-TYPE
  NO             9            283
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TLE1 MUTATED                                          0
  TLE1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TLE1 MUTATED                                       1
  TLE1 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TLE1 MUTATED                                                        7
  TLE1 WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TLE1 MUTATED                                                   1
  TLE1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TLE1 MUTATED                                                                   2
  TLE1 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TLE1 MUTATED                                                    0
  TLE1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TLE1 MUTATED                                                  1
  TLE1 WILD-TYPE                                               60
D653V9, multiclass
                                                                   clus
vv                                                                  TLE1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  TLE1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TLE1 MUTATED     8   1   1   2
  TLE1 WILD-TYPE 303  13  14  22
D653V10, multiclass
    clus
vv   TLE1 MUTATED TLE1 WILD-TYPE
  R0            8            303
  R1            1             13
  R2            1             14
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D653V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TLE1 MUTATED       2                         0
  TLE1 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TLE1 MUTATED                                           0     8
  TLE1 WILD-TYPE                                         1   235
D653V12, multiclass
                                           clus
vv                                          TLE1 MUTATED TLE1 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D653V13, binary
                cls
clus               0   1
  TLE1 MUTATED     0   9
  TLE1 WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLE1 MUTATED      0    9
  TLE1 WILD-TYPE    4  301
                        clus
vv                       TLE1 MUTATED TLE1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(654) Variable = ZNF285 MUTATION ANALYSIS
D654V1, survival
                  sevent
clus2                0   1
  ZNF285 MUTATED     5   2
  ZNF285 WILD-TYPE 225 137
  ZNF285 MUTATED ZNF285 WILD-TYPE 
               7              362 
  ZNF285 MUTATED ZNF285 WILD-TYPE 
               2              137 
$`ZNF285 MUTATED`
TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-7715 TCGA-BR-8369 TCGA-BR-8382 TCGA-CD-A4MH 
       34.68        19.33        33.63        14.04        25.05        12.20 
TCGA-VQ-A8P3 
       37.22 

$`ZNF285 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
            12.2              0.0 
  ZNF285 MUTATED ZNF285 WILD-TYPE 
           37.22           122.30 
  ZNF285 MUTATED ZNF285 WILD-TYPE 
           25.05            14.12 
[1] "12.2 - 37.2 (25.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D654V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF285 MUTATED         0        0        0        0         3         1
  ZNF285 WILD-TYPE       2       15       40       30        34        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF285 MUTATED           0          1          1          1        0
  ZNF285 WILD-TYPE         3         69         52         31       38
D654V3, multiclass
            clus
vv           ZNF285 MUTATED ZNF285 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF285 MUTATED     0   0   6   2
  ZNF285 WILD-TYPE  22  92 167  95
D654V4, multiclass
    clus
vv   ZNF285 MUTATED ZNF285 WILD-TYPE
  T1              0               22
  T2              0               92
  T3              6              167
  T4              2               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
  ZNF285 MUTATED     3   3   0   2
  ZNF285 WILD-TYPE 115 101  77  75
D654V5, multiclass
    clus
vv   ZNF285 MUTATED ZNF285 WILD-TYPE
  N0              3              115
  N1              3              101
  N2              0               77
  N3              2               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"
D654V6, binary
                  cls
clus                 0   1
  ZNF285 MUTATED     8   0
  ZNF285 WILD-TYPE 338  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF285 MUTATED      8    0
  ZNF285 WILD-TYPE  338   29
   clus
vv  ZNF285 MUTATED ZNF285 WILD-TYPE
  0              8              338
  1              0               29
[1] 2 2
[1] FALSE
D654V7, binary
                  cls
clus                 0   1
  ZNF285 MUTATED     7   2
  ZNF285 WILD-TYPE 138 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF285 MUTATED      7    2
  ZNF285 WILD-TYPE  138  246
        clus
vv       ZNF285 MUTATED ZNF285 WILD-TYPE
  FEMALE              7              138
  MALE                2              246
[1] 2 2
[1] FALSE
D654V8, binary
                  cls
clus                 0   1
  ZNF285 MUTATED     5   2
  ZNF285 WILD-TYPE 287  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF285 MUTATED      5    2
  ZNF285 WILD-TYPE  287   57
     clus
vv    ZNF285 MUTATED ZNF285 WILD-TYPE
  NO               5              287
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF285 MUTATED                                          0
  ZNF285 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF285 MUTATED                                       0
  ZNF285 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF285 MUTATED                                                        8
  ZNF285 WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF285 MUTATED                                                   0
  ZNF285 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF285 MUTATED                                                                   0
  ZNF285 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF285 MUTATED                                                    0
  ZNF285 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF285 MUTATED                                                  1
  ZNF285 WILD-TYPE                                               60
D654V9, multiclass
                                                                   clus
vv                                                                  ZNF285 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ZNF285 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF285 MUTATED     6   0   0   2
  ZNF285 WILD-TYPE 305  14  15  22
D654V10, multiclass
    clus
vv   ZNF285 MUTATED ZNF285 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D654V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF285 MUTATED       1                         0
  ZNF285 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF285 MUTATED                                           0     8
  ZNF285 WILD-TYPE                                         1   235
D654V12, multiclass
                                           clus
vv                                          ZNF285 MUTATED ZNF285 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D654V13, binary
                  cls
clus                 0   1
  ZNF285 MUTATED     0   8
  ZNF285 WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF285 MUTATED      0    8
  ZNF285 WILD-TYPE    4  302
                        clus
vv                       ZNF285 MUTATED ZNF285 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(655) Variable = PTOV1 MUTATION ANALYSIS
D655V1, survival
                 sevent
clus2               0   1
  PTOV1 MUTATED     7   4
  PTOV1 WILD-TYPE 223 135
  PTOV1 MUTATED PTOV1 WILD-TYPE 
             11             358 
  PTOV1 MUTATED PTOV1 WILD-TYPE 
              4             135 
$`PTOV1 MUTATED`
TCGA-BR-4280 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-8080 TCGA-BR-8368 TCGA-BR-8372 
        6.61        32.78        30.90         9.60         4.31        31.27 
TCGA-BR-8686 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-HU-A4GT TCGA-HU-A4H3 
       20.88         6.58        12.62         6.51        29.00 

$`PTOV1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-8369 
        0.26        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-8687 TCGA-BR-8690 
       24.79        31.96        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-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-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-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-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 

  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           14.35 
[1] "4.3 - 32.8 (12.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D655V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTOV1 MUTATED         0        0        2        0         3         0
  PTOV1 WILD-TYPE       2       15       38       30        34        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTOV1 MUTATED           1          1          1          3        0
  PTOV1 WILD-TYPE         2         69         52         29       38
D655V3, multiclass
            clus
vv           PTOV1 MUTATED PTOV1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              0              52
  STAGE III              1               2
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             3              29
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTOV1 MUTATED     0   3   4   4
  PTOV1 WILD-TYPE  22  89 169  93
D655V4, multiclass
    clus
vv   PTOV1 MUTATED PTOV1 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             4             169
  T4             4              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
  PTOV1 MUTATED     5   2   1   3
  PTOV1 WILD-TYPE 113 102  76  74
D655V5, multiclass
    clus
vv   PTOV1 MUTATED PTOV1 WILD-TYPE
  N0             5             113
  N1             2             102
  N2             1              76
  N3             3              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"
D655V6, binary
                 cls
clus                0   1
  PTOV1 MUTATED    11   0
  PTOV1 WILD-TYPE 335  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTOV1 MUTATED     11    0
  PTOV1 WILD-TYPE  335   29
   clus
vv  PTOV1 MUTATED PTOV1 WILD-TYPE
  0            11             335
  1             0              29
[1] 2 2
[1] FALSE
D655V7, binary
                 cls
clus                0   1
  PTOV1 MUTATED     6   5
  PTOV1 WILD-TYPE 139 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTOV1 MUTATED      6    5
  PTOV1 WILD-TYPE  139  243
        clus
vv       PTOV1 MUTATED PTOV1 WILD-TYPE
  FEMALE             6             139
  MALE               5             243
[1] 2 2
[1] FALSE
D655V8, binary
                 cls
clus                0   1
  PTOV1 MUTATED    10   0
  PTOV1 WILD-TYPE 282  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTOV1 MUTATED     10    0
  PTOV1 WILD-TYPE  282   59
     clus
vv    PTOV1 MUTATED PTOV1 WILD-TYPE
  NO             10             282
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PTOV1 MUTATED                                          0
  PTOV1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PTOV1 MUTATED                                       2
  PTOV1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTOV1 MUTATED                                                        6
  PTOV1 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PTOV1 MUTATED                                                   1
  PTOV1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTOV1 MUTATED                                                                   0
  PTOV1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PTOV1 MUTATED                                                    0
  PTOV1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PTOV1 MUTATED                                                  2
  PTOV1 WILD-TYPE                                               59
D655V9, multiclass
                                                                   clus
vv                                                                  PTOV1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  PTOV1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTOV1 MUTATED     8   0   0   1
  PTOV1 WILD-TYPE 303  14  15  23
D655V10, multiclass
    clus
vv   PTOV1 MUTATED PTOV1 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D655V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PTOV1 MUTATED       5                         0
  PTOV1 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTOV1 MUTATED                                           0     6
  PTOV1 WILD-TYPE                                         1   237
D655V12, multiclass
                                           clus
vv                                          PTOV1 MUTATED PTOV1 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D655V13, binary
                 cls
clus                0   1
  PTOV1 MUTATED     0  11
  PTOV1 WILD-TYPE   4 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTOV1 MUTATED      0   11
  PTOV1 WILD-TYPE    4  299
                        clus
vv                       PTOV1 MUTATED PTOV1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(656) Variable = SLC6A11 MUTATION ANALYSIS
D656V1, survival
                   sevent
clus2                 0   1
  SLC6A11 MUTATED     4   4
  SLC6A11 WILD-TYPE 226 135
  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
                8               361 
  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
                4               135 
$`SLC6A11 MUTATED`
TCGA-CG-4460 TCGA-BR-8366 TCGA-CD-5801 TCGA-CG-4443 TCGA-CG-5721 TCGA-CG-5733 
       21.99         0.95        13.18        29.98         6.02        21.07 
TCGA-MX-A5UJ TCGA-RD-A8N5 
       19.73        57.44 

$`SLC6A11 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        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-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-A8N6 TCGA-RD-A8N9 
       40.64       115.69       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-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 

  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
             0.95              0.00 
  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
            57.44            122.30 
  SLC6A11 MUTATED SLC6A11 WILD-TYPE 
            20.40             14.17 
[1] "0.9 - 57.4 (20.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D656V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC6A11 MUTATED         1        1        0        0         1         0
  SLC6A11 WILD-TYPE       1       14       40       30        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC6A11 MUTATED           0          5          0          0        2
  SLC6A11 WILD-TYPE         3         65         53         32       36
D656V3, multiclass
            clus
vv           SLC6A11 MUTATED SLC6A11 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 1                14
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               5                65
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC6A11 MUTATED     2   1   4   3
  SLC6A11 WILD-TYPE  20  91 169  94
D656V4, multiclass
    clus
vv   SLC6A11 MUTATED SLC6A11 WILD-TYPE
  T1               2                20
  T2               1                91
  T3               4               169
  T4               3                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
  SLC6A11 MUTATED     3   5   2   0
  SLC6A11 WILD-TYPE 115  99  75  77
D656V5, multiclass
    clus
vv   SLC6A11 MUTATED SLC6A11 WILD-TYPE
  N0               3               115
  N1               5                99
  N2               2                75
  N3               0                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"
D656V6, binary
                   cls
clus                  0   1
  SLC6A11 MUTATED     8   1
  SLC6A11 WILD-TYPE 338  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A11 MUTATED      8    1
  SLC6A11 WILD-TYPE  338   28
   clus
vv  SLC6A11 MUTATED SLC6A11 WILD-TYPE
  0               8               338
  1               1                28
[1] 2 2
[1] FALSE
D656V7, binary
                   cls
clus                  0   1
  SLC6A11 MUTATED     5   5
  SLC6A11 WILD-TYPE 140 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A11 MUTATED      5    5
  SLC6A11 WILD-TYPE  140  243
        clus
vv       SLC6A11 MUTATED SLC6A11 WILD-TYPE
  FEMALE               5               140
  MALE                 5               243
[1] 2 2
[1] FALSE
D656V8, binary
                   cls
clus                  0   1
  SLC6A11 MUTATED     7   1
  SLC6A11 WILD-TYPE 285  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A11 MUTATED      7    1
  SLC6A11 WILD-TYPE  285   58
     clus
vv    SLC6A11 MUTATED SLC6A11 WILD-TYPE
  NO                7               285
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC6A11 MUTATED                                          0
  SLC6A11 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC6A11 MUTATED                                       0
  SLC6A11 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC6A11 MUTATED                                                        4
  SLC6A11 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC6A11 MUTATED                                                   1
  SLC6A11 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC6A11 MUTATED                                                                   4
  SLC6A11 WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC6A11 MUTATED                                                    0
  SLC6A11 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC6A11 MUTATED                                                  1
  SLC6A11 WILD-TYPE                                               60
D656V9, multiclass
                                                                   clus
vv                                                                  SLC6A11 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  SLC6A11 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC6A11 MUTATED     8   0   1   1
  SLC6A11 WILD-TYPE 303  14  14  23
D656V10, multiclass
    clus
vv   SLC6A11 MUTATED SLC6A11 WILD-TYPE
  R0               8               303
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D656V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC6A11 MUTATED       1                         1
  SLC6A11 WILD-TYPE    86                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC6A11 MUTATED                                           0     4
  SLC6A11 WILD-TYPE                                         1   239
D656V12, multiclass
                                           clus
vv                                          SLC6A11 MUTATED SLC6A11 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D656V13, binary
                   cls
clus                  0   1
  SLC6A11 MUTATED     0   6
  SLC6A11 WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A11 MUTATED      0    6
  SLC6A11 WILD-TYPE    4  304
                        clus
vv                       SLC6A11 MUTATED SLC6A11 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(657) Variable = BRCA1 MUTATION ANALYSIS
D657V1, survival
                 sevent
clus2               0   1
  BRCA1 MUTATED     9   3
  BRCA1 WILD-TYPE 221 136
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             12             357 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
              3             136 
$`BRCA1 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-4455 TCGA-CG-4462 
        8.05        54.08         4.01        14.01        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-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-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-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 

  BRCA1 MUTATED BRCA1 WILD-TYPE 
           1.02            0.00 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
           65.1           122.3 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
          27.63           14.07 
[1] "1.0 - 65.1 (27.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D657V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRCA1 MUTATED         0        1        2        1         3         1
  BRCA1 WILD-TYPE       2       14       38       29        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BRCA1 MUTATED           0          0          1          3        2
  BRCA1 WILD-TYPE         3         70         52         29       36
D657V3, multiclass
            clus
vv           BRCA1 MUTATED BRCA1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BRCA1 MUTATED     1   4   3   6
  BRCA1 WILD-TYPE  21  88 170  91
D657V4, multiclass
    clus
vv   BRCA1 MUTATED BRCA1 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             3             170
  T4             6              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
  BRCA1 MUTATED     6   4   2   3
  BRCA1 WILD-TYPE 112 100  75  74
D657V5, multiclass
    clus
vv   BRCA1 MUTATED BRCA1 WILD-TYPE
  N0             6             112
  N1             4             100
  N2             2              75
  N3             3              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"
D657V6, binary
                 cls
clus                0   1
  BRCA1 MUTATED    13   2
  BRCA1 WILD-TYPE 333  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED     13    2
  BRCA1 WILD-TYPE  333   27
   clus
vv  BRCA1 MUTATED BRCA1 WILD-TYPE
  0            13             333
  1             2              27
[1] 2 2
[1] FALSE
D657V7, binary
                 cls
clus                0   1
  BRCA1 MUTATED     3  12
  BRCA1 WILD-TYPE 142 236
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED      3   12
  BRCA1 WILD-TYPE  142  236
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  FEMALE             3             142
  MALE              12             236
[1] 2 2
[1] FALSE
D657V8, binary
                 cls
clus                0   1
  BRCA1 MUTATED     9   0
  BRCA1 WILD-TYPE 283  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED      9    0
  BRCA1 WILD-TYPE  283   59
     clus
vv    BRCA1 MUTATED BRCA1 WILD-TYPE
  NO              9             283
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BRCA1 MUTATED                                          0
  BRCA1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BRCA1 MUTATED                                       2
  BRCA1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BRCA1 MUTATED                                                        4
  BRCA1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BRCA1 MUTATED                                                   1
  BRCA1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BRCA1 MUTATED                                                                   5
  BRCA1 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BRCA1 MUTATED                                                    0
  BRCA1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BRCA1 MUTATED                                                  3
  BRCA1 WILD-TYPE                                               58
D657V9, multiclass
                                                                   clus
vv                                                                  BRCA1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  BRCA1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BRCA1 MUTATED    12   0   1   1
  BRCA1 WILD-TYPE 299  14  14  23
D657V10, multiclass
    clus
vv   BRCA1 MUTATED BRCA1 WILD-TYPE
  R0            12             299
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D657V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BRCA1 MUTATED       5                         0
  BRCA1 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRCA1 MUTATED                                           0     5
  BRCA1 WILD-TYPE                                         1   238
D657V12, multiclass
                                           clus
vv                                          BRCA1 MUTATED BRCA1 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D657V13, binary
                 cls
clus                0   1
  BRCA1 MUTATED     0  10
  BRCA1 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED      0   10
  BRCA1 WILD-TYPE    4  300
                        clus
vv                       BRCA1 MUTATED BRCA1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(658) Variable = HAUS6 MUTATION ANALYSIS
D658V1, survival
                 sevent
clus2               0   1
  HAUS6 MUTATED     8   4
  HAUS6 WILD-TYPE 222 135
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             12             357 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              4             135 
$`HAUS6 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8536 
        6.97        34.68        32.78        31.96        16.14        12.43 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A6EY TCGA-HF-7132 TCGA-VQ-A8P2 
        6.02       105.07        28.96        11.44        77.29        38.14 

$`HAUS6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  HAUS6 MUTATED HAUS6 WILD-TYPE 
           6.02            0.00 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
         105.07          122.30 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
          30.46           14.07 
[1] "6.0 - 105.1 (30.5)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D658V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HAUS6 MUTATED         0        1        0        3         2         0
  HAUS6 WILD-TYPE       2       14       40       27        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HAUS6 MUTATED           0          3          2          0        2
  HAUS6 WILD-TYPE         3         67         51         32       36
D658V3, multiclass
            clus
vv           HAUS6 MUTATED HAUS6 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               3              27
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HAUS6 MUTATED     1   2   7   3
  HAUS6 WILD-TYPE  21  90 166  94
D658V4, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             7             166
  T4             3              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
  HAUS6 MUTATED     4   6   1   2
  HAUS6 WILD-TYPE 114  98  76  75
D658V5, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  N0             4             114
  N1             6              98
  N2             1              76
  N3             2              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"
D658V6, binary
                 cls
clus                0   1
  HAUS6 MUTATED    11   1
  HAUS6 WILD-TYPE 335  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED     11    1
  HAUS6 WILD-TYPE  335   28
   clus
vv  HAUS6 MUTATED HAUS6 WILD-TYPE
  0            11             335
  1             1              28
[1] 2 2
[1] FALSE
D658V7, binary
                 cls
clus                0   1
  HAUS6 MUTATED     4   9
  HAUS6 WILD-TYPE 141 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      4    9
  HAUS6 WILD-TYPE  141  239
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  FEMALE             4             141
  MALE               9             239
[1] 2 2
[1] FALSE
D658V8, binary
                 cls
clus                0   1
  HAUS6 MUTATED     9   3
  HAUS6 WILD-TYPE 283  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      9    3
  HAUS6 WILD-TYPE  283   56
     clus
vv    HAUS6 MUTATED HAUS6 WILD-TYPE
  NO              9             283
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HAUS6 MUTATED                                          0
  HAUS6 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HAUS6 MUTATED                                       0
  HAUS6 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HAUS6 MUTATED                                                        7
  HAUS6 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HAUS6 MUTATED                                                   2
  HAUS6 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HAUS6 MUTATED                                                                   2
  HAUS6 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HAUS6 MUTATED                                                    0
  HAUS6 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HAUS6 MUTATED                                                  2
  HAUS6 WILD-TYPE                                               59
D658V9, multiclass
                                                                   clus
vv                                                                  HAUS6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  HAUS6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HAUS6 MUTATED    11   1   0   1
  HAUS6 WILD-TYPE 300  13  15  23
D658V10, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  R0            11             300
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D658V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HAUS6 MUTATED       2                         0
  HAUS6 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HAUS6 MUTATED                                           0     6
  HAUS6 WILD-TYPE                                         1   237
D658V12, multiclass
                                           clus
vv                                          HAUS6 MUTATED HAUS6 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D658V13, binary
                 cls
clus                0   1
  HAUS6 MUTATED     0   7
  HAUS6 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      0    7
  HAUS6 WILD-TYPE    4  303
                        clus
vv                       HAUS6 MUTATED HAUS6 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(659) Variable = ARHGEF11 MUTATION ANALYSIS
D659V1, survival
                    sevent
clus2                  0   1
  ARHGEF11 MUTATED    13   7
  ARHGEF11 WILD-TYPE 217 132
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
                20                349 
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
                 7                132 
$`ARHGEF11 MUTATED`
TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8372 TCGA-BR-8487 
       30.90         9.67        34.68        35.84        31.27         1.12 
TCGA-CG-4465 TCGA-CG-5721 TCGA-D7-6519 TCGA-D7-6527 TCGA-FP-A9TM TCGA-HF-7132 
        9.01         6.02        20.55        10.26         6.21        77.29 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-MX-A5UJ 
       22.32        22.68         0.10         6.58        14.07        19.73 
TCGA-VQ-A8PM TCGA-VQ-AA6I 
        1.87        16.14 

$`ARHGEF11 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-D7-6520 
        7.99        25.71        12.66        20.91        19.13        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-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-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-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-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-A8P2 
        5.46        13.25        13.02        43.36        37.41        38.14 
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-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 

  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
               0.1                0.0 
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
             77.29             122.30 
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
            15.105             14.270 
[1] "0.1 - 77.3 (15.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D659V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARHGEF11 MUTATED         0        0        2        2         2         3
  ARHGEF11 WILD-TYPE       2       15       38       28        35        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF11 MUTATED           0          2          1          2        3
  ARHGEF11 WILD-TYPE         3         68         52         30       35
D659V3, multiclass
            clus
vv           ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  2                 38
  STAGE II                  2                 28
  STAGE IIA                 2                 35
  STAGE IIB                 3                 49
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                1                 52
  STAGE IIIC                2                 30
  STAGE IV                  3                 35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGEF11 MUTATED     2   5   6   7
  ARHGEF11 WILD-TYPE  20  87 167  90
D659V4, multiclass
    clus
vv   ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  T1                2                 20
  T2                5                 87
  T3                6                167
  T4                7                 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
  ARHGEF11 MUTATED     5   8   2   4
  ARHGEF11 WILD-TYPE 113  96  75  73
D659V5, multiclass
    clus
vv   ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  N0                5                113
  N1                8                 96
  N2                2                 75
  N3                4                 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"
D659V6, binary
                    cls
clus                   0   1
  ARHGEF11 MUTATED    20   1
  ARHGEF11 WILD-TYPE 326  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF11 MUTATED     20    1
  ARHGEF11 WILD-TYPE  326   28
   clus
vv  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  0               20                326
  1                1                 28
[1] 2 2
[1] FALSE
D659V7, binary
                    cls
clus                   0   1
  ARHGEF11 MUTATED    11  10
  ARHGEF11 WILD-TYPE 134 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF11 MUTATED     11   10
  ARHGEF11 WILD-TYPE  134  238
        clus
vv       ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  FEMALE               11                134
  MALE                 10                238
[1] 2 2
[1] FALSE
D659V8, binary
                    cls
clus                   0   1
  ARHGEF11 MUTATED    15   4
  ARHGEF11 WILD-TYPE 277  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF11 MUTATED     15    4
  ARHGEF11 WILD-TYPE  277   55
     clus
vv    ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  NO                15                277
  YES                4                 55
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARHGEF11 MUTATED                                          1
  ARHGEF11 WILD-TYPE                                        7
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARHGEF11 MUTATED                                       5
  ARHGEF11 WILD-TYPE                                    65
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARHGEF11 MUTATED                                                        8
  ARHGEF11 WILD-TYPE                                                    150
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARHGEF11 MUTATED                                                   1
  ARHGEF11 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARHGEF11 MUTATED                                                                   2
  ARHGEF11 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARHGEF11 MUTATED                                                    1
  ARHGEF11 WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARHGEF11 MUTATED                                                  3
  ARHGEF11 WILD-TYPE                                               58
D659V9, multiclass
                                                                   clus
vv                                                                  ARHGEF11 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 3
                                                                   clus
vv                                                                  ARHGEF11 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ARHGEF11 MUTATED    16   0   1   3
  ARHGEF11 WILD-TYPE 295  14  14  21
D659V10, multiclass
    clus
vv   ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  R0               16                295
  R1                0                 14
  R2                1                 14
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D659V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ARHGEF11 MUTATED       5                         0
  ARHGEF11 WILD-TYPE    82                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARHGEF11 MUTATED                                           0    13
  ARHGEF11 WILD-TYPE                                         1   230
D659V12, multiclass
                                           clus
vv                                          ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  ASIAN                                                    5                 82
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   13                230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D659V13, binary
                    cls
clus                   0   1
  ARHGEF11 MUTATED     0  16
  ARHGEF11 WILD-TYPE   4 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF11 MUTATED      0   16
  ARHGEF11 WILD-TYPE    4  294
                        clus
vv                       ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               16                294
[1] 2 2
[1] FALSE

Clustering(660) Variable = MGST2 MUTATION ANALYSIS
D660V1, survival
                 sevent
clus2               0   1
  MGST2 MUTATED     3   0
  MGST2 WILD-TYPE 227 139
  MGST2 MUTATED MGST2 WILD-TYPE 
              3             366 
  MGST2 MUTATED MGST2 WILD-TYPE 
              0             139 
$`MGST2 MUTATED`
TCGA-BR-6852 TCGA-BR-8078 TCGA-CD-A4MJ 
       44.94        29.59        12.62 

$`MGST2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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           14.22 
[1] "12.6 - 44.9 (29.6)" "0.0 - 122.3 (14.2)"
[1] "hr="     "9100000"
D660V2, 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       2       15       39       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MGST2 MUTATED           0          0          0          0        0
  MGST2 WILD-TYPE         3         70         53         32       38
D660V3, multiclass
            clus
vv           MGST2 MUTATED MGST2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MGST2 MUTATED     0   1   1   1
  MGST2 WILD-TYPE  22  91 172  96
D660V4, multiclass
    clus
vv   MGST2 MUTATED MGST2 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             1             172
  T4             1              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
  MGST2 MUTATED     3   0   0   0
  MGST2 WILD-TYPE 115 104  77  77
D660V5, multiclass
    clus
vv   MGST2 MUTATED MGST2 WILD-TYPE
  N0             3             115
  N1             0             104
  N2             0              77
  N3             0              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"
D660V6, binary
                 cls
clus                0   1
  MGST2 MUTATED     3   0
  MGST2 WILD-TYPE 343  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGST2 MUTATED      3    0
  MGST2 WILD-TYPE  343   29
   clus
vv  MGST2 MUTATED MGST2 WILD-TYPE
  0             3             343
  1             0              29
[1] 2 2
[1] FALSE
D660V7, binary
                 cls
clus                0   1
  MGST2 MUTATED     2   1
  MGST2 WILD-TYPE 143 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGST2 MUTATED      2    1
  MGST2 WILD-TYPE  143  247
        clus
vv       MGST2 MUTATED MGST2 WILD-TYPE
  FEMALE             2             143
  MALE               1             247
[1] 2 2
[1] FALSE
D660V8, binary
                 cls
clus                0   1
  MGST2 MUTATED     3   0
  MGST2 WILD-TYPE 289  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGST2 MUTATED      3    0
  MGST2 WILD-TYPE  289   59
     clus
vv    MGST2 MUTATED MGST2 WILD-TYPE
  NO              3             289
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MGST2 MUTATED                                          0
  MGST2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MGST2 MUTATED                                       0
  MGST2 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MGST2 MUTATED                                                        3
  MGST2 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MGST2 MUTATED                                                   0
  MGST2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MGST2 MUTATED                                                                   0
  MGST2 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MGST2 MUTATED                                                    0
  MGST2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MGST2 MUTATED                                                  0
  MGST2 WILD-TYPE                                               61
D660V9, multiclass
                                                                   clus
vv                                                                  MGST2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  MGST2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MGST2 MUTATED     2   0   0   0
  MGST2 WILD-TYPE 309  14  15  24
D660V10, multiclass
[1] "Remove cluster labels:" "MGST2 MUTATED"         
clus
  MGST2 MUTATED MGST2 WILD-TYPE 
              2             362 
     TCGA-CG-4444      TCGA-CG-4460      TCGA-CG-4475      TCGA-CG-4476 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5716      TCGA-CG-5727      TCGA-EQ-A4SO      TCGA-F1-6177 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-FP-A8CX      TCGA-HF-7131      TCGA-KB-A93G      TCGA-MX-A663 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4183      TCGA-BR-4184 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191      TCGA-BR-4201 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4362 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368      TCGA-BR-4369 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6709      TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6803      TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-7704      TCGA-BR-7707      TCGA-BR-7715      TCGA-BR-7716 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-7717      TCGA-BR-7722      TCGA-BR-7723      TCGA-BR-7851 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-7901      TCGA-BR-7957      TCGA-BR-7958      TCGA-BR-7959 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8058      TCGA-BR-8059      TCGA-BR-8060      TCGA-BR-8077 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8080      TCGA-BR-8081      TCGA-BR-8284      TCGA-BR-8285 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291      TCGA-BR-8295 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8297      TCGA-BR-8360      TCGA-BR-8361      TCGA-BR-8363 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366      TCGA-BR-8367 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370      TCGA-BR-8371 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8372      TCGA-BR-8373      TCGA-BR-8380      TCGA-BR-8381 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483      TCGA-BR-8484 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487      TCGA-BR-8588 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591      TCGA-BR-8592 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678      TCGA-BR-8679 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683      TCGA-BR-8686 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T      TCGA-BR-A44U 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ      TCGA-BR-A4CR 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV      TCGA-BR-A4IY 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2      TCGA-BR-A4J4 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4J5      TCGA-BR-A4J6      TCGA-BR-A4J7      TCGA-BR-A4J8 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5800      TCGA-CD-5801 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CD-5804      TCGA-CD-8524      TCGA-CD-8525      TCGA-CD-8526 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CD-8527      TCGA-CD-8528      TCGA-CD-8529      TCGA-CD-8530 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CD-8531      TCGA-CD-8532      TCGA-CD-8533      TCGA-CD-8534 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A487      TCGA-CG-4300 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4306 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4436      TCGA-CG-4437      TCGA-CG-4438      TCGA-CG-4440 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4441      TCGA-CG-4442      TCGA-CG-4443      TCGA-CG-4449 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4455      TCGA-CG-4462      TCGA-CG-4465      TCGA-CG-4466 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4469      TCGA-CG-4474      TCGA-CG-4477      TCGA-CG-5717 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5718      TCGA-CG-5719      TCGA-CG-5720      TCGA-CG-5721 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5722      TCGA-CG-5723      TCGA-CG-5724      TCGA-CG-5725 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5726      TCGA-CG-5728      TCGA-CG-5730      TCGA-CG-5732 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5733      TCGA-CG-5734      TCGA-D7-5577      TCGA-D7-5578 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-5579      TCGA-D7-6518      TCGA-D7-6519      TCGA-D7-6520 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6521      TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6525 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-8570      TCGA-D7-8572      TCGA-D7-8573      TCGA-D7-8574 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-8575      TCGA-D7-8576      TCGA-D7-8578      TCGA-D7-8579 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-A4YT      TCGA-D7-A4YU      TCGA-D7-A4YV      TCGA-D7-A4YX 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-A4YY      TCGA-D7-A4Z0      TCGA-D7-A6ET      TCGA-D7-A6EV 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-A6EX      TCGA-D7-A6EY      TCGA-D7-A6EZ      TCGA-D7-A6F0 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-A6F2      TCGA-D7-A747      TCGA-D7-A748      TCGA-D7-A74A 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-A74B      TCGA-EQ-5647      TCGA-F1-6874      TCGA-F1-6875 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-F1-A448      TCGA-F1-A72C      TCGA-FP-7735      TCGA-FP-7829 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209      TCGA-FP-8211 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-FP-8631      TCGA-FP-A4BE      TCGA-FP-A4BF      TCGA-FP-A9TM 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HF-7132      TCGA-HF-7133      TCGA-HF-7134      TCGA-HF-7136 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HF-A5NB      TCGA-HJ-7597      TCGA-HU-8238      TCGA-HU-8243 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-8244      TCGA-HU-8249      TCGA-HU-8602      TCGA-HU-8604 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-8608      TCGA-HU-8610      TCGA-HU-A4G2      TCGA-HU-A4G3 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4G6      TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4GF      TCGA-HU-A4GH      TCGA-HU-A4GJ      TCGA-HU-A4GN 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4GP      TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4GX      TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4H3      TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4H8      TCGA-HU-A4HB      TCGA-HU-A4HD      TCGA-IN-7806 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-IN-8462      TCGA-IN-8663      TCGA-IN-A6RI      TCGA-IN-A6RJ 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-IN-A6RL      TCGA-IN-A6RN      TCGA-IN-A6RO      TCGA-IN-A6RP 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-IN-A6RR      TCGA-IN-A6RS      TCGA-IN-A7NR      TCGA-IN-A7NT 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-IN-A7NU      TCGA-IN-AB1V      TCGA-IN-AB1X      TCGA-IP-7968 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-KB-A6F5      TCGA-KB-A6F7      TCGA-KB-A93J      TCGA-MX-A5UG 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-MX-A5UJ      TCGA-R5-A7ZI      TCGA-RD-A7BS      TCGA-RD-A7BT 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-RD-A7BW      TCGA-RD-A7C1      TCGA-RD-A8MV      TCGA-RD-A8MW 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-RD-A8N0      TCGA-RD-A8N1      TCGA-RD-A8N2      TCGA-RD-A8N4 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-RD-A8N5      TCGA-RD-A8N6      TCGA-RD-A8N9      TCGA-SW-A7EA 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-SW-A7EB      TCGA-VQ-A8DL      TCGA-VQ-A8DT      TCGA-VQ-A8DU 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-VQ-A8DV      TCGA-VQ-A8DZ      TCGA-VQ-A8E2      TCGA-VQ-A8E7 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-VQ-A8P2      TCGA-VQ-A8P3      TCGA-VQ-A8PE      TCGA-VQ-A8PK 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-VQ-A8PM      TCGA-VQ-A8PQ      TCGA-VQ-A91Q      TCGA-VQ-A91U 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-VQ-A91V      TCGA-VQ-A92D      TCGA-VQ-A94T      TCGA-VQ-AA64 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-VQ-AA68      TCGA-VQ-AA69      TCGA-VQ-AA6A      TCGA-VQ-AA6B 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-VQ-AA6F      TCGA-VQ-AA6G      TCGA-VQ-AA6I      TCGA-VQ-AA6J 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-VQ-AA6K      TCGA-ZA-A8F6 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
D660V11, continuous
[1] "Remove cluster labels:" "MGST2 MUTATED"         
clus
  MGST2 MUTATED MGST2 WILD-TYPE 
              2             341 
     TCGA-CG-4444      TCGA-CG-4460      TCGA-CG-4475      TCGA-CG-4476 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5727      TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-FP-A8CX 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HF-7131      TCGA-KB-A93G      TCGA-MX-A663      TCGA-B7-5816 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-B7-A5TI      TCGA-BR-4183      TCGA-BR-4184      TCGA-BR-4188 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4191      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4361 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-4362      TCGA-BR-4368      TCGA-BR-6452      TCGA-BR-6453 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6709      TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-6803      TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-7704      TCGA-BR-7707      TCGA-BR-7715      TCGA-BR-7716 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-7717      TCGA-BR-7722      TCGA-BR-7723      TCGA-BR-7851 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-7901      TCGA-BR-7957      TCGA-BR-7958      TCGA-BR-7959 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8058      TCGA-BR-8059      TCGA-BR-8060      TCGA-BR-8077 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8080      TCGA-BR-8081      TCGA-BR-8284      TCGA-BR-8285 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291      TCGA-BR-8295 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8297      TCGA-BR-8360      TCGA-BR-8361      TCGA-BR-8363 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366      TCGA-BR-8367 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370      TCGA-BR-8371 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8372      TCGA-BR-8373      TCGA-BR-8380      TCGA-BR-8381 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483      TCGA-BR-8484 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487      TCGA-BR-8588 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591      TCGA-BR-8592 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678      TCGA-BR-8679 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683      TCGA-BR-8686 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T      TCGA-BR-A44U 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ      TCGA-BR-A4CR 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV      TCGA-BR-A4IY 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2      TCGA-BR-A4J4 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4J5      TCGA-BR-A4J6      TCGA-BR-A4J8      TCGA-BR-A4PD 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QL 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-BR-A4QM      TCGA-CD-5804      TCGA-CD-8525      TCGA-CD-8526 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CD-8531      TCGA-CD-8535      TCGA-CD-A487      TCGA-CG-4301 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4436      TCGA-CG-4437 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4438      TCGA-CG-4440      TCGA-CG-4441      TCGA-CG-4442 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4443      TCGA-CG-4449      TCGA-CG-4455      TCGA-CG-4462 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4465      TCGA-CG-4466      TCGA-CG-4469      TCGA-CG-4474 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-4477      TCGA-CG-5717      TCGA-CG-5718      TCGA-CG-5719 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5720      TCGA-CG-5721      TCGA-CG-5722      TCGA-CG-5723 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5724      TCGA-CG-5725      TCGA-CG-5726      TCGA-CG-5728 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-CG-5730      TCGA-CG-5732      TCGA-CG-5733      TCGA-CG-5734 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-A6ET      TCGA-D7-A6EV      TCGA-D7-A6EX      TCGA-D7-A6EY 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-A6EZ      TCGA-D7-A6F0      TCGA-D7-A6F2      TCGA-D7-A747 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-D7-A748      TCGA-D7-A74A      TCGA-D7-A74B      TCGA-EQ-5647 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-EQ-8122      TCGA-F1-6874      TCGA-F1-6875      TCGA-F1-A448 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-F1-A72C      TCGA-FP-7735      TCGA-FP-7829      TCGA-FP-7916 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209      TCGA-FP-8210 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BE      TCGA-FP-A4BF 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-FP-A9TM      TCGA-HF-7132      TCGA-HF-7133      TCGA-HF-7134 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HF-7136      TCGA-HF-A5NB      TCGA-HJ-7597      TCGA-HU-8238 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-8243      TCGA-HU-8244      TCGA-HU-8249      TCGA-HU-8602 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610      TCGA-HU-A4G2 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8      TCGA-HU-A4G9 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF      TCGA-HU-A4GH 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4GJ      TCGA-HU-A4GN      TCGA-HU-A4GP      TCGA-HU-A4GQ 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX      TCGA-HU-A4GY 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3      TCGA-HU-A4H4 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8      TCGA-HU-A4HB 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-IN-8663      TCGA-IN-A6RI      TCGA-IN-A6RJ      TCGA-IN-A6RL 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-IN-A6RN      TCGA-IN-A6RO      TCGA-IN-A6RP      TCGA-IN-A6RR 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-IN-A6RS      TCGA-IN-A7NR      TCGA-IN-A7NT      TCGA-IN-A7NU 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-IN-AB1V      TCGA-IN-AB1X      TCGA-IP-7968      TCGA-KB-A6F5 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-KB-A6F7      TCGA-KB-A93J      TCGA-MX-A5UG      TCGA-MX-A5UJ 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-R5-A7ZI      TCGA-RD-A7BS      TCGA-RD-A7BT      TCGA-RD-A7BW 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-RD-A7C1      TCGA-RD-A8MV      TCGA-RD-A8MW      TCGA-RD-A8N0 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-RD-A8N1      TCGA-RD-A8N2      TCGA-RD-A8N4      TCGA-RD-A8N5 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-RD-A8N6      TCGA-RD-A8N9      TCGA-SW-A7EA      TCGA-SW-A7EB 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-VQ-A8DL      TCGA-VQ-A8DT      TCGA-VQ-A8DU      TCGA-VQ-A8DV 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-VQ-A8DZ      TCGA-VQ-A8E2      TCGA-VQ-A8E7      TCGA-VQ-A8P2 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-VQ-A8P3      TCGA-VQ-A8PE      TCGA-VQ-A8PK      TCGA-VQ-A8PM 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-VQ-A8PQ      TCGA-VQ-A91Q      TCGA-VQ-A91U      TCGA-VQ-A91V 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-VQ-A92D      TCGA-VQ-A94T      TCGA-VQ-AA64      TCGA-VQ-AA68 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-VQ-AA69      TCGA-VQ-AA6A      TCGA-VQ-AA6B      TCGA-VQ-AA6F 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-VQ-AA6G      TCGA-VQ-AA6I      TCGA-VQ-AA6J      TCGA-VQ-AA6K 
"MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" "MGST2 WILD-TYPE" 
     TCGA-ZA-A8F6 
"MGST2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MGST2 MUTATED       1                         0
  MGST2 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MGST2 MUTATED                                           0     2
  MGST2 WILD-TYPE                                         1   241
D660V12, multiclass
                                           clus
vv                                          MGST2 MUTATED MGST2 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D660V13, binary
                 cls
clus                0   1
  MGST2 MUTATED     0   3
  MGST2 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGST2 MUTATED      0    3
  MGST2 WILD-TYPE    4  307
                        clus
vv                       MGST2 MUTATED MGST2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(661) Variable = CD4 MUTATION ANALYSIS
D661V1, survival
               sevent
clus2             0   1
  CD4 MUTATED     9   2
  CD4 WILD-TYPE 221 137
  CD4 MUTATED CD4 WILD-TYPE 
           11           358 
  CD4 MUTATED CD4 WILD-TYPE 
            2           137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  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         14.12 
[1] "4.3 - 32.0 (21.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.4"
D661V2, 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       2       15       39       29        36        50
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CD4 MUTATED           0          2          1          2        1
  CD4 WILD-TYPE         3         68         52         30       37
D661V3, multiclass
            clus
vv           CD4 MUTATED CD4 WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             1            39
  STAGE II             1            29
  STAGE IIA            1            36
  STAGE IIB            2            50
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           1            52
  STAGE IIIC           2            30
  STAGE IV             1            37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CD4 MUTATED     0   2   6   3
  CD4 WILD-TYPE  22  90 167  94
D661V4, multiclass
    clus
vv   CD4 MUTATED CD4 WILD-TYPE
  T1           0            22
  T2           2            90
  T3           6           167
  T4           3            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
  CD4 MUTATED     2   4   2   3
  CD4 WILD-TYPE 116 100  75  74
D661V5, multiclass
    clus
vv   CD4 MUTATED CD4 WILD-TYPE
  N0           2           116
  N1           4           100
  N2           2            75
  N3           3            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"
D661V6, binary
               cls
clus              0   1
  CD4 MUTATED    10   1
  CD4 WILD-TYPE 336  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD4 MUTATED     10    1
  CD4 WILD-TYPE  336   28
   clus
vv  CD4 MUTATED CD4 WILD-TYPE
  0          10           336
  1           1            28
[1] 2 2
[1] FALSE
D661V7, binary
               cls
clus              0   1
  CD4 MUTATED     5   6
  CD4 WILD-TYPE 140 242
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD4 MUTATED      5    6
  CD4 WILD-TYPE  140  242
        clus
vv       CD4 MUTATED CD4 WILD-TYPE
  FEMALE           5           140
  MALE             6           242
[1] 2 2
[1] FALSE
D661V8, binary
               cls
clus              0   1
  CD4 MUTATED     9   1
  CD4 WILD-TYPE 283  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD4 MUTATED      9    1
  CD4 WILD-TYPE  283   58
     clus
vv    CD4 MUTATED CD4 WILD-TYPE
  NO            9           283
  YES           1            58
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CD4 MUTATED                                          0
  CD4 WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CD4 MUTATED                                       2
  CD4 WILD-TYPE                                    68
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD4 MUTATED                                                        4
  CD4 WILD-TYPE                                                    154
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CD4 MUTATED                                                   2
  CD4 WILD-TYPE                                                19
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD4 MUTATED                                                                   0
  CD4 WILD-TYPE                                                                68
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CD4 MUTATED                                                    0
  CD4 WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CD4 MUTATED                                                  3
  CD4 WILD-TYPE                                               58
D661V9, multiclass
                                                                   clus
vv                                                                  CD4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            3
                                                                   clus
vv                                                                  CD4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  CD4 MUTATED     9   0   0   0
  CD4 WILD-TYPE 302  14  15  24
D661V10, multiclass
    clus
vv   CD4 MUTATED CD4 WILD-TYPE
  R0           9           302
  R1           0            14
  R2           0            15
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D661V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CD4 MUTATED       5                         0
  CD4 WILD-TYPE    82                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD4 MUTATED                                           0     5
  CD4 WILD-TYPE                                         1   238
D661V12, multiclass
                                           clus
vv                                          CD4 MUTATED CD4 WILD-TYPE
  ASIAN                                               5            82
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               5           238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D661V13, binary
               cls
clus              0   1
  CD4 MUTATED     1   9
  CD4 WILD-TYPE   3 301
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD4 MUTATED      1    9
  CD4 WILD-TYPE    3  301
                        clus
vv                       CD4 MUTATED CD4 WILD-TYPE
  HISPANIC OR LATINO               1             3
  NOT HISPANIC OR LATINO           9           301
[1] 2 2
[1] FALSE

Clustering(662) Variable = RP1L1 MUTATION ANALYSIS
D662V1, survival
                 sevent
clus2               0   1
  RP1L1 MUTATED    18  12
  RP1L1 WILD-TYPE 212 127
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             30             339 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             12             127 
$`RP1L1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7707 
       26.70         6.97        30.90         9.67        34.68        35.84 
TCGA-BR-8384 TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4PE TCGA-CD-8529 
        3.72        31.96        13.87         7.53        20.42        12.30 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5734 
       12.43         6.58        11.77         6.02        65.10         7.99 
TCGA-D7-6818 TCGA-F1-A448 TCGA-FP-7829 TCGA-HU-8602 TCGA-HU-A4G9 TCGA-IN-A6RL 
       12.36        21.27        19.53        22.32        24.20        13.35 
TCGA-IN-A6RN TCGA-MX-A5UJ TCGA-VQ-A8DT TCGA-VQ-A8P2 TCGA-VQ-AA64 TCGA-VQ-AA6I 
       19.53        19.73        48.79        38.14        18.41        16.14 

$`RP1L1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 
       11.80        31.27        14.79         7.36        25.05         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-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-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-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-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-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-D7-6820 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-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-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-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-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       18.38        12.46         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-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-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        17.26 

  RP1L1 MUTATED RP1L1 WILD-TYPE 
           3.72            0.00 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
           65.1           122.3 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
          18.97           14.07 
[1] "3.7 - 65.1 (19.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D662V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RP1L1 MUTATED         0        1        3        1         3         3
  RP1L1 WILD-TYPE       2       14       37       29        34        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RP1L1 MUTATED           0          8          5          1        3
  RP1L1 WILD-TYPE         3         62         48         31       35
D662V3, multiclass
            clus
vv           RP1L1 MUTATED RP1L1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             8              62
  STAGE IIIB             5              48
  STAGE IIIC             1              31
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RP1L1 MUTATED     2   6  13   8
  RP1L1 WILD-TYPE  20  86 160  89
D662V4, multiclass
    clus
vv   RP1L1 MUTATED RP1L1 WILD-TYPE
  T1             2              20
  T2             6              86
  T3            13             160
  T4             8              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
  RP1L1 MUTATED    10   8   5   5
  RP1L1 WILD-TYPE 108  96  72  72
D662V5, multiclass
    clus
vv   RP1L1 MUTATED RP1L1 WILD-TYPE
  N0            10             108
  N1             8              96
  N2             5              72
  N3             5              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"
D662V6, binary
                 cls
clus                0   1
  RP1L1 MUTATED    28   2
  RP1L1 WILD-TYPE 318  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED     28    2
  RP1L1 WILD-TYPE  318   27
   clus
vv  RP1L1 MUTATED RP1L1 WILD-TYPE
  0            28             318
  1             2              27
[1] 2 2
[1] FALSE
D662V7, binary
                 cls
clus                0   1
  RP1L1 MUTATED    12  19
  RP1L1 WILD-TYPE 133 229
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED     12   19
  RP1L1 WILD-TYPE  133  229
        clus
vv       RP1L1 MUTATED RP1L1 WILD-TYPE
  FEMALE            12             133
  MALE              19             229
[1] 2 2
[1] FALSE
D662V8, binary
                 cls
clus                0   1
  RP1L1 MUTATED    21   7
  RP1L1 WILD-TYPE 271  52
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED     21    7
  RP1L1 WILD-TYPE  271   52
     clus
vv    RP1L1 MUTATED RP1L1 WILD-TYPE
  NO             21             271
  YES             7              52
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RP1L1 MUTATED                                          0
  RP1L1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RP1L1 MUTATED                                       4
  RP1L1 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RP1L1 MUTATED                                                       13
  RP1L1 WILD-TYPE                                                    145
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RP1L1 MUTATED                                                   4
  RP1L1 WILD-TYPE                                                17
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RP1L1 MUTATED                                                                   6
  RP1L1 WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RP1L1 MUTATED                                                    0
  RP1L1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RP1L1 MUTATED                                                  4
  RP1L1 WILD-TYPE                                               57
D662V9, multiclass
                                                                   clus
vv                                                                  RP1L1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  RP1L1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RP1L1 MUTATED    25   0   0   4
  RP1L1 WILD-TYPE 286  14  15  20
D662V10, multiclass
    clus
vv   RP1L1 MUTATED RP1L1 WILD-TYPE
  R0            25             286
  R1             0              14
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D662V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RP1L1 MUTATED       8                         0
  RP1L1 WILD-TYPE    79                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RP1L1 MUTATED                                           0    19
  RP1L1 WILD-TYPE                                         1   224
D662V12, multiclass
                                           clus
vv                                          RP1L1 MUTATED RP1L1 WILD-TYPE
  ASIAN                                                 8              79
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                19             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D662V13, binary
                 cls
clus                0   1
  RP1L1 MUTATED     1  23
  RP1L1 WILD-TYPE   3 287
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED      1   23
  RP1L1 WILD-TYPE    3  287
                        clus
vv                       RP1L1 MUTATED RP1L1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            23             287
[1] 2 2
[1] FALSE

Clustering(663) Variable = UVRAG MUTATION ANALYSIS
D663V1, survival
                 sevent
clus2               0   1
  UVRAG MUTATED     5   3
  UVRAG WILD-TYPE 225 136
  UVRAG MUTATED UVRAG WILD-TYPE 
              8             361 
  UVRAG MUTATED UVRAG WILD-TYPE 
              3             136 
$`UVRAG MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8591 TCGA-BR-A4QL 
       26.70         6.97         9.67        34.68        28.14        16.14 
TCGA-CG-5721 TCGA-CG-5723 
        6.02       105.07 

$`UVRAG WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  UVRAG MUTATED UVRAG WILD-TYPE 
           6.02            0.00 
  UVRAG MUTATED UVRAG WILD-TYPE 
         105.07          122.30 
  UVRAG MUTATED UVRAG WILD-TYPE 
          21.42           14.17 
[1] "6.0 - 105.1 (21.4)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D663V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UVRAG MUTATED         0        0        0        1         1         2
  UVRAG WILD-TYPE       2       15       40       29        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UVRAG MUTATED           0          1          1          1        1
  UVRAG WILD-TYPE         3         69         52         31       37
D663V3, multiclass
            clus
vv           UVRAG MUTATED UVRAG WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UVRAG MUTATED     0   1   4   4
  UVRAG WILD-TYPE  22  91 169  93
D663V4, multiclass
    clus
vv   UVRAG MUTATED UVRAG WILD-TYPE
  T1             0              22
  T2             1              91
  T3             4             169
  T4             4              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
  UVRAG MUTATED     3   4   0   2
  UVRAG WILD-TYPE 115 100  77  75
D663V5, multiclass
    clus
vv   UVRAG MUTATED UVRAG WILD-TYPE
  N0             3             115
  N1             4             100
  N2             0              77
  N3             2              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"
D663V6, binary
                 cls
clus                0   1
  UVRAG MUTATED    10   0
  UVRAG WILD-TYPE 336  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED     10    0
  UVRAG WILD-TYPE  336   29
   clus
vv  UVRAG MUTATED UVRAG WILD-TYPE
  0            10             336
  1             0              29
[1] 2 2
[1] FALSE
D663V7, binary
                 cls
clus                0   1
  UVRAG MUTATED     7   5
  UVRAG WILD-TYPE 138 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED      7    5
  UVRAG WILD-TYPE  138  243
        clus
vv       UVRAG MUTATED UVRAG WILD-TYPE
  FEMALE             7             138
  MALE               5             243
[1] 2 2
[1] FALSE
D663V8, binary
                 cls
clus                0   1
  UVRAG MUTATED     9   0
  UVRAG WILD-TYPE 283  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED      9    0
  UVRAG WILD-TYPE  283   59
     clus
vv    UVRAG MUTATED UVRAG WILD-TYPE
  NO              9             283
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  UVRAG MUTATED                                          0
  UVRAG WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  UVRAG MUTATED                                       1
  UVRAG WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UVRAG MUTATED                                                        9
  UVRAG WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  UVRAG MUTATED                                                   0
  UVRAG WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UVRAG MUTATED                                                                   2
  UVRAG WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  UVRAG MUTATED                                                    0
  UVRAG WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  UVRAG MUTATED                                                  0
  UVRAG WILD-TYPE                                               61
D663V9, multiclass
                                                                   clus
vv                                                                  UVRAG MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  UVRAG WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  UVRAG MUTATED     7   0   0   5
  UVRAG WILD-TYPE 304  14  15  19
D663V10, multiclass
    clus
vv   UVRAG MUTATED UVRAG WILD-TYPE
  R0             7             304
  R1             0              14
  R2             0              15
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D663V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  UVRAG MUTATED       0                         0
  UVRAG WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UVRAG MUTATED                                           0    10
  UVRAG WILD-TYPE                                         1   233
D663V12, multiclass
                                           clus
vv                                          UVRAG MUTATED UVRAG WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D663V13, binary
                 cls
clus                0   1
  UVRAG MUTATED     0  10
  UVRAG WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED      0   10
  UVRAG WILD-TYPE    4  300
                        clus
vv                       UVRAG MUTATED UVRAG WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(664) Variable = CHD1 MUTATION ANALYSIS
D664V1, survival
                sevent
clus2              0   1
  CHD1 MUTATED    11   2
  CHD1 WILD-TYPE 219 137
  CHD1 MUTATED CHD1 WILD-TYPE 
            13            356 
  CHD1 MUTATED CHD1 WILD-TYPE 
             2            137 
$`CHD1 MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8680 
       19.56         6.97         9.67        34.68        32.78        31.96 
TCGA-CG-4305 TCGA-CG-5721 TCGA-D7-5579 TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-VQ-A8P2 
       15.95         6.02        20.91        19.73        74.53        38.14 
TCGA-VQ-A91V 
       42.64 

$`CHD1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-D7-6518 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-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-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-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 

  CHD1 MUTATED CHD1 WILD-TYPE 
          6.02           0.00 
  CHD1 MUTATED CHD1 WILD-TYPE 
         74.53         122.30 
  CHD1 MUTATED CHD1 WILD-TYPE 
        20.910         14.055 
[1] "6.0 - 74.5 (20.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.5"
D664V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CHD1 MUTATED         0        0        0        1         2         0
  CHD1 WILD-TYPE       2       15       40       29        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHD1 MUTATED           0          5          0          1        3
  CHD1 WILD-TYPE         3         65         53         31       35
D664V3, multiclass
            clus
vv           CHD1 MUTATED CHD1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            5             65
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHD1 MUTATED     0   1   6   5
  CHD1 WILD-TYPE  22  91 167  92
D664V4, multiclass
    clus
vv   CHD1 MUTATED CHD1 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            6            167
  T4            5             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
  CHD1 MUTATED     2   5   4   1
  CHD1 WILD-TYPE 116  99  73  76
D664V5, multiclass
    clus
vv   CHD1 MUTATED CHD1 WILD-TYPE
  N0            2            116
  N1            5             99
  N2            4             73
  N3            1             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"
D664V6, binary
                cls
clus               0   1
  CHD1 MUTATED    10   2
  CHD1 WILD-TYPE 336  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED     10    2
  CHD1 WILD-TYPE  336   27
   clus
vv  CHD1 MUTATED CHD1 WILD-TYPE
  0           10            336
  1            2             27
[1] 2 2
[1] FALSE
D664V7, binary
                cls
clus               0   1
  CHD1 MUTATED     5   8
  CHD1 WILD-TYPE 140 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED      5    8
  CHD1 WILD-TYPE  140  240
        clus
vv       CHD1 MUTATED CHD1 WILD-TYPE
  FEMALE            5            140
  MALE              8            240
[1] 2 2
[1] FALSE
D664V8, binary
                cls
clus               0   1
  CHD1 MUTATED    11   2
  CHD1 WILD-TYPE 281  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED     11    2
  CHD1 WILD-TYPE  281   57
     clus
vv    CHD1 MUTATED CHD1 WILD-TYPE
  NO            11            281
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CHD1 MUTATED                                          0
  CHD1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CHD1 MUTATED                                       2
  CHD1 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CHD1 MUTATED                                                        5
  CHD1 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CHD1 MUTATED                                                   2
  CHD1 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CHD1 MUTATED                                                                   1
  CHD1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CHD1 MUTATED                                                    0
  CHD1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CHD1 MUTATED                                                  3
  CHD1 WILD-TYPE                                               58
D664V9, multiclass
                                                                   clus
vv                                                                  CHD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  CHD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CHD1 MUTATED     9   1   0   2
  CHD1 WILD-TYPE 302  13  15  22
D664V10, multiclass
    clus
vv   CHD1 MUTATED CHD1 WILD-TYPE
  R0            9            302
  R1            1             13
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D664V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CHD1 MUTATED       1                         0
  CHD1 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CHD1 MUTATED                                           0     9
  CHD1 WILD-TYPE                                         1   234
D664V12, multiclass
                                           clus
vv                                          CHD1 MUTATED CHD1 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D664V13, binary
                cls
clus               0   1
  CHD1 MUTATED     1   8
  CHD1 WILD-TYPE   3 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED      1    8
  CHD1 WILD-TYPE    3  302
                        clus
vv                       CHD1 MUTATED CHD1 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(665) Variable = ZMYND8 MUTATION ANALYSIS
D665V1, survival
                  sevent
clus2                0   1
  ZMYND8 MUTATED    14   3
  ZMYND8 WILD-TYPE 216 136
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
              17              352 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
               3              136 
$`ZMYND8 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 
       26.70        34.68         4.31        31.27         1.12        31.96 
TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-A6EV TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4G8 
       21.07        25.71        11.24        77.29        30.51        22.68 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H8 TCGA-IN-A7NR TCGA-VQ-A8P2 
       29.98         0.10        14.07         6.51        38.14 

$`ZMYND8 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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-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-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 

  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
             0.1              0.0 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
           77.29           122.30 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
          25.710           14.055 
[1] "0.1 - 77.3 (25.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.9"
D665V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZMYND8 MUTATED         0        0        2        1         3         3
  ZMYND8 WILD-TYPE       2       15       38       29        34        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZMYND8 MUTATED           0          3          0          3        2
  ZMYND8 WILD-TYPE         3         67         53         29       36
D665V3, multiclass
            clus
vv           ZMYND8 MUTATED ZMYND8 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              3               29
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZMYND8 MUTATED     1   6   4   6
  ZMYND8 WILD-TYPE  21  86 169  91
D665V4, multiclass
    clus
vv   ZMYND8 MUTATED ZMYND8 WILD-TYPE
  T1              1               21
  T2              6               86
  T3              4              169
  T4              6               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
  ZMYND8 MUTATED     4   6   4   4
  ZMYND8 WILD-TYPE 114  98  73  73
D665V5, multiclass
    clus
vv   ZMYND8 MUTATED ZMYND8 WILD-TYPE
  N0              4              114
  N1              6               98
  N2              4               73
  N3              4               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"
D665V6, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED    17   2
  ZMYND8 WILD-TYPE 329  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED     17    2
  ZMYND8 WILD-TYPE  329   27
   clus
vv  ZMYND8 MUTATED ZMYND8 WILD-TYPE
  0             17              329
  1              2               27
[1] 2 2
[1] FALSE
D665V7, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED    12   7
  ZMYND8 WILD-TYPE 133 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED     12    7
  ZMYND8 WILD-TYPE  133  241
        clus
vv       ZMYND8 MUTATED ZMYND8 WILD-TYPE
  FEMALE             12              133
  MALE                7              241
[1] 2 2
[1] FALSE
D665V8, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED    14   3
  ZMYND8 WILD-TYPE 278  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED     14    3
  ZMYND8 WILD-TYPE  278   56
     clus
vv    ZMYND8 MUTATED ZMYND8 WILD-TYPE
  NO              14              278
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZMYND8 MUTATED                                          0
  ZMYND8 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZMYND8 MUTATED                                       2
  ZMYND8 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZMYND8 MUTATED                                                        8
  ZMYND8 WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZMYND8 MUTATED                                                   3
  ZMYND8 WILD-TYPE                                                18
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZMYND8 MUTATED                                                                   1
  ZMYND8 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZMYND8 MUTATED                                                    0
  ZMYND8 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZMYND8 MUTATED                                                  5
  ZMYND8 WILD-TYPE                                               56
D665V9, multiclass
                                                                   clus
vv                                                                  ZMYND8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               5
                                                                   clus
vv                                                                  ZMYND8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZMYND8 MUTATED    15   1   0   2
  ZMYND8 WILD-TYPE 296  13  15  22
D665V10, multiclass
    clus
vv   ZMYND8 MUTATED ZMYND8 WILD-TYPE
  R0             15              296
  R1              1               13
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D665V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZMYND8 MUTATED       5                         0
  ZMYND8 WILD-TYPE    82                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZMYND8 MUTATED                                           0    11
  ZMYND8 WILD-TYPE                                         1   232
D665V12, multiclass
                                           clus
vv                                          ZMYND8 MUTATED ZMYND8 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D665V13, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED     0  15
  ZMYND8 WILD-TYPE   4 295
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED      0   15
  ZMYND8 WILD-TYPE    4  295
                        clus
vv                       ZMYND8 MUTATED ZMYND8 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             15              295
[1] 2 2
[1] FALSE

Clustering(666) Variable = GPATCH4 MUTATION ANALYSIS
D666V1, survival
                   sevent
clus2                 0   1
  GPATCH4 MUTATED     5   3
  GPATCH4 WILD-TYPE 225 136
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                8               361 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                3               136 
$`GPATCH4 MUTATED`
TCGA-BR-4201 TCGA-CD-8536 TCGA-CD-A4MG TCGA-D7-6526 TCGA-F1-6875 TCGA-HU-A4GN 
       30.90        12.43         6.58        17.19        72.23        29.98 
TCGA-VQ-A8DT TCGA-VQ-A8P2 
       48.79        38.14 

$`GPATCH4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-6527 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-A448 TCGA-F1-A72C TCGA-FP-7735 
        0.62         7.99        14.47        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-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 

  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
             6.58              0.00 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
            72.23            122.30 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
            30.44             14.07 
[1] "6.6 - 72.2 (30.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D666V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPATCH4 MUTATED         0        1        0        1         2         0
  GPATCH4 WILD-TYPE       2       14       40       29        35        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPATCH4 MUTATED           0          2          1          0        0
  GPATCH4 WILD-TYPE         3         68         52         32       38
D666V3, multiclass
            clus
vv           GPATCH4 MUTATED GPATCH4 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 0                40
  STAGE II                 1                29
  STAGE IIA                2                35
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GPATCH4 MUTATED     0   3   5   1
  GPATCH4 WILD-TYPE  22  89 168  96
D666V4, multiclass
    clus
vv   GPATCH4 MUTATED GPATCH4 WILD-TYPE
  T1               0                22
  T2               3                89
  T3               5               168
  T4               1                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
  GPATCH4 MUTATED     3   2   1   1
  GPATCH4 WILD-TYPE 115 102  76  76
D666V5, multiclass
    clus
vv   GPATCH4 MUTATED GPATCH4 WILD-TYPE
  N0               3               115
  N1               2               102
  N2               1                76
  N3               1                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"
D666V6, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED     8   0
  GPATCH4 WILD-TYPE 338  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      8    0
  GPATCH4 WILD-TYPE  338   29
   clus
vv  GPATCH4 MUTATED GPATCH4 WILD-TYPE
  0               8               338
  1               0                29
[1] 2 2
[1] FALSE
D666V7, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED     2   7
  GPATCH4 WILD-TYPE 143 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      2    7
  GPATCH4 WILD-TYPE  143  241
        clus
vv       GPATCH4 MUTATED GPATCH4 WILD-TYPE
  FEMALE               2               143
  MALE                 7               241
[1] 2 2
[1] FALSE
D666V8, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED     6   2
  GPATCH4 WILD-TYPE 286  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      6    2
  GPATCH4 WILD-TYPE  286   57
     clus
vv    GPATCH4 MUTATED GPATCH4 WILD-TYPE
  NO                6               286
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GPATCH4 MUTATED                                          0
  GPATCH4 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GPATCH4 MUTATED                                       1
  GPATCH4 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPATCH4 MUTATED                                                        4
  GPATCH4 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GPATCH4 MUTATED                                                   1
  GPATCH4 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPATCH4 MUTATED                                                                   1
  GPATCH4 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GPATCH4 MUTATED                                                    0
  GPATCH4 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GPATCH4 MUTATED                                                  2
  GPATCH4 WILD-TYPE                                               59
D666V9, multiclass
                                                                   clus
vv                                                                  GPATCH4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  GPATCH4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GPATCH4 MUTATED     6   0   0   2
  GPATCH4 WILD-TYPE 305  14  15  22
D666V10, multiclass
    clus
vv   GPATCH4 MUTATED GPATCH4 WILD-TYPE
  R0               6               305
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D666V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  GPATCH4 MUTATED       3                         1
  GPATCH4 WILD-TYPE    84                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPATCH4 MUTATED                                           0     4
  GPATCH4 WILD-TYPE                                         1   239
D666V12, multiclass
                                           clus
vv                                          GPATCH4 MUTATED GPATCH4 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D666V13, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED     0   7
  GPATCH4 WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      0    7
  GPATCH4 WILD-TYPE    4  303
                        clus
vv                       GPATCH4 MUTATED GPATCH4 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(667) Variable = MASTL MUTATION ANALYSIS
D667V1, survival
                 sevent
clus2               0   1
  MASTL MUTATED     8   4
  MASTL WILD-TYPE 222 135
  MASTL MUTATED MASTL WILD-TYPE 
             12             357 
  MASTL MUTATED MASTL WILD-TYPE 
              4             135 
$`MASTL MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8363 TCGA-BR-8680 TCGA-CD-5801 
       34.68        44.94        14.43         0.26        31.96        13.18 
TCGA-CG-5721 TCGA-CG-5728 TCGA-HU-A4H4 TCGA-IN-8663 TCGA-R5-A7ZI TCGA-VQ-A8P2 
        6.02        65.10        23.84         3.39        74.53        38.14 

$`MASTL WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  MASTL MUTATED MASTL WILD-TYPE 
           0.26            0.00 
  MASTL MUTATED MASTL WILD-TYPE 
          74.53          122.30 
  MASTL MUTATED MASTL WILD-TYPE 
          27.90           14.07 
[1] "0.3 - 74.5 (27.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D667V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MASTL MUTATED         0        0        2        0         2         2
  MASTL WILD-TYPE       2       15       38       30        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MASTL MUTATED           1          2          0          0        3
  MASTL WILD-TYPE         2         68         53         32       35
D667V3, multiclass
            clus
vv           MASTL MUTATED MASTL WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              1               2
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MASTL MUTATED     1   4   3   5
  MASTL WILD-TYPE  21  88 170  92
D667V4, multiclass
    clus
vv   MASTL MUTATED MASTL WILD-TYPE
  T1             1              21
  T2             4              88
  T3             3             170
  T4             5              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
  MASTL MUTATED     4   5   3   0
  MASTL WILD-TYPE 114  99  74  77
D667V5, multiclass
    clus
vv   MASTL MUTATED MASTL WILD-TYPE
  N0             4             114
  N1             5              99
  N2             3              74
  N3             0              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"
D667V6, binary
                 cls
clus                0   1
  MASTL MUTATED    11   2
  MASTL WILD-TYPE 335  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MASTL MUTATED     11    2
  MASTL WILD-TYPE  335   27
   clus
vv  MASTL MUTATED MASTL WILD-TYPE
  0            11             335
  1             2              27
[1] 2 2
[1] FALSE
D667V7, binary
                 cls
clus                0   1
  MASTL MUTATED     7   6
  MASTL WILD-TYPE 138 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MASTL MUTATED      7    6
  MASTL WILD-TYPE  138  242
        clus
vv       MASTL MUTATED MASTL WILD-TYPE
  FEMALE             7             138
  MALE               6             242
[1] 2 2
[1] FALSE
D667V8, binary
                 cls
clus                0   1
  MASTL MUTATED    10   1
  MASTL WILD-TYPE 282  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MASTL MUTATED     10    1
  MASTL WILD-TYPE  282   58
     clus
vv    MASTL MUTATED MASTL WILD-TYPE
  NO             10             282
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MASTL MUTATED                                          0
  MASTL WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MASTL MUTATED                                       1
  MASTL WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MASTL MUTATED                                                        6
  MASTL WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MASTL MUTATED                                                   1
  MASTL WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MASTL MUTATED                                                                   3
  MASTL WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MASTL MUTATED                                                    0
  MASTL WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MASTL MUTATED                                                  2
  MASTL WILD-TYPE                                               59
D667V9, multiclass
                                                                   clus
vv                                                                  MASTL MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  MASTL WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MASTL MUTATED    12   0   0   1
  MASTL WILD-TYPE 299  14  15  23
D667V10, multiclass
    clus
vv   MASTL MUTATED MASTL WILD-TYPE
  R0            12             299
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D667V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MASTL MUTATED       3                         0
  MASTL WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MASTL MUTATED                                           0     8
  MASTL WILD-TYPE                                         1   235
D667V12, multiclass
                                           clus
vv                                          MASTL MUTATED MASTL WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D667V13, binary
                 cls
clus                0   1
  MASTL MUTATED     1   9
  MASTL WILD-TYPE   3 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MASTL MUTATED      1    9
  MASTL WILD-TYPE    3  301
                        clus
vv                       MASTL MUTATED MASTL WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(668) Variable = KIRREL2 MUTATION ANALYSIS
D668V1, survival
                   sevent
clus2                 0   1
  KIRREL2 MUTATED    11   4
  KIRREL2 WILD-TYPE 219 135
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               15               354 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
                4               135 
$`KIRREL2 MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8487 TCGA-BR-8686 TCGA-BR-A4QL TCGA-CD-A4MG 
       34.68        32.78         1.12        20.88        16.14         6.58 
TCGA-CG-5721 TCGA-F1-6874 TCGA-FP-7735 TCGA-HF-7132 TCGA-HF-7134 TCGA-HU-A4GN 
        6.02        14.47         3.48        77.29        52.21        29.98 
TCGA-HU-A4GT TCGA-MX-A5UJ TCGA-VQ-A8P2 
        6.51        19.73        38.14 

$`KIRREL2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-F1-6875 
        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-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-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-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 

  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
             1.12              0.00 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
            77.29            122.30 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
            19.73             14.07 
[1] "1.1 - 77.3 (19.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D668V2, 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       2       14       37       29        31        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIRREL2 MUTATED           0          2          2          0        1
  KIRREL2 WILD-TYPE         3         68         51         32       37
D668V3, multiclass
            clus
vv           KIRREL2 MUTATED KIRREL2 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 3                37
  STAGE II                 1                29
  STAGE IIA                6                31
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               2                51
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  KIRREL2 MUTATED     1   5   7   3
  KIRREL2 WILD-TYPE  21  87 166  94
D668V4, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  T1               1                21
  T2               5                87
  T3               7               166
  T4               3                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
  KIRREL2 MUTATED     9   5   1   1
  KIRREL2 WILD-TYPE 109  99  76  76
D668V5, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  N0               9               109
  N1               5                99
  N2               1                76
  N3               1                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"
D668V6, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED    15   0
  KIRREL2 WILD-TYPE 331  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED     15    0
  KIRREL2 WILD-TYPE  331   29
   clus
vv  KIRREL2 MUTATED KIRREL2 WILD-TYPE
  0              15               331
  1               0                29
[1] 2 2
[1] FALSE
D668V7, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED     6  10
  KIRREL2 WILD-TYPE 139 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED      6   10
  KIRREL2 WILD-TYPE  139  238
        clus
vv       KIRREL2 MUTATED KIRREL2 WILD-TYPE
  FEMALE               6               139
  MALE                10               238
[1] 2 2
[1] FALSE
D668V8, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED    13   2
  KIRREL2 WILD-TYPE 279  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED     13    2
  KIRREL2 WILD-TYPE  279   57
     clus
vv    KIRREL2 MUTATED KIRREL2 WILD-TYPE
  NO               13               279
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIRREL2 MUTATED                                          0
  KIRREL2 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIRREL2 MUTATED                                       1
  KIRREL2 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIRREL2 MUTATED                                                        5
  KIRREL2 WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIRREL2 MUTATED                                                   2
  KIRREL2 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIRREL2 MUTATED                                                                   4
  KIRREL2 WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIRREL2 MUTATED                                                    0
  KIRREL2 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIRREL2 MUTATED                                                  4
  KIRREL2 WILD-TYPE                                               57
D668V9, multiclass
                                                                   clus
vv                                                                  KIRREL2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                4
                                                                   clus
vv                                                                  KIRREL2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  KIRREL2 MUTATED    15   0   0   0
  KIRREL2 WILD-TYPE 296  14  15  24
D668V10, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  R0              15               296
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D668V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  KIRREL2 MUTATED       4                         1
  KIRREL2 WILD-TYPE    83                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIRREL2 MUTATED                                           0     7
  KIRREL2 WILD-TYPE                                         1   236
D668V12, multiclass
                                           clus
vv                                          KIRREL2 MUTATED KIRREL2 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D668V13, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED     0  11
  KIRREL2 WILD-TYPE   4 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED      0   11
  KIRREL2 WILD-TYPE    4  299
                        clus
vv                       KIRREL2 MUTATED KIRREL2 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              11               299
[1] 2 2
[1] FALSE

Clustering(669) Variable = HSPB8 MUTATION ANALYSIS
D669V1, survival
                 sevent
clus2               0   1
  HSPB8 MUTATED     6   0
  HSPB8 WILD-TYPE 224 139
  HSPB8 MUTATED HSPB8 WILD-TYPE 
              6             363 
  HSPB8 MUTATED HSPB8 WILD-TYPE 
              0             139 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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          14.070 
[1] "6.5 - 38.1 (32.6)"  "0.0 - 122.3 (14.1)"
[1] "hr="     "9400000"
D669V2, 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       2       15       39       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSPB8 MUTATED           0          1          0          1        0
  HSPB8 WILD-TYPE         3         69         53         31       38
D669V3, multiclass
            clus
vv           HSPB8 MUTATED HSPB8 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HSPB8 MUTATED     0   1   2   3
  HSPB8 WILD-TYPE  22  91 171  94
D669V4, multiclass
    clus
vv   HSPB8 MUTATED HSPB8 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             2             171
  T4             3              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
  HSPB8 MUTATED     4   1   0   1
  HSPB8 WILD-TYPE 114 103  77  76
D669V5, multiclass
    clus
vv   HSPB8 MUTATED HSPB8 WILD-TYPE
  N0             4             114
  N1             1             103
  N2             0              77
  N3             1              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"
D669V6, binary
                 cls
clus                0   1
  HSPB8 MUTATED     6   0
  HSPB8 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPB8 MUTATED      6    0
  HSPB8 WILD-TYPE  340   29
   clus
vv  HSPB8 MUTATED HSPB8 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D669V7, binary
                 cls
clus                0   1
  HSPB8 MUTATED     5   1
  HSPB8 WILD-TYPE 140 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPB8 MUTATED      5    1
  HSPB8 WILD-TYPE  140  247
        clus
vv       HSPB8 MUTATED HSPB8 WILD-TYPE
  FEMALE             5             140
  MALE               1             247
[1] 2 2
[1] FALSE
D669V8, binary
                 cls
clus                0   1
  HSPB8 MUTATED     4   2
  HSPB8 WILD-TYPE 288  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPB8 MUTATED      4    2
  HSPB8 WILD-TYPE  288   57
     clus
vv    HSPB8 MUTATED HSPB8 WILD-TYPE
  NO              4             288
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HSPB8 MUTATED                                          0
  HSPB8 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HSPB8 MUTATED                                       0
  HSPB8 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HSPB8 MUTATED                                                        3
  HSPB8 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HSPB8 MUTATED                                                   2
  HSPB8 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HSPB8 MUTATED                                                                   0
  HSPB8 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HSPB8 MUTATED                                                    0
  HSPB8 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HSPB8 MUTATED                                                  1
  HSPB8 WILD-TYPE                                               60
D669V9, multiclass
                                                                   clus
vv                                                                  HSPB8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  HSPB8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HSPB8 MUTATED     5   1   0   0
  HSPB8 WILD-TYPE 306  13  15  24
D669V10, multiclass
    clus
vv   HSPB8 MUTATED HSPB8 WILD-TYPE
  R0             5             306
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D669V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HSPB8 MUTATED       1                         0
  HSPB8 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HSPB8 MUTATED                                           0     4
  HSPB8 WILD-TYPE                                         1   239
D669V12, multiclass
                                           clus
vv                                          HSPB8 MUTATED HSPB8 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D669V13, binary
                 cls
clus                0   1
  HSPB8 MUTATED     0   4
  HSPB8 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPB8 MUTATED      0    4
  HSPB8 WILD-TYPE    4  306
                        clus
vv                       HSPB8 MUTATED HSPB8 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(670) Variable = GTF3C4 MUTATION ANALYSIS
D670V1, survival
                  sevent
clus2                0   1
  GTF3C4 MUTATED    10   2
  GTF3C4 WILD-TYPE 220 137
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
              12              357 
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
               2              137 
$`GTF3C4 MUTATED`
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8591 
        9.34        34.68        32.25         4.31         1.12        28.14 
TCGA-BR-A4QL TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-A4YY TCGA-F1-6874 TCGA-VQ-A91V 
       16.14       105.07        65.10        13.78        14.47        42.64 

$`GTF3C4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       20.81         1.71        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 

  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
            1.12             0.00 
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
          105.07           122.30 
  GTF3C4 MUTATED GTF3C4 WILD-TYPE 
           22.14            14.07 
[1] "1.1 - 105.1 (22.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "3.1"
D670V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GTF3C4 MUTATED         0        0        3        1         2         1
  GTF3C4 WILD-TYPE       2       15       37       29        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GTF3C4 MUTATED           0          1          2          1        0
  GTF3C4 WILD-TYPE         3         69         51         31       38
D670V3, multiclass
            clus
vv           GTF3C4 MUTATED GTF3C4 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              2               51
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GTF3C4 MUTATED     0   4   5   2
  GTF3C4 WILD-TYPE  22  88 168  95
D670V4, multiclass
    clus
vv   GTF3C4 MUTATED GTF3C4 WILD-TYPE
  T1              0               22
  T2              4               88
  T3              5              168
  T4              2               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
  GTF3C4 MUTATED     6   2   1   3
  GTF3C4 WILD-TYPE 112 102  76  74
D670V5, multiclass
    clus
vv   GTF3C4 MUTATED GTF3C4 WILD-TYPE
  N0              6              112
  N1              2              102
  N2              1               76
  N3              3               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"
D670V6, binary
                  cls
clus                 0   1
  GTF3C4 MUTATED    13   0
  GTF3C4 WILD-TYPE 333  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C4 MUTATED     13    0
  GTF3C4 WILD-TYPE  333   29
   clus
vv  GTF3C4 MUTATED GTF3C4 WILD-TYPE
  0             13              333
  1              0               29
[1] 2 2
[1] FALSE
D670V7, binary
                  cls
clus                 0   1
  GTF3C4 MUTATED     7   6
  GTF3C4 WILD-TYPE 138 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C4 MUTATED      7    6
  GTF3C4 WILD-TYPE  138  242
        clus
vv       GTF3C4 MUTATED GTF3C4 WILD-TYPE
  FEMALE              7              138
  MALE                6              242
[1] 2 2
[1] FALSE
D670V8, binary
                  cls
clus                 0   1
  GTF3C4 MUTATED     9   2
  GTF3C4 WILD-TYPE 283  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C4 MUTATED      9    2
  GTF3C4 WILD-TYPE  283   57
     clus
vv    GTF3C4 MUTATED GTF3C4 WILD-TYPE
  NO               9              283
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GTF3C4 MUTATED                                          0
  GTF3C4 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GTF3C4 MUTATED                                       0
  GTF3C4 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GTF3C4 MUTATED                                                       10
  GTF3C4 WILD-TYPE                                                    148
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GTF3C4 MUTATED                                                   0
  GTF3C4 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GTF3C4 MUTATED                                                                   2
  GTF3C4 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GTF3C4 MUTATED                                                    0
  GTF3C4 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GTF3C4 MUTATED                                                  1
  GTF3C4 WILD-TYPE                                               60
D670V9, multiclass
                                                                   clus
vv                                                                  GTF3C4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  GTF3C4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GTF3C4 MUTATED    11   0   0   2
  GTF3C4 WILD-TYPE 300  14  15  22
D670V10, multiclass
    clus
vv   GTF3C4 MUTATED GTF3C4 WILD-TYPE
  R0             11              300
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D670V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GTF3C4 MUTATED       0                         0
  GTF3C4 WILD-TYPE    87                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GTF3C4 MUTATED                                           0    10
  GTF3C4 WILD-TYPE                                         1   233
D670V12, multiclass
                                           clus
vv                                          GTF3C4 MUTATED GTF3C4 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D670V13, binary
                  cls
clus                 0   1
  GTF3C4 MUTATED     0  10
  GTF3C4 WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C4 MUTATED      0   10
  GTF3C4 WILD-TYPE    4  300
                        clus
vv                       GTF3C4 MUTATED GTF3C4 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(671) Variable = PPP3CA MUTATION ANALYSIS
D671V1, survival
                  sevent
clus2                0   1
  PPP3CA MUTATED     9   3
  PPP3CA WILD-TYPE 221 136
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              12              357 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
               3              136 
$`PPP3CA MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-7958 TCGA-CD-8536 TCGA-CG-4465 
       21.99         6.97        35.84        29.56        12.43         9.01 
TCGA-CG-5721 TCGA-FP-7998 TCGA-HU-8249 TCGA-HU-A4H4 TCGA-SW-A7EA TCGA-VQ-A8P2 
        6.02        22.29        28.96        23.84        19.04        38.14 

$`PPP3CA WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-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-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 

  PPP3CA MUTATED PPP3CA WILD-TYPE 
            6.02             0.00 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
           38.14           122.30 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
           22.14            14.07 
[1] "6.0 - 38.1 (22.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D671V2, 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       2       15       38       29        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP3CA MUTATED           0          3          1          1        3
  PPP3CA WILD-TYPE         3         67         52         31       35
D671V3, multiclass
            clus
vv           PPP3CA MUTATED PPP3CA WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PPP3CA MUTATED     0   3   3   6
  PPP3CA WILD-TYPE  22  89 170  91
D671V4, multiclass
    clus
vv   PPP3CA MUTATED PPP3CA WILD-TYPE
  T1              0               22
  T2              3               89
  T3              3              170
  T4              6               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
  PPP3CA MUTATED     4   4   2   2
  PPP3CA WILD-TYPE 114 100  75  75
D671V5, multiclass
    clus
vv   PPP3CA MUTATED PPP3CA WILD-TYPE
  N0              4              114
  N1              4              100
  N2              2               75
  N3              2               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"
D671V6, binary
                  cls
clus                 0   1
  PPP3CA MUTATED     8   2
  PPP3CA WILD-TYPE 338  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      8    2
  PPP3CA WILD-TYPE  338   27
   clus
vv  PPP3CA MUTATED PPP3CA WILD-TYPE
  0              8              338
  1              2               27
[1] 2 2
[1] FALSE
D671V7, binary
                  cls
clus                 0   1
  PPP3CA MUTATED     5   7
  PPP3CA WILD-TYPE 140 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      5    7
  PPP3CA WILD-TYPE  140  241
        clus
vv       PPP3CA MUTATED PPP3CA WILD-TYPE
  FEMALE              5              140
  MALE                7              241
[1] 2 2
[1] FALSE
D671V8, binary
                  cls
clus                 0   1
  PPP3CA MUTATED    10   1
  PPP3CA WILD-TYPE 282  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED     10    1
  PPP3CA WILD-TYPE  282   58
     clus
vv    PPP3CA MUTATED PPP3CA WILD-TYPE
  NO              10              282
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PPP3CA MUTATED                                          0
  PPP3CA WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PPP3CA MUTATED                                       3
  PPP3CA WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPP3CA MUTATED                                                        4
  PPP3CA WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PPP3CA MUTATED                                                   1
  PPP3CA WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPP3CA MUTATED                                                                   2
  PPP3CA WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PPP3CA MUTATED                                                    0
  PPP3CA WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PPP3CA MUTATED                                                  2
  PPP3CA WILD-TYPE                                               59
D671V9, multiclass
                                                                   clus
vv                                                                  PPP3CA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  PPP3CA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PPP3CA MUTATED     9   0   2   1
  PPP3CA WILD-TYPE 302  14  13  23
D671V10, multiclass
    clus
vv   PPP3CA MUTATED PPP3CA WILD-TYPE
  R0              9              302
  R1              0               14
  R2              2               13
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D671V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PPP3CA MUTATED       3                         0
  PPP3CA WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPP3CA MUTATED                                           0     6
  PPP3CA WILD-TYPE                                         1   237
D671V12, multiclass
                                           clus
vv                                          PPP3CA MUTATED PPP3CA WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D671V13, binary
                  cls
clus                 0   1
  PPP3CA MUTATED     1   7
  PPP3CA WILD-TYPE   3 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      1    7
  PPP3CA WILD-TYPE    3  303
                        clus
vv                       PPP3CA MUTATED PPP3CA WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(672) Variable = NOB1 MUTATION ANALYSIS
D672V1, survival
                sevent
clus2              0   1
  NOB1 MUTATED     5   1
  NOB1 WILD-TYPE 225 138
  NOB1 MUTATED NOB1 WILD-TYPE 
             6            363 
  NOB1 MUTATED NOB1 WILD-TYPE 
             1            138 
$`NOB1 MUTATED`
TCGA-B7-5816 TCGA-BR-7707 TCGA-BR-8487 TCGA-CG-4305 TCGA-CG-4306 TCGA-HU-A4H6 
       26.70        35.84         1.12        15.95         1.02        21.17 

$`NOB1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-A4H8 TCGA-HU-A4HB 
       12.95        29.00        23.84        23.80        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 

  NOB1 MUTATED NOB1 WILD-TYPE 
          1.02           0.00 
  NOB1 MUTATED NOB1 WILD-TYPE 
         35.84         122.30 
  NOB1 MUTATED NOB1 WILD-TYPE 
         18.56          14.17 
[1] "1.0 - 35.8 (18.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.2"
D672V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOB1 MUTATED         0        0        1        1         1         1
  NOB1 WILD-TYPE       2       15       39       29        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOB1 MUTATED           0          1          0          0        1
  NOB1 WILD-TYPE         3         69         53         32       37
D672V3, multiclass
            clus
vv           NOB1 MUTATED NOB1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOB1 MUTATED     0   2   3   1
  NOB1 WILD-TYPE  22  90 170  96
D672V4, multiclass
    clus
vv   NOB1 MUTATED NOB1 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            3            170
  T4            1             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
  NOB1 MUTATED     3   1   2   0
  NOB1 WILD-TYPE 115 103  75  77
D672V5, multiclass
    clus
vv   NOB1 MUTATED NOB1 WILD-TYPE
  N0            3            115
  N1            1            103
  N2            2             75
  N3            0             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"
D672V6, binary
                cls
clus               0   1
  NOB1 MUTATED     6   1
  NOB1 WILD-TYPE 340  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOB1 MUTATED      6    1
  NOB1 WILD-TYPE  340   28
   clus
vv  NOB1 MUTATED NOB1 WILD-TYPE
  0            6            340
  1            1             28
[1] 2 2
[1] FALSE
D672V7, binary
                cls
clus               0   1
  NOB1 MUTATED     5   2
  NOB1 WILD-TYPE 140 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOB1 MUTATED      5    2
  NOB1 WILD-TYPE  140  246
        clus
vv       NOB1 MUTATED NOB1 WILD-TYPE
  FEMALE            5            140
  MALE              2            246
[1] 2 2
[1] FALSE
D672V8, binary
                cls
clus               0   1
  NOB1 MUTATED     5   0
  NOB1 WILD-TYPE 287  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOB1 MUTATED      5    0
  NOB1 WILD-TYPE  287   59
     clus
vv    NOB1 MUTATED NOB1 WILD-TYPE
  NO             5            287
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NOB1 MUTATED                                          0
  NOB1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NOB1 MUTATED                                       1
  NOB1 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NOB1 MUTATED                                                        5
  NOB1 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NOB1 MUTATED                                                   0
  NOB1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NOB1 MUTATED                                                                   0
  NOB1 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NOB1 MUTATED                                                    0
  NOB1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NOB1 MUTATED                                                  1
  NOB1 WILD-TYPE                                               60
D672V9, multiclass
                                                                   clus
vv                                                                  NOB1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  NOB1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NOB1 MUTATED     5   0   1   1
  NOB1 WILD-TYPE 306  14  14  23
D672V10, multiclass
    clus
vv   NOB1 MUTATED NOB1 WILD-TYPE
  R0            5            306
  R1            0             14
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D672V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NOB1 MUTATED       1                         0
  NOB1 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOB1 MUTATED                                           0     4
  NOB1 WILD-TYPE                                         1   239
D672V12, multiclass
                                           clus
vv                                          NOB1 MUTATED NOB1 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D672V13, binary
                cls
clus               0   1
  NOB1 MUTATED     0   5
  NOB1 WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOB1 MUTATED      0    5
  NOB1 WILD-TYPE    4  305
                        clus
vv                       NOB1 MUTATED NOB1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(673) Variable = C15ORF52 MUTATION ANALYSIS
D673V1, survival
                    sevent
clus2                  0   1
  C15ORF52 MUTATED     4   1
  C15ORF52 WILD-TYPE 226 138
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 5                364 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 1                138 
$`C15ORF52 MUTATED`
TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MG TCGA-HF-7132 TCGA-HU-A4GT 
        1.12        28.14         6.58        77.29         6.51 

$`C15ORF52 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
              1.12               0.00 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
             77.29             122.30 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
              6.58              14.35 
[1] "1.1 - 77.3 (6.6)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "2"  
D673V2, 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       2       15       40       29        34        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C15ORF52 MUTATED           0          0          0          1        0
  C15ORF52 WILD-TYPE         3         70         53         31       38
D673V3, multiclass
            clus
vv           C15ORF52 MUTATED C15ORF52 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  1                 29
  STAGE IIA                 3                 34
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                0                 53
  STAGE IIIC                1                 31
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C15ORF52 MUTATED     0   1   3   1
  C15ORF52 WILD-TYPE  22  91 170  96
D673V4, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  T1                0                 22
  T2                1                 91
  T3                3                170
  T4                1                 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
  C15ORF52 MUTATED     3   1   0   1
  C15ORF52 WILD-TYPE 115 103  77  76
D673V5, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  N0                3                115
  N1                1                103
  N2                0                 77
  N3                1                 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"
D673V6, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED     6   0
  C15ORF52 WILD-TYPE 340  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED      6    0
  C15ORF52 WILD-TYPE  340   29
   clus
vv  C15ORF52 MUTATED C15ORF52 WILD-TYPE
  0                6                340
  1                0                 29
[1] 2 2
[1] FALSE
D673V7, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED     3   3
  C15ORF52 WILD-TYPE 142 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED      3    3
  C15ORF52 WILD-TYPE  142  245
        clus
vv       C15ORF52 MUTATED C15ORF52 WILD-TYPE
  FEMALE                3                142
  MALE                  3                245
[1] 2 2
[1] FALSE
D673V8, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED     4   1
  C15ORF52 WILD-TYPE 288  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED      4    1
  C15ORF52 WILD-TYPE  288   58
     clus
vv    C15ORF52 MUTATED C15ORF52 WILD-TYPE
  NO                 4                288
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C15ORF52 MUTATED                                          0
  C15ORF52 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C15ORF52 MUTATED                                       1
  C15ORF52 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C15ORF52 MUTATED                                                        3
  C15ORF52 WILD-TYPE                                                    155
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C15ORF52 MUTATED                                                   1
  C15ORF52 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C15ORF52 MUTATED                                                                   0
  C15ORF52 WILD-TYPE                                                                68
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C15ORF52 MUTATED                                                    0
  C15ORF52 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C15ORF52 MUTATED                                                  1
  C15ORF52 WILD-TYPE                                               60
D673V9, multiclass
                                                                   clus
vv                                                                  C15ORF52 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  C15ORF52 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C15ORF52 MUTATED     4   0   0   1
  C15ORF52 WILD-TYPE 307  14  15  23
D673V10, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  R0                4                307
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D673V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C15ORF52 MUTATED       2                         0
  C15ORF52 WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C15ORF52 MUTATED                                           0     3
  C15ORF52 WILD-TYPE                                         1   240
D673V12, multiclass
                                           clus
vv                                          C15ORF52 MUTATED C15ORF52 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D673V13, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED     0   5
  C15ORF52 WILD-TYPE   4 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED      0    5
  C15ORF52 WILD-TYPE    4  305
                        clus
vv                       C15ORF52 MUTATED C15ORF52 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                5                305
[1] 2 2
[1] FALSE

Clustering(674) Variable = MEN1 MUTATION ANALYSIS
D674V1, survival
                sevent
clus2              0   1
  MEN1 MUTATED     6   2
  MEN1 WILD-TYPE 224 137
  MEN1 MUTATED MEN1 WILD-TYPE 
             8            361 
  MEN1 MUTATED MEN1 WILD-TYPE 
             2            137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       33.40         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-ZA-A8F6 
       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         14.070 
[1] "12.4 - 105.1 (22.0)" "0.0 - 122.3 (14.1)" 
[1] "hr=" "2.3"
D674V2, 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       2       15       39       29        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MEN1 MUTATED           0          1          2          1        0
  MEN1 WILD-TYPE         3         69         51         31       38
D674V3, multiclass
            clus
vv           MEN1 MUTATED MEN1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            2             51
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MEN1 MUTATED     2   1   5   2
  MEN1 WILD-TYPE  20  91 168  95
D674V4, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  T1            2             20
  T2            1             91
  T3            5            168
  T4            2             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
  MEN1 MUTATED     2   4   0   3
  MEN1 WILD-TYPE 116 100  77  74
D674V5, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  N0            2            116
  N1            4            100
  N2            0             77
  N3            3             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"
D674V6, binary
                cls
clus               0   1
  MEN1 MUTATED    10   0
  MEN1 WILD-TYPE 336  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED     10    0
  MEN1 WILD-TYPE  336   29
   clus
vv  MEN1 MUTATED MEN1 WILD-TYPE
  0           10            336
  1            0             29
[1] 2 2
[1] FALSE
D674V7, binary
                cls
clus               0   1
  MEN1 MUTATED     5   5
  MEN1 WILD-TYPE 140 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      5    5
  MEN1 WILD-TYPE  140  243
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  FEMALE            5            140
  MALE              5            243
[1] 2 2
[1] FALSE
D674V8, binary
                cls
clus               0   1
  MEN1 MUTATED     6   2
  MEN1 WILD-TYPE 286  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      6    2
  MEN1 WILD-TYPE  286   57
     clus
vv    MEN1 MUTATED MEN1 WILD-TYPE
  NO             6            286
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MEN1 MUTATED                                          1
  MEN1 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MEN1 MUTATED                                       2
  MEN1 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MEN1 MUTATED                                                        5
  MEN1 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MEN1 MUTATED                                                   1
  MEN1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MEN1 MUTATED                                                                   0
  MEN1 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MEN1 MUTATED                                                    0
  MEN1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MEN1 MUTATED                                                  1
  MEN1 WILD-TYPE                                               60
D674V9, multiclass
                                                                   clus
vv                                                                  MEN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  MEN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MEN1 MUTATED     6   1   0   2
  MEN1 WILD-TYPE 305  13  15  22
D674V10, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  R0            6            305
  R1            1             13
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D674V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MEN1 MUTATED       2                         0
  MEN1 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MEN1 MUTATED                                           0     7
  MEN1 WILD-TYPE                                         1   236
D674V12, multiclass
                                           clus
vv                                          MEN1 MUTATED MEN1 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D674V13, binary
                cls
clus               0   1
  MEN1 MUTATED     1   7
  MEN1 WILD-TYPE   3 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED      1    7
  MEN1 WILD-TYPE    3  303
                        clus
vv                       MEN1 MUTATED MEN1 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(675) Variable = MAPK15 MUTATION ANALYSIS
D675V1, survival
                  sevent
clus2                0   1
  MAPK15 MUTATED     5   1
  MAPK15 WILD-TYPE 225 138
  MAPK15 MUTATED MAPK15 WILD-TYPE 
               6              363 
  MAPK15 MUTATED MAPK15 WILD-TYPE 
               1              138 
$`MAPK15 MUTATED`
TCGA-BR-6452 TCGA-BR-7707 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5728 TCGA-HU-8602 
       34.68        35.84        15.95         1.02        65.10        22.32 

$`MAPK15 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  MAPK15 MUTATED MAPK15 WILD-TYPE 
            1.02             0.00 
  MAPK15 MUTATED MAPK15 WILD-TYPE 
            65.1            122.3 
  MAPK15 MUTATED MAPK15 WILD-TYPE 
           28.50            14.07 
[1] "1.0 - 65.1 (28.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.2"
D675V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAPK15 MUTATED         0        0        2        1         1         1
  MAPK15 WILD-TYPE       2       15       38       29        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAPK15 MUTATED           0          0          0          0        2
  MAPK15 WILD-TYPE         3         70         53         32       36
D675V3, multiclass
            clus
vv           MAPK15 MUTATED MAPK15 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAPK15 MUTATED     0   3   2   2
  MAPK15 WILD-TYPE  22  89 171  95
D675V4, multiclass
    clus
vv   MAPK15 MUTATED MAPK15 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              2              171
  T4              2               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
  MAPK15 MUTATED     4   2   2   0
  MAPK15 WILD-TYPE 114 102  75  77
D675V5, multiclass
    clus
vv   MAPK15 MUTATED MAPK15 WILD-TYPE
  N0              4              114
  N1              2              102
  N2              2               75
  N3              0               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"
D675V6, binary
                  cls
clus                 0   1
  MAPK15 MUTATED     7   1
  MAPK15 WILD-TYPE 339  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAPK15 MUTATED      7    1
  MAPK15 WILD-TYPE  339   28
   clus
vv  MAPK15 MUTATED MAPK15 WILD-TYPE
  0              7              339
  1              1               28
[1] 2 2
[1] FALSE
D675V7, binary
                  cls
clus                 0   1
  MAPK15 MUTATED     6   2
  MAPK15 WILD-TYPE 139 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAPK15 MUTATED      6    2
  MAPK15 WILD-TYPE  139  246
        clus
vv       MAPK15 MUTATED MAPK15 WILD-TYPE
  FEMALE              6              139
  MALE                2              246
[1] 2 2
[1] FALSE
D675V8, binary
                  cls
clus                 0   1
  MAPK15 MUTATED     4   0
  MAPK15 WILD-TYPE 288  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAPK15 MUTATED      4    0
  MAPK15 WILD-TYPE  288   59
     clus
vv    MAPK15 MUTATED MAPK15 WILD-TYPE
  NO               4              288
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MAPK15 MUTATED                                          0
  MAPK15 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MAPK15 MUTATED                                       1
  MAPK15 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAPK15 MUTATED                                                        6
  MAPK15 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MAPK15 MUTATED                                                   0
  MAPK15 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAPK15 MUTATED                                                                   1
  MAPK15 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MAPK15 MUTATED                                                    0
  MAPK15 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MAPK15 MUTATED                                                  0
  MAPK15 WILD-TYPE                                               61
D675V9, multiclass
                                                                   clus
vv                                                                  MAPK15 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  MAPK15 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAPK15 MUTATED     5   0   1   2
  MAPK15 WILD-TYPE 306  14  14  22
D675V10, multiclass
    clus
vv   MAPK15 MUTATED MAPK15 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D675V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAPK15 MUTATED       1                         0
  MAPK15 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAPK15 MUTATED                                           0     4
  MAPK15 WILD-TYPE                                         1   239
D675V12, multiclass
                                           clus
vv                                          MAPK15 MUTATED MAPK15 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D675V13, binary
                  cls
clus                 0   1
  MAPK15 MUTATED     0   5
  MAPK15 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAPK15 MUTATED      0    5
  MAPK15 WILD-TYPE    4  305
                        clus
vv                       MAPK15 MUTATED MAPK15 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(676) Variable = DDX50 MUTATION ANALYSIS
D676V1, survival
                 sevent
clus2               0   1
  DDX50 MUTATED     7   3
  DDX50 WILD-TYPE 223 136
  DDX50 MUTATED DDX50 WILD-TYPE 
             10             359 
  DDX50 MUTATED DDX50 WILD-TYPE 
              3             136 
$`DDX50 MUTATED`
TCGA-BR-4201 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-5721 
       30.90        36.16        35.84         1.12         6.58         6.02 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-VQ-A8P2 
       22.32        22.68         0.10        38.14 

$`DDX50 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  DDX50 MUTATED DDX50 WILD-TYPE 
            0.1             0.0 
  DDX50 MUTATED DDX50 WILD-TYPE 
          38.14          122.30 
  DDX50 MUTATED DDX50 WILD-TYPE 
          22.50           14.17 
[1] "0.1 - 38.1 (22.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D676V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX50 MUTATED         1        1        1        0         2         2
  DDX50 WILD-TYPE       1       14       39       30        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDX50 MUTATED           0          1          0          1        2
  DDX50 WILD-TYPE         3         69         53         31       36
D676V3, multiclass
            clus
vv           DDX50 MUTATED DDX50 WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX50 MUTATED     2   2   3   5
  DDX50 WILD-TYPE  20  90 170  92
D676V4, multiclass
    clus
vv   DDX50 MUTATED DDX50 WILD-TYPE
  T1             2              20
  T2             2              90
  T3             3             170
  T4             5              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
  DDX50 MUTATED     5   4   2   0
  DDX50 WILD-TYPE 113 100  75  77
D676V5, multiclass
    clus
vv   DDX50 MUTATED DDX50 WILD-TYPE
  N0             5             113
  N1             4             100
  N2             2              75
  N3             0              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"
D676V6, binary
                 cls
clus                0   1
  DDX50 MUTATED    11   0
  DDX50 WILD-TYPE 335  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX50 MUTATED     11    0
  DDX50 WILD-TYPE  335   29
   clus
vv  DDX50 MUTATED DDX50 WILD-TYPE
  0            11             335
  1             0              29
[1] 2 2
[1] FALSE
D676V7, binary
                 cls
clus                0   1
  DDX50 MUTATED     6   6
  DDX50 WILD-TYPE 139 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX50 MUTATED      6    6
  DDX50 WILD-TYPE  139  242
        clus
vv       DDX50 MUTATED DDX50 WILD-TYPE
  FEMALE             6             139
  MALE               6             242
[1] 2 2
[1] FALSE
D676V8, binary
                 cls
clus                0   1
  DDX50 MUTATED    10   1
  DDX50 WILD-TYPE 282  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX50 MUTATED     10    1
  DDX50 WILD-TYPE  282   58
     clus
vv    DDX50 MUTATED DDX50 WILD-TYPE
  NO             10             282
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DDX50 MUTATED                                          0
  DDX50 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DDX50 MUTATED                                       3
  DDX50 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DDX50 MUTATED                                                        5
  DDX50 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DDX50 MUTATED                                                   1
  DDX50 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DDX50 MUTATED                                                                   1
  DDX50 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DDX50 MUTATED                                                    1
  DDX50 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DDX50 MUTATED                                                  1
  DDX50 WILD-TYPE                                               60
D676V9, multiclass
                                                                   clus
vv                                                                  DDX50 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  DDX50 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DDX50 MUTATED     8   0   0   2
  DDX50 WILD-TYPE 303  14  15  22
D676V10, multiclass
    clus
vv   DDX50 MUTATED DDX50 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D676V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DDX50 MUTATED       4                         1
  DDX50 WILD-TYPE    83                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDX50 MUTATED                                           0     6
  DDX50 WILD-TYPE                                         1   237
D676V12, multiclass
                                           clus
vv                                          DDX50 MUTATED DDX50 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D676V13, binary
                 cls
clus                0   1
  DDX50 MUTATED     0  10
  DDX50 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX50 MUTATED      0   10
  DDX50 WILD-TYPE    4  300
                        clus
vv                       DDX50 MUTATED DDX50 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(677) Variable = ATP6V1H MUTATION ANALYSIS
D677V1, survival
                   sevent
clus2                 0   1
  ATP6V1H MUTATED     7   6
  ATP6V1H WILD-TYPE 223 133
  ATP6V1H MUTATED ATP6V1H WILD-TYPE 
               13               356 
  ATP6V1H MUTATED ATP6V1H WILD-TYPE 
                6               133 
$`ATP6V1H MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8369 TCGA-BR-A4IZ 
        6.97         9.34        34.68        32.25        14.04         8.98 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-HU-8602 TCGA-HU-A4GT TCGA-VQ-A8P2 TCGA-VQ-A94T 
       20.42        16.14        22.32         6.51        38.14        11.24 
TCGA-VQ-AA64 
       18.41 

$`ATP6V1H WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4J1 
       34.98         1.48        27.55        28.57        12.89         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-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-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-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-AA68 TCGA-VQ-AA69 
       20.81         1.71        42.64        66.81        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 

  ATP6V1H MUTATED ATP6V1H WILD-TYPE 
             6.51              0.00 
  ATP6V1H MUTATED ATP6V1H WILD-TYPE 
            38.14            122.30 
  ATP6V1H MUTATED ATP6V1H WILD-TYPE 
            16.14             14.22 
[1] "6.5 - 38.1 (16.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D677V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP6V1H MUTATED         0        0        1        0         2         2
  ATP6V1H WILD-TYPE       2       15       39       30        35        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1H MUTATED           0          2          5          0        0
  ATP6V1H WILD-TYPE         3         68         48         32       38
D677V3, multiclass
            clus
vv           ATP6V1H MUTATED ATP6V1H WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               5                48
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ATP6V1H MUTATED     0   1   7   4
  ATP6V1H WILD-TYPE  22  91 166  93
D677V4, multiclass
    clus
vv   ATP6V1H MUTATED ATP6V1H WILD-TYPE
  T1               0                22
  T2               1                91
  T3               7               166
  T4               4                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
  ATP6V1H MUTATED     5   3   3   2
  ATP6V1H WILD-TYPE 113 101  74  75
D677V5, multiclass
    clus
vv   ATP6V1H MUTATED ATP6V1H WILD-TYPE
  N0               5               113
  N1               3               101
  N2               3                74
  N3               2                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"
D677V6, binary
                   cls
clus                  0   1
  ATP6V1H MUTATED    12   0
  ATP6V1H WILD-TYPE 334  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1H MUTATED     12    0
  ATP6V1H WILD-TYPE  334   29
   clus
vv  ATP6V1H MUTATED ATP6V1H WILD-TYPE
  0              12               334
  1               0                29
[1] 2 2
[1] FALSE
D677V7, binary
                   cls
clus                  0   1
  ATP6V1H MUTATED     8   5
  ATP6V1H WILD-TYPE 137 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1H MUTATED      8    5
  ATP6V1H WILD-TYPE  137  243
        clus
vv       ATP6V1H MUTATED ATP6V1H WILD-TYPE
  FEMALE               8               137
  MALE                 5               243
[1] 2 2
[1] FALSE
D677V8, binary
                   cls
clus                  0   1
  ATP6V1H MUTATED    11   2
  ATP6V1H WILD-TYPE 281  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1H MUTATED     11    2
  ATP6V1H WILD-TYPE  281   57
     clus
vv    ATP6V1H MUTATED ATP6V1H WILD-TYPE
  NO               11               281
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ATP6V1H MUTATED                                          0
  ATP6V1H WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ATP6V1H MUTATED                                       3
  ATP6V1H WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATP6V1H MUTATED                                                        7
  ATP6V1H WILD-TYPE                                                    151
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ATP6V1H MUTATED                                                   1
  ATP6V1H WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATP6V1H MUTATED                                                                   1
  ATP6V1H WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ATP6V1H MUTATED                                                    0
  ATP6V1H WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ATP6V1H MUTATED                                                  1
  ATP6V1H WILD-TYPE                                               60
D677V9, multiclass
                                                                   clus
vv                                                                  ATP6V1H MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  ATP6V1H WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ATP6V1H MUTATED    11   0   0   2
  ATP6V1H WILD-TYPE 300  14  15  22
D677V10, multiclass
    clus
vv   ATP6V1H MUTATED ATP6V1H WILD-TYPE
  R0              11               300
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D677V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ATP6V1H MUTATED       3                         0
  ATP6V1H WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATP6V1H MUTATED                                           0     9
  ATP6V1H WILD-TYPE                                         1   234
D677V12, multiclass
                                           clus
vv                                          ATP6V1H MUTATED ATP6V1H WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D677V13, binary
                   cls
clus                  0   1
  ATP6V1H MUTATED     0  10
  ATP6V1H WILD-TYPE   4 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1H MUTATED      0   10
  ATP6V1H WILD-TYPE    4  300
                        clus
vv                       ATP6V1H MUTATED ATP6V1H WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              10               300
[1] 2 2
[1] FALSE

Clustering(678) Variable = KIAA1609 MUTATION ANALYSIS
D678V1, survival
                    sevent
clus2                  0   1
  KIAA1609 MUTATED     7   1
  KIAA1609 WILD-TYPE 223 138
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
                 8                361 
  KIAA1609 MUTATED KIAA1609 WILD-TYPE 
                 1                138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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              14.07 
[1] "6.0 - 38.1 (30.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "4.4"
D678V2, 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       2       14       40       30        37        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1609 MUTATED           0          1          0          3        1
  KIAA1609 WILD-TYPE         3         69         53         29       37
D678V3, multiclass
            clus
vv           KIAA1609 MUTATED KIAA1609 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 0                 37
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                0                 53
  STAGE IIIC                3                 29
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1609 MUTATED     1   0   0   6
  KIAA1609 WILD-TYPE  21  92 173  91
D678V4, multiclass
    clus
vv   KIAA1609 MUTATED KIAA1609 WILD-TYPE
  T1                1                 21
  T2                0                 92
  T3                0                173
  T4                6                 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
  KIAA1609 MUTATED     2   3   1   2
  KIAA1609 WILD-TYPE 116 101  76  75
D678V5, multiclass
    clus
vv   KIAA1609 MUTATED KIAA1609 WILD-TYPE
  N0                2                116
  N1                3                101
  N2                1                 76
  N3                2                 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"
D678V6, binary
                    cls
clus                   0   1
  KIAA1609 MUTATED     8   0
  KIAA1609 WILD-TYPE 338  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1609 MUTATED      8    0
  KIAA1609 WILD-TYPE  338   29
   clus
vv  KIAA1609 MUTATED KIAA1609 WILD-TYPE
  0                8                338
  1                0                 29
[1] 2 2
[1] FALSE
D678V7, binary
                    cls
clus                   0   1
  KIAA1609 MUTATED     4   4
  KIAA1609 WILD-TYPE 141 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1609 MUTATED      4    4
  KIAA1609 WILD-TYPE  141  244
        clus
vv       KIAA1609 MUTATED KIAA1609 WILD-TYPE
  FEMALE                4                141
  MALE                  4                244
[1] 2 2
[1] FALSE
D678V8, binary
                    cls
clus                   0   1
  KIAA1609 MUTATED     6   2
  KIAA1609 WILD-TYPE 286  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1609 MUTATED      6    2
  KIAA1609 WILD-TYPE  286   57
     clus
vv    KIAA1609 MUTATED KIAA1609 WILD-TYPE
  NO                 6                286
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA1609 MUTATED                                          0
  KIAA1609 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA1609 MUTATED                                       0
  KIAA1609 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1609 MUTATED                                                        4
  KIAA1609 WILD-TYPE                                                    154
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA1609 MUTATED                                                   2
  KIAA1609 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1609 MUTATED                                                                   1
  KIAA1609 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA1609 MUTATED                                                    0
  KIAA1609 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA1609 MUTATED                                                  1
  KIAA1609 WILD-TYPE                                               60
D678V9, multiclass
                                                                   clus
vv                                                                  KIAA1609 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  KIAA1609 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1609 MUTATED     6   1   0   1
  KIAA1609 WILD-TYPE 305  13  15  23
D678V10, multiclass
    clus
vv   KIAA1609 MUTATED KIAA1609 WILD-TYPE
  R0                6                305
  R1                1                 13
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D678V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1609 MUTATED       1                         0
  KIAA1609 WILD-TYPE    86                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1609 MUTATED                                           0     5
  KIAA1609 WILD-TYPE                                         1   238
D678V12, multiclass
                                           clus
vv                                          KIAA1609 MUTATED KIAA1609 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D678V13, binary
                    cls
clus                   0   1
  KIAA1609 MUTATED     0   5
  KIAA1609 WILD-TYPE   4 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1609 MUTATED      0    5
  KIAA1609 WILD-TYPE    4  305
                        clus
vv                       KIAA1609 MUTATED KIAA1609 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                5                305
[1] 2 2
[1] FALSE

Clustering(679) Variable = ITPR2 MUTATION ANALYSIS
D679V1, survival
                 sevent
clus2               0   1
  ITPR2 MUTATED    16   8
  ITPR2 WILD-TYPE 214 131
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             24             345 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
              8             131 
$`ITPR2 MUTATED`
TCGA-CG-4460 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8361 
       21.99         9.34         9.67        34.68         6.18        31.10 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-5801 TCGA-CD-8536 TCGA-CG-5721 
        1.12        27.12        31.96        13.18        12.43         6.02 
TCGA-CG-5723 TCGA-D7-5577 TCGA-D7-A4YV TCGA-F1-6874 TCGA-FP-8631 TCGA-HU-8249 
      105.07        25.71         5.92        14.47         0.56        28.96 
TCGA-HU-8602 TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-R5-A7ZR 
       22.32         8.98         0.10        14.07        19.73         6.08 

$`ITPR2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-4267 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         4.08         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-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-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-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-D7-5578 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-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-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-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       24.39        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-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       11.77        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-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 

  ITPR2 MUTATED ITPR2 WILD-TYPE 
            0.1             0.0 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
         105.07          122.30 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
         13.625          14.430 
[1] "0.1 - 105.1 (13.6)" "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D679V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITPR2 MUTATED         0        0        2        2         4         2
  ITPR2 WILD-TYPE       2       15       38       28        33        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ITPR2 MUTATED           1          6          1          2        3
  ITPR2 WILD-TYPE         2         64         52         30       35
D679V3, multiclass
            clus
vv           ITPR2 MUTATED ITPR2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               2              28
  STAGE IIA              4              33
  STAGE IIB              2              50
  STAGE III              1               2
  STAGE IIIA             6              64
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITPR2 MUTATED     2   4  10   8
  ITPR2 WILD-TYPE  20  88 163  89
D679V4, multiclass
    clus
vv   ITPR2 MUTATED ITPR2 WILD-TYPE
  T1             2              20
  T2             4              88
  T3            10             163
  T4             8              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
  ITPR2 MUTATED     7  10   6   1
  ITPR2 WILD-TYPE 111  94  71  76
D679V5, multiclass
    clus
vv   ITPR2 MUTATED ITPR2 WILD-TYPE
  N0             7             111
  N1            10              94
  N2             6              71
  N3             1              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"
D679V6, binary
                 cls
clus                0   1
  ITPR2 MUTATED    24   2
  ITPR2 WILD-TYPE 322  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED     24    2
  ITPR2 WILD-TYPE  322   27
   clus
vv  ITPR2 MUTATED ITPR2 WILD-TYPE
  0            24             322
  1             2              27
[1] 2 2
[1] FALSE
D679V7, binary
                 cls
clus                0   1
  ITPR2 MUTATED    14  13
  ITPR2 WILD-TYPE 131 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED     14   13
  ITPR2 WILD-TYPE  131  235
        clus
vv       ITPR2 MUTATED ITPR2 WILD-TYPE
  FEMALE            14             131
  MALE              13             235
[1] 2 2
[1] FALSE
D679V8, binary
                 cls
clus                0   1
  ITPR2 MUTATED    23   0
  ITPR2 WILD-TYPE 269  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED     23    0
  ITPR2 WILD-TYPE  269   59
     clus
vv    ITPR2 MUTATED ITPR2 WILD-TYPE
  NO             23             269
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ITPR2 MUTATED                                          0
  ITPR2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ITPR2 MUTATED                                       2
  ITPR2 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ITPR2 MUTATED                                                       12
  ITPR2 WILD-TYPE                                                    146
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ITPR2 MUTATED                                                   0
  ITPR2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ITPR2 MUTATED                                                                   5
  ITPR2 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ITPR2 MUTATED                                                    0
  ITPR2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ITPR2 MUTATED                                                  8
  ITPR2 WILD-TYPE                                               53
D679V9, multiclass
                                                                   clus
vv                                                                  ITPR2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              8
                                                                   clus
vv                                                                  ITPR2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               53
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ITPR2 MUTATED    20   0   1   5
  ITPR2 WILD-TYPE 291  14  14  19
D679V10, multiclass
    clus
vv   ITPR2 MUTATED ITPR2 WILD-TYPE
  R0            20             291
  R1             0              14
  R2             1              14
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D679V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ITPR2 MUTATED       8                         1
  ITPR2 WILD-TYPE    79                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ITPR2 MUTATED                                           0    15
  ITPR2 WILD-TYPE                                         1   228
D679V12, multiclass
                                           clus
vv                                          ITPR2 MUTATED ITPR2 WILD-TYPE
  ASIAN                                                 8              79
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D679V13, binary
                 cls
clus                0   1
  ITPR2 MUTATED     0  24
  ITPR2 WILD-TYPE   4 286
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      0   24
  ITPR2 WILD-TYPE    4  286
                        clus
vv                       ITPR2 MUTATED ITPR2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            24             286
[1] 2 2
[1] FALSE

Clustering(680) Variable = NUP35 MUTATION ANALYSIS
D680V1, survival
                 sevent
clus2               0   1
  NUP35 MUTATED     4   1
  NUP35 WILD-TYPE 226 138
  NUP35 MUTATED NUP35 WILD-TYPE 
              5             364 
  NUP35 MUTATED NUP35 WILD-TYPE 
              1             138 
$`NUP35 MUTATED`
TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8687 TCGA-CG-5723 TCGA-HU-A4G8 
       35.84        29.59         8.22       105.07        22.68 

$`NUP35 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  NUP35 MUTATED NUP35 WILD-TYPE 
           8.22            0.00 
  NUP35 MUTATED NUP35 WILD-TYPE 
         105.07          122.30 
  NUP35 MUTATED NUP35 WILD-TYPE 
          29.59           14.12 
[1] "8.2 - 105.1 (29.6)" "0.0 - 122.3 (14.1)"
[1] "hr=" "3.2"
D680V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NUP35 MUTATED         0        0        1        1         0         2
  NUP35 WILD-TYPE       2       15       39       29        37        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUP35 MUTATED           0          0          0          2        0
  NUP35 WILD-TYPE         3         70         53         30       38
D680V3, multiclass
            clus
vv           NUP35 MUTATED NUP35 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NUP35 MUTATED     0   2   1   3
  NUP35 WILD-TYPE  22  90 172  94
D680V4, multiclass
    clus
vv   NUP35 MUTATED NUP35 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             1             172
  T4             3              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
  NUP35 MUTATED     2   2   1   1
  NUP35 WILD-TYPE 116 102  76  76
D680V5, multiclass
    clus
vv   NUP35 MUTATED NUP35 WILD-TYPE
  N0             2             116
  N1             2             102
  N2             1              76
  N3             1              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"
D680V6, binary
                 cls
clus                0   1
  NUP35 MUTATED     6   0
  NUP35 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP35 MUTATED      6    0
  NUP35 WILD-TYPE  340   29
   clus
vv  NUP35 MUTATED NUP35 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D680V7, binary
                 cls
clus                0   1
  NUP35 MUTATED     4   2
  NUP35 WILD-TYPE 141 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP35 MUTATED      4    2
  NUP35 WILD-TYPE  141  246
        clus
vv       NUP35 MUTATED NUP35 WILD-TYPE
  FEMALE             4             141
  MALE               2             246
[1] 2 2
[1] FALSE
D680V8, binary
                 cls
clus                0   1
  NUP35 MUTATED     5   0
  NUP35 WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP35 MUTATED      5    0
  NUP35 WILD-TYPE  287   59
     clus
vv    NUP35 MUTATED NUP35 WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NUP35 MUTATED                                          0
  NUP35 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NUP35 MUTATED                                       2
  NUP35 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NUP35 MUTATED                                                        4
  NUP35 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NUP35 MUTATED                                                   0
  NUP35 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NUP35 MUTATED                                                                   0
  NUP35 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NUP35 MUTATED                                                    0
  NUP35 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NUP35 MUTATED                                                  0
  NUP35 WILD-TYPE                                               61
D680V9, multiclass
                                                                   clus
vv                                                                  NUP35 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  NUP35 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NUP35 MUTATED     4   1   0   0
  NUP35 WILD-TYPE 307  13  15  24
D680V10, multiclass
    clus
vv   NUP35 MUTATED NUP35 WILD-TYPE
  R0             4             307
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D680V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NUP35 MUTATED       1                         0
  NUP35 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NUP35 MUTATED                                           0     3
  NUP35 WILD-TYPE                                         1   240
D680V12, multiclass
                                           clus
vv                                          NUP35 MUTATED NUP35 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D680V13, binary
                 cls
clus                0   1
  NUP35 MUTATED     0   4
  NUP35 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP35 MUTATED      0    4
  NUP35 WILD-TYPE    4  306
                        clus
vv                       NUP35 MUTATED NUP35 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(681) Variable = LIMCH1 MUTATION ANALYSIS
D681V1, survival
                  sevent
clus2                0   1
  LIMCH1 MUTATED     7   5
  LIMCH1 WILD-TYPE 223 134
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              12              357 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
               5              134 
$`LIMCH1 MUTATED`
TCGA-B7-5816 TCGA-BR-7707 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CD-A48C TCGA-CD-A4MI 
       26.70        35.84         1.12        16.14        11.61        11.77 
TCGA-CG-5728 TCGA-D7-6525 TCGA-D7-A6EY TCGA-IN-7806 TCGA-IN-A6RJ TCGA-MX-A5UJ 
       65.10        13.35        11.44        36.36        12.46        19.73 

$`LIMCH1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
       12.30        11.31        12.43         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-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-D7-6526 
       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-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-7808 TCGA-IN-8462 
       21.17        14.07        15.68        33.40         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        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 

  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
            1.12             0.00 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
            65.1            122.3 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
          14.745           14.270 
[1] "1.1 - 65.1 (14.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D681V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LIMCH1 MUTATED         0        1        2        0         1         3
  LIMCH1 WILD-TYPE       2       14       38       30        36        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LIMCH1 MUTATED           0          3          2          0        0
  LIMCH1 WILD-TYPE         3         67         51         32       38
D681V3, multiclass
            clus
vv           LIMCH1 MUTATED LIMCH1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              2               51
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LIMCH1 MUTATED     1   3   7   1
  LIMCH1 WILD-TYPE  21  89 166  96
D681V4, multiclass
    clus
vv   LIMCH1 MUTATED LIMCH1 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              7              166
  T4              1               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
  LIMCH1 MUTATED     5   3   2   2
  LIMCH1 WILD-TYPE 113 101  75  75
D681V5, multiclass
    clus
vv   LIMCH1 MUTATED LIMCH1 WILD-TYPE
  N0              5              113
  N1              3              101
  N2              2               75
  N3              2               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"
D681V6, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED    12   0
  LIMCH1 WILD-TYPE 334  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED     12    0
  LIMCH1 WILD-TYPE  334   29
   clus
vv  LIMCH1 MUTATED LIMCH1 WILD-TYPE
  0             12              334
  1              0               29
[1] 2 2
[1] FALSE
D681V7, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED     8   4
  LIMCH1 WILD-TYPE 137 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED      8    4
  LIMCH1 WILD-TYPE  137  244
        clus
vv       LIMCH1 MUTATED LIMCH1 WILD-TYPE
  FEMALE              8              137
  MALE                4              244
[1] 2 2
[1] FALSE
D681V8, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED    11   0
  LIMCH1 WILD-TYPE 281  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED     11    0
  LIMCH1 WILD-TYPE  281   59
     clus
vv    LIMCH1 MUTATED LIMCH1 WILD-TYPE
  NO              11              281
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LIMCH1 MUTATED                                          0
  LIMCH1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LIMCH1 MUTATED                                       3
  LIMCH1 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LIMCH1 MUTATED                                                        6
  LIMCH1 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LIMCH1 MUTATED                                                   0
  LIMCH1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LIMCH1 MUTATED                                                                   1
  LIMCH1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LIMCH1 MUTATED                                                    0
  LIMCH1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LIMCH1 MUTATED                                                  2
  LIMCH1 WILD-TYPE                                               59
D681V9, multiclass
                                                                   clus
vv                                                                  LIMCH1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  LIMCH1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LIMCH1 MUTATED    10   0   0   0
  LIMCH1 WILD-TYPE 301  14  15  24
D681V10, multiclass
    clus
vv   LIMCH1 MUTATED LIMCH1 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D681V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  LIMCH1 MUTATED       2                         0
  LIMCH1 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LIMCH1 MUTATED                                           0     9
  LIMCH1 WILD-TYPE                                         1   234
D681V12, multiclass
                                           clus
vv                                          LIMCH1 MUTATED LIMCH1 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D681V13, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED     0  11
  LIMCH1 WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED      0   11
  LIMCH1 WILD-TYPE    4  299
                        clus
vv                       LIMCH1 MUTATED LIMCH1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(682) Variable = NAGPA MUTATION ANALYSIS
D682V1, survival
                 sevent
clus2               0   1
  NAGPA MUTATED     5   1
  NAGPA WILD-TYPE 225 138
  NAGPA MUTATED NAGPA WILD-TYPE 
              6             363 
  NAGPA MUTATED NAGPA WILD-TYPE 
              1             138 
$`NAGPA MUTATED`
TCGA-BR-6852 TCGA-BR-8284 TCGA-BR-8487 TCGA-CG-5730 TCGA-HU-A4G3 TCGA-HU-A4GF 
       44.94         8.05         1.12         4.01         5.59        25.81 

$`NAGPA WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        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 

  NAGPA MUTATED NAGPA WILD-TYPE 
           1.12            0.00 
  NAGPA MUTATED NAGPA WILD-TYPE 
          44.94          122.30 
  NAGPA MUTATED NAGPA WILD-TYPE 
           6.82           14.43 
[1] "1.1 - 44.9 (6.8)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.6"
D682V2, 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       1       15       40       30        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NAGPA MUTATED           0          0          0          1        1
  NAGPA WILD-TYPE         3         70         53         31       37
D682V3, multiclass
            clus
vv           NAGPA MUTATED NAGPA WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NAGPA MUTATED     1   2   3   1
  NAGPA WILD-TYPE  21  90 170  96
D682V4, multiclass
    clus
vv   NAGPA MUTATED NAGPA WILD-TYPE
  T1             1              21
  T2             2              90
  T3             3             170
  T4             1              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
  NAGPA MUTATED     3   2   1   1
  NAGPA WILD-TYPE 115 102  76  76
D682V5, multiclass
    clus
vv   NAGPA MUTATED NAGPA WILD-TYPE
  N0             3             115
  N1             2             102
  N2             1              76
  N3             1              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"
D682V6, binary
                 cls
clus                0   1
  NAGPA MUTATED     5   1
  NAGPA WILD-TYPE 341  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAGPA MUTATED      5    1
  NAGPA WILD-TYPE  341   28
   clus
vv  NAGPA MUTATED NAGPA WILD-TYPE
  0             5             341
  1             1              28
[1] 2 2
[1] FALSE
D682V7, binary
                 cls
clus                0   1
  NAGPA MUTATED     4   3
  NAGPA WILD-TYPE 141 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAGPA MUTATED      4    3
  NAGPA WILD-TYPE  141  245
        clus
vv       NAGPA MUTATED NAGPA WILD-TYPE
  FEMALE             4             141
  MALE               3             245
[1] 2 2
[1] FALSE
D682V8, binary
                 cls
clus                0   1
  NAGPA MUTATED     6   0
  NAGPA WILD-TYPE 286  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAGPA MUTATED      6    0
  NAGPA WILD-TYPE  286   59
     clus
vv    NAGPA MUTATED NAGPA WILD-TYPE
  NO              6             286
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NAGPA MUTATED                                          0
  NAGPA WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NAGPA MUTATED                                       0
  NAGPA WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NAGPA MUTATED                                                        3
  NAGPA WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NAGPA MUTATED                                                   0
  NAGPA WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NAGPA MUTATED                                                                   2
  NAGPA WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NAGPA MUTATED                                                    0
  NAGPA WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NAGPA MUTATED                                                  2
  NAGPA WILD-TYPE                                               59
D682V9, multiclass
                                                                   clus
vv                                                                  NAGPA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  NAGPA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NAGPA MUTATED     6   0   1   0
  NAGPA WILD-TYPE 305  14  14  24
D682V10, multiclass
    clus
vv   NAGPA MUTATED NAGPA WILD-TYPE
  R0             6             305
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D682V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NAGPA MUTATED       2                         1
  NAGPA WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NAGPA MUTATED                                           0     3
  NAGPA WILD-TYPE                                         1   240
D682V12, multiclass
                                           clus
vv                                          NAGPA MUTATED NAGPA WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D682V13, binary
                 cls
clus                0   1
  NAGPA MUTATED     0   6
  NAGPA WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAGPA MUTATED      0    6
  NAGPA WILD-TYPE    4  304
                        clus
vv                       NAGPA MUTATED NAGPA WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(683) Variable = PDS5A MUTATION ANALYSIS
D683V1, survival
                 sevent
clus2               0   1
  PDS5A MUTATED    14   2
  PDS5A WILD-TYPE 216 137
  PDS5A MUTATED PDS5A WILD-TYPE 
             16             353 
  PDS5A MUTATED PDS5A WILD-TYPE 
              2             137 
$`PDS5A MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-8531 
       26.70         6.97        34.68         1.12        31.96        12.59 
TCGA-CG-4462 TCGA-CG-5721 TCGA-D7-5579 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-A4GN 
        0.00         6.02        20.91        11.08        77.29        29.98 
TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-MX-A666 TCGA-VQ-A8P2 
       29.00        14.07        14.04        38.14 

$`PDS5A WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-D7-6518 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-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-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-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-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 

  PDS5A MUTATED PDS5A WILD-TYPE 
            0.0             0.1 
  PDS5A MUTATED PDS5A WILD-TYPE 
          77.29          122.30 
  PDS5A MUTATED PDS5A WILD-TYPE 
          17.49           14.27 
[1] "0.0 - 77.3 (17.5)"  "0.1 - 122.3 (14.3)"
[1] "hr=" "3.7"
D683V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PDS5A MUTATED         0        0        1        1         5         2
  PDS5A WILD-TYPE       2       15       39       29        32        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PDS5A MUTATED           0          4          0          1        3
  PDS5A WILD-TYPE         3         66         53         31       35
D683V3, multiclass
            clus
vv           PDS5A MUTATED PDS5A WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              5              32
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PDS5A MUTATED     1   3   7   6
  PDS5A WILD-TYPE  21  89 166  91
D683V4, multiclass
    clus
vv   PDS5A MUTATED PDS5A WILD-TYPE
  T1             1              21
  T2             3              89
  T3             7             166
  T4             6              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
  PDS5A MUTATED     5   7   2   2
  PDS5A WILD-TYPE 113  97  75  75
D683V5, multiclass
    clus
vv   PDS5A MUTATED PDS5A WILD-TYPE
  N0             5             113
  N1             7              97
  N2             2              75
  N3             2              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"
D683V6, binary
                 cls
clus                0   1
  PDS5A MUTATED    13   2
  PDS5A WILD-TYPE 333  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5A MUTATED     13    2
  PDS5A WILD-TYPE  333   27
   clus
vv  PDS5A MUTATED PDS5A WILD-TYPE
  0            13             333
  1             2              27
[1] 2 2
[1] FALSE
D683V7, binary
                 cls
clus                0   1
  PDS5A MUTATED     6  11
  PDS5A WILD-TYPE 139 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5A MUTATED      6   11
  PDS5A WILD-TYPE  139  237
        clus
vv       PDS5A MUTATED PDS5A WILD-TYPE
  FEMALE             6             139
  MALE              11             237
[1] 2 2
[1] FALSE
D683V8, binary
                 cls
clus                0   1
  PDS5A MUTATED    11   4
  PDS5A WILD-TYPE 281  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5A MUTATED     11    4
  PDS5A WILD-TYPE  281   55
     clus
vv    PDS5A MUTATED PDS5A WILD-TYPE
  NO             11             281
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PDS5A MUTATED                                          0
  PDS5A WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PDS5A MUTATED                                       4
  PDS5A WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PDS5A MUTATED                                                        5
  PDS5A WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PDS5A MUTATED                                                   3
  PDS5A WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PDS5A MUTATED                                                                   2
  PDS5A WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PDS5A MUTATED                                                    0
  PDS5A WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PDS5A MUTATED                                                  3
  PDS5A WILD-TYPE                                               58
D683V9, multiclass
                                                                   clus
vv                                                                  PDS5A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  PDS5A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PDS5A MUTATED    13   1   1   1
  PDS5A WILD-TYPE 298  13  14  23
D683V10, multiclass
    clus
vv   PDS5A MUTATED PDS5A WILD-TYPE
  R0            13             298
  R1             1              13
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D683V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PDS5A MUTATED       5                         1
  PDS5A WILD-TYPE    82                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PDS5A MUTATED                                           0     8
  PDS5A WILD-TYPE                                         1   235
D683V12, multiclass
                                           clus
vv                                          PDS5A MUTATED PDS5A WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D683V13, binary
                 cls
clus                0   1
  PDS5A MUTATED     0  13
  PDS5A WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5A MUTATED      0   13
  PDS5A WILD-TYPE    4  297
                        clus
vv                       PDS5A MUTATED PDS5A WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(684) Variable = CEP110 MUTATION ANALYSIS
D684V1, survival
                  sevent
clus2                0   1
  CEP110 MUTATED     7   8
  CEP110 WILD-TYPE 223 131
  CEP110 MUTATED CEP110 WILD-TYPE 
              15              354 
  CEP110 MUTATED CEP110 WILD-TYPE 
               8              131 
$`CEP110 MUTATED`
TCGA-CG-4460 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8680 
       21.99        32.78        25.61         6.18         0.26        31.96 
TCGA-BR-A4QL TCGA-CD-A4MI TCGA-CG-5726 TCGA-FP-A4BF TCGA-HF-7132 TCGA-HU-A4H8 
       16.14        11.77        28.96         5.52        77.29        14.07 
TCGA-IN-A6RL TCGA-SW-A7EA TCGA-VQ-A8P2 
       13.35        19.04        38.14 

$`CEP110 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-6706 
       13.68        19.33        39.12        26.10         9.17        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-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-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-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-A9TM 
       59.54         5.03        13.58         0.56        11.08         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-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-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        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 

  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            14.12 
[1] "0.3 - 77.3 (19.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D684V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CEP110 MUTATED         0        1        3        1         2         0
  CEP110 WILD-TYPE       2       14       37       29        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP110 MUTATED           0          4          2          0        2
  CEP110 WILD-TYPE         3         66         51         32       36
D684V3, multiclass
            clus
vv           CEP110 MUTATED CEP110 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                3               37
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              2               51
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CEP110 MUTATED     2   4   6   3
  CEP110 WILD-TYPE  20  88 167  94
D684V4, multiclass
    clus
vv   CEP110 MUTATED CEP110 WILD-TYPE
  T1              2               20
  T2              4               88
  T3              6              167
  T4              3               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
  CEP110 MUTATED     5   6   2   2
  CEP110 WILD-TYPE 113  98  75  75
D684V5, multiclass
    clus
vv   CEP110 MUTATED CEP110 WILD-TYPE
  N0              5              113
  N1              6               98
  N2              2               75
  N3              2               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"
D684V6, binary
                  cls
clus                 0   1
  CEP110 MUTATED    13   2
  CEP110 WILD-TYPE 333  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP110 MUTATED     13    2
  CEP110 WILD-TYPE  333   27
   clus
vv  CEP110 MUTATED CEP110 WILD-TYPE
  0             13              333
  1              2               27
[1] 2 2
[1] FALSE
D684V7, binary
                  cls
clus                 0   1
  CEP110 MUTATED     6   9
  CEP110 WILD-TYPE 139 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP110 MUTATED      6    9
  CEP110 WILD-TYPE  139  239
        clus
vv       CEP110 MUTATED CEP110 WILD-TYPE
  FEMALE              6              139
  MALE                9              239
[1] 2 2
[1] FALSE
D684V8, binary
                  cls
clus                 0   1
  CEP110 MUTATED    12   2
  CEP110 WILD-TYPE 280  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP110 MUTATED     12    2
  CEP110 WILD-TYPE  280   57
     clus
vv    CEP110 MUTATED CEP110 WILD-TYPE
  NO              12              280
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CEP110 MUTATED                                          1
  CEP110 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CEP110 MUTATED                                       1
  CEP110 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CEP110 MUTATED                                                        6
  CEP110 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CEP110 MUTATED                                                   2
  CEP110 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CEP110 MUTATED                                                                   3
  CEP110 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CEP110 MUTATED                                                    0
  CEP110 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CEP110 MUTATED                                                  2
  CEP110 WILD-TYPE                                               59
D684V9, multiclass
                                                                   clus
vv                                                                  CEP110 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  CEP110 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CEP110 MUTATED    12   1   1   0
  CEP110 WILD-TYPE 299  13  14  24
D684V10, multiclass
    clus
vv   CEP110 MUTATED CEP110 WILD-TYPE
  R0             12              299
  R1              1               13
  R2              1               14
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D684V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CEP110 MUTATED       3                         0
  CEP110 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CEP110 MUTATED                                           0     9
  CEP110 WILD-TYPE                                         1   234
D684V12, multiclass
                                           clus
vv                                          CEP110 MUTATED CEP110 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D684V13, binary
                  cls
clus                 0   1
  CEP110 MUTATED     0  11
  CEP110 WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP110 MUTATED      0   11
  CEP110 WILD-TYPE    4  299
                        clus
vv                       CEP110 MUTATED CEP110 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(685) Variable = DPAGT1 MUTATION ANALYSIS
D685V1, survival
                  sevent
clus2                0   1
  DPAGT1 MUTATED     2   2
  DPAGT1 WILD-TYPE 228 137
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
               4              365 
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
               2              137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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           14.170 
[1] "6.6 - 74.5 (28.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D685V2, 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       2       15       40       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DPAGT1 MUTATED           1          1          0          0        1
  DPAGT1 WILD-TYPE         2         69         53         32       37
D685V3, multiclass
            clus
vv           DPAGT1 MUTATED DPAGT1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               1                2
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DPAGT1 MUTATED     1   0   2   3
  DPAGT1 WILD-TYPE  21  92 171  94
D685V4, multiclass
    clus
vv   DPAGT1 MUTATED DPAGT1 WILD-TYPE
  T1              1               21
  T2              0               92
  T3              2              171
  T4              3               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
  DPAGT1 MUTATED     2   2   1   0
  DPAGT1 WILD-TYPE 116 102  76  77
D685V5, multiclass
    clus
vv   DPAGT1 MUTATED DPAGT1 WILD-TYPE
  N0              2              116
  N1              2              102
  N2              1               76
  N3              0               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"
D685V6, binary
                  cls
clus                 0   1
  DPAGT1 MUTATED     5   1
  DPAGT1 WILD-TYPE 341  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DPAGT1 MUTATED      5    1
  DPAGT1 WILD-TYPE  341   28
   clus
vv  DPAGT1 MUTATED DPAGT1 WILD-TYPE
  0              5              341
  1              1               28
[1] 2 2
[1] FALSE
D685V7, binary
                  cls
clus                 0   1
  DPAGT1 MUTATED     2   4
  DPAGT1 WILD-TYPE 143 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DPAGT1 MUTATED      2    4
  DPAGT1 WILD-TYPE  143  244
        clus
vv       DPAGT1 MUTATED DPAGT1 WILD-TYPE
  FEMALE              2              143
  MALE                4              244
[1] 2 2
[1] FALSE
D685V8, binary
                  cls
clus                 0   1
  DPAGT1 MUTATED     4   1
  DPAGT1 WILD-TYPE 288  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DPAGT1 MUTATED      4    1
  DPAGT1 WILD-TYPE  288   58
     clus
vv    DPAGT1 MUTATED DPAGT1 WILD-TYPE
  NO               4              288
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DPAGT1 MUTATED                                          0
  DPAGT1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DPAGT1 MUTATED                                       2
  DPAGT1 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DPAGT1 MUTATED                                                        1
  DPAGT1 WILD-TYPE                                                    157
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DPAGT1 MUTATED                                                   0
  DPAGT1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DPAGT1 MUTATED                                                                   2
  DPAGT1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DPAGT1 MUTATED                                                    0
  DPAGT1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DPAGT1 MUTATED                                                  1
  DPAGT1 WILD-TYPE                                               60
D685V9, multiclass
                                                                   clus
vv                                                                  DPAGT1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  DPAGT1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DPAGT1 MUTATED     4   0   0   1
  DPAGT1 WILD-TYPE 307  14  15  23
D685V10, multiclass
    clus
vv   DPAGT1 MUTATED DPAGT1 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D685V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DPAGT1 MUTATED       1                         0
  DPAGT1 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DPAGT1 MUTATED                                           0     4
  DPAGT1 WILD-TYPE                                         1   239
D685V12, multiclass
                                           clus
vv                                          DPAGT1 MUTATED DPAGT1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D685V13, binary
                  cls
clus                 0   1
  DPAGT1 MUTATED     1   4
  DPAGT1 WILD-TYPE   3 306
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DPAGT1 MUTATED      1    4
  DPAGT1 WILD-TYPE    3  306
                        clus
vv                       DPAGT1 MUTATED DPAGT1 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              4              306
[1] 2 2
[1] FALSE

Clustering(686) Variable = KCNH4 MUTATION ANALYSIS
D686V1, survival
                 sevent
clus2               0   1
  KCNH4 MUTATED     8   3
  KCNH4 WILD-TYPE 222 136
  KCNH4 MUTATED KCNH4 WILD-TYPE 
             11             358 
  KCNH4 MUTATED KCNH4 WILD-TYPE 
              3             136 
$`KCNH4 MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-A4IY TCGA-BR-A4QL 
       34.68        32.78        31.10         1.12        12.89        16.14 
TCGA-CD-A4MG TCGA-CG-4437 TCGA-FP-A4BE TCGA-HU-A4GH TCGA-RD-A7BW 
        6.58         8.05        11.08        11.77         5.13 

$`KCNH4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  KCNH4 MUTATED KCNH4 WILD-TYPE 
           1.12            0.00 
  KCNH4 MUTATED KCNH4 WILD-TYPE 
          34.68          122.30 
  KCNH4 MUTATED KCNH4 WILD-TYPE 
          11.77           14.45 
[1] "1.1 - 34.7 (11.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D686V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNH4 MUTATED         0        1        1        1         5         1
  KCNH4 WILD-TYPE       2       14       39       29        32        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNH4 MUTATED           0          0          1          1        0
  KCNH4 WILD-TYPE         3         70         52         31       38
D686V3, multiclass
            clus
vv           KCNH4 MUTATED KCNH4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              5              32
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNH4 MUTATED     1   2   6   2
  KCNH4 WILD-TYPE  21  90 167  95
D686V4, multiclass
    clus
vv   KCNH4 MUTATED KCNH4 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             6             167
  T4             2              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
  KCNH4 MUTATED     8   1   1   1
  KCNH4 WILD-TYPE 110 103  76  76
D686V5, multiclass
    clus
vv   KCNH4 MUTATED KCNH4 WILD-TYPE
  N0             8             110
  N1             1             103
  N2             1              76
  N3             1              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"
D686V6, binary
                 cls
clus                0   1
  KCNH4 MUTATED    11   0
  KCNH4 WILD-TYPE 335  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH4 MUTATED     11    0
  KCNH4 WILD-TYPE  335   29
   clus
vv  KCNH4 MUTATED KCNH4 WILD-TYPE
  0            11             335
  1             0              29
[1] 2 2
[1] FALSE
D686V7, binary
                 cls
clus                0   1
  KCNH4 MUTATED     6   5
  KCNH4 WILD-TYPE 139 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH4 MUTATED      6    5
  KCNH4 WILD-TYPE  139  243
        clus
vv       KCNH4 MUTATED KCNH4 WILD-TYPE
  FEMALE             6             139
  MALE               5             243
[1] 2 2
[1] FALSE
D686V8, binary
                 cls
clus                0   1
  KCNH4 MUTATED     9   2
  KCNH4 WILD-TYPE 283  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH4 MUTATED      9    2
  KCNH4 WILD-TYPE  283   57
     clus
vv    KCNH4 MUTATED KCNH4 WILD-TYPE
  NO              9             283
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KCNH4 MUTATED                                          0
  KCNH4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KCNH4 MUTATED                                       2
  KCNH4 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNH4 MUTATED                                                        7
  KCNH4 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KCNH4 MUTATED                                                   0
  KCNH4 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNH4 MUTATED                                                                   1
  KCNH4 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KCNH4 MUTATED                                                    0
  KCNH4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KCNH4 MUTATED                                                  1
  KCNH4 WILD-TYPE                                               60
D686V9, multiclass
                                                                   clus
vv                                                                  KCNH4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  KCNH4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCNH4 MUTATED    10   0   0   0
  KCNH4 WILD-TYPE 301  14  15  24
D686V10, multiclass
    clus
vv   KCNH4 MUTATED KCNH4 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D686V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCNH4 MUTATED       3                         1
  KCNH4 WILD-TYPE    84                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNH4 MUTATED                                           0     6
  KCNH4 WILD-TYPE                                         1   237
D686V12, multiclass
                                           clus
vv                                          KCNH4 MUTATED KCNH4 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D686V13, binary
                 cls
clus                0   1
  KCNH4 MUTATED     0  10
  KCNH4 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH4 MUTATED      0   10
  KCNH4 WILD-TYPE    4  300
                        clus
vv                       KCNH4 MUTATED KCNH4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(687) Variable = TCF20 MUTATION ANALYSIS
D687V1, survival
                 sevent
clus2               0   1
  TCF20 MUTATED     9   5
  TCF20 WILD-TYPE 221 134
  TCF20 MUTATED TCF20 WILD-TYPE 
             14             355 
  TCF20 MUTATED TCF20 WILD-TYPE 
              5             134 
$`TCF20 MUTATED`
TCGA-BR-4184 TCGA-BR-8285 TCGA-BR-8368 TCGA-BR-8680 TCGA-CD-5800 TCGA-CD-5813 
        6.97         0.56         4.31        31.96        13.15        12.39 
TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A6EY TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-IN-8462 
        6.02       105.07        11.44         0.10         6.51        18.81 
TCGA-MX-A5UJ TCGA-R5-A7ZI 
       19.73        74.53 

$`TCF20 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
         11.915          14.470 
[1] "0.1 - 105.1 (11.9)" "0.0 - 122.3 (14.5)"
[1] "hr=" "1"  
D687V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TCF20 MUTATED         0        0        1        3         1         1
  TCF20 WILD-TYPE       2       15       39       27        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TCF20 MUTATED           0          2          1          2        3
  TCF20 WILD-TYPE         3         68         52         30       35
D687V3, multiclass
            clus
vv           TCF20 MUTATED TCF20 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               3              27
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TCF20 MUTATED     0   3   7   5
  TCF20 WILD-TYPE  22  89 166  92
D687V4, multiclass
    clus
vv   TCF20 MUTATED TCF20 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             7             166
  T4             5              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
  TCF20 MUTATED     4   6   3   2
  TCF20 WILD-TYPE 114  98  74  75
D687V5, multiclass
    clus
vv   TCF20 MUTATED TCF20 WILD-TYPE
  N0             4             114
  N1             6              98
  N2             3              74
  N3             2              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"
D687V6, binary
                 cls
clus                0   1
  TCF20 MUTATED    13   2
  TCF20 WILD-TYPE 333  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF20 MUTATED     13    2
  TCF20 WILD-TYPE  333   27
   clus
vv  TCF20 MUTATED TCF20 WILD-TYPE
  0            13             333
  1             2              27
[1] 2 2
[1] FALSE
D687V7, binary
                 cls
clus                0   1
  TCF20 MUTATED    10   7
  TCF20 WILD-TYPE 135 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF20 MUTATED     10    7
  TCF20 WILD-TYPE  135  241
        clus
vv       TCF20 MUTATED TCF20 WILD-TYPE
  FEMALE            10             135
  MALE               7             241
[1] 2 2
[1] FALSE
D687V8, binary
                 cls
clus                0   1
  TCF20 MUTATED    14   0
  TCF20 WILD-TYPE 278  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF20 MUTATED     14    0
  TCF20 WILD-TYPE  278   59
     clus
vv    TCF20 MUTATED TCF20 WILD-TYPE
  NO             14             278
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TCF20 MUTATED                                          0
  TCF20 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TCF20 MUTATED                                       1
  TCF20 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TCF20 MUTATED                                                        7
  TCF20 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TCF20 MUTATED                                                   1
  TCF20 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TCF20 MUTATED                                                                   2
  TCF20 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TCF20 MUTATED                                                    1
  TCF20 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TCF20 MUTATED                                                  5
  TCF20 WILD-TYPE                                               56
D687V9, multiclass
                                                                   clus
vv                                                                  TCF20 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              5
                                                                   clus
vv                                                                  TCF20 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TCF20 MUTATED    12   0   0   4
  TCF20 WILD-TYPE 299  14  15  20
D687V10, multiclass
    clus
vv   TCF20 MUTATED TCF20 WILD-TYPE
  R0            12             299
  R1             0              14
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D687V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TCF20 MUTATED       5                         0
  TCF20 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TCF20 MUTATED                                           0    10
  TCF20 WILD-TYPE                                         1   233
D687V12, multiclass
                                           clus
vv                                          TCF20 MUTATED TCF20 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D687V13, binary
                 cls
clus                0   1
  TCF20 MUTATED     1  14
  TCF20 WILD-TYPE   3 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCF20 MUTATED      1   14
  TCF20 WILD-TYPE    3  296
                        clus
vv                       TCF20 MUTATED TCF20 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(688) Variable = EPB41 MUTATION ANALYSIS
D688V1, survival
                 sevent
clus2               0   1
  EPB41 MUTATED     6   5
  EPB41 WILD-TYPE 224 134
  EPB41 MUTATED EPB41 WILD-TYPE 
             11             358 
  EPB41 MUTATED EPB41 WILD-TYPE 
              5             134 
$`EPB41 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6705 TCGA-BR-7707 TCGA-BR-8363 TCGA-BR-8382 
        6.97        34.68        25.61        35.84         0.26        25.05 
TCGA-BR-8487 TCGA-D7-A6EY TCGA-HU-A4GU TCGA-HU-A4GX TCGA-VQ-A8P2 
        1.12        11.44         6.58        20.25        38.14 

$`EPB41 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-6706 
       19.33        39.12        26.10         9.17        32.78        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-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-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-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 

  EPB41 MUTATED EPB41 WILD-TYPE 
           0.26            0.00 
  EPB41 MUTATED EPB41 WILD-TYPE 
          38.14          122.30 
  EPB41 MUTATED EPB41 WILD-TYPE 
          20.25           14.22 
[1] "0.3 - 38.1 (20.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D688V2, 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       2       15       38       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPB41 MUTATED           0          3          2          2        1
  EPB41 WILD-TYPE         3         67         51         30       37
D688V3, multiclass
            clus
vv           EPB41 MUTATED EPB41 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPB41 MUTATED     0   2   6   5
  EPB41 WILD-TYPE  22  90 167  92
D688V4, multiclass
    clus
vv   EPB41 MUTATED EPB41 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             6             167
  T4             5              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
  EPB41 MUTATED     5   3   2   3
  EPB41 WILD-TYPE 113 101  75  74
D688V5, multiclass
    clus
vv   EPB41 MUTATED EPB41 WILD-TYPE
  N0             5             113
  N1             3             101
  N2             2              75
  N3             3              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"
D688V6, binary
                 cls
clus                0   1
  EPB41 MUTATED    12   0
  EPB41 WILD-TYPE 334  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB41 MUTATED     12    0
  EPB41 WILD-TYPE  334   29
   clus
vv  EPB41 MUTATED EPB41 WILD-TYPE
  0            12             334
  1             0              29
[1] 2 2
[1] FALSE
D688V7, binary
                 cls
clus                0   1
  EPB41 MUTATED    10   3
  EPB41 WILD-TYPE 135 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB41 MUTATED     10    3
  EPB41 WILD-TYPE  135  245
        clus
vv       EPB41 MUTATED EPB41 WILD-TYPE
  FEMALE            10             135
  MALE               3             245
[1] 2 2
[1] FALSE
D688V8, binary
                 cls
clus                0   1
  EPB41 MUTATED    10   1
  EPB41 WILD-TYPE 282  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB41 MUTATED     10    1
  EPB41 WILD-TYPE  282   58
     clus
vv    EPB41 MUTATED EPB41 WILD-TYPE
  NO             10             282
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EPB41 MUTATED                                          0
  EPB41 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EPB41 MUTATED                                       2
  EPB41 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPB41 MUTATED                                                        9
  EPB41 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EPB41 MUTATED                                                   1
  EPB41 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPB41 MUTATED                                                                   0
  EPB41 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EPB41 MUTATED                                                    0
  EPB41 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EPB41 MUTATED                                                  1
  EPB41 WILD-TYPE                                               60
D688V9, multiclass
                                                                   clus
vv                                                                  EPB41 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  EPB41 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EPB41 MUTATED    10   0   0   3
  EPB41 WILD-TYPE 301  14  15  21
D688V10, multiclass
    clus
vv   EPB41 MUTATED EPB41 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D688V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EPB41 MUTATED       2                         0
  EPB41 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPB41 MUTATED                                           0    11
  EPB41 WILD-TYPE                                         1   232
D688V12, multiclass
                                           clus
vv                                          EPB41 MUTATED EPB41 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D688V13, binary
                 cls
clus                0   1
  EPB41 MUTATED     0  12
  EPB41 WILD-TYPE   4 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPB41 MUTATED      0   12
  EPB41 WILD-TYPE    4  298
                        clus
vv                       EPB41 MUTATED EPB41 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(689) Variable = ARSJ MUTATION ANALYSIS
D689V1, survival
                sevent
clus2              0   1
  ARSJ MUTATED     5   1
  ARSJ WILD-TYPE 225 138
  ARSJ MUTATED ARSJ WILD-TYPE 
             6            363 
  ARSJ MUTATED ARSJ WILD-TYPE 
             1            138 
$`ARSJ MUTATED`
TCGA-CD-8536 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-A4YV TCGA-F1-A72C TCGA-MX-A5UJ 
       12.43       105.07        65.10         5.92        11.38        19.73 

$`ARSJ WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-FP-7735 
        0.62         7.99        14.47        72.23        21.27         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 

  ARSJ MUTATED ARSJ WILD-TYPE 
          5.92           0.00 
  ARSJ MUTATED ARSJ WILD-TYPE 
        105.07         122.30 
  ARSJ MUTATED ARSJ WILD-TYPE 
         16.08          14.27 
[1] "5.9 - 105.1 (16.1)" "0.0 - 122.3 (14.3)"
[1] "hr=" "3.1"
D689V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARSJ MUTATED         0        0        1        2         1         1
  ARSJ WILD-TYPE       2       15       39       28        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARSJ MUTATED           0          1          0          0        0
  ARSJ WILD-TYPE         3         69         53         32       38
D689V3, multiclass
            clus
vv           ARSJ MUTATED ARSJ WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              2             28
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ARSJ MUTATED     0   2   4   0
  ARSJ WILD-TYPE  22  90 169  97
D689V4, multiclass
    clus
vv   ARSJ MUTATED ARSJ WILD-TYPE
  T1            0             22
  T2            2             90
  T3            4            169
  T4            0             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
  ARSJ MUTATED     3   2   1   0
  ARSJ WILD-TYPE 115 102  76  77
D689V5, multiclass
    clus
vv   ARSJ MUTATED ARSJ WILD-TYPE
  N0            3            115
  N1            2            102
  N2            1             76
  N3            0             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"
D689V6, binary
                cls
clus               0   1
  ARSJ MUTATED     6   0
  ARSJ WILD-TYPE 340  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARSJ MUTATED      6    0
  ARSJ WILD-TYPE  340   29
   clus
vv  ARSJ MUTATED ARSJ WILD-TYPE
  0            6            340
  1            0             29
[1] 2 2
[1] FALSE
D689V7, binary
                cls
clus               0   1
  ARSJ MUTATED     3   3
  ARSJ WILD-TYPE 142 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARSJ MUTATED      3    3
  ARSJ WILD-TYPE  142  245
        clus
vv       ARSJ MUTATED ARSJ WILD-TYPE
  FEMALE            3            142
  MALE              3            245
[1] 2 2
[1] FALSE
D689V8, binary
                cls
clus               0   1
  ARSJ MUTATED     5   0
  ARSJ WILD-TYPE 287  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARSJ MUTATED      5    0
  ARSJ WILD-TYPE  287   59
     clus
vv    ARSJ MUTATED ARSJ WILD-TYPE
  NO             5            287
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARSJ MUTATED                                          0
  ARSJ WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARSJ MUTATED                                       0
  ARSJ WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARSJ MUTATED                                                        2
  ARSJ WILD-TYPE                                                    156
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARSJ MUTATED                                                   0
  ARSJ WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARSJ MUTATED                                                                   2
  ARSJ WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARSJ MUTATED                                                    0
  ARSJ WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARSJ MUTATED                                                  2
  ARSJ WILD-TYPE                                               59
D689V9, multiclass
                                                                   clus
vv                                                                  ARSJ MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  ARSJ WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ARSJ MUTATED     6   0   0   0
  ARSJ WILD-TYPE 305  14  15  24
D689V10, multiclass
    clus
vv   ARSJ MUTATED ARSJ WILD-TYPE
  R0            6            305
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D689V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ARSJ MUTATED       2                         0
  ARSJ WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARSJ MUTATED                                           0     2
  ARSJ WILD-TYPE                                         1   241
D689V12, multiclass
                                           clus
vv                                          ARSJ MUTATED ARSJ WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D689V13, binary
                cls
clus               0   1
  ARSJ MUTATED     0   4
  ARSJ WILD-TYPE   4 306
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARSJ MUTATED      0    4
  ARSJ WILD-TYPE    4  306
                        clus
vv                       ARSJ MUTATED ARSJ WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            4            306
[1] 2 2
[1] FALSE

Clustering(690) Variable = PNMT MUTATION ANALYSIS
D690V1, survival
                sevent
clus2              0   1
  PNMT MUTATED     8   1
  PNMT WILD-TYPE 222 138
  PNMT MUTATED PNMT WILD-TYPE 
             9            360 
  PNMT MUTATED PNMT WILD-TYPE 
             1            138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  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          14.22 
[1] "1.0 - 77.3 (32.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "4.3"
D690V2, 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       1       15       40       28        35        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PNMT MUTATED           0          0          0          0        2
  PNMT WILD-TYPE         3         70         53         32       36
D690V3, multiclass
            clus
vv           PNMT MUTATED PNMT WILD-TYPE
  STAGE I               1              1
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              2             28
  STAGE IIA             2             35
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PNMT MUTATED     1   2   4   3
  PNMT WILD-TYPE  21  90 169  94
D690V4, multiclass
    clus
vv   PNMT MUTATED PNMT WILD-TYPE
  T1            1             21
  T2            2             90
  T3            4            169
  T4            3             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
  PNMT MUTATED     3   6   1   0
  PNMT WILD-TYPE 115  98  76  77
D690V5, multiclass
    clus
vv   PNMT MUTATED PNMT WILD-TYPE
  N0            3            115
  N1            6             98
  N2            1             76
  N3            0             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"
D690V6, binary
                cls
clus               0   1
  PNMT MUTATED     9   1
  PNMT WILD-TYPE 337  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  PNMT MUTATED      9    1
  PNMT WILD-TYPE  337   28
   clus
vv  PNMT MUTATED PNMT WILD-TYPE
  0            9            337
  1            1             28
[1] 2 2
[1] FALSE
D690V7, binary
                cls
clus               0   1
  PNMT MUTATED     2   9
  PNMT WILD-TYPE 143 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  PNMT MUTATED      2    9
  PNMT WILD-TYPE  143  239
        clus
vv       PNMT MUTATED PNMT WILD-TYPE
  FEMALE            2            143
  MALE              9            239
[1] 2 2
[1] FALSE
D690V8, binary
                cls
clus               0   1
  PNMT MUTATED     7   2
  PNMT WILD-TYPE 285  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  PNMT MUTATED      7    2
  PNMT WILD-TYPE  285   57
     clus
vv    PNMT MUTATED PNMT WILD-TYPE
  NO             7            285
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PNMT MUTATED                                          0
  PNMT WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PNMT MUTATED                                       2
  PNMT WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PNMT MUTATED                                                        5
  PNMT WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PNMT MUTATED                                                   2
  PNMT WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PNMT MUTATED                                                                   2
  PNMT WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PNMT MUTATED                                                    0
  PNMT WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PNMT MUTATED                                                  0
  PNMT WILD-TYPE                                               61
D690V9, multiclass
                                                                   clus
vv                                                                  PNMT MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  PNMT WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PNMT MUTATED     9   0   1   1
  PNMT WILD-TYPE 302  14  14  23
D690V10, multiclass
    clus
vv   PNMT MUTATED PNMT WILD-TYPE
  R0            9            302
  R1            0             14
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D690V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PNMT MUTATED       2                         1
  PNMT WILD-TYPE    85                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PNMT MUTATED                                           0     5
  PNMT WILD-TYPE                                         1   238
D690V12, multiclass
                                           clus
vv                                          PNMT MUTATED PNMT WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D690V13, binary
                cls
clus               0   1
  PNMT MUTATED     0   7
  PNMT WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  PNMT MUTATED      0    7
  PNMT WILD-TYPE    4  303
                        clus
vv                       PNMT MUTATED PNMT WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(691) Variable = AP3M2 MUTATION ANALYSIS
D691V1, survival
                 sevent
clus2               0   1
  AP3M2 MUTATED     8   4
  AP3M2 WILD-TYPE 222 135
  AP3M2 MUTATED AP3M2 WILD-TYPE 
             12             357 
  AP3M2 MUTATED AP3M2 WILD-TYPE 
              4             135 
$`AP3M2 MUTATED`
TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-7717 TCGA-BR-8589 TCGA-CG-4305 
       30.90         9.57        34.68        18.15        27.12        15.95 
TCGA-CG-5734 TCGA-HF-A5NB TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4GX TCGA-MX-A5UJ 
        7.99        30.51        24.20         6.51        20.25        19.73 

$`AP3M2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-F1-6874 
        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-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-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-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 

  AP3M2 MUTATED AP3M2 WILD-TYPE 
           6.51            0.00 
  AP3M2 MUTATED AP3M2 WILD-TYPE 
          34.68          122.30 
  AP3M2 MUTATED AP3M2 WILD-TYPE 
          19.99           14.07 
[1] "6.5 - 34.7 (20.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D691V2, 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       2       14       40       28        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AP3M2 MUTATED           0          2          1          2        1
  AP3M2 WILD-TYPE         3         68         52         30       37
D691V3, multiclass
            clus
vv           AP3M2 MUTATED AP3M2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               2              28
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AP3M2 MUTATED     1   3   4   4
  AP3M2 WILD-TYPE  21  89 169  93
D691V4, multiclass
    clus
vv   AP3M2 MUTATED AP3M2 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             4             169
  T4             4              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
  AP3M2 MUTATED     3   5   2   1
  AP3M2 WILD-TYPE 115  99  75  76
D691V5, multiclass
    clus
vv   AP3M2 MUTATED AP3M2 WILD-TYPE
  N0             3             115
  N1             5              99
  N2             2              75
  N3             1              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"
D691V6, binary
                 cls
clus                0   1
  AP3M2 MUTATED    12   0
  AP3M2 WILD-TYPE 334  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3M2 MUTATED     12    0
  AP3M2 WILD-TYPE  334   29
   clus
vv  AP3M2 MUTATED AP3M2 WILD-TYPE
  0            12             334
  1             0              29
[1] 2 2
[1] FALSE
D691V7, binary
                 cls
clus                0   1
  AP3M2 MUTATED     7   5
  AP3M2 WILD-TYPE 138 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3M2 MUTATED      7    5
  AP3M2 WILD-TYPE  138  243
        clus
vv       AP3M2 MUTATED AP3M2 WILD-TYPE
  FEMALE             7             138
  MALE               5             243
[1] 2 2
[1] FALSE
D691V8, binary
                 cls
clus                0   1
  AP3M2 MUTATED    10   1
  AP3M2 WILD-TYPE 282  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3M2 MUTATED     10    1
  AP3M2 WILD-TYPE  282   58
     clus
vv    AP3M2 MUTATED AP3M2 WILD-TYPE
  NO             10             282
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AP3M2 MUTATED                                          0
  AP3M2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AP3M2 MUTATED                                       1
  AP3M2 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AP3M2 MUTATED                                                        6
  AP3M2 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AP3M2 MUTATED                                                   1
  AP3M2 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AP3M2 MUTATED                                                                   1
  AP3M2 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AP3M2 MUTATED                                                    0
  AP3M2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AP3M2 MUTATED                                                  3
  AP3M2 WILD-TYPE                                               58
D691V9, multiclass
                                                                   clus
vv                                                                  AP3M2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  AP3M2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AP3M2 MUTATED     9   1   0   2
  AP3M2 WILD-TYPE 302  13  15  22
D691V10, multiclass
    clus
vv   AP3M2 MUTATED AP3M2 WILD-TYPE
  R0             9             302
  R1             1              13
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D691V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AP3M2 MUTATED       3                         0
  AP3M2 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AP3M2 MUTATED                                           0     6
  AP3M2 WILD-TYPE                                         1   237
D691V12, multiclass
                                           clus
vv                                          AP3M2 MUTATED AP3M2 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D691V13, binary
                 cls
clus                0   1
  AP3M2 MUTATED     0   9
  AP3M2 WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3M2 MUTATED      0    9
  AP3M2 WILD-TYPE    4  301
                        clus
vv                       AP3M2 MUTATED AP3M2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(692) Variable = EHBP1 MUTATION ANALYSIS
D692V1, survival
                 sevent
clus2               0   1
  EHBP1 MUTATED    10   3
  EHBP1 WILD-TYPE 220 136
  EHBP1 MUTATED EHBP1 WILD-TYPE 
             13             356 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
              3             136 
$`EHBP1 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8297 TCGA-BR-8483 TCGA-BR-8683 
       30.90        34.68        29.59         7.40         5.39         9.86 
TCGA-CG-5721 TCGA-CG-5723 TCGA-IN-A6RN TCGA-IN-A7NU TCGA-R5-A805 TCGA-SW-A7EA 
        6.02       105.07        19.53        11.70         9.24        19.04 
TCGA-VQ-A8P2 
       38.14 

$`EHBP1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
          19.04           14.22 
[1] "5.4 - 105.1 (19.0)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.9"
D692V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EHBP1 MUTATED         0        0        2        1         2         1
  EHBP1 WILD-TYPE       2       15       38       29        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EHBP1 MUTATED           0          2          3          1        1
  EHBP1 WILD-TYPE         3         68         50         31       37
D692V3, multiclass
            clus
vv           EHBP1 MUTATED EHBP1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             3              50
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EHBP1 MUTATED     1   4   4   5
  EHBP1 WILD-TYPE  21  88 169  92
D692V4, multiclass
    clus
vv   EHBP1 MUTATED EHBP1 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             4             169
  T4             5              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
  EHBP1 MUTATED     4   3   4   2
  EHBP1 WILD-TYPE 114 101  73  75
D692V5, multiclass
    clus
vv   EHBP1 MUTATED EHBP1 WILD-TYPE
  N0             4             114
  N1             3             101
  N2             4              73
  N3             2              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"
D692V6, binary
                 cls
clus                0   1
  EHBP1 MUTATED    14   0
  EHBP1 WILD-TYPE 332  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED     14    0
  EHBP1 WILD-TYPE  332   29
   clus
vv  EHBP1 MUTATED EHBP1 WILD-TYPE
  0            14             332
  1             0              29
[1] 2 2
[1] FALSE
D692V7, binary
                 cls
clus                0   1
  EHBP1 MUTATED     5   9
  EHBP1 WILD-TYPE 140 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED      5    9
  EHBP1 WILD-TYPE  140  239
        clus
vv       EHBP1 MUTATED EHBP1 WILD-TYPE
  FEMALE             5             140
  MALE               9             239
[1] 2 2
[1] FALSE
D692V8, binary
                 cls
clus                0   1
  EHBP1 MUTATED    11   1
  EHBP1 WILD-TYPE 281  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED     11    1
  EHBP1 WILD-TYPE  281   58
     clus
vv    EHBP1 MUTATED EHBP1 WILD-TYPE
  NO             11             281
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EHBP1 MUTATED                                          0
  EHBP1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EHBP1 MUTATED                                       2
  EHBP1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EHBP1 MUTATED                                                        6
  EHBP1 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EHBP1 MUTATED                                                   1
  EHBP1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EHBP1 MUTATED                                                                   4
  EHBP1 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EHBP1 MUTATED                                                    0
  EHBP1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EHBP1 MUTATED                                                  1
  EHBP1 WILD-TYPE                                               60
D692V9, multiclass
                                                                   clus
vv                                                                  EHBP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  EHBP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EHBP1 MUTATED    12   0   0   1
  EHBP1 WILD-TYPE 299  14  15  23
D692V10, multiclass
    clus
vv   EHBP1 MUTATED EHBP1 WILD-TYPE
  R0            12             299
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D692V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EHBP1 MUTATED       1                         0
  EHBP1 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EHBP1 MUTATED                                           0    10
  EHBP1 WILD-TYPE                                         1   233
D692V12, multiclass
                                           clus
vv                                          EHBP1 MUTATED EHBP1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D692V13, binary
                 cls
clus                0   1
  EHBP1 MUTATED     0  10
  EHBP1 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED      0   10
  EHBP1 WILD-TYPE    4  300
                        clus
vv                       EHBP1 MUTATED EHBP1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(693) Variable = CRAT MUTATION ANALYSIS
D693V1, survival
                sevent
clus2              0   1
  CRAT MUTATED     7   3
  CRAT WILD-TYPE 223 136
  CRAT MUTATED CRAT WILD-TYPE 
            10            359 
  CRAT MUTATED CRAT WILD-TYPE 
             3            136 
$`CRAT MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4201 TCGA-BR-8363 TCGA-CG-4466 TCGA-CG-5721 
       26.70        19.56        30.90         0.26        18.97         6.02 
TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-A4G8 TCGA-HU-A4GX 
       26.47        24.39        22.68        20.25 

$`CRAT WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        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-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-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-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-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-8249 TCGA-HU-8602 
       52.21        30.51         1.51         5.92        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 

  CRAT MUTATED CRAT WILD-TYPE 
          0.26           0.00 
  CRAT MUTATED CRAT WILD-TYPE 
          30.9          122.3 
  CRAT MUTATED CRAT WILD-TYPE 
        21.465         14.070 
[1] "0.3 - 30.9 (21.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D693V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CRAT MUTATED         1        1        3        0         0         2
  CRAT WILD-TYPE       1       14       37       30        37        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CRAT MUTATED           0          0          0          2        1
  CRAT WILD-TYPE         3         70         53         30       37
D693V3, multiclass
            clus
vv           CRAT MUTATED CRAT WILD-TYPE
  STAGE I               1              1
  STAGE IA              1             14
  STAGE IB              3             37
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CRAT MUTATED     2   4   1   4
  CRAT WILD-TYPE  20  88 172  93
D693V4, multiclass
    clus
vv   CRAT MUTATED CRAT WILD-TYPE
  T1            2             20
  T2            4             88
  T3            1            172
  T4            4             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
  CRAT MUTATED     5   4   1   1
  CRAT WILD-TYPE 113 100  76  76
D693V5, multiclass
    clus
vv   CRAT MUTATED CRAT WILD-TYPE
  N0            5            113
  N1            4            100
  N2            1             76
  N3            1             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"
D693V6, binary
                cls
clus               0   1
  CRAT MUTATED    10   0
  CRAT WILD-TYPE 336  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRAT MUTATED     10    0
  CRAT WILD-TYPE  336   29
   clus
vv  CRAT MUTATED CRAT WILD-TYPE
  0           10            336
  1            0             29
[1] 2 2
[1] FALSE
D693V7, binary
                cls
clus               0   1
  CRAT MUTATED     9   3
  CRAT WILD-TYPE 136 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRAT MUTATED      9    3
  CRAT WILD-TYPE  136  245
        clus
vv       CRAT MUTATED CRAT WILD-TYPE
  FEMALE            9            136
  MALE              3            245
[1] 2 2
[1] FALSE
D693V8, binary
                cls
clus               0   1
  CRAT MUTATED    11   0
  CRAT WILD-TYPE 281  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRAT MUTATED     11    0
  CRAT WILD-TYPE  281   59
     clus
vv    CRAT MUTATED CRAT WILD-TYPE
  NO            11            281
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CRAT MUTATED                                          1
  CRAT WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CRAT MUTATED                                       4
  CRAT WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CRAT MUTATED                                                        4
  CRAT WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CRAT MUTATED                                                   0
  CRAT WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CRAT MUTATED                                                                   2
  CRAT WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CRAT MUTATED                                                    0
  CRAT WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CRAT MUTATED                                                  1
  CRAT WILD-TYPE                                               60
D693V9, multiclass
                                                                   clus
vv                                                                  CRAT MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  CRAT WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CRAT MUTATED     8   0   0   2
  CRAT WILD-TYPE 303  14  15  22
D693V10, multiclass
    clus
vv   CRAT MUTATED CRAT WILD-TYPE
  R0            8            303
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D693V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CRAT MUTATED       3                         1
  CRAT WILD-TYPE    84                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CRAT MUTATED                                           0     6
  CRAT WILD-TYPE                                         1   237
D693V12, multiclass
                                           clus
vv                                          CRAT MUTATED CRAT WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D693V13, binary
                cls
clus               0   1
  CRAT MUTATED     0  10
  CRAT WILD-TYPE   4 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRAT MUTATED      0   10
  CRAT WILD-TYPE    4  300
                        clus
vv                       CRAT MUTATED CRAT WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           10            300
[1] 2 2
[1] FALSE

Clustering(694) Variable = SMAP2 MUTATION ANALYSIS
D694V1, survival
                 sevent
clus2               0   1
  SMAP2 MUTATED     3   2
  SMAP2 WILD-TYPE 227 137
  SMAP2 MUTATED SMAP2 WILD-TYPE 
              5             364 
  SMAP2 MUTATED SMAP2 WILD-TYPE 
              2             137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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           14.22 
[1] "9.7 - 36.2 (30.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D694V2, 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       2       14       40       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMAP2 MUTATED           0          2          0          0        0
  SMAP2 WILD-TYPE         3         68         53         32       38
D694V3, multiclass
            clus
vv           SMAP2 MUTATED SMAP2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMAP2 MUTATED     1   0   3   0
  SMAP2 WILD-TYPE  21  92 170  97
D694V4, multiclass
    clus
vv   SMAP2 MUTATED SMAP2 WILD-TYPE
  T1             1              21
  T2             0              92
  T3             3             170
  T4             0              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
  SMAP2 MUTATED     2   1   1   0
  SMAP2 WILD-TYPE 116 103  76  77
D694V5, multiclass
    clus
vv   SMAP2 MUTATED SMAP2 WILD-TYPE
  N0             2             116
  N1             1             103
  N2             1              76
  N3             0              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"
D694V6, binary
                 cls
clus                0   1
  SMAP2 MUTATED     5   0
  SMAP2 WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAP2 MUTATED      5    0
  SMAP2 WILD-TYPE  341   29
   clus
vv  SMAP2 MUTATED SMAP2 WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D694V7, binary
                 cls
clus                0   1
  SMAP2 MUTATED     2   3
  SMAP2 WILD-TYPE 143 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAP2 MUTATED      2    3
  SMAP2 WILD-TYPE  143  245
        clus
vv       SMAP2 MUTATED SMAP2 WILD-TYPE
  FEMALE             2             143
  MALE               3             245
[1] 2 2
[1] FALSE
D694V8, binary
                 cls
clus                0   1
  SMAP2 MUTATED     5   0
  SMAP2 WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAP2 MUTATED      5    0
  SMAP2 WILD-TYPE  287   59
     clus
vv    SMAP2 MUTATED SMAP2 WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SMAP2 MUTATED                                          0
  SMAP2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SMAP2 MUTATED                                       0
  SMAP2 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMAP2 MUTATED                                                        4
  SMAP2 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SMAP2 MUTATED                                                   0
  SMAP2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMAP2 MUTATED                                                                   0
  SMAP2 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SMAP2 MUTATED                                                    1
  SMAP2 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SMAP2 MUTATED                                                  0
  SMAP2 WILD-TYPE                                               61
D694V9, multiclass
                                                                   clus
vv                                                                  SMAP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  SMAP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SMAP2 MUTATED     3   0   0   1
  SMAP2 WILD-TYPE 308  14  15  23
D694V10, multiclass
    clus
vv   SMAP2 MUTATED SMAP2 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D694V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SMAP2 MUTATED       1                         0
  SMAP2 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMAP2 MUTATED                                           0     4
  SMAP2 WILD-TYPE                                         1   239
D694V12, multiclass
                                           clus
vv                                          SMAP2 MUTATED SMAP2 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D694V13, binary
                 cls
clus                0   1
  SMAP2 MUTATED     0   5
  SMAP2 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAP2 MUTATED      0    5
  SMAP2 WILD-TYPE    4  305
                        clus
vv                       SMAP2 MUTATED SMAP2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(695) Variable = APITD1 MUTATION ANALYSIS
D695V1, survival
                  sevent
clus2                0   1
  APITD1 MUTATED     1   4
  APITD1 WILD-TYPE 229 135
  APITD1 MUTATED APITD1 WILD-TYPE 
               5              364 
  APITD1 MUTATED APITD1 WILD-TYPE 
               4              135 
$`APITD1 MUTATED`
TCGA-BR-4257 TCGA-BR-8361 TCGA-BR-8382 TCGA-CD-A4MI TCGA-D7-A4YV 
        9.67        31.10        25.05        11.77         5.92 

$`APITD1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  APITD1 MUTATED APITD1 WILD-TYPE 
            5.92             0.00 
  APITD1 MUTATED APITD1 WILD-TYPE 
            31.1            122.3 
  APITD1 MUTATED APITD1 WILD-TYPE 
           11.77            14.35 
[1] "5.9 - 31.1 (11.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.3"
D695V2, 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       2       15       40       30        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  APITD1 MUTATED           0          1          0          2        0
  APITD1 WILD-TYPE         3         69         53         30       38
D695V3, multiclass
            clus
vv           APITD1 MUTATED APITD1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  APITD1 MUTATED     0   0   2   2
  APITD1 WILD-TYPE  22  92 171  95
D695V4, multiclass
    clus
vv   APITD1 MUTATED APITD1 WILD-TYPE
  T1              0               22
  T2              0               92
  T3              2              171
  T4              2               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
  APITD1 MUTATED     0   2   1   1
  APITD1 WILD-TYPE 118 102  76  76
D695V5, multiclass
    clus
vv   APITD1 MUTATED APITD1 WILD-TYPE
  N0              0              118
  N1              2              102
  N2              1               76
  N3              1               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"
D695V6, binary
                  cls
clus                 0   1
  APITD1 MUTATED     5   0
  APITD1 WILD-TYPE 341  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  APITD1 MUTATED      5    0
  APITD1 WILD-TYPE  341   29
   clus
vv  APITD1 MUTATED APITD1 WILD-TYPE
  0              5              341
  1              0               29
[1] 2 2
[1] FALSE
D695V7, binary
                  cls
clus                 0   1
  APITD1 MUTATED     4   1
  APITD1 WILD-TYPE 141 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  APITD1 MUTATED      4    1
  APITD1 WILD-TYPE  141  247
        clus
vv       APITD1 MUTATED APITD1 WILD-TYPE
  FEMALE              4              141
  MALE                1              247
[1] 2 2
[1] FALSE
D695V8, binary
                  cls
clus                 0   1
  APITD1 MUTATED     5   0
  APITD1 WILD-TYPE 287  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  APITD1 MUTATED      5    0
  APITD1 WILD-TYPE  287   59
     clus
vv    APITD1 MUTATED APITD1 WILD-TYPE
  NO               5              287
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  APITD1 MUTATED                                          0
  APITD1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  APITD1 MUTATED                                       0
  APITD1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  APITD1 MUTATED                                                        4
  APITD1 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  APITD1 MUTATED                                                   0
  APITD1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  APITD1 MUTATED                                                                   0
  APITD1 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  APITD1 MUTATED                                                    0
  APITD1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  APITD1 MUTATED                                                  1
  APITD1 WILD-TYPE                                               60
D695V9, multiclass
                                                                   clus
vv                                                                  APITD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  APITD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  APITD1 MUTATED     3   0   0   1
  APITD1 WILD-TYPE 308  14  15  23
D695V10, multiclass
    clus
vv   APITD1 MUTATED APITD1 WILD-TYPE
  R0              3              308
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D695V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  APITD1 MUTATED       1                         0
  APITD1 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  APITD1 MUTATED                                           0     4
  APITD1 WILD-TYPE                                         1   239
D695V12, multiclass
                                           clus
vv                                          APITD1 MUTATED APITD1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D695V13, binary
                  cls
clus                 0   1
  APITD1 MUTATED     0   5
  APITD1 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  APITD1 MUTATED      0    5
  APITD1 WILD-TYPE    4  305
                        clus
vv                       APITD1 MUTATED APITD1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(696) Variable = KIFAP3 MUTATION ANALYSIS
D696V1, survival
                  sevent
clus2                0   1
  KIFAP3 MUTATED    10   4
  KIFAP3 WILD-TYPE 220 135
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
              14              355 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               4              135 
$`KIFAP3 MUTATED`
TCGA-CG-4460 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-7715 TCGA-BR-8360 
       21.99        30.90         9.34        34.68        33.63         6.18 
TCGA-BR-8369 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-D7-8572 TCGA-HU-A4G8 TCGA-HU-A4H8 
       14.04         6.58        12.62        16.80        22.68        14.07 
TCGA-KB-A6F7 TCGA-VQ-A8P2 
       63.62        38.14 

$`KIFAP3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-D7-8573 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-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-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-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 

  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
            6.18             0.00 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
           63.62           122.30 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
          19.395           14.170 
[1] "6.2 - 63.6 (19.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D696V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIFAP3 MUTATED         0        0        3        0         4         2
  KIFAP3 WILD-TYPE       2       15       37       30        33        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIFAP3 MUTATED           0          1          1          0        1
  KIFAP3 WILD-TYPE         3         69         52         32       37
D696V3, multiclass
            clus
vv           KIFAP3 MUTATED KIFAP3 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                0               30
  STAGE IIA               4               33
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIFAP3 MUTATED     2   3   6   2
  KIFAP3 WILD-TYPE  20  89 167  95
D696V4, multiclass
    clus
vv   KIFAP3 MUTATED KIFAP3 WILD-TYPE
  T1              2               20
  T2              3               89
  T3              6              167
  T4              2               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
  KIFAP3 MUTATED     5   6   1   1
  KIFAP3 WILD-TYPE 113  98  76  76
D696V5, multiclass
    clus
vv   KIFAP3 MUTATED KIFAP3 WILD-TYPE
  N0              5              113
  N1              6               98
  N2              1               76
  N3              1               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"
D696V6, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED    13   1
  KIFAP3 WILD-TYPE 333  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED     13    1
  KIFAP3 WILD-TYPE  333   28
   clus
vv  KIFAP3 MUTATED KIFAP3 WILD-TYPE
  0             13              333
  1              1               28
[1] 2 2
[1] FALSE
D696V7, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED     6   8
  KIFAP3 WILD-TYPE 139 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED      6    8
  KIFAP3 WILD-TYPE  139  240
        clus
vv       KIFAP3 MUTATED KIFAP3 WILD-TYPE
  FEMALE              6              139
  MALE                8              240
[1] 2 2
[1] FALSE
D696V8, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED    12   2
  KIFAP3 WILD-TYPE 280  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED     12    2
  KIFAP3 WILD-TYPE  280   57
     clus
vv    KIFAP3 MUTATED KIFAP3 WILD-TYPE
  NO              12              280
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIFAP3 MUTATED                                          0
  KIFAP3 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIFAP3 MUTATED                                       2
  KIFAP3 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIFAP3 MUTATED                                                        7
  KIFAP3 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIFAP3 MUTATED                                                   1
  KIFAP3 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIFAP3 MUTATED                                                                   3
  KIFAP3 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIFAP3 MUTATED                                                    0
  KIFAP3 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIFAP3 MUTATED                                                  1
  KIFAP3 WILD-TYPE                                               60
D696V9, multiclass
                                                                   clus
vv                                                                  KIFAP3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  KIFAP3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KIFAP3 MUTATED     8   0   1   2
  KIFAP3 WILD-TYPE 303  14  14  22
D696V10, multiclass
    clus
vv   KIFAP3 MUTATED KIFAP3 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D696V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KIFAP3 MUTATED       4                         0
  KIFAP3 WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIFAP3 MUTATED                                           0     8
  KIFAP3 WILD-TYPE                                         1   235
D696V12, multiclass
                                           clus
vv                                          KIFAP3 MUTATED KIFAP3 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D696V13, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED     0  11
  KIFAP3 WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED      0   11
  KIFAP3 WILD-TYPE    4  299
                        clus
vv                       KIFAP3 MUTATED KIFAP3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(697) Variable = ELL2 MUTATION ANALYSIS
D697V1, survival
                sevent
clus2              0   1
  ELL2 MUTATED     8   6
  ELL2 WILD-TYPE 222 133
  ELL2 MUTATED ELL2 WILD-TYPE 
            14            355 
  ELL2 MUTATED ELL2 WILD-TYPE 
             6            133 
$`ELL2 MUTATED`
TCGA-BR-4253 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-A4QL TCGA-CD-A4MI TCGA-CG-4437 
        4.08         6.18        34.68        16.14        11.77         8.05 
TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A6EY TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4H2 
        6.02       105.07        11.44        77.29        22.32        12.95 
TCGA-RD-A7BW TCGA-VQ-A8P2 
        5.13        38.14 

$`ELL2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-4279 
       18.35        30.90         4.08         9.34         9.67         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-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-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-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-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-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-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 

  ELL2 MUTATED ELL2 WILD-TYPE 
          4.08           0.00 
  ELL2 MUTATED ELL2 WILD-TYPE 
        105.07         122.30 
  ELL2 MUTATED ELL2 WILD-TYPE 
         12.36          14.43 
[1] "4.1 - 105.1 (12.4)" "0.0 - 122.3 (14.4)"
[1] "hr=" "1"  
D697V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ELL2 MUTATED         0        0        2        3         1         1
  ELL2 WILD-TYPE       2       15       38       27        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ELL2 MUTATED           0          4          3          0        1
  ELL2 WILD-TYPE         3         66         50         32       37
D697V3, multiclass
            clus
vv           ELL2 MUTATED ELL2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              3             27
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            4             66
  STAGE IIIB            3             50
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ELL2 MUTATED     0   5   6   4
  ELL2 WILD-TYPE  22  87 167  93
D697V4, multiclass
    clus
vv   ELL2 MUTATED ELL2 WILD-TYPE
  T1            0             22
  T2            5             87
  T3            6            167
  T4            4             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
  ELL2 MUTATED     5   7   0   3
  ELL2 WILD-TYPE 113  97  77  74
D697V5, multiclass
    clus
vv   ELL2 MUTATED ELL2 WILD-TYPE
  N0            5            113
  N1            7             97
  N2            0             77
  N3            3             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"
D697V6, binary
                cls
clus               0   1
  ELL2 MUTATED    15   0
  ELL2 WILD-TYPE 331  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELL2 MUTATED     15    0
  ELL2 WILD-TYPE  331   29
   clus
vv  ELL2 MUTATED ELL2 WILD-TYPE
  0           15            331
  1            0             29
[1] 2 2
[1] FALSE
D697V7, binary
                cls
clus               0   1
  ELL2 MUTATED     8   7
  ELL2 WILD-TYPE 137 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELL2 MUTATED      8    7
  ELL2 WILD-TYPE  137  241
        clus
vv       ELL2 MUTATED ELL2 WILD-TYPE
  FEMALE            8            137
  MALE              7            241
[1] 2 2
[1] FALSE
D697V8, binary
                cls
clus               0   1
  ELL2 MUTATED    11   3
  ELL2 WILD-TYPE 281  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELL2 MUTATED     11    3
  ELL2 WILD-TYPE  281   56
     clus
vv    ELL2 MUTATED ELL2 WILD-TYPE
  NO            11            281
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ELL2 MUTATED                                          0
  ELL2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ELL2 MUTATED                                       2
  ELL2 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ELL2 MUTATED                                                        7
  ELL2 WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ELL2 MUTATED                                                   2
  ELL2 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ELL2 MUTATED                                                                   2
  ELL2 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ELL2 MUTATED                                                    0
  ELL2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ELL2 MUTATED                                                  2
  ELL2 WILD-TYPE                                               59
D697V9, multiclass
                                                                   clus
vv                                                                  ELL2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  ELL2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ELL2 MUTATED    11   0   0   3
  ELL2 WILD-TYPE 300  14  15  21
D697V10, multiclass
    clus
vv   ELL2 MUTATED ELL2 WILD-TYPE
  R0           11            300
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D697V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ELL2 MUTATED       3                         0
  ELL2 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ELL2 MUTATED                                           0     8
  ELL2 WILD-TYPE                                         1   235
D697V12, multiclass
                                           clus
vv                                          ELL2 MUTATED ELL2 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D697V13, binary
                cls
clus               0   1
  ELL2 MUTATED     0  10
  ELL2 WILD-TYPE   4 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELL2 MUTATED      0   10
  ELL2 WILD-TYPE    4  300
                        clus
vv                       ELL2 MUTATED ELL2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           10            300
[1] 2 2
[1] FALSE

Clustering(698) Variable = CEP290 MUTATION ANALYSIS
D698V1, survival
                  sevent
clus2                0   1
  CEP290 MUTATED     9   4
  CEP290 WILD-TYPE 221 135
  CEP290 MUTATED CEP290 WILD-TYPE 
              13              356 
  CEP290 MUTATED CEP290 WILD-TYPE 
               4              135 
$`CEP290 MUTATED`
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7197 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8680 
        9.67        34.68         9.21         6.18        31.10        31.96 
TCGA-BR-A4J1 TCGA-CD-A487 TCGA-CD-A4MG TCGA-D7-A4YV TCGA-HF-7134 TCGA-HU-A4G8 
        0.72        12.30         6.58         5.92        52.21        22.68 
TCGA-HU-A4GT 
        6.51 

$`CEP290 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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 

  CEP290 MUTATED CEP290 WILD-TYPE 
            0.72             0.00 
  CEP290 MUTATED CEP290 WILD-TYPE 
           52.21           122.30 
  CEP290 MUTATED CEP290 WILD-TYPE 
            9.67            14.45 
[1] "0.7 - 52.2 (9.7)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D698V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CEP290 MUTATED         1        1        0        1         4         3
  CEP290 WILD-TYPE       1       14       40       29        33        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP290 MUTATED           0          1          0          1        1
  CEP290 WILD-TYPE         3         69         53         31       37
D698V3, multiclass
            clus
vv           CEP290 MUTATED CEP290 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               4               33
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CEP290 MUTATED     2   0   8   3
  CEP290 WILD-TYPE  20  92 165  94
D698V4, multiclass
    clus
vv   CEP290 MUTATED CEP290 WILD-TYPE
  T1              2               20
  T2              0               92
  T3              8              165
  T4              3               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
  CEP290 MUTATED     6   5   2   0
  CEP290 WILD-TYPE 112  99  75  77
D698V5, multiclass
    clus
vv   CEP290 MUTATED CEP290 WILD-TYPE
  N0              6              112
  N1              5               99
  N2              2               75
  N3              0               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"
D698V6, binary
                  cls
clus                 0   1
  CEP290 MUTATED    12   1
  CEP290 WILD-TYPE 334  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED     12    1
  CEP290 WILD-TYPE  334   28
   clus
vv  CEP290 MUTATED CEP290 WILD-TYPE
  0             12              334
  1              1               28
[1] 2 2
[1] FALSE
D698V7, binary
                  cls
clus                 0   1
  CEP290 MUTATED     6   8
  CEP290 WILD-TYPE 139 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED      6    8
  CEP290 WILD-TYPE  139  240
        clus
vv       CEP290 MUTATED CEP290 WILD-TYPE
  FEMALE              6              139
  MALE                8              240
[1] 2 2
[1] FALSE
D698V8, binary
                  cls
clus                 0   1
  CEP290 MUTATED    13   0
  CEP290 WILD-TYPE 279  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED     13    0
  CEP290 WILD-TYPE  279   59
     clus
vv    CEP290 MUTATED CEP290 WILD-TYPE
  NO              13              279
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CEP290 MUTATED                                          0
  CEP290 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CEP290 MUTATED                                       3
  CEP290 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CEP290 MUTATED                                                        6
  CEP290 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CEP290 MUTATED                                                   0
  CEP290 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CEP290 MUTATED                                                                   2
  CEP290 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CEP290 MUTATED                                                    0
  CEP290 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CEP290 MUTATED                                                  3
  CEP290 WILD-TYPE                                               58
D698V9, multiclass
                                                                   clus
vv                                                                  CEP290 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  CEP290 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CEP290 MUTATED    11   0   0   1
  CEP290 WILD-TYPE 300  14  15  23
D698V10, multiclass
    clus
vv   CEP290 MUTATED CEP290 WILD-TYPE
  R0             11              300
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D698V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CEP290 MUTATED       6                         1
  CEP290 WILD-TYPE    81                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CEP290 MUTATED                                           0     6
  CEP290 WILD-TYPE                                         1   237
D698V12, multiclass
                                           clus
vv                                          CEP290 MUTATED CEP290 WILD-TYPE
  ASIAN                                                  6               81
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D698V13, binary
                  cls
clus                 0   1
  CEP290 MUTATED     0  13
  CEP290 WILD-TYPE   4 297
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED      0   13
  CEP290 WILD-TYPE    4  297
                        clus
vv                       CEP290 MUTATED CEP290 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             13              297
[1] 2 2
[1] FALSE

Clustering(699) Variable = MBD2 MUTATION ANALYSIS
D699V1, survival
                sevent
clus2              0   1
  MBD2 MUTATED     5   3
  MBD2 WILD-TYPE 225 136
  MBD2 MUTATED MBD2 WILD-TYPE 
             8            361 
  MBD2 MUTATED MBD2 WILD-TYPE 
             3            136 
$`MBD2 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8372 
       21.99         6.97        34.68        31.10         0.26        31.27 
TCGA-HU-A4G8 TCGA-HU-A4GT 
       22.68         6.51 

$`MBD2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  MBD2 MUTATED MBD2 WILD-TYPE 
          0.26           0.00 
  MBD2 MUTATED MBD2 WILD-TYPE 
         34.68         122.30 
  MBD2 MUTATED MBD2 WILD-TYPE 
        22.335         14.170 
[1] "0.3 - 34.7 (22.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D699V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MBD2 MUTATED         0        0        1        0         2         1
  MBD2 WILD-TYPE       2       15       39       30        35        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MBD2 MUTATED           0          1          0          2        2
  MBD2 WILD-TYPE         3         69         53         30       36
D699V3, multiclass
            clus
vv           MBD2 MUTATED MBD2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MBD2 MUTATED     0   1   4   4
  MBD2 WILD-TYPE  22  91 169  93
D699V4, multiclass
    clus
vv   MBD2 MUTATED MBD2 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            4            169
  T4            4             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
  MBD2 MUTATED     3   3   2   1
  MBD2 WILD-TYPE 115 101  75  76
D699V5, multiclass
    clus
vv   MBD2 MUTATED MBD2 WILD-TYPE
  N0            3            115
  N1            3            101
  N2            2             75
  N3            1             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"
D699V6, binary
                cls
clus               0   1
  MBD2 MUTATED     7   1
  MBD2 WILD-TYPE 339  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD2 MUTATED      7    1
  MBD2 WILD-TYPE  339   28
   clus
vv  MBD2 MUTATED MBD2 WILD-TYPE
  0            7            339
  1            1             28
[1] 2 2
[1] FALSE
D699V7, binary
                cls
clus               0   1
  MBD2 MUTATED     7   2
  MBD2 WILD-TYPE 138 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD2 MUTATED      7    2
  MBD2 WILD-TYPE  138  246
        clus
vv       MBD2 MUTATED MBD2 WILD-TYPE
  FEMALE            7            138
  MALE              2            246
[1] 2 2
[1] FALSE
D699V8, binary
                cls
clus               0   1
  MBD2 MUTATED     8   0
  MBD2 WILD-TYPE 284  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD2 MUTATED      8    0
  MBD2 WILD-TYPE  284   59
     clus
vv    MBD2 MUTATED MBD2 WILD-TYPE
  NO             8            284
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MBD2 MUTATED                                          0
  MBD2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MBD2 MUTATED                                       1
  MBD2 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MBD2 MUTATED                                                        6
  MBD2 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MBD2 MUTATED                                                   0
  MBD2 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MBD2 MUTATED                                                                   1
  MBD2 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MBD2 MUTATED                                                    0
  MBD2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MBD2 MUTATED                                                  1
  MBD2 WILD-TYPE                                               60
D699V9, multiclass
                                                                   clus
vv                                                                  MBD2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  MBD2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MBD2 MUTATED     5   0   1   2
  MBD2 WILD-TYPE 306  14  14  22
D699V10, multiclass
    clus
vv   MBD2 MUTATED MBD2 WILD-TYPE
  R0            5            306
  R1            0             14
  R2            1             14
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D699V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MBD2 MUTATED       2                         0
  MBD2 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MBD2 MUTATED                                           0     6
  MBD2 WILD-TYPE                                         1   237
D699V12, multiclass
                                           clus
vv                                          MBD2 MUTATED MBD2 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D699V13, binary
                cls
clus               0   1
  MBD2 MUTATED     0   8
  MBD2 WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD2 MUTATED      0    8
  MBD2 WILD-TYPE    4  302
                        clus
vv                       MBD2 MUTATED MBD2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(700) Variable = DDX43 MUTATION ANALYSIS
D700V1, survival
                 sevent
clus2               0   1
  DDX43 MUTATED     7   5
  DDX43 WILD-TYPE 223 134
  DDX43 MUTATED DDX43 WILD-TYPE 
             12             357 
  DDX43 MUTATED DDX43 WILD-TYPE 
              5             134 
$`DDX43 MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-4306 TCGA-CG-4441 
        6.97         9.34         1.12        16.14         1.02        14.01 
TCGA-D7-8572 TCGA-F1-A448 TCGA-HU-A4G6 TCGA-IP-7968 TCGA-VQ-A8DT TCGA-VQ-AA6B 
       16.80        21.27        24.26         2.53        48.79        32.94 

$`DDX43 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-A4G8 
       22.82        21.07         0.76        24.30         5.59        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-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-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-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        28.41        38.93        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       27.55        12.43        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 
         15.075          14.270 
[1] "1.0 - 48.8 (15.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D700V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDX43 MUTATED         0        1        0        0         1         1
  DDX43 WILD-TYPE       2       14       40       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDX43 MUTATED           0          2          5          0        1
  DDX43 WILD-TYPE         3         68         48         32       37
D700V3, multiclass
            clus
vv           DDX43 MUTATED DDX43 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             5              48
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX43 MUTATED     1   2   9   0
  DDX43 WILD-TYPE  21  90 164  97
D700V4, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             9             164
  T4             0              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
  DDX43 MUTATED     2   2   5   3
  DDX43 WILD-TYPE 116 102  72  74
D700V5, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  N0             2             116
  N1             2             102
  N2             5              72
  N3             3              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"
D700V6, binary
                 cls
clus                0   1
  DDX43 MUTATED     9   1
  DDX43 WILD-TYPE 337  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      9    1
  DDX43 WILD-TYPE  337   28
   clus
vv  DDX43 MUTATED DDX43 WILD-TYPE
  0             9             337
  1             1              28
[1] 2 2
[1] FALSE
D700V7, binary
                 cls
clus                0   1
  DDX43 MUTATED     3  10
  DDX43 WILD-TYPE 142 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      3   10
  DDX43 WILD-TYPE  142  238
        clus
vv       DDX43 MUTATED DDX43 WILD-TYPE
  FEMALE             3             142
  MALE              10             238
[1] 2 2
[1] FALSE
D700V8, binary
                 cls
clus                0   1
  DDX43 MUTATED     6   3
  DDX43 WILD-TYPE 286  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      6    3
  DDX43 WILD-TYPE  286   56
     clus
vv    DDX43 MUTATED DDX43 WILD-TYPE
  NO              6             286
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DDX43 MUTATED                                          0
  DDX43 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DDX43 MUTATED                                       0
  DDX43 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DDX43 MUTATED                                                        8
  DDX43 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DDX43 MUTATED                                                   1
  DDX43 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DDX43 MUTATED                                                                   3
  DDX43 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DDX43 MUTATED                                                    1
  DDX43 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DDX43 MUTATED                                                  0
  DDX43 WILD-TYPE                                               61
D700V9, multiclass
                                                                   clus
vv                                                                  DDX43 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  DDX43 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DDX43 MUTATED     9   0   1   3
  DDX43 WILD-TYPE 302  14  14  21
D700V10, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  R0             9             302
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D700V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DDX43 MUTATED       1                         0
  DDX43 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDX43 MUTATED                                           0     9
  DDX43 WILD-TYPE                                         1   234
D700V12, multiclass
                                           clus
vv                                          DDX43 MUTATED DDX43 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D700V13, binary
                 cls
clus                0   1
  DDX43 MUTATED     1   8
  DDX43 WILD-TYPE   3 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      1    8
  DDX43 WILD-TYPE    3  302
                        clus
vv                       DDX43 MUTATED DDX43 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(701) Variable = DDHD1 MUTATION ANALYSIS
D701V1, survival
                 sevent
clus2               0   1
  DDHD1 MUTATED     7   3
  DDHD1 WILD-TYPE 223 136
  DDHD1 MUTATED DDHD1 WILD-TYPE 
             10             359 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
              3             136 
$`DDHD1 MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8081 TCGA-CG-4438 
       11.70         6.97        30.90        34.68        32.25        54.08 
TCGA-D7-A6EY TCGA-F1-6874 TCGA-F1-A448 TCGA-HU-A4G8 
       11.44        14.47        21.27        22.68 

$`DDHD1 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        7.99         8.05         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-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 

  DDHD1 MUTATED DDHD1 WILD-TYPE 
           6.97            0.00 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
          54.08          122.30 
  DDHD1 MUTATED DDHD1 WILD-TYPE 
         21.975          14.070 
[1] "7.0 - 54.1 (22.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D701V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DDHD1 MUTATED         0        0        2        0         1         3
  DDHD1 WILD-TYPE       2       15       38       30        36        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDHD1 MUTATED           0          2          2          0        2
  DDHD1 WILD-TYPE         3         68         51         32       36
D701V3, multiclass
            clus
vv           DDHD1 MUTATED DDHD1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDHD1 MUTATED     0   3   5   5
  DDHD1 WILD-TYPE  22  89 168  92
D701V4, multiclass
    clus
vv   DDHD1 MUTATED DDHD1 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             5             168
  T4             5              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
  DDHD1 MUTATED     6   2   2   2
  DDHD1 WILD-TYPE 112 102  75  75
D701V5, multiclass
    clus
vv   DDHD1 MUTATED DDHD1 WILD-TYPE
  N0             6             112
  N1             2             102
  N2             2              75
  N3             2              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"
D701V6, binary
                 cls
clus                0   1
  DDHD1 MUTATED    12   0
  DDHD1 WILD-TYPE 334  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD1 MUTATED     12    0
  DDHD1 WILD-TYPE  334   29
   clus
vv  DDHD1 MUTATED DDHD1 WILD-TYPE
  0            12             334
  1             0              29
[1] 2 2
[1] FALSE
D701V7, binary
                 cls
clus                0   1
  DDHD1 MUTATED     7   6
  DDHD1 WILD-TYPE 138 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD1 MUTATED      7    6
  DDHD1 WILD-TYPE  138  242
        clus
vv       DDHD1 MUTATED DDHD1 WILD-TYPE
  FEMALE             7             138
  MALE               6             242
[1] 2 2
[1] FALSE
D701V8, binary
                 cls
clus                0   1
  DDHD1 MUTATED     9   1
  DDHD1 WILD-TYPE 283  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD1 MUTATED      9    1
  DDHD1 WILD-TYPE  283   58
     clus
vv    DDHD1 MUTATED DDHD1 WILD-TYPE
  NO              9             283
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DDHD1 MUTATED                                          0
  DDHD1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DDHD1 MUTATED                                       2
  DDHD1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DDHD1 MUTATED                                                        6
  DDHD1 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DDHD1 MUTATED                                                   1
  DDHD1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DDHD1 MUTATED                                                                   3
  DDHD1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DDHD1 MUTATED                                                    0
  DDHD1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DDHD1 MUTATED                                                  1
  DDHD1 WILD-TYPE                                               60
D701V9, multiclass
                                                                   clus
vv                                                                  DDHD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  DDHD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DDHD1 MUTATED     8   0   0   4
  DDHD1 WILD-TYPE 303  14  15  20
D701V10, multiclass
    clus
vv   DDHD1 MUTATED DDHD1 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D701V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DDHD1 MUTATED       1                         0
  DDHD1 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DDHD1 MUTATED                                           0    11
  DDHD1 WILD-TYPE                                         1   232
D701V12, multiclass
                                           clus
vv                                          DDHD1 MUTATED DDHD1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D701V13, binary
                 cls
clus                0   1
  DDHD1 MUTATED     1  11
  DDHD1 WILD-TYPE   3 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD1 MUTATED      1   11
  DDHD1 WILD-TYPE    3  299
                        clus
vv                       DDHD1 MUTATED DDHD1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(702) Variable = TMEM64 MUTATION ANALYSIS
D702V1, survival
                  sevent
clus2                0   1
  TMEM64 MUTATED     6   1
  TMEM64 WILD-TYPE 224 138
  TMEM64 MUTATED TMEM64 WILD-TYPE 
               7              362 
  TMEM64 MUTATED TMEM64 WILD-TYPE 
               1              138 
$`TMEM64 MUTATED`
TCGA-BR-6452 TCGA-BR-7707 TCGA-CD-8525 TCGA-CD-8536 TCGA-CG-4300 TCGA-MX-A5UJ 
       34.68        35.84        12.59        12.43        20.02        19.73 
TCGA-VQ-AA6J 
       27.55 

$`TMEM64 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-4305 TCGA-CG-4306 
       11.77        12.62         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-AA6K TCGA-ZA-A8F6 
       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 
           20.02            14.12 
[1] "12.4 - 35.8 (20.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "3.5"
D702V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM64 MUTATED         0        0        1        1         1         0
  TMEM64 WILD-TYPE       2       15       39       29        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM64 MUTATED           0          2          2          0        0
  TMEM64 WILD-TYPE         3         68         51         32       38
D702V3, multiclass
            clus
vv           TMEM64 MUTATED TMEM64 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              2               51
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TMEM64 MUTATED     0   1   5   1
  TMEM64 WILD-TYPE  22  91 168  96
D702V4, multiclass
    clus
vv   TMEM64 MUTATED TMEM64 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              5              168
  T4              1               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
  TMEM64 MUTATED     3   1   3   0
  TMEM64 WILD-TYPE 115 103  74  77
D702V5, multiclass
    clus
vv   TMEM64 MUTATED TMEM64 WILD-TYPE
  N0              3              115
  N1              1              103
  N2              3               74
  N3              0               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"
D702V6, binary
                  cls
clus                 0   1
  TMEM64 MUTATED     7   0
  TMEM64 WILD-TYPE 339  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM64 MUTATED      7    0
  TMEM64 WILD-TYPE  339   29
   clus
vv  TMEM64 MUTATED TMEM64 WILD-TYPE
  0              7              339
  1              0               29
[1] 2 2
[1] FALSE
D702V7, binary
                  cls
clus                 0   1
  TMEM64 MUTATED     4   3
  TMEM64 WILD-TYPE 141 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM64 MUTATED      4    3
  TMEM64 WILD-TYPE  141  245
        clus
vv       TMEM64 MUTATED TMEM64 WILD-TYPE
  FEMALE              4              141
  MALE                3              245
[1] 2 2
[1] FALSE
D702V8, binary
                  cls
clus                 0   1
  TMEM64 MUTATED     5   1
  TMEM64 WILD-TYPE 287  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM64 MUTATED      5    1
  TMEM64 WILD-TYPE  287   58
     clus
vv    TMEM64 MUTATED TMEM64 WILD-TYPE
  NO               5              287
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TMEM64 MUTATED                                          0
  TMEM64 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TMEM64 MUTATED                                       0
  TMEM64 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM64 MUTATED                                                        4
  TMEM64 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TMEM64 MUTATED                                                   1
  TMEM64 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM64 MUTATED                                                                   1
  TMEM64 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TMEM64 MUTATED                                                    0
  TMEM64 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TMEM64 MUTATED                                                  1
  TMEM64 WILD-TYPE                                               60
D702V9, multiclass
                                                                   clus
vv                                                                  TMEM64 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  TMEM64 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TMEM64 MUTATED     7   0   0   0
  TMEM64 WILD-TYPE 304  14  15  24
D702V10, multiclass
    clus
vv   TMEM64 MUTATED TMEM64 WILD-TYPE
  R0              7              304
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D702V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TMEM64 MUTATED       2                         1
  TMEM64 WILD-TYPE    85                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM64 MUTATED                                           0     3
  TMEM64 WILD-TYPE                                         1   240
D702V12, multiclass
                                           clus
vv                                          TMEM64 MUTATED TMEM64 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D702V13, binary
                  cls
clus                 0   1
  TMEM64 MUTATED     0   5
  TMEM64 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM64 MUTATED      0    5
  TMEM64 WILD-TYPE    4  305
                        clus
vv                       TMEM64 MUTATED TMEM64 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(703) Variable = ECSIT MUTATION ANALYSIS
D703V1, survival
                 sevent
clus2               0   1
  ECSIT MUTATED     3   3
  ECSIT WILD-TYPE 227 136
  ECSIT MUTATED ECSIT WILD-TYPE 
              6             363 
  ECSIT MUTATED ECSIT WILD-TYPE 
              3             136 
$`ECSIT MUTATED`
TCGA-MX-A663 TCGA-BR-4280 TCGA-BR-8059 TCGA-BR-8487 TCGA-HF-A5NB TCGA-HU-A4H8 
        9.86         6.61        14.43         1.12        30.51        14.07 

$`ECSIT WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15        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-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-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-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 

  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          14.470 
[1] "1.1 - 30.5 (12.0)"  "0.0 - 122.3 (14.5)"
[1] "hr=" "1.8"
D703V2, 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       2       15       39       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ECSIT MUTATED           2          0          0          1        0
  ECSIT WILD-TYPE         1         70         53         31       38
D703V3, multiclass
            clus
vv           ECSIT MUTATED ECSIT WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              2               1
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ECSIT MUTATED     1   1   2   2
  ECSIT WILD-TYPE  21  91 171  95
D703V4, multiclass
    clus
vv   ECSIT MUTATED ECSIT WILD-TYPE
  T1             1              21
  T2             1              91
  T3             2             171
  T4             2              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
  ECSIT MUTATED     2   3   0   1
  ECSIT WILD-TYPE 116 101  77  76
D703V5, multiclass
    clus
vv   ECSIT MUTATED ECSIT WILD-TYPE
  N0             2             116
  N1             3             101
  N2             0              77
  N3             1              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"
D703V6, binary
                 cls
clus                0   1
  ECSIT MUTATED     6   0
  ECSIT WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ECSIT MUTATED      6    0
  ECSIT WILD-TYPE  340   29
   clus
vv  ECSIT MUTATED ECSIT WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D703V7, binary
                 cls
clus                0   1
  ECSIT MUTATED     3   3
  ECSIT WILD-TYPE 142 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ECSIT MUTATED      3    3
  ECSIT WILD-TYPE  142  245
        clus
vv       ECSIT MUTATED ECSIT WILD-TYPE
  FEMALE             3             142
  MALE               3             245
[1] 2 2
[1] FALSE
D703V8, binary
                 cls
clus                0   1
  ECSIT MUTATED     5   1
  ECSIT WILD-TYPE 287  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ECSIT MUTATED      5    1
  ECSIT WILD-TYPE  287   58
     clus
vv    ECSIT MUTATED ECSIT WILD-TYPE
  NO              5             287
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ECSIT MUTATED                                          0
  ECSIT WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ECSIT MUTATED                                       0
  ECSIT WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ECSIT MUTATED                                                        3
  ECSIT WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ECSIT MUTATED                                                   1
  ECSIT WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ECSIT MUTATED                                                                   1
  ECSIT WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ECSIT MUTATED                                                    0
  ECSIT WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ECSIT MUTATED                                                  1
  ECSIT WILD-TYPE                                               60
D703V9, multiclass
                                                                   clus
vv                                                                  ECSIT MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  ECSIT WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ECSIT MUTATED     4   1   0   1
  ECSIT WILD-TYPE 307  13  15  23
D703V10, multiclass
    clus
vv   ECSIT MUTATED ECSIT WILD-TYPE
  R0             4             307
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D703V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ECSIT MUTATED       1                         0
  ECSIT WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ECSIT MUTATED                                           0     4
  ECSIT WILD-TYPE                                         1   239
D703V12, multiclass
                                           clus
vv                                          ECSIT MUTATED ECSIT WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D703V13, binary
                 cls
clus                0   1
  ECSIT MUTATED     0   5
  ECSIT WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ECSIT MUTATED      0    5
  ECSIT WILD-TYPE    4  305
                        clus
vv                       ECSIT MUTATED ECSIT WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(704) Variable = KIAA1543 MUTATION ANALYSIS
D704V1, survival
                    sevent
clus2                  0   1
  KIAA1543 MUTATED    11   5
  KIAA1543 WILD-TYPE 219 134
  KIAA1543 MUTATED KIAA1543 WILD-TYPE 
                16                353 
  KIAA1543 MUTATED KIAA1543 WILD-TYPE 
                 5                134 
$`KIAA1543 MUTATED`
TCGA-BR-4257 TCGA-BR-6852 TCGA-BR-8591 TCGA-BR-A4J4 TCGA-CD-5813 TCGA-CG-4306 
        9.67        44.94        28.14         0.53        12.39         1.02 
TCGA-CG-4465 TCGA-CG-5721 TCGA-D7-A4YV TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4GT 
        9.01         6.02         5.92        77.29        30.51         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-MX-A5UJ 
        6.58        20.25        23.84        19.73 

$`KIAA1543 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4J5 TCGA-BR-A4J6 
       12.89         8.98         0.72        14.17        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-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-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-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-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
        0.10         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-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 

  KIAA1543 MUTATED KIAA1543 WILD-TYPE 
              0.53               0.00 
  KIAA1543 MUTATED KIAA1543 WILD-TYPE 
             77.29             122.30 
  KIAA1543 MUTATED KIAA1543 WILD-TYPE 
             11.03              14.43 
[1] "0.5 - 77.3 (11.0)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D704V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1543 MUTATED         0        0        0        2         2         3
  KIAA1543 WILD-TYPE       2       15       40       28        35        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1543 MUTATED           0          2          1          3        3
  KIAA1543 WILD-TYPE         3         68         52         29       35
D704V3, multiclass
            clus
vv           KIAA1543 MUTATED KIAA1543 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  2                 28
  STAGE IIA                 2                 35
  STAGE IIB                 3                 49
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                1                 52
  STAGE IIIC                3                 29
  STAGE IV                  3                 35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1543 MUTATED     0   2   7   7
  KIAA1543 WILD-TYPE  22  90 166  90
D704V4, multiclass
    clus
vv   KIAA1543 MUTATED KIAA1543 WILD-TYPE
  T1                0                 22
  T2                2                 90
  T3                7                166
  T4                7                 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
  KIAA1543 MUTATED     4   4   5   3
  KIAA1543 WILD-TYPE 114 100  72  74
D704V5, multiclass
    clus
vv   KIAA1543 MUTATED KIAA1543 WILD-TYPE
  N0                4                114
  N1                4                100
  N2                5                 72
  N3                3                 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"
D704V6, binary
                    cls
clus                   0   1
  KIAA1543 MUTATED    15   2
  KIAA1543 WILD-TYPE 331  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1543 MUTATED     15    2
  KIAA1543 WILD-TYPE  331   27
   clus
vv  KIAA1543 MUTATED KIAA1543 WILD-TYPE
  0               15                331
  1                2                 27
[1] 2 2
[1] FALSE
D704V7, binary
                    cls
clus                   0   1
  KIAA1543 MUTATED    10   7
  KIAA1543 WILD-TYPE 135 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1543 MUTATED     10    7
  KIAA1543 WILD-TYPE  135  241
        clus
vv       KIAA1543 MUTATED KIAA1543 WILD-TYPE
  FEMALE               10                135
  MALE                  7                241
[1] 2 2
[1] FALSE
D704V8, binary
                    cls
clus                   0   1
  KIAA1543 MUTATED    11   2
  KIAA1543 WILD-TYPE 281  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1543 MUTATED     11    2
  KIAA1543 WILD-TYPE  281   57
     clus
vv    KIAA1543 MUTATED KIAA1543 WILD-TYPE
  NO                11                281
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA1543 MUTATED                                          0
  KIAA1543 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA1543 MUTATED                                       3
  KIAA1543 WILD-TYPE                                    67
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1543 MUTATED                                                        6
  KIAA1543 WILD-TYPE                                                    152
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA1543 MUTATED                                                   3
  KIAA1543 WILD-TYPE                                                18
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1543 MUTATED                                                                   1
  KIAA1543 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA1543 MUTATED                                                    0
  KIAA1543 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA1543 MUTATED                                                  4
  KIAA1543 WILD-TYPE                                               57
D704V9, multiclass
                                                                   clus
vv                                                                  KIAA1543 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 4
                                                                   clus
vv                                                                  KIAA1543 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1543 MUTATED    11   1   2   2
  KIAA1543 WILD-TYPE 300  13  13  22
D704V10, multiclass
    clus
vv   KIAA1543 MUTATED KIAA1543 WILD-TYPE
  R0               11                300
  R1                1                 13
  R2                2                 13
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D704V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1543 MUTATED       6                         0
  KIAA1543 WILD-TYPE    81                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1543 MUTATED                                           0     6
  KIAA1543 WILD-TYPE                                         1   237
D704V12, multiclass
                                           clus
vv                                          KIAA1543 MUTATED KIAA1543 WILD-TYPE
  ASIAN                                                    6                 81
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D704V13, binary
                    cls
clus                   0   1
  KIAA1543 MUTATED     0  12
  KIAA1543 WILD-TYPE   4 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1543 MUTATED      0   12
  KIAA1543 WILD-TYPE    4  298
                        clus
vv                       KIAA1543 MUTATED KIAA1543 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               12                298
[1] 2 2
[1] FALSE

Clustering(705) Variable = UPK2 MUTATION ANALYSIS
D705V1, survival
                sevent
clus2              0   1
  UPK2 MUTATED     2   2
  UPK2 WILD-TYPE 228 137
  UPK2 MUTATED UPK2 WILD-TYPE 
             4            365 
  UPK2 MUTATED UPK2 WILD-TYPE 
             2            137 
$`UPK2 MUTATED`
TCGA-BR-8081 TCGA-BR-8360 TCGA-CD-A4MG TCGA-CG-4465 
       32.25         6.18         6.58         9.01 

$`UPK2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  UPK2 MUTATED UPK2 WILD-TYPE 
          6.18           0.00 
  UPK2 MUTATED UPK2 WILD-TYPE 
         32.25         122.30 
  UPK2 MUTATED UPK2 WILD-TYPE 
         7.795         14.430 
[1] "6.2 - 32.2 (7.8)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.9"
D705V2, 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       2       15       40       30        35        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UPK2 MUTATED           0          0          0          0        1
  UPK2 WILD-TYPE         3         70         53         32       37
D705V3, multiclass
            clus
vv           UPK2 MUTATED UPK2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  UPK2 MUTATED     0   0   2   2
  UPK2 WILD-TYPE  22  92 171  95
D705V4, multiclass
    clus
vv   UPK2 MUTATED UPK2 WILD-TYPE
  T1            0             22
  T2            0             92
  T3            2            171
  T4            2             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
  UPK2 MUTATED     3   0   0   1
  UPK2 WILD-TYPE 115 104  77  76
D705V5, multiclass
    clus
vv   UPK2 MUTATED UPK2 WILD-TYPE
  N0            3            115
  N1            0            104
  N2            0             77
  N3            1             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"
D705V6, binary
                cls
clus               0   1
  UPK2 MUTATED     3   1
  UPK2 WILD-TYPE 343  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPK2 MUTATED      3    1
  UPK2 WILD-TYPE  343   28
   clus
vv  UPK2 MUTATED UPK2 WILD-TYPE
  0            3            343
  1            1             28
[1] 2 2
[1] FALSE
D705V7, binary
                cls
clus               0   1
  UPK2 MUTATED     2   2
  UPK2 WILD-TYPE 143 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPK2 MUTATED      2    2
  UPK2 WILD-TYPE  143  246
        clus
vv       UPK2 MUTATED UPK2 WILD-TYPE
  FEMALE            2            143
  MALE              2            246
[1] 2 2
[1] FALSE
D705V8, binary
                cls
clus               0   1
  UPK2 MUTATED     3   0
  UPK2 WILD-TYPE 289  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPK2 MUTATED      3    0
  UPK2 WILD-TYPE  289   59
     clus
vv    UPK2 MUTATED UPK2 WILD-TYPE
  NO             3            289
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  UPK2 MUTATED                                          0
  UPK2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  UPK2 MUTATED                                       2
  UPK2 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UPK2 MUTATED                                                        1
  UPK2 WILD-TYPE                                                    157
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  UPK2 MUTATED                                                   0
  UPK2 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UPK2 MUTATED                                                                   1
  UPK2 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  UPK2 MUTATED                                                    0
  UPK2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  UPK2 MUTATED                                                  0
  UPK2 WILD-TYPE                                               61
D705V9, multiclass
                                                                   clus
vv                                                                  UPK2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  UPK2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  UPK2 MUTATED     2   0   1   0
  UPK2 WILD-TYPE 309  14  14  24
D705V10, multiclass
    clus
vv   UPK2 MUTATED UPK2 WILD-TYPE
  R0            2            309
  R1            0             14
  R2            1             14
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D705V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  UPK2 MUTATED       1                         0
  UPK2 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UPK2 MUTATED                                           0     2
  UPK2 WILD-TYPE                                         1   241
D705V12, multiclass
                                           clus
vv                                          UPK2 MUTATED UPK2 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D705V13, binary
                cls
clus               0   1
  UPK2 MUTATED     0   3
  UPK2 WILD-TYPE   4 307
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPK2 MUTATED      0    3
  UPK2 WILD-TYPE    4  307
                        clus
vv                       UPK2 MUTATED UPK2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            3            307
[1] 2 2
[1] FALSE

Clustering(706) Variable = IGFBP7 MUTATION ANALYSIS
D706V1, survival
                  sevent
clus2                0   1
  IGFBP7 MUTATED     2   1
  IGFBP7 WILD-TYPE 228 138
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               3              366 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               1              138 
$`IGFBP7 MUTATED`
TCGA-BR-8487 TCGA-CG-5733 TCGA-FP-A4BE 
        1.12        21.07        11.08 

$`IGFBP7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
            1.12             0.00 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
           21.07           122.30 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
           11.08            14.35 
[1] "1.1 - 21.1 (11.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D706V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IGFBP7 MUTATED         0        0        1        0         2         0
  IGFBP7 WILD-TYPE       2       15       39       30        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGFBP7 MUTATED           0          1          0          0        0
  IGFBP7 WILD-TYPE         3         69         53         32       38
D706V3, multiclass
            clus
vv           IGFBP7 MUTATED IGFBP7 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IGFBP7 MUTATED     0   2   2   0
  IGFBP7 WILD-TYPE  22  90 171  97
D706V4, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              2              171
  T4              0               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
  IGFBP7 MUTATED     3   0   1   0
  IGFBP7 WILD-TYPE 115 104  76  77
D706V5, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  N0              3              115
  N1              0              104
  N2              1               76
  N3              0               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"
D706V6, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     4   0
  IGFBP7 WILD-TYPE 342  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      4    0
  IGFBP7 WILD-TYPE  342   29
   clus
vv  IGFBP7 MUTATED IGFBP7 WILD-TYPE
  0              4              342
  1              0               29
[1] 2 2
[1] FALSE
D706V7, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     2   2
  IGFBP7 WILD-TYPE 143 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      2    2
  IGFBP7 WILD-TYPE  143  246
        clus
vv       IGFBP7 MUTATED IGFBP7 WILD-TYPE
  FEMALE              2              143
  MALE                2              246
[1] 2 2
[1] FALSE
D706V8, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     2   1
  IGFBP7 WILD-TYPE 290  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      2    1
  IGFBP7 WILD-TYPE  290   58
     clus
vv    IGFBP7 MUTATED IGFBP7 WILD-TYPE
  NO               2              290
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IGFBP7 MUTATED                                          0
  IGFBP7 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IGFBP7 MUTATED                                       0
  IGFBP7 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IGFBP7 MUTATED                                                        2
  IGFBP7 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IGFBP7 MUTATED                                                   0
  IGFBP7 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IGFBP7 MUTATED                                                                   2
  IGFBP7 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IGFBP7 MUTATED                                                    0
  IGFBP7 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IGFBP7 MUTATED                                                  0
  IGFBP7 WILD-TYPE                                               61
D706V9, multiclass
                                                                   clus
vv                                                                  IGFBP7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  IGFBP7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IGFBP7 MUTATED     4   0   0   0
  IGFBP7 WILD-TYPE 307  14  15  24
D706V10, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D706V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  IGFBP7 MUTATED       0                         1
  IGFBP7 WILD-TYPE    87                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IGFBP7 MUTATED                                           0     1
  IGFBP7 WILD-TYPE                                         1   242
D706V12, multiclass
[1] "Remove cluster labels:" "IGFBP7 MUTATED"        
clus
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               2              338 
      TCGA-EQ-A4SO       TCGA-F1-6177       TCGA-FP-A8CX       TCGA-KB-A93G 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-MX-A663       TCGA-B7-5816       TCGA-B7-5818       TCGA-B7-A5TI 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-B7-A5TJ       TCGA-B7-A5TK       TCGA-B7-A5TN       TCGA-BR-4183 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-4184       TCGA-BR-4187       TCGA-BR-4188       TCGA-BR-4191 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-4201       TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-4257       TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-4292       TCGA-BR-4294       TCGA-BR-4357       TCGA-BR-4361 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-4362       TCGA-BR-4363       TCGA-BR-4366       TCGA-BR-4368 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-4369       TCGA-BR-4370       TCGA-BR-4371       TCGA-BR-6452 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-6453       TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-6457       TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-6565       TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-6707       TCGA-BR-6709       TCGA-BR-6710       TCGA-BR-6801 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-6802       TCGA-BR-6803       TCGA-BR-6852       TCGA-BR-7196 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-7197       TCGA-BR-7703       TCGA-BR-7704       TCGA-BR-7707 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717       TCGA-BR-7722 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901       TCGA-BR-7957 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058       TCGA-BR-8059 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8060       TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8285       TCGA-BR-8286 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8289       TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8297 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8373       TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8384       TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8486       TCGA-BR-8588       TCGA-BR-8589       TCGA-BR-8590 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676       TCGA-BR-8677 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680       TCGA-BR-8682 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J5       TCGA-BR-A4J6 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-A4J7       TCGA-BR-A4J8       TCGA-BR-A4PD       TCGA-BR-A4PE 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-BR-A4PF       TCGA-BR-A4QI       TCGA-BR-A4QL       TCGA-BR-A4QM 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-5798       TCGA-CD-5799       TCGA-CD-5800       TCGA-CD-5801 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-5802       TCGA-CD-5803       TCGA-CD-5804       TCGA-CD-5813 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-8524       TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8527 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-8528       TCGA-CD-8529       TCGA-CD-8530       TCGA-CD-8531 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-8532       TCGA-CD-8533       TCGA-CD-8534       TCGA-CD-8535 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-8536       TCGA-CD-A486       TCGA-CD-A487       TCGA-CD-A489 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-A48A       TCGA-CD-A48C       TCGA-CD-A4MG       TCGA-CD-A4MH 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-CD-A4MI       TCGA-CD-A4MJ       TCGA-D7-5577       TCGA-D7-5578 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-5579       TCGA-D7-6518       TCGA-D7-6519       TCGA-D7-6520 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-6521       TCGA-D7-6522       TCGA-D7-6524       TCGA-D7-6525 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-6526       TCGA-D7-6527       TCGA-D7-6528       TCGA-D7-6815 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-6817       TCGA-D7-6818       TCGA-D7-6820       TCGA-D7-6822 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-8570       TCGA-D7-8572       TCGA-D7-8573       TCGA-D7-8574 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-8575       TCGA-D7-8576       TCGA-D7-8578       TCGA-D7-8579 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-A4YT       TCGA-D7-A4YU       TCGA-D7-A4YV       TCGA-D7-A4YX 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-A4YY       TCGA-D7-A4Z0       TCGA-D7-A6ET       TCGA-D7-A6EV 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-A6EX       TCGA-D7-A6EY       TCGA-D7-A6EZ       TCGA-D7-A6F0 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-A6F2       TCGA-D7-A747       TCGA-D7-A748       TCGA-D7-A74A 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-D7-A74B       TCGA-EQ-5647       TCGA-EQ-8122       TCGA-F1-6874 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-F1-6875       TCGA-F1-A448       TCGA-F1-A72C       TCGA-FP-7735 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-FP-7829       TCGA-FP-7916       TCGA-FP-7998       TCGA-FP-8099 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-FP-8209       TCGA-FP-8210       TCGA-FP-8211       TCGA-FP-8631 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-FP-A4BF       TCGA-FP-A9TM       TCGA-HJ-7597       TCGA-HU-8238 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-8243       TCGA-HU-8244       TCGA-HU-8249       TCGA-HU-8602 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-8604       TCGA-HU-8608       TCGA-HU-8610       TCGA-HU-A4G2 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-A4G3       TCGA-HU-A4G6       TCGA-HU-A4G8       TCGA-HU-A4G9 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-A4GC       TCGA-HU-A4GD       TCGA-HU-A4GF       TCGA-HU-A4GH 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-A4GJ       TCGA-HU-A4GN       TCGA-HU-A4GP       TCGA-HU-A4GQ 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX       TCGA-HU-A4GY 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3       TCGA-HU-A4H4 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8       TCGA-HU-A4HB 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808       TCGA-IN-8462 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-IN-8663       TCGA-IN-A6RI       TCGA-IN-A6RJ       TCGA-IN-A6RL 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-IN-A6RN       TCGA-IN-A6RO       TCGA-IN-A6RP       TCGA-IN-A6RR 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-IN-A6RS       TCGA-IN-A7NR       TCGA-IN-A7NT       TCGA-IN-A7NU 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-IN-AB1V       TCGA-IN-AB1X       TCGA-IP-7968       TCGA-KB-A93J 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-MX-A5UG       TCGA-MX-A5UJ       TCGA-MX-A666       TCGA-R5-A7O7 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-R5-A7ZE       TCGA-R5-A7ZF       TCGA-R5-A7ZI       TCGA-R5-A7ZR 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-R5-A804       TCGA-R5-A805       TCGA-RD-A7BS       TCGA-RD-A7BT 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-RD-A7BW       TCGA-RD-A7C1       TCGA-RD-A8MV       TCGA-RD-A8MW 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-RD-A8N0       TCGA-RD-A8N1       TCGA-RD-A8N2       TCGA-RD-A8N4 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-RD-A8N5       TCGA-RD-A8N6       TCGA-RD-A8N9       TCGA-SW-A7EA 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-SW-A7EB       TCGA-VQ-A8DL       TCGA-VQ-A8DU       TCGA-VQ-A8DV 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-VQ-A8DZ       TCGA-VQ-A8E2       TCGA-VQ-A8E7       TCGA-VQ-A8P2 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-VQ-A8P3       TCGA-VQ-A8PE       TCGA-VQ-A8PK       TCGA-VQ-A8PM 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-VQ-A8PQ       TCGA-VQ-A91U       TCGA-VQ-A92D       TCGA-VQ-AA64 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-VQ-AA68       TCGA-VQ-AA69       TCGA-VQ-AA6A       TCGA-VQ-AA6B 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-VQ-AA6F       TCGA-VQ-AA6G       TCGA-VQ-AA6I       TCGA-VQ-AA6J 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
      TCGA-VQ-AA6K       TCGA-ZA-A8F6 
"IGFBP7 WILD-TYPE" "IGFBP7 WILD-TYPE" 
D706V13, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     0   2
  IGFBP7 WILD-TYPE   4 308
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      0    2
  IGFBP7 WILD-TYPE    4  308
                        clus
vv                       IGFBP7 MUTATED IGFBP7 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              2              308
[1] 2 2
[1] FALSE

Clustering(707) Variable = ARPC5L MUTATION ANALYSIS
D707V1, survival
                  sevent
clus2                0   1
  ARPC5L MUTATED     1   1
  ARPC5L WILD-TYPE 229 138
  ARPC5L MUTATED ARPC5L WILD-TYPE 
               2              367 
  ARPC5L MUTATED ARPC5L WILD-TYPE 
               1              138 
$`ARPC5L MUTATED`
TCGA-BR-8078 TCGA-R5-A804 
       29.59         4.60 

$`ARPC5L WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  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           14.270 
[1] "4.6 - 29.6 (17.1)"  "0.0 - 122.3 (14.3)"
[1] "Remove cluster labels:" "ARPC5L MUTATED"        
D707V2, 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       2       15       40       30        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARPC5L MUTATED           0          0          0          0        1
  ARPC5L WILD-TYPE         3         70         53         32       37
D707V3, multiclass
[1] "Remove cluster labels:" "ARPC5L MUTATED"        
clus
  ARPC5L MUTATED ARPC5L WILD-TYPE 
               2              370 
      TCGA-CG-4444       TCGA-CG-4460       TCGA-CG-4475       TCGA-CG-4476 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5716       TCGA-CG-5727       TCGA-EQ-A4SO       TCGA-F1-6177 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-FP-A8CX       TCGA-HF-7131       TCGA-KB-A93G       TCGA-MX-A663 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-B7-A5TI       TCGA-B7-A5TJ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-B7-A5TK       TCGA-B7-A5TN       TCGA-BR-4183       TCGA-BR-4184 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4267       TCGA-BR-4279 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4280       TCGA-BR-4361       TCGA-BR-4368       TCGA-BR-6452 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6453       TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6457       TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6565       TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6707       TCGA-BR-6709       TCGA-BR-6710       TCGA-BR-6801 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6802       TCGA-BR-6803       TCGA-BR-6852       TCGA-BR-7196 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7197       TCGA-BR-7703       TCGA-BR-7704       TCGA-BR-7707 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717       TCGA-BR-7722 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901       TCGA-BR-7957 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058       TCGA-BR-8059 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8060       TCGA-BR-8077       TCGA-BR-8080       TCGA-BR-8081 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8284       TCGA-BR-8285       TCGA-BR-8286       TCGA-BR-8289 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8297       TCGA-BR-8360 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364       TCGA-BR-8365 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368       TCGA-BR-8369 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372       TCGA-BR-8373 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382       TCGA-BR-8384 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485       TCGA-BR-8486 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589       TCGA-BR-8590 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676       TCGA-BR-8677 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680       TCGA-BR-8682 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J5       TCGA-BR-A4J6 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4J7       TCGA-BR-A4J8       TCGA-BR-A4PD       TCGA-BR-A4PE 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4PF       TCGA-BR-A4QI       TCGA-BR-A4QL       TCGA-BR-A4QM 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-5798       TCGA-CD-5799       TCGA-CD-5800       TCGA-CD-5801 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-5802       TCGA-CD-5803       TCGA-CD-5813       TCGA-CD-8524 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8527       TCGA-CD-8528 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8529       TCGA-CD-8530       TCGA-CD-8531       TCGA-CD-8532 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8533       TCGA-CD-8534       TCGA-CD-8535       TCGA-CD-8536 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-A486       TCGA-CD-A487       TCGA-CD-A489       TCGA-CD-A48A 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-A48C       TCGA-CD-A4MG       TCGA-CD-A4MH       TCGA-CD-A4MI 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-A4MJ       TCGA-CG-4300       TCGA-CG-4301       TCGA-CG-4304 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4305       TCGA-CG-4306       TCGA-CG-4436       TCGA-CG-4437 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4438       TCGA-CG-4440       TCGA-CG-4441       TCGA-CG-4442 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4443       TCGA-CG-4449       TCGA-CG-4455       TCGA-CG-4462 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4465       TCGA-CG-4466       TCGA-CG-4469       TCGA-CG-4474 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4477       TCGA-CG-5717       TCGA-CG-5718       TCGA-CG-5719 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5720       TCGA-CG-5721       TCGA-CG-5722       TCGA-CG-5723 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5724       TCGA-CG-5725       TCGA-CG-5726       TCGA-CG-5728 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5730       TCGA-CG-5732       TCGA-CG-5733       TCGA-CG-5734 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6520       TCGA-D7-6522       TCGA-D7-6524       TCGA-D7-6525 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6526       TCGA-D7-6527       TCGA-D7-6528       TCGA-D7-6815 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6817       TCGA-D7-6818       TCGA-D7-6820       TCGA-D7-6822 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-8570       TCGA-D7-8572       TCGA-D7-8573       TCGA-D7-8574 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-8575       TCGA-D7-8576       TCGA-D7-8578       TCGA-D7-8579 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A4YT       TCGA-D7-A4YU       TCGA-D7-A4YV       TCGA-D7-A4YX 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A4YY       TCGA-D7-A4Z0       TCGA-D7-A6ET       TCGA-D7-A6EV 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A6EX       TCGA-D7-A6EY       TCGA-D7-A6EZ       TCGA-D7-A6F0 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A6F2       TCGA-D7-A747       TCGA-D7-A748       TCGA-D7-A74A 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A74B       TCGA-EQ-5647       TCGA-EQ-8122       TCGA-F1-6874 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-F1-6875       TCGA-F1-A448       TCGA-F1-A72C       TCGA-FP-7735 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-FP-7829       TCGA-FP-7916       TCGA-FP-7998       TCGA-FP-8099 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-FP-8209       TCGA-FP-8210       TCGA-FP-8211       TCGA-FP-8631 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-FP-A4BE       TCGA-FP-A4BF       TCGA-HF-7132       TCGA-HF-7133 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HF-7134       TCGA-HF-7136       TCGA-HF-A5NB       TCGA-HJ-7597 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-8243       TCGA-HU-8244       TCGA-HU-8249       TCGA-HU-8602 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-8604       TCGA-HU-8608       TCGA-HU-8610       TCGA-HU-A4G2 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4G3       TCGA-HU-A4G6       TCGA-HU-A4G8       TCGA-HU-A4G9 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GC       TCGA-HU-A4GD       TCGA-HU-A4GF       TCGA-HU-A4GH 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GJ       TCGA-HU-A4GN       TCGA-HU-A4GP       TCGA-HU-A4GQ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX       TCGA-HU-A4GY 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3       TCGA-HU-A4H4 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8       TCGA-HU-A4HB 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       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-MX-A666 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-R5-A7O7       TCGA-R5-A7ZE       TCGA-R5-A7ZF       TCGA-R5-A7ZI 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-R5-A7ZR       TCGA-R5-A805       TCGA-RD-A7BS       TCGA-RD-A7BT 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A7BW       TCGA-RD-A7C1       TCGA-RD-A8MV       TCGA-RD-A8MW 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A8N0       TCGA-RD-A8N1       TCGA-RD-A8N2       TCGA-RD-A8N4 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A8N5       TCGA-RD-A8N6       TCGA-RD-A8N9       TCGA-SW-A7EA 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-SW-A7EB       TCGA-VQ-A8DL       TCGA-VQ-A8DT       TCGA-VQ-A8DU 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8DV       TCGA-VQ-A8DZ       TCGA-VQ-A8E2       TCGA-VQ-A8E7 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8P2       TCGA-VQ-A8P3       TCGA-VQ-A8PE       TCGA-VQ-A8PK 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8PM       TCGA-VQ-A8PQ       TCGA-VQ-A91Q       TCGA-VQ-A91U 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A91V       TCGA-VQ-A92D       TCGA-VQ-A94T       TCGA-VQ-AA64 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA68       TCGA-VQ-AA69       TCGA-VQ-AA6A       TCGA-VQ-AA6B 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA6F       TCGA-VQ-AA6G       TCGA-VQ-AA6I       TCGA-VQ-AA6J 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA6K       TCGA-ZA-A8F6 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
                  vv
clus                T1  T2  T3  T4
  ARPC5L MUTATED     1   0   1   1
  ARPC5L WILD-TYPE  21  92 172  96
D707V4, multiclass
    clus
vv   ARPC5L MUTATED ARPC5L WILD-TYPE
  T1              1               21
  T2              0               92
  T3              1              172
  T4              1               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
  ARPC5L MUTATED     1   0   1   0
  ARPC5L WILD-TYPE 117 104  76  77
D707V5, multiclass
[1] "Remove cluster labels:" "ARPC5L MUTATED"        
clus
  ARPC5L MUTATED ARPC5L WILD-TYPE 
               2              374 
      TCGA-CG-4444       TCGA-CG-4460       TCGA-CG-4475       TCGA-CG-4476 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5716       TCGA-CG-5727       TCGA-EQ-A4SO       TCGA-F1-6177 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-FP-A8CX       TCGA-HF-7131       TCGA-KB-A93G       TCGA-MX-A663 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-B7-A5TI       TCGA-BR-4183 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4184       TCGA-BR-4188       TCGA-BR-4191       TCGA-BR-4253 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4255       TCGA-BR-4256       TCGA-BR-4267       TCGA-BR-4279 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4280       TCGA-BR-4361       TCGA-BR-4362       TCGA-BR-4368 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6452       TCGA-BR-6453       TCGA-BR-6454       TCGA-BR-6455 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6456       TCGA-BR-6457       TCGA-BR-6458       TCGA-BR-6563 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6564       TCGA-BR-6565       TCGA-BR-6566       TCGA-BR-6705 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6706       TCGA-BR-6707       TCGA-BR-6709       TCGA-BR-6710 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803       TCGA-BR-6852 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703       TCGA-BR-7704 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7707       TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7722       TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7957       TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8059       TCGA-BR-8060       TCGA-BR-8077       TCGA-BR-8080 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8285       TCGA-BR-8286 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8289       TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8297 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8373       TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8384       TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8486       TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8590       TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8677       TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8682       TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8690       TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A453       TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4IU       TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4J1       TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J5 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4J6       TCGA-BR-A4J8       TCGA-BR-A4PD       TCGA-BR-A4PE 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4PF       TCGA-BR-A4QI       TCGA-BR-A4QL       TCGA-BR-A4QM 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-5798       TCGA-CD-5799       TCGA-CD-5800       TCGA-CD-5801 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-5802       TCGA-CD-5803       TCGA-CD-5804       TCGA-CD-5813 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8524       TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8527 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8528       TCGA-CD-8529       TCGA-CD-8530       TCGA-CD-8531 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8532       TCGA-CD-8533       TCGA-CD-8534       TCGA-CD-8535 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8536       TCGA-CD-A486       TCGA-CD-A487       TCGA-CD-A489 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-A48A       TCGA-CD-A48C       TCGA-CD-A4MG       TCGA-CD-A4MH 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-A4MI       TCGA-CD-A4MJ       TCGA-CG-4300       TCGA-CG-4301 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4304       TCGA-CG-4305       TCGA-CG-4306       TCGA-CG-4436 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4437       TCGA-CG-4438       TCGA-CG-4440       TCGA-CG-4441 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4442       TCGA-CG-4443       TCGA-CG-4449       TCGA-CG-4455 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466       TCGA-CG-4469 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4474       TCGA-CG-4477       TCGA-CG-5717       TCGA-CG-5718 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5719       TCGA-CG-5720       TCGA-CG-5721       TCGA-CG-5722 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5723       TCGA-CG-5724       TCGA-CG-5725       TCGA-CG-5726 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5728       TCGA-CG-5730       TCGA-CG-5732       TCGA-CG-5733 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5734       TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6518       TCGA-D7-6519       TCGA-D7-6520       TCGA-D7-6521 
"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-FP-A9TM       TCGA-HF-7132       TCGA-HF-7133 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HF-7134       TCGA-HF-7136       TCGA-HF-A5NB       TCGA-HJ-7597 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-8238       TCGA-HU-8243       TCGA-HU-8244       TCGA-HU-8249 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-8602       TCGA-HU-8604       TCGA-HU-8608       TCGA-HU-8610 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6       TCGA-HU-A4G8 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD       TCGA-HU-A4GF 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GH       TCGA-HU-A4GJ       TCGA-HU-A4GN       TCGA-HU-A4GP 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GQ       TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4HB       TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-8462       TCGA-IN-8663       TCGA-IN-A6RI       TCGA-IN-A6RJ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A6RL       TCGA-IN-A6RN       TCGA-IN-A6RO       TCGA-IN-A6RP 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A6RR       TCGA-IN-A6RS       TCGA-IN-A7NR       TCGA-IN-A7NT 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A7NU       TCGA-IN-AB1V       TCGA-IN-AB1X       TCGA-IP-7968 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-KB-A6F5       TCGA-KB-A6F7       TCGA-KB-A93J       TCGA-MX-A5UG 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-MX-A5UJ       TCGA-R5-A7O7       TCGA-R5-A7ZE       TCGA-R5-A7ZF 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-R5-A7ZI       TCGA-R5-A805       TCGA-RD-A7BS       TCGA-RD-A7BT 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A7BW       TCGA-RD-A7C1       TCGA-RD-A8MV       TCGA-RD-A8MW 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A8N0       TCGA-RD-A8N1       TCGA-RD-A8N2       TCGA-RD-A8N4 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A8N5       TCGA-RD-A8N6       TCGA-RD-A8N9       TCGA-SW-A7EA 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-SW-A7EB       TCGA-VQ-A8DL       TCGA-VQ-A8DT       TCGA-VQ-A8DU 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8DV       TCGA-VQ-A8DZ       TCGA-VQ-A8E2       TCGA-VQ-A8E7 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8P2       TCGA-VQ-A8P3       TCGA-VQ-A8PE       TCGA-VQ-A8PK 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8PM       TCGA-VQ-A8PQ       TCGA-VQ-A91Q       TCGA-VQ-A91U 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A91V       TCGA-VQ-A92D       TCGA-VQ-A94T       TCGA-VQ-AA64 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA68       TCGA-VQ-AA69       TCGA-VQ-AA6A       TCGA-VQ-AA6B 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA6F       TCGA-VQ-AA6G       TCGA-VQ-AA6I       TCGA-VQ-AA6J 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA6K       TCGA-ZA-A8F6 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
D707V6, binary
                  cls
clus                 0   1
  ARPC5L MUTATED     2   1
  ARPC5L WILD-TYPE 344  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARPC5L MUTATED      2    1
  ARPC5L WILD-TYPE  344   28
   clus
vv  ARPC5L MUTATED ARPC5L WILD-TYPE
  0              2              344
  1              1               28
[1] 2 2
[1] FALSE
D707V7, binary
                  cls
clus                 0   1
  ARPC5L MUTATED     2   1
  ARPC5L WILD-TYPE 143 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARPC5L MUTATED      2    1
  ARPC5L WILD-TYPE  143  247
        clus
vv       ARPC5L MUTATED ARPC5L WILD-TYPE
  FEMALE              2              143
  MALE                1              247
[1] 2 2
[1] FALSE
D707V8, binary
                  cls
clus                 0   1
  ARPC5L MUTATED     2   0
  ARPC5L WILD-TYPE 290  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARPC5L MUTATED      2    0
  ARPC5L WILD-TYPE  290   59
     clus
vv    ARPC5L MUTATED ARPC5L WILD-TYPE
  NO               2              290
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARPC5L MUTATED                                          0
  ARPC5L WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARPC5L MUTATED                                       1
  ARPC5L WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARPC5L MUTATED                                                        2
  ARPC5L WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARPC5L MUTATED                                                   0
  ARPC5L WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARPC5L MUTATED                                                                   0
  ARPC5L WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARPC5L MUTATED                                                    0
  ARPC5L WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARPC5L MUTATED                                                  0
  ARPC5L WILD-TYPE                                               61
D707V9, multiclass
                                                                   clus
vv                                                                  ARPC5L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  ARPC5L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARPC5L MUTATED     1   0   0   1
  ARPC5L WILD-TYPE 310  14  15  23
D707V10, multiclass
[1] "Remove cluster labels:" "ARPC5L MUTATED"        
clus
  ARPC5L MUTATED ARPC5L WILD-TYPE 
               2              362 
      TCGA-CG-4444       TCGA-CG-4460       TCGA-CG-4475       TCGA-CG-4476 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5716       TCGA-CG-5727       TCGA-EQ-A4SO       TCGA-F1-6177 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-FP-A8CX       TCGA-HF-7131       TCGA-KB-A93G       TCGA-MX-A663 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-BR-4183       TCGA-BR-4184 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4187       TCGA-BR-4188       TCGA-BR-4191       TCGA-BR-4201 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256       TCGA-BR-4257 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4294 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4357       TCGA-BR-4361       TCGA-BR-4362       TCGA-BR-4363 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4366       TCGA-BR-4368       TCGA-BR-4369       TCGA-BR-4370 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-4371       TCGA-BR-6452       TCGA-BR-6453       TCGA-BR-6454 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457       TCGA-BR-6458 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565       TCGA-BR-6566 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707       TCGA-BR-6709 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7704       TCGA-BR-7707       TCGA-BR-7715       TCGA-BR-7716 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7717       TCGA-BR-7722       TCGA-BR-7723       TCGA-BR-7851 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-7901       TCGA-BR-7957       TCGA-BR-7958       TCGA-BR-7959 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8058       TCGA-BR-8059       TCGA-BR-8060       TCGA-BR-8077 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8080       TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8285 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8286       TCGA-BR-8289       TCGA-BR-8291       TCGA-BR-8295 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8297       TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8364       TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8368       TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8372       TCGA-BR-8373       TCGA-BR-8380       TCGA-BR-8381 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8382       TCGA-BR-8384       TCGA-BR-8483       TCGA-BR-8484 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8485       TCGA-BR-8486       TCGA-BR-8487       TCGA-BR-8588 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8589       TCGA-BR-8590       TCGA-BR-8591       TCGA-BR-8592 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8676       TCGA-BR-8677       TCGA-BR-8678       TCGA-BR-8679 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8680       TCGA-BR-8682       TCGA-BR-8683       TCGA-BR-8686 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-8687       TCGA-BR-8690       TCGA-BR-A44T       TCGA-BR-A44U 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A452       TCGA-BR-A453       TCGA-BR-A4CQ       TCGA-BR-A4CR 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4CS       TCGA-BR-A4IU       TCGA-BR-A4IV       TCGA-BR-A4IY 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4IZ       TCGA-BR-A4J1       TCGA-BR-A4J2       TCGA-BR-A4J4 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-BR-A4J5       TCGA-BR-A4J6       TCGA-BR-A4J7       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-5800       TCGA-CD-5801 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-5804       TCGA-CD-8524       TCGA-CD-8525       TCGA-CD-8526 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8527       TCGA-CD-8528       TCGA-CD-8529       TCGA-CD-8530 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8531       TCGA-CD-8532       TCGA-CD-8533       TCGA-CD-8534 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8535       TCGA-CD-8536       TCGA-CD-A487       TCGA-CG-4300 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305       TCGA-CG-4306 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4436       TCGA-CG-4437       TCGA-CG-4438       TCGA-CG-4440 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4441       TCGA-CG-4442       TCGA-CG-4443       TCGA-CG-4449 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4455       TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4469       TCGA-CG-4474       TCGA-CG-4477       TCGA-CG-5717 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5718       TCGA-CG-5719       TCGA-CG-5720       TCGA-CG-5721 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5722       TCGA-CG-5723       TCGA-CG-5724       TCGA-CG-5725 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5726       TCGA-CG-5728       TCGA-CG-5730       TCGA-CG-5732 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5733       TCGA-CG-5734       TCGA-D7-5577       TCGA-D7-5578 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-5579       TCGA-D7-6518       TCGA-D7-6519       TCGA-D7-6520 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6521       TCGA-D7-6522       TCGA-D7-6524       TCGA-D7-6525 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6526       TCGA-D7-6527       TCGA-D7-6528       TCGA-D7-6815 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6817       TCGA-D7-6818       TCGA-D7-6820       TCGA-D7-6822 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-8570       TCGA-D7-8572       TCGA-D7-8573       TCGA-D7-8574 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-8575       TCGA-D7-8576       TCGA-D7-8578       TCGA-D7-8579 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A4YT       TCGA-D7-A4YU       TCGA-D7-A4YV       TCGA-D7-A4YX 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A4YY       TCGA-D7-A4Z0       TCGA-D7-A6ET       TCGA-D7-A6EV 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A6EX       TCGA-D7-A6EY       TCGA-D7-A6EZ       TCGA-D7-A6F0 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A6F2       TCGA-D7-A747       TCGA-D7-A748       TCGA-D7-A74A 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-A74B       TCGA-EQ-5647       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-7998       TCGA-FP-8099       TCGA-FP-8209       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-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GJ       TCGA-HU-A4GN 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GP       TCGA-HU-A4GQ       TCGA-HU-A4GT       TCGA-HU-A4GU 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GX       TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4H3       TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4H8       TCGA-HU-A4HB       TCGA-HU-A4HD       TCGA-IN-7806 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-8462       TCGA-IN-8663       TCGA-IN-A6RI       TCGA-IN-A6RJ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A6RL       TCGA-IN-A6RN       TCGA-IN-A6RO       TCGA-IN-A6RP 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A6RR       TCGA-IN-A6RS       TCGA-IN-A7NR       TCGA-IN-A7NT 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A7NU       TCGA-IN-AB1V       TCGA-IN-AB1X       TCGA-IP-7968 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-KB-A6F5       TCGA-KB-A6F7       TCGA-KB-A93J       TCGA-MX-A5UG 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-MX-A5UJ       TCGA-R5-A7ZI       TCGA-RD-A7BS       TCGA-RD-A7BT 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A7BW       TCGA-RD-A7C1       TCGA-RD-A8MV       TCGA-RD-A8MW 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A8N0       TCGA-RD-A8N1       TCGA-RD-A8N2       TCGA-RD-A8N4 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A8N5       TCGA-RD-A8N6       TCGA-RD-A8N9       TCGA-SW-A7EA 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-SW-A7EB       TCGA-VQ-A8DL       TCGA-VQ-A8DT       TCGA-VQ-A8DU 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8DV       TCGA-VQ-A8DZ       TCGA-VQ-A8E2       TCGA-VQ-A8E7 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8P2       TCGA-VQ-A8P3       TCGA-VQ-A8PE       TCGA-VQ-A8PK 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8PM       TCGA-VQ-A8PQ       TCGA-VQ-A91Q       TCGA-VQ-A91U 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A91V       TCGA-VQ-A92D       TCGA-VQ-A94T       TCGA-VQ-AA64 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA68       TCGA-VQ-AA69       TCGA-VQ-AA6A       TCGA-VQ-AA6B 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA6F       TCGA-VQ-AA6G       TCGA-VQ-AA6I       TCGA-VQ-AA6J 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA6K       TCGA-ZA-A8F6 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
D707V11, continuous
[1] "Remove cluster labels:" "ARPC5L MUTATED"        
clus
  ARPC5L MUTATED ARPC5L WILD-TYPE 
               1              342 
      TCGA-CG-4444       TCGA-CG-4460       TCGA-CG-4475       TCGA-CG-4476 
"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-B7-5816 
"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-5804       TCGA-CD-8525 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CD-8526       TCGA-CD-8531       TCGA-CD-8535       TCGA-CD-A487 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305       TCGA-CG-4436 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4437       TCGA-CG-4438       TCGA-CG-4440       TCGA-CG-4441 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4442       TCGA-CG-4443       TCGA-CG-4449       TCGA-CG-4455 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466       TCGA-CG-4469 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-4474       TCGA-CG-4477       TCGA-CG-5717       TCGA-CG-5718 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5719       TCGA-CG-5720       TCGA-CG-5721       TCGA-CG-5722 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5723       TCGA-CG-5724       TCGA-CG-5725       TCGA-CG-5726 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5728       TCGA-CG-5730       TCGA-CG-5732       TCGA-CG-5733 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-CG-5734       TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-D7-6518       TCGA-D7-6519       TCGA-D7-6520       TCGA-D7-6521 
"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-FP-A9TM       TCGA-HF-7132       TCGA-HF-7133 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HF-7134       TCGA-HF-7136       TCGA-HF-A5NB       TCGA-HJ-7597 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-8238       TCGA-HU-8243       TCGA-HU-8244       TCGA-HU-8249 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-8602       TCGA-HU-8604       TCGA-HU-8608       TCGA-HU-8610 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6       TCGA-HU-A4G8 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD       TCGA-HU-A4GF 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GH       TCGA-HU-A4GJ       TCGA-HU-A4GN       TCGA-HU-A4GP 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GQ       TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-HU-A4HB       TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-8462       TCGA-IN-8663       TCGA-IN-A6RI       TCGA-IN-A6RJ 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A6RL       TCGA-IN-A6RN       TCGA-IN-A6RO       TCGA-IN-A6RP 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A6RR       TCGA-IN-A6RS       TCGA-IN-A7NR       TCGA-IN-A7NT 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-IN-A7NU       TCGA-IN-AB1V       TCGA-IN-AB1X       TCGA-IP-7968 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-KB-A6F5       TCGA-KB-A6F7       TCGA-KB-A93J       TCGA-MX-A5UG 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-MX-A5UJ       TCGA-R5-A7ZI       TCGA-RD-A7BS       TCGA-RD-A7BT 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A7BW       TCGA-RD-A7C1       TCGA-RD-A8MV       TCGA-RD-A8MW 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A8N0       TCGA-RD-A8N1       TCGA-RD-A8N2       TCGA-RD-A8N4 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-RD-A8N5       TCGA-RD-A8N6       TCGA-RD-A8N9       TCGA-SW-A7EA 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-SW-A7EB       TCGA-VQ-A8DL       TCGA-VQ-A8DT       TCGA-VQ-A8DU 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8DV       TCGA-VQ-A8DZ       TCGA-VQ-A8E2       TCGA-VQ-A8E7 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8P2       TCGA-VQ-A8P3       TCGA-VQ-A8PE       TCGA-VQ-A8PK 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A8PM       TCGA-VQ-A8PQ       TCGA-VQ-A91Q       TCGA-VQ-A91U 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-A91V       TCGA-VQ-A92D       TCGA-VQ-A94T       TCGA-VQ-AA64 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA68       TCGA-VQ-AA69       TCGA-VQ-AA6A       TCGA-VQ-AA6B 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA6F       TCGA-VQ-AA6G       TCGA-VQ-AA6I       TCGA-VQ-AA6J 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
      TCGA-VQ-AA6K       TCGA-ZA-A8F6 
"ARPC5L WILD-TYPE" "ARPC5L WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ARPC5L MUTATED       0                         1
  ARPC5L WILD-TYPE    87                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARPC5L MUTATED                                           0     2
  ARPC5L WILD-TYPE                                         1   241
D707V12, multiclass
                                           clus
vv                                          ARPC5L MUTATED ARPC5L WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D707V13, binary
                  cls
clus                 0   1
  ARPC5L MUTATED     0   3
  ARPC5L WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARPC5L MUTATED      0    3
  ARPC5L WILD-TYPE    4  307
                        clus
vv                       ARPC5L MUTATED ARPC5L WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(708) Variable = TEX13A MUTATION ANALYSIS
D708V1, survival
                  sevent
clus2                0   1
  TEX13A MUTATED     4   0
  TEX13A WILD-TYPE 226 139
  TEX13A MUTATED TEX13A WILD-TYPE 
               4              365 
  TEX13A MUTATED TEX13A WILD-TYPE 
               0              139 
$`TEX13A MUTATED`
TCGA-BR-7707 TCGA-CD-8536 TCGA-CG-5723 TCGA-MX-A666 
       35.84        12.43       105.07        14.04 

$`TEX13A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        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 

  TEX13A MUTATED TEX13A WILD-TYPE 
           12.43             0.00 
  TEX13A MUTATED TEX13A WILD-TYPE 
          105.07           122.30 
  TEX13A MUTATED TEX13A WILD-TYPE 
           24.94            14.27 
[1] "12.4 - 105.1 (24.9)" "0.0 - 122.3 (14.3)" 
[1] "hr="     "9300000"
D708V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TEX13A MUTATED         1        0        1        2         1         0
  TEX13A WILD-TYPE       1       15       39       28        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TEX13A MUTATED           0          0          0          0        0
  TEX13A WILD-TYPE         3         70         53         32       38
D708V3, multiclass
            clus
vv           TEX13A MUTATED TEX13A WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TEX13A MUTATED     1   3   1   0
  TEX13A WILD-TYPE  21  89 172  97
D708V4, multiclass
    clus
vv   TEX13A MUTATED TEX13A WILD-TYPE
  T1              1               21
  T2              3               89
  T3              1              172
  T4              0               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
  TEX13A MUTATED     2   2   0   0
  TEX13A WILD-TYPE 116 102  77  77
D708V5, multiclass
    clus
vv   TEX13A MUTATED TEX13A WILD-TYPE
  N0              2              116
  N1              2              102
  N2              0               77
  N3              0               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"
D708V6, binary
                  cls
clus                 0   1
  TEX13A MUTATED     3   0
  TEX13A WILD-TYPE 343  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TEX13A MUTATED      3    0
  TEX13A WILD-TYPE  343   29
   clus
vv  TEX13A MUTATED TEX13A WILD-TYPE
  0              3              343
  1              0               29
[1] 2 2
[1] FALSE
D708V7, binary
                  cls
clus                 0   1
  TEX13A MUTATED     1   4
  TEX13A WILD-TYPE 144 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TEX13A MUTATED      1    4
  TEX13A WILD-TYPE  144  244
        clus
vv       TEX13A MUTATED TEX13A WILD-TYPE
  FEMALE              1              144
  MALE                4              244
[1] 2 2
[1] FALSE
D708V8, binary
                  cls
clus                 0   1
  TEX13A MUTATED     5   0
  TEX13A WILD-TYPE 287  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TEX13A MUTATED      5    0
  TEX13A WILD-TYPE  287   59
     clus
vv    TEX13A MUTATED TEX13A WILD-TYPE
  NO               5              287
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TEX13A MUTATED                                          0
  TEX13A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TEX13A MUTATED                                       0
  TEX13A WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TEX13A MUTATED                                                        5
  TEX13A WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TEX13A MUTATED                                                   0
  TEX13A WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TEX13A MUTATED                                                                   0
  TEX13A WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TEX13A MUTATED                                                    0
  TEX13A WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TEX13A MUTATED                                                  0
  TEX13A WILD-TYPE                                               61
D708V9, multiclass
                                                                   clus
vv                                                                  TEX13A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  TEX13A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TEX13A MUTATED     4   0   0   0
  TEX13A WILD-TYPE 307  14  15  24
D708V10, multiclass
    clus
vv   TEX13A MUTATED TEX13A WILD-TYPE
  R0              4              307
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D708V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TEX13A MUTATED       1                         1
  TEX13A WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TEX13A MUTATED                                           0     2
  TEX13A WILD-TYPE                                         1   241
D708V12, multiclass
                                           clus
vv                                          TEX13A MUTATED TEX13A WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D708V13, binary
                  cls
clus                 0   1
  TEX13A MUTATED     0   4
  TEX13A WILD-TYPE   4 306
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TEX13A MUTATED      0    4
  TEX13A WILD-TYPE    4  306
                        clus
vv                       TEX13A MUTATED TEX13A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              306
[1] 2 2
[1] FALSE

Clustering(709) Variable = KCNQ1 MUTATION ANALYSIS
D709V1, survival
                 sevent
clus2               0   1
  KCNQ1 MUTATED     5   1
  KCNQ1 WILD-TYPE 225 138
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
              6             363 
  KCNQ1 MUTATED KCNQ1 WILD-TYPE 
              1             138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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           14.17 
[1] "0.9 - 38.1 (30.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.9"
D709V2, 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       2       15       40       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNQ1 MUTATED           0          1          0          2        2
  KCNQ1 WILD-TYPE         3         69         53         30       36
D709V3, multiclass
            clus
vv           KCNQ1 MUTATED KCNQ1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNQ1 MUTATED     0   0   2   4
  KCNQ1 WILD-TYPE  22  92 171  93
D709V4, multiclass
    clus
vv   KCNQ1 MUTATED KCNQ1 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             2             171
  T4             4              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
  KCNQ1 MUTATED     1   1   2   2
  KCNQ1 WILD-TYPE 117 103  75  75
D709V5, multiclass
    clus
vv   KCNQ1 MUTATED KCNQ1 WILD-TYPE
  N0             1             117
  N1             1             103
  N2             2              75
  N3             2              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"
D709V6, binary
                 cls
clus                0   1
  KCNQ1 MUTATED     4   2
  KCNQ1 WILD-TYPE 342  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNQ1 MUTATED      4    2
  KCNQ1 WILD-TYPE  342   27
   clus
vv  KCNQ1 MUTATED KCNQ1 WILD-TYPE
  0             4             342
  1             2              27
[1] 2 2
[1] FALSE
D709V7, binary
                 cls
clus                0   1
  KCNQ1 MUTATED     2   4
  KCNQ1 WILD-TYPE 143 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNQ1 MUTATED      2    4
  KCNQ1 WILD-TYPE  143  244
        clus
vv       KCNQ1 MUTATED KCNQ1 WILD-TYPE
  FEMALE             2             143
  MALE               4             244
[1] 2 2
[1] FALSE
D709V8, binary
                 cls
clus                0   1
  KCNQ1 MUTATED     3   2
  KCNQ1 WILD-TYPE 289  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNQ1 MUTATED      3    2
  KCNQ1 WILD-TYPE  289   57
     clus
vv    KCNQ1 MUTATED KCNQ1 WILD-TYPE
  NO              3             289
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KCNQ1 MUTATED                                          0
  KCNQ1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KCNQ1 MUTATED                                       0
  KCNQ1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNQ1 MUTATED                                                        3
  KCNQ1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KCNQ1 MUTATED                                                   2
  KCNQ1 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNQ1 MUTATED                                                                   0
  KCNQ1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KCNQ1 MUTATED                                                    0
  KCNQ1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KCNQ1 MUTATED                                                  1
  KCNQ1 WILD-TYPE                                               60
D709V9, multiclass
                                                                   clus
vv                                                                  KCNQ1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  KCNQ1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCNQ1 MUTATED     4   1   1   0
  KCNQ1 WILD-TYPE 307  13  14  24
D709V10, multiclass
    clus
vv   KCNQ1 MUTATED KCNQ1 WILD-TYPE
  R0             4             307
  R1             1              13
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D709V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCNQ1 MUTATED       1                         0
  KCNQ1 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNQ1 MUTATED                                           0     3
  KCNQ1 WILD-TYPE                                         1   240
D709V12, multiclass
                                           clus
vv                                          KCNQ1 MUTATED KCNQ1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D709V13, binary
                 cls
clus                0   1
  KCNQ1 MUTATED     0   3
  KCNQ1 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNQ1 MUTATED      0    3
  KCNQ1 WILD-TYPE    4  307
                        clus
vv                       KCNQ1 MUTATED KCNQ1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(710) Variable = HAPLN1 MUTATION ANALYSIS
D710V1, survival
                  sevent
clus2                0   1
  HAPLN1 MUTATED     5   3
  HAPLN1 WILD-TYPE 225 136
  HAPLN1 MUTATED HAPLN1 WILD-TYPE 
               8              361 
  HAPLN1 MUTATED HAPLN1 WILD-TYPE 
               3              136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       11.44         0.69        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-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-F1-6875 
        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-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 

  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           14.070 
[1] "1.0 - 32.8 (25.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D710V2, 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       1       15       39       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HAPLN1 MUTATED           0          0          0          3        2
  HAPLN1 WILD-TYPE         3         70         53         29       36
D710V3, multiclass
            clus
vv           HAPLN1 MUTATED HAPLN1 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              3               29
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HAPLN1 MUTATED     1   1   2   5
  HAPLN1 WILD-TYPE  21  91 171  92
D710V4, multiclass
    clus
vv   HAPLN1 MUTATED HAPLN1 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              2              171
  T4              5               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
  HAPLN1 MUTATED     3   2   2   2
  HAPLN1 WILD-TYPE 115 102  75  75
D710V5, multiclass
    clus
vv   HAPLN1 MUTATED HAPLN1 WILD-TYPE
  N0              3              115
  N1              2              102
  N2              2               75
  N3              2               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"
D710V6, binary
                  cls
clus                 0   1
  HAPLN1 MUTATED     6   2
  HAPLN1 WILD-TYPE 340  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HAPLN1 MUTATED      6    2
  HAPLN1 WILD-TYPE  340   27
   clus
vv  HAPLN1 MUTATED HAPLN1 WILD-TYPE
  0              6              340
  1              2               27
[1] 2 2
[1] FALSE
D710V7, binary
                  cls
clus                 0   1
  HAPLN1 MUTATED     5   4
  HAPLN1 WILD-TYPE 140 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HAPLN1 MUTATED      5    4
  HAPLN1 WILD-TYPE  140  244
        clus
vv       HAPLN1 MUTATED HAPLN1 WILD-TYPE
  FEMALE              5              140
  MALE                4              244
[1] 2 2
[1] FALSE
D710V8, binary
                  cls
clus                 0   1
  HAPLN1 MUTATED     8   0
  HAPLN1 WILD-TYPE 284  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HAPLN1 MUTATED      8    0
  HAPLN1 WILD-TYPE  284   59
     clus
vv    HAPLN1 MUTATED HAPLN1 WILD-TYPE
  NO               8              284
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HAPLN1 MUTATED                                          0
  HAPLN1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HAPLN1 MUTATED                                       0
  HAPLN1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HAPLN1 MUTATED                                                        6
  HAPLN1 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HAPLN1 MUTATED                                                   1
  HAPLN1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HAPLN1 MUTATED                                                                   2
  HAPLN1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HAPLN1 MUTATED                                                    0
  HAPLN1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HAPLN1 MUTATED                                                  0
  HAPLN1 WILD-TYPE                                               61
D710V9, multiclass
                                                                   clus
vv                                                                  HAPLN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  HAPLN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HAPLN1 MUTATED     7   0   2   0
  HAPLN1 WILD-TYPE 304  14  13  24
D710V10, multiclass
    clus
vv   HAPLN1 MUTATED HAPLN1 WILD-TYPE
  R0              7              304
  R1              0               14
  R2              2               13
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D710V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  HAPLN1 MUTATED       0                         1
  HAPLN1 WILD-TYPE    87                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HAPLN1 MUTATED                                           0     6
  HAPLN1 WILD-TYPE                                         1   237
D710V12, multiclass
                                           clus
vv                                          HAPLN1 MUTATED HAPLN1 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D710V13, binary
                  cls
clus                 0   1
  HAPLN1 MUTATED     0   7
  HAPLN1 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HAPLN1 MUTATED      0    7
  HAPLN1 WILD-TYPE    4  303
                        clus
vv                       HAPLN1 MUTATED HAPLN1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(711) Variable = AXIN1 MUTATION ANALYSIS
D711V1, survival
                 sevent
clus2               0   1
  AXIN1 MUTATED     7   6
  AXIN1 WILD-TYPE 223 133
  AXIN1 MUTATED AXIN1 WILD-TYPE 
             13             356 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              6             133 
$`AXIN1 MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6705 TCGA-BR-8361 TCGA-BR-8487 
       19.56         6.97         9.67        25.61        31.10         1.12 
TCGA-BR-A4J8 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-D7-6820 TCGA-HU-A4GU TCGA-IN-A6RR 
       13.51        16.14         6.58        11.31         6.58         6.74 
TCGA-VQ-A8P2 
       38.14 

$`AXIN1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-6706 TCGA-BR-6707 
       39.12        26.10         9.17        32.78        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-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-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-D7-6822 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-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-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-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 

  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           14.45 
[1] "1.1 - 38.1 (11.3)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.5"
D711V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AXIN1 MUTATED         1        0        0        0         2         2
  AXIN1 WILD-TYPE       1       15       40       30        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AXIN1 MUTATED           0          3          3          2        0
  AXIN1 WILD-TYPE         3         67         50         30       38
D711V3, multiclass
            clus
vv           AXIN1 MUTATED AXIN1 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             3              50
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AXIN1 MUTATED     1   1   8   3
  AXIN1 WILD-TYPE  21  91 165  94
D711V4, multiclass
    clus
vv   AXIN1 MUTATED AXIN1 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             8             165
  T4             3              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
  AXIN1 MUTATED     2   6   1   4
  AXIN1 WILD-TYPE 116  98  76  73
D711V5, multiclass
    clus
vv   AXIN1 MUTATED AXIN1 WILD-TYPE
  N0             2             116
  N1             6              98
  N2             1              76
  N3             4              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"
D711V6, binary
                 cls
clus                0   1
  AXIN1 MUTATED    12   0
  AXIN1 WILD-TYPE 334  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED     12    0
  AXIN1 WILD-TYPE  334   29
   clus
vv  AXIN1 MUTATED AXIN1 WILD-TYPE
  0            12             334
  1             0              29
[1] 2 2
[1] FALSE
D711V7, binary
                 cls
clus                0   1
  AXIN1 MUTATED     6   8
  AXIN1 WILD-TYPE 139 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      6    8
  AXIN1 WILD-TYPE  139  240
        clus
vv       AXIN1 MUTATED AXIN1 WILD-TYPE
  FEMALE             6             139
  MALE               8             240
[1] 2 2
[1] FALSE
D711V8, binary
                 cls
clus                0   1
  AXIN1 MUTATED    13   1
  AXIN1 WILD-TYPE 279  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED     13    1
  AXIN1 WILD-TYPE  279   58
     clus
vv    AXIN1 MUTATED AXIN1 WILD-TYPE
  NO             13             279
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AXIN1 MUTATED                                          0
  AXIN1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AXIN1 MUTATED                                       3
  AXIN1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AXIN1 MUTATED                                                        9
  AXIN1 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AXIN1 MUTATED                                                   1
  AXIN1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AXIN1 MUTATED                                                                   0
  AXIN1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AXIN1 MUTATED                                                    0
  AXIN1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AXIN1 MUTATED                                                  1
  AXIN1 WILD-TYPE                                               60
D711V9, multiclass
                                                                   clus
vv                                                                  AXIN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  AXIN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AXIN1 MUTATED    10   0   0   2
  AXIN1 WILD-TYPE 301  14  15  22
D711V10, multiclass
    clus
vv   AXIN1 MUTATED AXIN1 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D711V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AXIN1 MUTATED       2                         1
  AXIN1 WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AXIN1 MUTATED                                           0    11
  AXIN1 WILD-TYPE                                         1   232
D711V12, multiclass
                                           clus
vv                                          AXIN1 MUTATED AXIN1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D711V13, binary
                 cls
clus                0   1
  AXIN1 MUTATED     0  13
  AXIN1 WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      0   13
  AXIN1 WILD-TYPE    4  297
                        clus
vv                       AXIN1 MUTATED AXIN1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(712) Variable = AOC3 MUTATION ANALYSIS
D712V1, survival
                sevent
clus2              0   1
  AOC3 MUTATED     5   3
  AOC3 WILD-TYPE 225 136
  AOC3 MUTATED AOC3 WILD-TYPE 
             8            361 
  AOC3 MUTATED AOC3 WILD-TYPE 
             3            136 
$`AOC3 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CG-4306 
       21.99        34.68         1.12        28.14        16.14         1.02 
TCGA-D7-A4YY TCGA-R5-A7ZI 
       13.78        74.53 

$`AOC3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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 

  AOC3 MUTATED AOC3 WILD-TYPE 
          1.02           0.00 
  AOC3 MUTATED AOC3 WILD-TYPE 
         74.53         122.30 
  AOC3 MUTATED AOC3 WILD-TYPE 
        19.065         14.170 
[1] "1.0 - 74.5 (19.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D712V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AOC3 MUTATED         0        0        0        0         2         0
  AOC3 WILD-TYPE       2       15       40       30        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AOC3 MUTATED           0          0          2          1        4
  AOC3 WILD-TYPE         3         70         51         31       34
D712V3, multiclass
            clus
vv           AOC3 MUTATED AOC3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            2             51
  STAGE IIIC            1             31
  STAGE IV              4             34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AOC3 MUTATED     1   0   5   4
  AOC3 WILD-TYPE  21  92 168  93
D712V4, multiclass
    clus
vv   AOC3 MUTATED AOC3 WILD-TYPE
  T1            1             21
  T2            0             92
  T3            5            168
  T4            4             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
  AOC3 MUTATED     2   3   2   3
  AOC3 WILD-TYPE 116 101  75  74
D712V5, multiclass
    clus
vv   AOC3 MUTATED AOC3 WILD-TYPE
  N0            2            116
  N1            3            101
  N2            2             75
  N3            3             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"
D712V6, binary
                cls
clus               0   1
  AOC3 MUTATED     8   3
  AOC3 WILD-TYPE 338  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOC3 MUTATED      8    3
  AOC3 WILD-TYPE  338   26
   clus
vv  AOC3 MUTATED AOC3 WILD-TYPE
  0            8            338
  1            3             26
[1] 2 2
[1] FALSE
D712V7, binary
                cls
clus               0   1
  AOC3 MUTATED     8   3
  AOC3 WILD-TYPE 137 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOC3 MUTATED      8    3
  AOC3 WILD-TYPE  137  245
        clus
vv       AOC3 MUTATED AOC3 WILD-TYPE
  FEMALE            8            137
  MALE              3            245
[1] 2 2
[1] FALSE
D712V8, binary
                cls
clus               0   1
  AOC3 MUTATED     6   1
  AOC3 WILD-TYPE 286  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOC3 MUTATED      6    1
  AOC3 WILD-TYPE  286   58
     clus
vv    AOC3 MUTATED AOC3 WILD-TYPE
  NO             6            286
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AOC3 MUTATED                                          0
  AOC3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AOC3 MUTATED                                       1
  AOC3 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AOC3 MUTATED                                                        9
  AOC3 WILD-TYPE                                                    149
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AOC3 MUTATED                                                   0
  AOC3 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AOC3 MUTATED                                                                   1
  AOC3 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AOC3 MUTATED                                                    0
  AOC3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AOC3 MUTATED                                                  0
  AOC3 WILD-TYPE                                               61
D712V9, multiclass
                                                                   clus
vv                                                                  AOC3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  AOC3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AOC3 MUTATED     6   0   2   3
  AOC3 WILD-TYPE 305  14  13  21
D712V10, multiclass
    clus
vv   AOC3 MUTATED AOC3 WILD-TYPE
  R0            6            305
  R1            0             14
  R2            2             13
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D712V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  AOC3 MUTATED       0                         0
  AOC3 WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AOC3 MUTATED                                           0     9
  AOC3 WILD-TYPE                                         1   234
D712V12, multiclass
                                           clus
vv                                          AOC3 MUTATED AOC3 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D712V13, binary
                cls
clus               0   1
  AOC3 MUTATED     1   8
  AOC3 WILD-TYPE   3 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOC3 MUTATED      1    8
  AOC3 WILD-TYPE    3  302
                        clus
vv                       AOC3 MUTATED AOC3 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(713) Variable = ANKRD23 MUTATION ANALYSIS
D713V1, survival
                   sevent
clus2                 0   1
  ANKRD23 MUTATED     4   2
  ANKRD23 WILD-TYPE 226 137
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                6               363 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                2               137 
$`ANKRD23 MUTATED`
TCGA-BR-4256 TCGA-BR-7707 TCGA-BR-A4QL TCGA-CG-5728 TCGA-HU-A4GT TCGA-VQ-A8P2 
        9.34        35.84        16.14        65.10         6.51        38.14 

$`ANKRD23 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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             14.17 
[1] "6.5 - 65.1 (26.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.5"
D713V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKRD23 MUTATED         0        0        2        0         1         0
  ANKRD23 WILD-TYPE       2       15       38       30        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD23 MUTATED           0          1          1          0        0
  ANKRD23 WILD-TYPE         3         69         52         32       38
D713V3, multiclass
            clus
vv           ANKRD23 MUTATED ANKRD23 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD23 MUTATED     0   2   2   1
  ANKRD23 WILD-TYPE  22  90 171  96
D713V4, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  T1               0                22
  T2               2                90
  T3               2               171
  T4               1                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
  ANKRD23 MUTATED     3   2   0   1
  ANKRD23 WILD-TYPE 115 102  77  76
D713V5, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  N0               3               115
  N1               2               102
  N2               0                77
  N3               1                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"
D713V6, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     6   0
  ANKRD23 WILD-TYPE 340  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      6    0
  ANKRD23 WILD-TYPE  340   29
   clus
vv  ANKRD23 MUTATED ANKRD23 WILD-TYPE
  0               6               340
  1               0                29
[1] 2 2
[1] FALSE
D713V7, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     4   2
  ANKRD23 WILD-TYPE 141 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      4    2
  ANKRD23 WILD-TYPE  141  246
        clus
vv       ANKRD23 MUTATED ANKRD23 WILD-TYPE
  FEMALE               4               141
  MALE                 2               246
[1] 2 2
[1] FALSE
D713V8, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     4   1
  ANKRD23 WILD-TYPE 288  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      4    1
  ANKRD23 WILD-TYPE  288   58
     clus
vv    ANKRD23 MUTATED ANKRD23 WILD-TYPE
  NO                4               288
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ANKRD23 MUTATED                                          0
  ANKRD23 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ANKRD23 MUTATED                                       0
  ANKRD23 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANKRD23 MUTATED                                                        3
  ANKRD23 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ANKRD23 MUTATED                                                   1
  ANKRD23 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANKRD23 MUTATED                                                                   1
  ANKRD23 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ANKRD23 MUTATED                                                    0
  ANKRD23 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ANKRD23 MUTATED                                                  1
  ANKRD23 WILD-TYPE                                               60
D713V9, multiclass
                                                                   clus
vv                                                                  ANKRD23 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  ANKRD23 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ANKRD23 MUTATED     5   0   0   1
  ANKRD23 WILD-TYPE 306  14  15  23
D713V10, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  R0               5               306
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D713V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ANKRD23 MUTATED       1                         0
  ANKRD23 WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANKRD23 MUTATED                                           0     4
  ANKRD23 WILD-TYPE                                         1   239
D713V12, multiclass
                                           clus
vv                                          ANKRD23 MUTATED ANKRD23 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D713V13, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     0   4
  ANKRD23 WILD-TYPE   4 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      0    4
  ANKRD23 WILD-TYPE    4  306
                        clus
vv                       ANKRD23 MUTATED ANKRD23 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4               306
[1] 2 2
[1] FALSE

Clustering(714) Variable = SOHLH2 MUTATION ANALYSIS
D714V1, survival
                  sevent
clus2                0   1
  SOHLH2 MUTATED     9   8
  SOHLH2 WILD-TYPE 221 131
  SOHLH2 MUTATED SOHLH2 WILD-TYPE 
              17              352 
  SOHLH2 MUTATED SOHLH2 WILD-TYPE 
               8              131 
$`SOHLH2 MUTATED`
TCGA-BR-4184 TCGA-BR-8297 TCGA-BR-8367 TCGA-BR-8485 TCGA-BR-A4PD TCGA-BR-A4QI 
        6.97         7.40        26.33         9.21        20.65        21.44 
TCGA-CD-8525 TCGA-CD-8536 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5733 
       12.59        12.43        11.31         6.58         9.01        21.07 
TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H2 TCGA-IN-A6RI 
       24.20        29.98         0.10        12.95        18.38 

$`SOHLH2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       32.52        13.51        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-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-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH 
       12.82         6.31        12.30        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-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-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-A4GU TCGA-HU-A4GX 
       11.77        21.37         8.98         6.51         6.58        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-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 

  SOHLH2 MUTATED SOHLH2 WILD-TYPE 
             0.1              0.0 
  SOHLH2 MUTATED SOHLH2 WILD-TYPE 
           29.98           122.30 
  SOHLH2 MUTATED SOHLH2 WILD-TYPE 
           12.59            14.45 
[1] "0.1 - 30.0 (12.6)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.5"
D714V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SOHLH2 MUTATED         1        1        0        1         4         1
  SOHLH2 WILD-TYPE       1       14       40       29        33        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SOHLH2 MUTATED           0          3          2          3        1
  SOHLH2 WILD-TYPE         3         67         51         29       37
D714V3, multiclass
            clus
vv           SOHLH2 MUTATED SOHLH2 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               4               33
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              2               51
  STAGE IIIC              3               29
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SOHLH2 MUTATED     2   2   8   5
  SOHLH2 WILD-TYPE  20  90 165  92
D714V4, multiclass
    clus
vv   SOHLH2 MUTATED SOHLH2 WILD-TYPE
  T1              2               20
  T2              2               90
  T3              8              165
  T4              5               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
  SOHLH2 MUTATED     7   3   2   5
  SOHLH2 WILD-TYPE 111 101  75  72
D714V5, multiclass
    clus
vv   SOHLH2 MUTATED SOHLH2 WILD-TYPE
  N0              7              111
  N1              3              101
  N2              2               75
  N3              5               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"
D714V6, binary
                  cls
clus                 0   1
  SOHLH2 MUTATED    15   1
  SOHLH2 WILD-TYPE 331  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SOHLH2 MUTATED     15    1
  SOHLH2 WILD-TYPE  331   28
   clus
vv  SOHLH2 MUTATED SOHLH2 WILD-TYPE
  0             15              331
  1              1               28
[1] 2 2
[1] FALSE
D714V7, binary
                  cls
clus                 0   1
  SOHLH2 MUTATED     8   9
  SOHLH2 WILD-TYPE 137 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SOHLH2 MUTATED      8    9
  SOHLH2 WILD-TYPE  137  239
        clus
vv       SOHLH2 MUTATED SOHLH2 WILD-TYPE
  FEMALE              8              137
  MALE                9              239
[1] 2 2
[1] FALSE
D714V8, binary
                  cls
clus                 0   1
  SOHLH2 MUTATED    15   1
  SOHLH2 WILD-TYPE 277  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SOHLH2 MUTATED     15    1
  SOHLH2 WILD-TYPE  277   58
     clus
vv    SOHLH2 MUTATED SOHLH2 WILD-TYPE
  NO              15              277
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SOHLH2 MUTATED                                          0
  SOHLH2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SOHLH2 MUTATED                                       4
  SOHLH2 WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SOHLH2 MUTATED                                                        7
  SOHLH2 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SOHLH2 MUTATED                                                   1
  SOHLH2 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SOHLH2 MUTATED                                                                   1
  SOHLH2 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SOHLH2 MUTATED                                                    0
  SOHLH2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SOHLH2 MUTATED                                                  4
  SOHLH2 WILD-TYPE                                               57
D714V9, multiclass
                                                                   clus
vv                                                                  SOHLH2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  SOHLH2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SOHLH2 MUTATED    13   0   1   1
  SOHLH2 WILD-TYPE 298  14  14  23
D714V10, multiclass
    clus
vv   SOHLH2 MUTATED SOHLH2 WILD-TYPE
  R0             13              298
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D714V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SOHLH2 MUTATED       8                         0
  SOHLH2 WILD-TYPE    79                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SOHLH2 MUTATED                                           0     7
  SOHLH2 WILD-TYPE                                         1   236
D714V12, multiclass
                                           clus
vv                                          SOHLH2 MUTATED SOHLH2 WILD-TYPE
  ASIAN                                                  8               79
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D714V13, binary
                  cls
clus                 0   1
  SOHLH2 MUTATED     0  15
  SOHLH2 WILD-TYPE   4 295
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SOHLH2 MUTATED      0   15
  SOHLH2 WILD-TYPE    4  295
                        clus
vv                       SOHLH2 MUTATED SOHLH2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             15              295
[1] 2 2
[1] FALSE

Clustering(715) Variable = SLC26A7 MUTATION ANALYSIS
D715V1, survival
                   sevent
clus2                 0   1
  SLC26A7 MUTATED    13   1
  SLC26A7 WILD-TYPE 217 138
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               14               355 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
                1               138 
$`SLC26A7 MUTATED`
TCGA-BR-6452 TCGA-BR-8381 TCGA-BR-8591 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-CD-A48A 
       34.68         7.36        28.14        20.65        16.14        12.43 
TCGA-CG-5721 TCGA-D7-6817 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-A4GX TCGA-HU-A4H8 
        6.02        12.79        21.27        11.08        20.25        14.07 
TCGA-MX-A5UJ TCGA-R5-A7O7 
       19.73        45.67 

$`SLC26A7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79        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-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        32.52        13.51        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-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-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-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        15.98        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-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-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 

  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
             6.02              0.00 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
            45.67            122.30 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
           17.935            14.170 
[1] "6.0 - 45.7 (17.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "5.9"
D715V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC26A7 MUTATED         0        0        1        0         3         2
  SLC26A7 WILD-TYPE       2       15       39       30        34        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC26A7 MUTATED           0          2          2          2        2
  SLC26A7 WILD-TYPE         3         68         51         30       36
D715V3, multiclass
            clus
vv           SLC26A7 MUTATED SLC26A7 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                3                34
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               2                51
  STAGE IIIC               2                30
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC26A7 MUTATED     2   1   8   4
  SLC26A7 WILD-TYPE  20  91 165  93
D715V4, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  T1               2                20
  T2               1                91
  T3               8               165
  T4               4                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
  SLC26A7 MUTATED     4   4   2   4
  SLC26A7 WILD-TYPE 114 100  75  73
D715V5, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  N0               4               114
  N1               4               100
  N2               2                75
  N3               4                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"
D715V6, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED    14   1
  SLC26A7 WILD-TYPE 332  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED     14    1
  SLC26A7 WILD-TYPE  332   28
   clus
vv  SLC26A7 MUTATED SLC26A7 WILD-TYPE
  0              14               332
  1               1                28
[1] 2 2
[1] FALSE
D715V7, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED     6   9
  SLC26A7 WILD-TYPE 139 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED      6    9
  SLC26A7 WILD-TYPE  139  239
        clus
vv       SLC26A7 MUTATED SLC26A7 WILD-TYPE
  FEMALE               6               139
  MALE                 9               239
[1] 2 2
[1] FALSE
D715V8, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED    10   4
  SLC26A7 WILD-TYPE 282  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED     10    4
  SLC26A7 WILD-TYPE  282   55
     clus
vv    SLC26A7 MUTATED SLC26A7 WILD-TYPE
  NO               10               282
  YES               4                55
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC26A7 MUTATED                                          0
  SLC26A7 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC26A7 MUTATED                                       1
  SLC26A7 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC26A7 MUTATED                                                        8
  SLC26A7 WILD-TYPE                                                    150
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC26A7 MUTATED                                                   1
  SLC26A7 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC26A7 MUTATED                                                                   1
  SLC26A7 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC26A7 MUTATED                                                    0
  SLC26A7 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC26A7 MUTATED                                                  4
  SLC26A7 WILD-TYPE                                               57
D715V9, multiclass
                                                                   clus
vv                                                                  SLC26A7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                4
                                                                   clus
vv                                                                  SLC26A7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC26A7 MUTATED    12   0   0   1
  SLC26A7 WILD-TYPE 299  14  15  23
D715V10, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  R0              12               299
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D715V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC26A7 MUTATED       3                         1
  SLC26A7 WILD-TYPE    84                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC26A7 MUTATED                                           0    10
  SLC26A7 WILD-TYPE                                         1   233
D715V12, multiclass
                                           clus
vv                                          SLC26A7 MUTATED SLC26A7 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D715V13, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED     2  12
  SLC26A7 WILD-TYPE   2 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED      2   12
  SLC26A7 WILD-TYPE    2  298
                        clus
vv                       SLC26A7 MUTATED SLC26A7 WILD-TYPE
  HISPANIC OR LATINO                   2                 2
  NOT HISPANIC OR LATINO              12               298
[1] 2 2
[1] FALSE

Clustering(716) Variable = RHOBTB2 MUTATION ANALYSIS
D716V1, survival
                   sevent
clus2                 0   1
  RHOBTB2 MUTATED     9  10
  RHOBTB2 WILD-TYPE 221 129
  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE 
               19               350 
  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE 
               10               129 
$`RHOBTB2 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8484 
        6.97        30.90         9.67        34.68         0.26        25.18 
TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5718 TCGA-CG-5728 TCGA-CG-5733 
       28.14        16.14         6.58        36.00        65.10        21.07 
TCGA-D7-A6EY TCGA-FP-A9TM TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GT TCGA-R5-A7ZI 
       11.44         6.21        22.32        29.98         6.51        74.53 
TCGA-VQ-A8P2 
       38.14 

$`RHOBTB2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39         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-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-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-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-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-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-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-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 

  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE 
             0.26              0.00 
  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE 
            74.53            122.30 
  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE 
            22.32             14.07 
[1] "0.3 - 74.5 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D716V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RHOBTB2 MUTATED         0        0        2        1         4         1
  RHOBTB2 WILD-TYPE       2       15       38       29        33        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RHOBTB2 MUTATED           0          4          2          1        2
  RHOBTB2 WILD-TYPE         3         66         51         31       36
D716V3, multiclass
            clus
vv           RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 1                29
  STAGE IIA                4                33
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               4                66
  STAGE IIIB               2                51
  STAGE IIIC               1                31
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RHOBTB2 MUTATED     1   6   6   6
  RHOBTB2 WILD-TYPE  21  86 167  91
D716V4, multiclass
    clus
vv   RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  T1               1                21
  T2               6                86
  T3               6               167
  T4               6                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
  RHOBTB2 MUTATED     6   7   2   3
  RHOBTB2 WILD-TYPE 112  97  75  74
D716V5, multiclass
    clus
vv   RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  N0               6               112
  N1               7                97
  N2               2                75
  N3               3                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"
D716V6, binary
                   cls
clus                  0   1
  RHOBTB2 MUTATED    18   1
  RHOBTB2 WILD-TYPE 328  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RHOBTB2 MUTATED     18    1
  RHOBTB2 WILD-TYPE  328   28
   clus
vv  RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  0              18               328
  1               1                28
[1] 2 2
[1] FALSE
D716V7, binary
                   cls
clus                  0   1
  RHOBTB2 MUTATED    13   7
  RHOBTB2 WILD-TYPE 132 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RHOBTB2 MUTATED     13    7
  RHOBTB2 WILD-TYPE  132  241
        clus
vv       RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  FEMALE              13               132
  MALE                 7               241
[1] 2 2
[1] FALSE
D716V8, binary
                   cls
clus                  0   1
  RHOBTB2 MUTATED    16   2
  RHOBTB2 WILD-TYPE 276  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RHOBTB2 MUTATED     16    2
  RHOBTB2 WILD-TYPE  276   57
     clus
vv    RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  NO               16               276
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RHOBTB2 MUTATED                                          0
  RHOBTB2 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RHOBTB2 MUTATED                                       3
  RHOBTB2 WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RHOBTB2 MUTATED                                                       10
  RHOBTB2 WILD-TYPE                                                    148
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RHOBTB2 MUTATED                                                   1
  RHOBTB2 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RHOBTB2 MUTATED                                                                   3
  RHOBTB2 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RHOBTB2 MUTATED                                                    0
  RHOBTB2 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RHOBTB2 MUTATED                                                  3
  RHOBTB2 WILD-TYPE                                               58
D716V9, multiclass
                                                                   clus
vv                                                                  RHOBTB2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  RHOBTB2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RHOBTB2 MUTATED    15   0   0   4
  RHOBTB2 WILD-TYPE 296  14  15  20
D716V10, multiclass
    clus
vv   RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  R0              15               296
  R1               0                14
  R2               0                15
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D716V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  RHOBTB2 MUTATED       4                         0
  RHOBTB2 WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RHOBTB2 MUTATED                                           0    13
  RHOBTB2 WILD-TYPE                                         1   230
D716V12, multiclass
                                           clus
vv                                          RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D716V13, binary
                   cls
clus                  0   1
  RHOBTB2 MUTATED     1  15
  RHOBTB2 WILD-TYPE   3 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RHOBTB2 MUTATED      1   15
  RHOBTB2 WILD-TYPE    3  295
                        clus
vv                       RHOBTB2 MUTATED RHOBTB2 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              15               295
[1] 2 2
[1] FALSE

Clustering(717) Variable = DGKA MUTATION ANALYSIS
D717V1, survival
                sevent
clus2              0   1
  DGKA MUTATED     4   4
  DGKA WILD-TYPE 226 135
  DGKA MUTATED DGKA WILD-TYPE 
             8            361 
  DGKA MUTATED DGKA WILD-TYPE 
             4            135 
$`DGKA MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6566 TCGA-BR-7723 TCGA-CD-5802 TCGA-CG-4469 
        6.97        30.90        32.78        28.73        13.35         7.07 
TCGA-HU-8602 TCGA-HU-A4H8 
       22.32        14.07 

$`DGKA WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-4477 
       19.07        12.03         0.00         9.01        18.97        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-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 

  DGKA MUTATED DGKA WILD-TYPE 
          6.97           0.00 
  DGKA MUTATED DGKA WILD-TYPE 
         32.78         122.30 
  DGKA MUTATED DGKA WILD-TYPE 
        18.195         14.270 
[1] "7.0 - 32.8 (18.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D717V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DGKA MUTATED         0        0        1        1         1         1
  DGKA WILD-TYPE       2       15       39       29        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DGKA MUTATED           0          2          1          0        1
  DGKA WILD-TYPE         3         68         52         32       37
D717V3, multiclass
            clus
vv           DGKA MUTATED DGKA WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DGKA MUTATED     1   1   5   2
  DGKA WILD-TYPE  21  91 168  95
D717V4, multiclass
    clus
vv   DGKA MUTATED DGKA WILD-TYPE
  T1            1             21
  T2            1             91
  T3            5            168
  T4            2             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
  DGKA MUTATED     4   2   0   2
  DGKA WILD-TYPE 114 102  77  75
D717V5, multiclass
    clus
vv   DGKA MUTATED DGKA WILD-TYPE
  N0            4            114
  N1            2            102
  N2            0             77
  N3            2             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"
D717V6, binary
                cls
clus               0   1
  DGKA MUTATED     8   0
  DGKA WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKA MUTATED      8    0
  DGKA WILD-TYPE  338   29
   clus
vv  DGKA MUTATED DGKA WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D717V7, binary
                cls
clus               0   1
  DGKA MUTATED     4   5
  DGKA WILD-TYPE 141 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKA MUTATED      4    5
  DGKA WILD-TYPE  141  243
        clus
vv       DGKA MUTATED DGKA WILD-TYPE
  FEMALE            4            141
  MALE              5            243
[1] 2 2
[1] FALSE
D717V8, binary
                cls
clus               0   1
  DGKA MUTATED     6   1
  DGKA WILD-TYPE 286  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKA MUTATED      6    1
  DGKA WILD-TYPE  286   58
     clus
vv    DGKA MUTATED DGKA WILD-TYPE
  NO             6            286
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DGKA MUTATED                                          0
  DGKA WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DGKA MUTATED                                       1
  DGKA WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DGKA MUTATED                                                        6
  DGKA WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DGKA MUTATED                                                   0
  DGKA WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DGKA MUTATED                                                                   1
  DGKA WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DGKA MUTATED                                                    0
  DGKA WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DGKA MUTATED                                                  1
  DGKA WILD-TYPE                                               60
D717V9, multiclass
                                                                   clus
vv                                                                  DGKA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  DGKA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DGKA MUTATED     4   1   0   3
  DGKA WILD-TYPE 307  13  15  21
D717V10, multiclass
    clus
vv   DGKA MUTATED DGKA WILD-TYPE
  R0            4            307
  R1            1             13
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D717V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DGKA MUTATED       3                         0
  DGKA WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DGKA MUTATED                                           0     5
  DGKA WILD-TYPE                                         1   238
D717V12, multiclass
                                           clus
vv                                          DGKA MUTATED DGKA WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D717V13, binary
                cls
clus               0   1
  DGKA MUTATED     0   8
  DGKA WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKA MUTATED      0    8
  DGKA WILD-TYPE    4  302
                        clus
vv                       DGKA MUTATED DGKA WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(718) Variable = KIAA1797 MUTATION ANALYSIS
D718V1, survival
                    sevent
clus2                  0   1
  KIAA1797 MUTATED    14   3
  KIAA1797 WILD-TYPE 216 136
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                17                352 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                 3                136 
$`KIAA1797 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 
       28.73         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-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-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-5724 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 
        0.99         0.99        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-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-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-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 

  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
              1.12               0.00 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
            105.07             122.30 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
             27.12              14.04 
[1] "1.1 - 105.1 (27.1)" "0.0 - 122.3 (14.0)"
[1] "hr=" "3"  
D718V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1797 MUTATED         0        1        2        3         2         3
  KIAA1797 WILD-TYPE       2       14       38       27        35        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1797 MUTATED           1          1          2          1        2
  KIAA1797 WILD-TYPE         2         69         51         31       36
D718V3, multiclass
            clus
vv           KIAA1797 MUTATED KIAA1797 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  2                 38
  STAGE II                  3                 27
  STAGE IIA                 2                 35
  STAGE IIB                 3                 49
  STAGE III                 1                  2
  STAGE IIIA                1                 69
  STAGE IIIB                2                 51
  STAGE IIIC                1                 31
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1797 MUTATED     2   4   5   7
  KIAA1797 WILD-TYPE  20  88 168  90
D718V4, multiclass
    clus
vv   KIAA1797 MUTATED KIAA1797 WILD-TYPE
  T1                2                 20
  T2                4                 88
  T3                5                168
  T4                7                 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
  KIAA1797 MUTATED     6  10   2   1
  KIAA1797 WILD-TYPE 112  94  75  76
D718V5, multiclass
    clus
vv   KIAA1797 MUTATED KIAA1797 WILD-TYPE
  N0                6                112
  N1               10                 94
  N2                2                 75
  N3                1                 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"
D718V6, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED    18   1
  KIAA1797 WILD-TYPE 328  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED     18    1
  KIAA1797 WILD-TYPE  328   28
   clus
vv  KIAA1797 MUTATED KIAA1797 WILD-TYPE
  0               18                328
  1                1                 28
[1] 2 2
[1] FALSE
D718V7, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED     9  10
  KIAA1797 WILD-TYPE 136 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED      9   10
  KIAA1797 WILD-TYPE  136  238
        clus
vv       KIAA1797 MUTATED KIAA1797 WILD-TYPE
  FEMALE                9                136
  MALE                 10                238
[1] 2 2
[1] FALSE
D718V8, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED    13   2
  KIAA1797 WILD-TYPE 279  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED     13    2
  KIAA1797 WILD-TYPE  279   57
     clus
vv    KIAA1797 MUTATED KIAA1797 WILD-TYPE
  NO                13                279
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA1797 MUTATED                                          0
  KIAA1797 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA1797 MUTATED                                       2
  KIAA1797 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1797 MUTATED                                                       11
  KIAA1797 WILD-TYPE                                                    147
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA1797 MUTATED                                                   0
  KIAA1797 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1797 MUTATED                                                                   4
  KIAA1797 WILD-TYPE                                                                64
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA1797 MUTATED                                                    0
  KIAA1797 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA1797 MUTATED                                                  2
  KIAA1797 WILD-TYPE                                               59
D718V9, multiclass
                                                                   clus
vv                                                                  KIAA1797 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  KIAA1797 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1797 MUTATED    16   0   0   2
  KIAA1797 WILD-TYPE 295  14  15  22
D718V10, multiclass
    clus
vv   KIAA1797 MUTATED KIAA1797 WILD-TYPE
  R0               16                295
  R1                0                 14
  R2                0                 15
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D718V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1797 MUTATED       4                         0
  KIAA1797 WILD-TYPE    83                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1797 MUTATED                                           0    10
  KIAA1797 WILD-TYPE                                         1   233
D718V12, multiclass
                                           clus
vv                                          KIAA1797 MUTATED KIAA1797 WILD-TYPE
  ASIAN                                                    4                 83
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   10                233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D718V13, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED     0  14
  KIAA1797 WILD-TYPE   4 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED      0   14
  KIAA1797 WILD-TYPE    4  296
                        clus
vv                       KIAA1797 MUTATED KIAA1797 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               14                296
[1] 2 2
[1] FALSE

Clustering(719) Variable = SERPINB10 MUTATION ANALYSIS
D719V1, survival
                     sevent
clus2                   0   1
  SERPINB10 MUTATED     7   1
  SERPINB10 WILD-TYPE 223 138
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                  8                 361 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                  1                 138 
$`SERPINB10 MUTATED`
TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-A4Z0 
       44.94        29.59        31.96         6.58         6.02        14.76 
TCGA-HF-7132 TCGA-HU-A4H8 
       77.29        14.07 

$`SERPINB10 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
               6.02                0.00 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
              77.29              122.30 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
             22.175              14.170 
[1] "6.0 - 77.3 (22.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "4.2"
D719V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPINB10 MUTATED         0        0        1        1         2         2
  SERPINB10 WILD-TYPE       2       15       39       29        35        50
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB10 MUTATED           0          0          0          0        2
  SERPINB10 WILD-TYPE         3         70         53         32       36
D719V3, multiclass
            clus
vv           SERPINB10 MUTATED SERPINB10 WILD-TYPE
  STAGE I                    0                   2
  STAGE IA                   0                  15
  STAGE IB                   1                  39
  STAGE II                   1                  29
  STAGE IIA                  2                  35
  STAGE IIB                  2                  50
  STAGE III                  0                   3
  STAGE IIIA                 0                  70
  STAGE IIIB                 0                  53
  STAGE IIIC                 0                  32
  STAGE IV                   2                  36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  SERPINB10 MUTATED     1   2   2   3
  SERPINB10 WILD-TYPE  21  90 171  94
D719V4, multiclass
    clus
vv   SERPINB10 MUTATED SERPINB10 WILD-TYPE
  T1                 1                  21
  T2                 2                  90
  T3                 2                 171
  T4                 3                  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
  SERPINB10 MUTATED     3   3   2   0
  SERPINB10 WILD-TYPE 115 101  75  77
D719V5, multiclass
    clus
vv   SERPINB10 MUTATED SERPINB10 WILD-TYPE
  N0                 3                 115
  N1                 3                 101
  N2                 2                  75
  N3                 0                  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"
D719V6, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED     7   1
  SERPINB10 WILD-TYPE 339  28
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED      7    1
  SERPINB10 WILD-TYPE  339   28
   clus
vv  SERPINB10 MUTATED SERPINB10 WILD-TYPE
  0                 7                 339
  1                 1                  28
[1] 2 2
[1] FALSE
D719V7, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED     3   5
  SERPINB10 WILD-TYPE 142 243
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED      3    5
  SERPINB10 WILD-TYPE  142  243
        clus
vv       SERPINB10 MUTATED SERPINB10 WILD-TYPE
  FEMALE                 3                 142
  MALE                   5                 243
[1] 2 2
[1] FALSE
D719V8, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED     6   2
  SERPINB10 WILD-TYPE 286  57
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED      6    2
  SERPINB10 WILD-TYPE  286   57
     clus
vv    SERPINB10 MUTATED SERPINB10 WILD-TYPE
  NO                  6                 286
  YES                 2                  57
[1] 2 2
[1] FALSE
                     vv
clus                  STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SERPINB10 MUTATED                                          0
  SERPINB10 WILD-TYPE                                        8
                     vv
clus                  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SERPINB10 MUTATED                                       1
  SERPINB10 WILD-TYPE                                    69
                     vv
clus                  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SERPINB10 MUTATED                                                        2
  SERPINB10 WILD-TYPE                                                    156
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SERPINB10 MUTATED                                                   2
  SERPINB10 WILD-TYPE                                                19
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SERPINB10 MUTATED                                                                   1
  SERPINB10 WILD-TYPE                                                                67
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SERPINB10 MUTATED                                                    0
  SERPINB10 WILD-TYPE                                                  5
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SERPINB10 MUTATED                                                  2
  SERPINB10 WILD-TYPE                                               59
D719V9, multiclass
                                                                   clus
vv                                                                  SERPINB10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  2
                                                                   clus
vv                                                                  SERPINB10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                            8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                              69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                  19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                  5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                   59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  SERPINB10 MUTATED     7   0   0   0
  SERPINB10 WILD-TYPE 304  14  15  24
D719V10, multiclass
    clus
vv   SERPINB10 MUTATED SERPINB10 WILD-TYPE
  R0                 7                 304
  R1                 0                  14
  R2                 0                  15
  RX                 0                  24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D719V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN
  SERPINB10 MUTATED       3                         0
  SERPINB10 WILD-TYPE    84                         9
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SERPINB10 MUTATED                                           0     3
  SERPINB10 WILD-TYPE                                         1   240
D719V12, multiclass
                                           clus
vv                                          SERPINB10 MUTATED
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                 0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                     3
                                           clus
vv                                          SERPINB10 WILD-TYPE
  ASIAN                                                      84
  BLACK OR AFRICAN AMERICAN                                   9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   1
  WHITE                                                     240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D719V13, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED     0   6
  SERPINB10 WILD-TYPE   4 304
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED      0    6
  SERPINB10 WILD-TYPE    4  304
                        clus
vv                       SERPINB10 MUTATED SERPINB10 WILD-TYPE
  HISPANIC OR LATINO                     0                   4
  NOT HISPANIC OR LATINO                 6                 304
[1] 2 2
[1] FALSE

Clustering(720) Variable = SMCHD1 MUTATION ANALYSIS
D720V1, survival
                  sevent
clus2                0   1
  SMCHD1 MUTATED     9   3
  SMCHD1 WILD-TYPE 221 136
  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
              12              357 
  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
               3              136 
$`SMCHD1 MUTATED`
TCGA-EQ-A4SO TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8678 
       16.24         6.97        30.90        35.84        32.25        24.79 
TCGA-BR-8680 TCGA-BR-A4PE TCGA-CD-A4MG TCGA-CG-4437 TCGA-HU-A4G8 TCGA-HU-A4GH 
       31.96        20.42         6.58         8.05        22.68        11.77 

$`SMCHD1 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       26.73        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-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-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-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 

  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
            6.58             0.00 
  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
           35.84           122.30 
  SMCHD1 MUTATED SMCHD1 WILD-TYPE 
           21.55            14.07 
[1] "6.6 - 35.8 (21.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D720V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMCHD1 MUTATED         0        2        3        1         1         2
  SMCHD1 WILD-TYPE       2       13       37       29        36        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMCHD1 MUTATED           0          1          1          0        1
  SMCHD1 WILD-TYPE         3         69         52         32       37
D720V3, multiclass
            clus
vv           SMCHD1 MUTATED SMCHD1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                2               13
  STAGE IB                3               37
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SMCHD1 MUTATED     2   5   3   3
  SMCHD1 WILD-TYPE  20  87 170  94
D720V4, multiclass
    clus
vv   SMCHD1 MUTATED SMCHD1 WILD-TYPE
  T1              2               20
  T2              5               87
  T3              3              170
  T4              3               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
  SMCHD1 MUTATED     7   5   1   0
  SMCHD1 WILD-TYPE 111  99  76  77
D720V5, multiclass
    clus
vv   SMCHD1 MUTATED SMCHD1 WILD-TYPE
  N0              7              111
  N1              5               99
  N2              1               76
  N3              0               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"
D720V6, binary
                  cls
clus                 0   1
  SMCHD1 MUTATED    11   1
  SMCHD1 WILD-TYPE 335  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SMCHD1 MUTATED     11    1
  SMCHD1 WILD-TYPE  335   28
   clus
vv  SMCHD1 MUTATED SMCHD1 WILD-TYPE
  0             11              335
  1              1               28
[1] 2 2
[1] FALSE
D720V7, binary
                  cls
clus                 0   1
  SMCHD1 MUTATED     6   8
  SMCHD1 WILD-TYPE 139 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SMCHD1 MUTATED      6    8
  SMCHD1 WILD-TYPE  139  240
        clus
vv       SMCHD1 MUTATED SMCHD1 WILD-TYPE
  FEMALE              6              139
  MALE                8              240
[1] 2 2
[1] FALSE
D720V8, binary
                  cls
clus                 0   1
  SMCHD1 MUTATED    11   2
  SMCHD1 WILD-TYPE 281  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SMCHD1 MUTATED     11    2
  SMCHD1 WILD-TYPE  281   57
     clus
vv    SMCHD1 MUTATED SMCHD1 WILD-TYPE
  NO              11              281
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SMCHD1 MUTATED                                          0
  SMCHD1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SMCHD1 MUTATED                                       2
  SMCHD1 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMCHD1 MUTATED                                                        8
  SMCHD1 WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SMCHD1 MUTATED                                                   0
  SMCHD1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMCHD1 MUTATED                                                                   1
  SMCHD1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SMCHD1 MUTATED                                                    0
  SMCHD1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SMCHD1 MUTATED                                                  2
  SMCHD1 WILD-TYPE                                               59
D720V9, multiclass
                                                                   clus
vv                                                                  SMCHD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  SMCHD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SMCHD1 MUTATED     9   0   0   3
  SMCHD1 WILD-TYPE 302  14  15  21
D720V10, multiclass
    clus
vv   SMCHD1 MUTATED SMCHD1 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D720V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SMCHD1 MUTATED       5                         0
  SMCHD1 WILD-TYPE    82                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMCHD1 MUTATED                                           0     8
  SMCHD1 WILD-TYPE                                         1   235
D720V12, multiclass
                                           clus
vv                                          SMCHD1 MUTATED SMCHD1 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D720V13, binary
                  cls
clus                 0   1
  SMCHD1 MUTATED     0  13
  SMCHD1 WILD-TYPE   4 297
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SMCHD1 MUTATED      0   13
  SMCHD1 WILD-TYPE    4  297
                        clus
vv                       SMCHD1 MUTATED SMCHD1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             13              297
[1] 2 2
[1] FALSE

Clustering(721) Variable = MOCS2 MUTATION ANALYSIS
D721V1, survival
                 sevent
clus2               0   1
  MOCS2 MUTATED     2   2
  MOCS2 WILD-TYPE 228 137
  MOCS2 MUTATED MOCS2 WILD-TYPE 
              4             365 
  MOCS2 MUTATED MOCS2 WILD-TYPE 
              2             137 
$`MOCS2 MUTATED`
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-8361 TCGA-HF-7132 
       18.35        30.90        31.10        77.29 

$`MOCS2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  MOCS2 MUTATED MOCS2 WILD-TYPE 
          18.35            0.00 
  MOCS2 MUTATED MOCS2 WILD-TYPE 
          77.29          122.30 
  MOCS2 MUTATED MOCS2 WILD-TYPE 
          31.00           14.07 
[1] "18.4 - 77.3 (31.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D721V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MOCS2 MUTATED         0        0        0        1         0         0
  MOCS2 WILD-TYPE       2       15       40       29        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MOCS2 MUTATED           0          0          0          1        1
  MOCS2 WILD-TYPE         3         70         53         31       37
D721V3, multiclass
            clus
vv           MOCS2 MUTATED MOCS2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MOCS2 MUTATED     0   2   0   2
  MOCS2 WILD-TYPE  22  90 173  95
D721V4, multiclass
    clus
vv   MOCS2 MUTATED MOCS2 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             0             173
  T4             2              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
  MOCS2 MUTATED     0   2   2   0
  MOCS2 WILD-TYPE 118 102  75  77
D721V5, multiclass
    clus
vv   MOCS2 MUTATED MOCS2 WILD-TYPE
  N0             0             118
  N1             2             102
  N2             2              75
  N3             0              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"
D721V6, binary
                 cls
clus                0   1
  MOCS2 MUTATED     5   0
  MOCS2 WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCS2 MUTATED      5    0
  MOCS2 WILD-TYPE  341   29
   clus
vv  MOCS2 MUTATED MOCS2 WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D721V7, binary
                 cls
clus                0   1
  MOCS2 MUTATED     3   2
  MOCS2 WILD-TYPE 142 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCS2 MUTATED      3    2
  MOCS2 WILD-TYPE  142  246
        clus
vv       MOCS2 MUTATED MOCS2 WILD-TYPE
  FEMALE             3             142
  MALE               2             246
[1] 2 2
[1] FALSE
D721V8, binary
                 cls
clus                0   1
  MOCS2 MUTATED     3   1
  MOCS2 WILD-TYPE 289  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCS2 MUTATED      3    1
  MOCS2 WILD-TYPE  289   58
     clus
vv    MOCS2 MUTATED MOCS2 WILD-TYPE
  NO              3             289
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MOCS2 MUTATED                                          0
  MOCS2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MOCS2 MUTATED                                       0
  MOCS2 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MOCS2 MUTATED                                                        4
  MOCS2 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MOCS2 MUTATED                                                   1
  MOCS2 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MOCS2 MUTATED                                                                   0
  MOCS2 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MOCS2 MUTATED                                                    0
  MOCS2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MOCS2 MUTATED                                                  0
  MOCS2 WILD-TYPE                                               61
D721V9, multiclass
                                                                   clus
vv                                                                  MOCS2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  MOCS2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MOCS2 MUTATED     2   0   0   3
  MOCS2 WILD-TYPE 309  14  15  21
D721V10, multiclass
    clus
vv   MOCS2 MUTATED MOCS2 WILD-TYPE
  R0             2             309
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D721V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MOCS2 MUTATED       0                         0
  MOCS2 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MOCS2 MUTATED                                           0     4
  MOCS2 WILD-TYPE                                         1   239
D721V12, multiclass
                                           clus
vv                                          MOCS2 MUTATED MOCS2 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D721V13, binary
                 cls
clus                0   1
  MOCS2 MUTATED     0   4
  MOCS2 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOCS2 MUTATED      0    4
  MOCS2 WILD-TYPE    4  306
                        clus
vv                       MOCS2 MUTATED MOCS2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(722) Variable = DGKD MUTATION ANALYSIS
D722V1, survival
                sevent
clus2              0   1
  DGKD MUTATED     4   2
  DGKD WILD-TYPE 226 137
  DGKD MUTATED DGKD WILD-TYPE 
             6            363 
  DGKD MUTATED DGKD WILD-TYPE 
             2            137 
$`DGKD MUTATED`
TCGA-BR-4201 TCGA-BR-8487 TCGA-CD-8525 TCGA-HF-7134 TCGA-HU-8602 TCGA-HU-A4GQ 
       30.90         1.12        12.59        52.21        22.32         0.10 

$`DGKD WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        6.21        77.29        63.06        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-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 

  DGKD MUTATED DGKD WILD-TYPE 
           0.1            0.0 
  DGKD MUTATED DGKD WILD-TYPE 
         52.21         122.30 
  DGKD MUTATED DGKD WILD-TYPE 
        17.455         14.270 
[1] "0.1 - 52.2 (17.5)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D722V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DGKD MUTATED         0        1        0        0         1         1
  DGKD WILD-TYPE       2       14       40       30        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DGKD MUTATED           0          1          0          1        0
  DGKD WILD-TYPE         3         69         53         31       38
D722V3, multiclass
            clus
vv           DGKD MUTATED DGKD WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DGKD MUTATED     1   1   2   2
  DGKD WILD-TYPE  21  91 171  95
D722V4, multiclass
    clus
vv   DGKD MUTATED DGKD WILD-TYPE
  T1            1             21
  T2            1             91
  T3            2            171
  T4            2             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
  DGKD MUTATED     3   1   1   0
  DGKD WILD-TYPE 115 103  76  77
D722V5, multiclass
    clus
vv   DGKD MUTATED DGKD WILD-TYPE
  N0            3            115
  N1            1            103
  N2            1             76
  N3            0             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"
D722V6, binary
                cls
clus               0   1
  DGKD MUTATED     6   0
  DGKD WILD-TYPE 340  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKD MUTATED      6    0
  DGKD WILD-TYPE  340   29
   clus
vv  DGKD MUTATED DGKD WILD-TYPE
  0            6            340
  1            0             29
[1] 2 2
[1] FALSE
D722V7, binary
                cls
clus               0   1
  DGKD MUTATED     4   2
  DGKD WILD-TYPE 141 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKD MUTATED      4    2
  DGKD WILD-TYPE  141  246
        clus
vv       DGKD MUTATED DGKD WILD-TYPE
  FEMALE            4            141
  MALE              2            246
[1] 2 2
[1] FALSE
D722V8, binary
                cls
clus               0   1
  DGKD MUTATED     5   1
  DGKD WILD-TYPE 287  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKD MUTATED      5    1
  DGKD WILD-TYPE  287   58
     clus
vv    DGKD MUTATED DGKD WILD-TYPE
  NO             5            287
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DGKD MUTATED                                          0
  DGKD WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DGKD MUTATED                                       1
  DGKD WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DGKD MUTATED                                                        2
  DGKD WILD-TYPE                                                    156
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DGKD MUTATED                                                   1
  DGKD WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DGKD MUTATED                                                                   1
  DGKD WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DGKD MUTATED                                                    0
  DGKD WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DGKD MUTATED                                                  1
  DGKD WILD-TYPE                                               60
D722V9, multiclass
                                                                   clus
vv                                                                  DGKD MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  DGKD WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DGKD MUTATED     5   0   0   1
  DGKD WILD-TYPE 306  14  15  23
D722V10, multiclass
    clus
vv   DGKD MUTATED DGKD WILD-TYPE
  R0            5            306
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D722V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DGKD MUTATED       3                         0
  DGKD WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DGKD MUTATED                                           0     2
  DGKD WILD-TYPE                                         1   241
D722V12, multiclass
                                           clus
vv                                          DGKD MUTATED DGKD WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D722V13, binary
                cls
clus               0   1
  DGKD MUTATED     0   5
  DGKD WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  DGKD MUTATED      0    5
  DGKD WILD-TYPE    4  305
                        clus
vv                       DGKD MUTATED DGKD WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(723) Variable = THEMIS MUTATION ANALYSIS
D723V1, survival
                  sevent
clus2                0   1
  THEMIS MUTATED     6   4
  THEMIS WILD-TYPE 224 135
  THEMIS MUTATED THEMIS WILD-TYPE 
              10              359 
  THEMIS MUTATED THEMIS WILD-TYPE 
               4              135 
$`THEMIS MUTATED`
TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8680 TCGA-BR-A4QL 
        6.97         7.43        30.90        34.68        31.96        16.14 
TCGA-CG-5723 TCGA-MX-A5UJ TCGA-VQ-A8P2 TCGA-ZA-A8F6 
      105.07        19.73        38.14        17.26 

$`THEMIS WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        26.70        11.70        19.56        11.01 
TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4253 
        9.47         9.44         6.61         4.64        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-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-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-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 
       54.12        26.04        16.14        27.55        12.43 

  THEMIS MUTATED THEMIS WILD-TYPE 
            6.97             0.00 
  THEMIS MUTATED THEMIS WILD-TYPE 
          105.07           122.30 
  THEMIS MUTATED THEMIS WILD-TYPE 
          25.315           14.070 
[1] "7.0 - 105.1 (25.3)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D723V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  THEMIS MUTATED         1        0        1        1         1         0
  THEMIS WILD-TYPE       1       15       39       29        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  THEMIS MUTATED           0          3          1          0        1
  THEMIS WILD-TYPE         3         67         52         32       37
D723V3, multiclass
            clus
vv           THEMIS MUTATED THEMIS WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  THEMIS MUTATED     1   3   4   2
  THEMIS WILD-TYPE  21  89 169  95
D723V4, multiclass
    clus
vv   THEMIS MUTATED THEMIS WILD-TYPE
  T1              1               21
  T2              3               89
  T3              4              169
  T4              2               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
  THEMIS MUTATED     2   5   2   1
  THEMIS WILD-TYPE 116  99  75  76
D723V5, multiclass
    clus
vv   THEMIS MUTATED THEMIS WILD-TYPE
  N0              2              116
  N1              5               99
  N2              2               75
  N3              1               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"
D723V6, binary
                  cls
clus                 0   1
  THEMIS MUTATED     7   1
  THEMIS WILD-TYPE 339  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      7    1
  THEMIS WILD-TYPE  339   28
   clus
vv  THEMIS MUTATED THEMIS WILD-TYPE
  0              7              339
  1              1               28
[1] 2 2
[1] FALSE
D723V7, binary
                  cls
clus                 0   1
  THEMIS MUTATED     5   6
  THEMIS WILD-TYPE 140 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      5    6
  THEMIS WILD-TYPE  140  242
        clus
vv       THEMIS MUTATED THEMIS WILD-TYPE
  FEMALE              5              140
  MALE                6              242
[1] 2 2
[1] FALSE
D723V8, binary
                  cls
clus                 0   1
  THEMIS MUTATED    10   1
  THEMIS WILD-TYPE 282  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED     10    1
  THEMIS WILD-TYPE  282   58
     clus
vv    THEMIS MUTATED THEMIS WILD-TYPE
  NO              10              282
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  THEMIS MUTATED                                          0
  THEMIS WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  THEMIS MUTATED                                       0
  THEMIS WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  THEMIS MUTATED                                                        7
  THEMIS WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  THEMIS MUTATED                                                   1
  THEMIS WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  THEMIS MUTATED                                                                   1
  THEMIS WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  THEMIS MUTATED                                                    0
  THEMIS WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  THEMIS MUTATED                                                  2
  THEMIS WILD-TYPE                                               59
D723V9, multiclass
                                                                   clus
vv                                                                  THEMIS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  THEMIS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  THEMIS MUTATED     8   0   0   3
  THEMIS WILD-TYPE 303  14  15  21
D723V10, multiclass
    clus
vv   THEMIS MUTATED THEMIS WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D723V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  THEMIS MUTATED       1                         1
  THEMIS WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  THEMIS MUTATED                                           0     8
  THEMIS WILD-TYPE                                         1   235
D723V12, multiclass
                                           clus
vv                                          THEMIS MUTATED THEMIS WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D723V13, binary
                  cls
clus                 0   1
  THEMIS MUTATED     0   9
  THEMIS WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      0    9
  THEMIS WILD-TYPE    4  301
                        clus
vv                       THEMIS MUTATED THEMIS WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(724) Variable = BMPR2 MUTATION ANALYSIS
D724V1, survival
                 sevent
clus2               0   1
  BMPR2 MUTATED    15   3
  BMPR2 WILD-TYPE 215 136
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             18             351 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
              3             136 
$`BMPR2 MUTATED`
TCGA-B7-A5TI TCGA-BR-4257 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8588 
       19.56         9.67        44.94        29.59        32.25        12.79 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4465 TCGA-CG-5723 TCGA-CG-5728 
        6.58        12.62        15.95         9.01       105.07        65.10 
TCGA-D7-6524 TCGA-F1-6874 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-VQ-A8P2 
       17.85        14.47        30.51        22.68        20.25        38.14 

$`BMPR2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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-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-D7-6525 
       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-F1-6875 
        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-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 

  BMPR2 MUTATED BMPR2 WILD-TYPE 
           6.58            0.00 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
         105.07          122.30 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
         19.905          14.040 
[1] "6.6 - 105.1 (19.9)" "0.0 - 122.3 (14.0)"
[1] "hr=" "3.2"
D724V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BMPR2 MUTATED         0        0        3        3         2         5
  BMPR2 WILD-TYPE       2       15       37       27        35        47
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BMPR2 MUTATED           0          1          0          3        1
  BMPR2 WILD-TYPE         3         69         53         29       37
D724V3, multiclass
            clus
vv           BMPR2 MUTATED BMPR2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               3              27
  STAGE IIA              2              35
  STAGE IIB              5              47
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BMPR2 MUTATED     0   6   3   9
  BMPR2 WILD-TYPE  22  86 170  88
D724V4, multiclass
    clus
vv   BMPR2 MUTATED BMPR2 WILD-TYPE
  T1             0              22
  T2             6              86
  T3             3             170
  T4             9              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
  BMPR2 MUTATED     9   5   1   3
  BMPR2 WILD-TYPE 109  99  76  74
D724V5, multiclass
    clus
vv   BMPR2 MUTATED BMPR2 WILD-TYPE
  N0             9             109
  N1             5              99
  N2             1              76
  N3             3              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"
D724V6, binary
                 cls
clus                0   1
  BMPR2 MUTATED    18   1
  BMPR2 WILD-TYPE 328  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     18    1
  BMPR2 WILD-TYPE  328   28
   clus
vv  BMPR2 MUTATED BMPR2 WILD-TYPE
  0            18             328
  1             1              28
[1] 2 2
[1] FALSE
D724V7, binary
                 cls
clus                0   1
  BMPR2 MUTATED    10   9
  BMPR2 WILD-TYPE 135 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     10    9
  BMPR2 WILD-TYPE  135  239
        clus
vv       BMPR2 MUTATED BMPR2 WILD-TYPE
  FEMALE            10             135
  MALE               9             239
[1] 2 2
[1] FALSE
D724V8, binary
                 cls
clus                0   1
  BMPR2 MUTATED    15   2
  BMPR2 WILD-TYPE 277  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     15    2
  BMPR2 WILD-TYPE  277   57
     clus
vv    BMPR2 MUTATED BMPR2 WILD-TYPE
  NO             15             277
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BMPR2 MUTATED                                          0
  BMPR2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BMPR2 MUTATED                                       6
  BMPR2 WILD-TYPE                                    64
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BMPR2 MUTATED                                                        8
  BMPR2 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BMPR2 MUTATED                                                   2
  BMPR2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BMPR2 MUTATED                                                                   3
  BMPR2 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BMPR2 MUTATED                                                    0
  BMPR2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BMPR2 MUTATED                                                  0
  BMPR2 WILD-TYPE                                               61
D724V9, multiclass
                                                                   clus
vv                                                                  BMPR2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  BMPR2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BMPR2 MUTATED    11   2   1   1
  BMPR2 WILD-TYPE 300  12  14  23
D724V10, multiclass
    clus
vv   BMPR2 MUTATED BMPR2 WILD-TYPE
  R0            11             300
  R1             2              12
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D724V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BMPR2 MUTATED       4                         0
  BMPR2 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BMPR2 MUTATED                                           0    10
  BMPR2 WILD-TYPE                                         1   233
D724V12, multiclass
                                           clus
vv                                          BMPR2 MUTATED BMPR2 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D724V13, binary
                 cls
clus                0   1
  BMPR2 MUTATED     0  13
  BMPR2 WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED      0   13
  BMPR2 WILD-TYPE    4  297
                        clus
vv                       BMPR2 MUTATED BMPR2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(725) Variable = R3HDM2 MUTATION ANALYSIS
D725V1, survival
                  sevent
clus2                0   1
  R3HDM2 MUTATED     4   2
  R3HDM2 WILD-TYPE 226 137
  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
               6              363 
  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
               2              137 
$`R3HDM2 MUTATED`
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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-8524 TCGA-CD-8525 
       13.18        13.35        11.21        12.10        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-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-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 

  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
            6.18             0.00 
  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
           74.53           122.30 
  R3HDM2 MUTATED R3HDM2 WILD-TYPE 
          19.545           14.270 
[1] "6.2 - 74.5 (19.5)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D725V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  R3HDM2 MUTATED         0        0        0        1         1         1
  R3HDM2 WILD-TYPE       2       15       40       29        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  R3HDM2 MUTATED           0          0          0          1        2
  R3HDM2 WILD-TYPE         3         70         53         31       36
D725V3, multiclass
            clus
vv           R3HDM2 MUTATED R3HDM2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  R3HDM2 MUTATED     1   0   3   4
  R3HDM2 WILD-TYPE  21  92 170  93
D725V4, multiclass
    clus
vv   R3HDM2 MUTATED R3HDM2 WILD-TYPE
  T1              1               21
  T2              0               92
  T3              3              170
  T4              4               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
  R3HDM2 MUTATED     3   1   0   2
  R3HDM2 WILD-TYPE 115 103  77  75
D725V5, multiclass
    clus
vv   R3HDM2 MUTATED R3HDM2 WILD-TYPE
  N0              3              115
  N1              1              103
  N2              0               77
  N3              2               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"
D725V6, binary
                  cls
clus                 0   1
  R3HDM2 MUTATED     6   2
  R3HDM2 WILD-TYPE 340  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM2 MUTATED      6    2
  R3HDM2 WILD-TYPE  340   27
   clus
vv  R3HDM2 MUTATED R3HDM2 WILD-TYPE
  0              6              340
  1              2               27
[1] 2 2
[1] FALSE
D725V7, binary
                  cls
clus                 0   1
  R3HDM2 MUTATED     6   3
  R3HDM2 WILD-TYPE 139 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM2 MUTATED      6    3
  R3HDM2 WILD-TYPE  139  245
        clus
vv       R3HDM2 MUTATED R3HDM2 WILD-TYPE
  FEMALE              6              139
  MALE                3              245
[1] 2 2
[1] FALSE
D725V8, binary
                  cls
clus                 0   1
  R3HDM2 MUTATED     5   0
  R3HDM2 WILD-TYPE 287  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM2 MUTATED      5    0
  R3HDM2 WILD-TYPE  287   59
     clus
vv    R3HDM2 MUTATED R3HDM2 WILD-TYPE
  NO               5              287
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  R3HDM2 MUTATED                                          0
  R3HDM2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  R3HDM2 MUTATED                                       3
  R3HDM2 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  R3HDM2 MUTATED                                                        4
  R3HDM2 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  R3HDM2 MUTATED                                                   1
  R3HDM2 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  R3HDM2 MUTATED                                                                   1
  R3HDM2 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  R3HDM2 MUTATED                                                    0
  R3HDM2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  R3HDM2 MUTATED                                                  0
  R3HDM2 WILD-TYPE                                               61
D725V9, multiclass
                                                                   clus
vv                                                                  R3HDM2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  R3HDM2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  R3HDM2 MUTATED     4   0   1   3
  R3HDM2 WILD-TYPE 307  14  14  21
D725V10, multiclass
    clus
vv   R3HDM2 MUTATED R3HDM2 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              1               14
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D725V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  R3HDM2 MUTATED       1                         0
  R3HDM2 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  R3HDM2 MUTATED                                           0     7
  R3HDM2 WILD-TYPE                                         1   236
D725V12, multiclass
                                           clus
vv                                          R3HDM2 MUTATED R3HDM2 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D725V13, binary
                  cls
clus                 0   1
  R3HDM2 MUTATED     1   7
  R3HDM2 WILD-TYPE   3 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM2 MUTATED      1    7
  R3HDM2 WILD-TYPE    3  303
                        clus
vv                       R3HDM2 MUTATED R3HDM2 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(726) Variable = BLMH MUTATION ANALYSIS
D726V1, survival
                sevent
clus2              0   1
  BLMH MUTATED     3   2
  BLMH WILD-TYPE 227 137
  BLMH MUTATED BLMH WILD-TYPE 
             5            364 
  BLMH MUTATED BLMH WILD-TYPE 
             2            137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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          14.45 
[1] "6.5 - 23.8 (11.4)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.5"
D726V2, 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       2       15       39       30        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BLMH MUTATED           0          0          0          0        0
  BLMH WILD-TYPE         3         70         53         32       38
D726V3, multiclass
            clus
vv           BLMH MUTATED BLMH WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BLMH MUTATED     1   2   2   0
  BLMH WILD-TYPE  21  90 171  97
D726V4, multiclass
    clus
vv   BLMH MUTATED BLMH WILD-TYPE
  T1            1             21
  T2            2             90
  T3            2            171
  T4            0             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
  BLMH MUTATED     2   1   2   0
  BLMH WILD-TYPE 116 103  75  77
D726V5, multiclass
    clus
vv   BLMH MUTATED BLMH WILD-TYPE
  N0            2            116
  N1            1            103
  N2            2             75
  N3            0             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"
D726V6, binary
                cls
clus               0   1
  BLMH MUTATED     5   0
  BLMH WILD-TYPE 341  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  BLMH MUTATED      5    0
  BLMH WILD-TYPE  341   29
   clus
vv  BLMH MUTATED BLMH WILD-TYPE
  0            5            341
  1            0             29
[1] 2 2
[1] FALSE
D726V7, binary
                cls
clus               0   1
  BLMH MUTATED     3   2
  BLMH WILD-TYPE 142 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  BLMH MUTATED      3    2
  BLMH WILD-TYPE  142  246
        clus
vv       BLMH MUTATED BLMH WILD-TYPE
  FEMALE            3            142
  MALE              2            246
[1] 2 2
[1] FALSE
D726V8, binary
                cls
clus               0   1
  BLMH MUTATED     5   0
  BLMH WILD-TYPE 287  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  BLMH MUTATED      5    0
  BLMH WILD-TYPE  287   59
     clus
vv    BLMH MUTATED BLMH WILD-TYPE
  NO             5            287
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BLMH MUTATED                                          0
  BLMH WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BLMH MUTATED                                       1
  BLMH WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BLMH MUTATED                                                        1
  BLMH WILD-TYPE                                                    157
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BLMH MUTATED                                                   0
  BLMH WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BLMH MUTATED                                                                   0
  BLMH WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BLMH MUTATED                                                    0
  BLMH WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BLMH MUTATED                                                  3
  BLMH WILD-TYPE                                               58
D726V9, multiclass
                                                                   clus
vv                                                                  BLMH MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  BLMH WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BLMH MUTATED     4   0   0   0
  BLMH WILD-TYPE 307  14  15  24
D726V10, multiclass
    clus
vv   BLMH MUTATED BLMH WILD-TYPE
  R0            4            307
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D726V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BLMH MUTATED       4                         0
  BLMH WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BLMH MUTATED                                           0     1
  BLMH WILD-TYPE                                         1   242
D726V12, multiclass
                                           clus
vv                                          BLMH MUTATED BLMH WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                1            242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D726V13, binary
                cls
clus               0   1
  BLMH MUTATED     0   5
  BLMH WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  BLMH MUTATED      0    5
  BLMH WILD-TYPE    4  305
                        clus
vv                       BLMH MUTATED BLMH WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(727) Variable = PLEKHO1 MUTATION ANALYSIS
D727V1, survival
                   sevent
clus2                 0   1
  PLEKHO1 MUTATED     3   1
  PLEKHO1 WILD-TYPE 227 138
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
                4               365 
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
                1               138 
$`PLEKHO1 MUTATED`
TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8680 TCGA-CG-5723 
       34.68         0.26        31.96       105.07 

$`PLEKHO1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
             0.26              0.00 
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
           105.07            122.30 
  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE 
            33.32             14.17 
[1] "0.3 - 105.1 (33.3)" "0.0 - 122.3 (14.2)"
[1] "hr=" "2.5"
D727V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLEKHO1 MUTATED         1        0        1        1         1         0
  PLEKHO1 WILD-TYPE       1       15       39       29        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHO1 MUTATED           0          0          0          0        1
  PLEKHO1 WILD-TYPE         3         70         53         32       37
D727V3, multiclass
            clus
vv           PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHO1 MUTATED     2   2   1   1
  PLEKHO1 WILD-TYPE  20  90 172  96
D727V4, multiclass
    clus
vv   PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  T1               2                20
  T2               2                90
  T3               1               172
  T4               1                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
  PLEKHO1 MUTATED     2   2   1   0
  PLEKHO1 WILD-TYPE 116 102  76  77
D727V5, multiclass
    clus
vv   PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  N0               2               116
  N1               2               102
  N2               1                76
  N3               0                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"
D727V6, binary
                   cls
clus                  0   1
  PLEKHO1 MUTATED     5   1
  PLEKHO1 WILD-TYPE 341  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHO1 MUTATED      5    1
  PLEKHO1 WILD-TYPE  341   28
   clus
vv  PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  0               5               341
  1               1                28
[1] 2 2
[1] FALSE
D727V7, binary
                   cls
clus                  0   1
  PLEKHO1 MUTATED     4   3
  PLEKHO1 WILD-TYPE 141 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHO1 MUTATED      4    3
  PLEKHO1 WILD-TYPE  141  245
        clus
vv       PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  FEMALE               4               141
  MALE                 3               245
[1] 2 2
[1] FALSE
D727V8, binary
                   cls
clus                  0   1
  PLEKHO1 MUTATED     5   0
  PLEKHO1 WILD-TYPE 287  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHO1 MUTATED      5    0
  PLEKHO1 WILD-TYPE  287   59
     clus
vv    PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  NO                5               287
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PLEKHO1 MUTATED                                          0
  PLEKHO1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PLEKHO1 MUTATED                                       0
  PLEKHO1 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLEKHO1 MUTATED                                                        6
  PLEKHO1 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PLEKHO1 MUTATED                                                   0
  PLEKHO1 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLEKHO1 MUTATED                                                                   0
  PLEKHO1 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PLEKHO1 MUTATED                                                    0
  PLEKHO1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PLEKHO1 MUTATED                                                  1
  PLEKHO1 WILD-TYPE                                               60
D727V9, multiclass
                                                                   clus
vv                                                                  PLEKHO1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  PLEKHO1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PLEKHO1 MUTATED     5   0   0   2
  PLEKHO1 WILD-TYPE 306  14  15  22
D727V10, multiclass
    clus
vv   PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  R0               5               306
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D727V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PLEKHO1 MUTATED       1                         1
  PLEKHO1 WILD-TYPE    86                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLEKHO1 MUTATED                                           0     4
  PLEKHO1 WILD-TYPE                                         1   239
D727V12, multiclass
                                           clus
vv                                          PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D727V13, binary
                   cls
clus                  0   1
  PLEKHO1 MUTATED     0   6
  PLEKHO1 WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHO1 MUTATED      0    6
  PLEKHO1 WILD-TYPE    4  304
                        clus
vv                       PLEKHO1 MUTATED PLEKHO1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(728) Variable = INPP5F MUTATION ANALYSIS
D728V1, survival
                  sevent
clus2                0   1
  INPP5F MUTATED    10   3
  INPP5F WILD-TYPE 220 136
  INPP5F MUTATED INPP5F WILD-TYPE 
              13              356 
  INPP5F MUTATED INPP5F WILD-TYPE 
               3              136 
$`INPP5F MUTATED`
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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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 

  INPP5F MUTATED INPP5F WILD-TYPE 
            0.26             0.00 
  INPP5F MUTATED INPP5F WILD-TYPE 
          105.07           122.30 
  INPP5F MUTATED INPP5F WILD-TYPE 
           28.14            14.07 
[1] "0.3 - 105.1 (28.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.2"
D728V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INPP5F MUTATED         0        0        2        1         4         1
  INPP5F WILD-TYPE       2       15       38       29        33        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INPP5F MUTATED           0          2          0          1        2
  INPP5F WILD-TYPE         3         68         53         31       36
D728V3, multiclass
            clus
vv           INPP5F MUTATED INPP5F WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               4               33
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  INPP5F MUTATED     1   4   5   5
  INPP5F WILD-TYPE  21  88 168  92
D728V4, multiclass
    clus
vv   INPP5F MUTATED INPP5F WILD-TYPE
  T1              1               21
  T2              4               88
  T3              5              168
  T4              5               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
  INPP5F MUTATED     8   2   2   1
  INPP5F WILD-TYPE 110 102  75  76
D728V5, multiclass
    clus
vv   INPP5F MUTATED INPP5F WILD-TYPE
  N0              8              110
  N1              2              102
  N2              2               75
  N3              1               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"
D728V6, binary
                  cls
clus                 0   1
  INPP5F MUTATED    13   2
  INPP5F WILD-TYPE 333  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPP5F MUTATED     13    2
  INPP5F WILD-TYPE  333   27
   clus
vv  INPP5F MUTATED INPP5F WILD-TYPE
  0             13              333
  1              2               27
[1] 2 2
[1] FALSE
D728V7, binary
                  cls
clus                 0   1
  INPP5F MUTATED     9   6
  INPP5F WILD-TYPE 136 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPP5F MUTATED      9    6
  INPP5F WILD-TYPE  136  242
        clus
vv       INPP5F MUTATED INPP5F WILD-TYPE
  FEMALE              9              136
  MALE                6              242
[1] 2 2
[1] FALSE
D728V8, binary
                  cls
clus                 0   1
  INPP5F MUTATED    11   1
  INPP5F WILD-TYPE 281  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPP5F MUTATED     11    1
  INPP5F WILD-TYPE  281   58
     clus
vv    INPP5F MUTATED INPP5F WILD-TYPE
  NO              11              281
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  INPP5F MUTATED                                          0
  INPP5F WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  INPP5F MUTATED                                       1
  INPP5F WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  INPP5F MUTATED                                                       10
  INPP5F WILD-TYPE                                                    148
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  INPP5F MUTATED                                                   1
  INPP5F WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  INPP5F MUTATED                                                                   0
  INPP5F WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  INPP5F MUTATED                                                    0
  INPP5F WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  INPP5F MUTATED                                                  3
  INPP5F WILD-TYPE                                               58
D728V9, multiclass
                                                                   clus
vv                                                                  INPP5F MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  INPP5F WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  INPP5F MUTATED    11   0   1   3
  INPP5F WILD-TYPE 300  14  14  21
D728V10, multiclass
    clus
vv   INPP5F MUTATED INPP5F WILD-TYPE
  R0             11              300
  R1              0               14
  R2              1               14
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D728V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  INPP5F MUTATED       2                         0
  INPP5F WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INPP5F MUTATED                                           0    11
  INPP5F WILD-TYPE                                         1   232
D728V12, multiclass
                                           clus
vv                                          INPP5F MUTATED INPP5F WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D728V13, binary
                  cls
clus                 0   1
  INPP5F MUTATED     0  12
  INPP5F WILD-TYPE   4 298
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPP5F MUTATED      0   12
  INPP5F WILD-TYPE    4  298
                        clus
vv                       INPP5F MUTATED INPP5F WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             12              298
[1] 2 2
[1] FALSE

Clustering(729) Variable = NLRC5 MUTATION ANALYSIS
D729V1, survival
                 sevent
clus2               0   1
  NLRC5 MUTATED    12   7
  NLRC5 WILD-TYPE 218 132
  NLRC5 MUTATED NLRC5 WILD-TYPE 
             19             350 
  NLRC5 MUTATED NLRC5 WILD-TYPE 
              7             132 
$`NLRC5 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-7707 TCGA-BR-8363 TCGA-BR-8591 
       21.99         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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
        5.92        36.43        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-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-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-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 

  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           14.35 
[1] "0.3 - 105.1 (13.8)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D729V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NLRC5 MUTATED         0        0        4        2         1         2
  NLRC5 WILD-TYPE       2       15       36       28        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NLRC5 MUTATED           0          2          2          3        4
  NLRC5 WILD-TYPE         3         68         51         29       34
D729V3, multiclass
            clus
vv           NLRC5 MUTATED NLRC5 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               4              36
  STAGE II               2              28
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             3              29
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NLRC5 MUTATED     1   5   6   9
  NLRC5 WILD-TYPE  21  87 167  88
D729V4, multiclass
    clus
vv   NLRC5 MUTATED NLRC5 WILD-TYPE
  T1             1              21
  T2             5              87
  T3             6             167
  T4             9              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
  NLRC5 MUTATED     8   5   1   6
  NLRC5 WILD-TYPE 110  99  76  71
D729V5, multiclass
    clus
vv   NLRC5 MUTATED NLRC5 WILD-TYPE
  N0             8             110
  N1             5              99
  N2             1              76
  N3             6              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"
D729V6, binary
                 cls
clus                0   1
  NLRC5 MUTATED    19   3
  NLRC5 WILD-TYPE 327  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED     19    3
  NLRC5 WILD-TYPE  327   26
   clus
vv  NLRC5 MUTATED NLRC5 WILD-TYPE
  0            19             327
  1             3              26
[1] 2 2
[1] FALSE
D729V7, binary
                 cls
clus                0   1
  NLRC5 MUTATED    12  11
  NLRC5 WILD-TYPE 133 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED     12   11
  NLRC5 WILD-TYPE  133  237
        clus
vv       NLRC5 MUTATED NLRC5 WILD-TYPE
  FEMALE            12             133
  MALE              11             237
[1] 2 2
[1] FALSE
D729V8, binary
                 cls
clus                0   1
  NLRC5 MUTATED    15   3
  NLRC5 WILD-TYPE 277  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED     15    3
  NLRC5 WILD-TYPE  277   56
     clus
vv    NLRC5 MUTATED NLRC5 WILD-TYPE
  NO             15             277
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NLRC5 MUTATED                                          0
  NLRC5 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NLRC5 MUTATED                                       4
  NLRC5 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NLRC5 MUTATED                                                       11
  NLRC5 WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NLRC5 MUTATED                                                   2
  NLRC5 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NLRC5 MUTATED                                                                   5
  NLRC5 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NLRC5 MUTATED                                                    0
  NLRC5 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NLRC5 MUTATED                                                  1
  NLRC5 WILD-TYPE                                               60
D729V9, multiclass
                                                                   clus
vv                                                                  NLRC5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  NLRC5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NLRC5 MUTATED    15   1   2   4
  NLRC5 WILD-TYPE 296  13  13  20
D729V10, multiclass
    clus
vv   NLRC5 MUTATED NLRC5 WILD-TYPE
  R0            15             296
  R1             1              13
  R2             2              13
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D729V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NLRC5 MUTATED       3                         0
  NLRC5 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NLRC5 MUTATED                                           0    13
  NLRC5 WILD-TYPE                                         1   230
D729V12, multiclass
                                           clus
vv                                          NLRC5 MUTATED NLRC5 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D729V13, binary
                 cls
clus                0   1
  NLRC5 MUTATED     2  14
  NLRC5 WILD-TYPE   2 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC5 MUTATED      2   14
  NLRC5 WILD-TYPE    2  296
                        clus
vv                       NLRC5 MUTATED NLRC5 WILD-TYPE
  HISPANIC OR LATINO                 2               2
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(730) Variable = MYCT1 MUTATION ANALYSIS
D730V1, survival
                 sevent
clus2               0   1
  MYCT1 MUTATED     5   2
  MYCT1 WILD-TYPE 225 137
  MYCT1 MUTATED MYCT1 WILD-TYPE 
              7             362 
  MYCT1 MUTATED MYCT1 WILD-TYPE 
              2             137 
$`MYCT1 MUTATED`
TCGA-BR-6452 TCGA-BR-8485 TCGA-CD-8527 TCGA-CG-4469 TCGA-FP-8099 TCGA-IN-A6RP 
       34.68         9.21         7.17         7.07        17.06         6.44 
TCGA-VQ-A91V 
       42.64 

$`MYCT1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-8209 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        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-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 

  MYCT1 MUTATED MYCT1 WILD-TYPE 
           6.44            0.00 
  MYCT1 MUTATED MYCT1 WILD-TYPE 
          42.64          122.30 
  MYCT1 MUTATED MYCT1 WILD-TYPE 
           9.21           14.35 
[1] "6.4 - 42.6 (9.2)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D730V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYCT1 MUTATED         0        0        0        1         2         0
  MYCT1 WILD-TYPE       2       15       40       29        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MYCT1 MUTATED           0          1          0          2        1
  MYCT1 WILD-TYPE         3         69         53         30       37
D730V3, multiclass
            clus
vv           MYCT1 MUTATED MYCT1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYCT1 MUTATED     1   1   4   1
  MYCT1 WILD-TYPE  21  91 169  96
D730V4, multiclass
    clus
vv   MYCT1 MUTATED MYCT1 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             4             169
  T4             1              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
  MYCT1 MUTATED     2   2   1   3
  MYCT1 WILD-TYPE 116 102  76  74
D730V5, multiclass
    clus
vv   MYCT1 MUTATED MYCT1 WILD-TYPE
  N0             2             116
  N1             2             102
  N2             1              76
  N3             3              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"
D730V6, binary
                 cls
clus                0   1
  MYCT1 MUTATED     7   0
  MYCT1 WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCT1 MUTATED      7    0
  MYCT1 WILD-TYPE  339   29
   clus
vv  MYCT1 MUTATED MYCT1 WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D730V7, binary
                 cls
clus                0   1
  MYCT1 MUTATED     4   4
  MYCT1 WILD-TYPE 141 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCT1 MUTATED      4    4
  MYCT1 WILD-TYPE  141  244
        clus
vv       MYCT1 MUTATED MYCT1 WILD-TYPE
  FEMALE             4             141
  MALE               4             244
[1] 2 2
[1] FALSE
D730V8, binary
                 cls
clus                0   1
  MYCT1 MUTATED     4   2
  MYCT1 WILD-TYPE 288  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCT1 MUTATED      4    2
  MYCT1 WILD-TYPE  288   57
     clus
vv    MYCT1 MUTATED MYCT1 WILD-TYPE
  NO              4             288
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MYCT1 MUTATED                                          0
  MYCT1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MYCT1 MUTATED                                       0
  MYCT1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MYCT1 MUTATED                                                        5
  MYCT1 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MYCT1 MUTATED                                                   0
  MYCT1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MYCT1 MUTATED                                                                   2
  MYCT1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MYCT1 MUTATED                                                    0
  MYCT1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MYCT1 MUTATED                                                  1
  MYCT1 WILD-TYPE                                               60
D730V9, multiclass
                                                                   clus
vv                                                                  MYCT1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  MYCT1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYCT1 MUTATED     6   1   0   1
  MYCT1 WILD-TYPE 305  13  15  23
D730V10, multiclass
    clus
vv   MYCT1 MUTATED MYCT1 WILD-TYPE
  R0             6             305
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D730V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MYCT1 MUTATED       1                         0
  MYCT1 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MYCT1 MUTATED                                           0     5
  MYCT1 WILD-TYPE                                         1   238
D730V12, multiclass
                                           clus
vv                                          MYCT1 MUTATED MYCT1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D730V13, binary
                 cls
clus                0   1
  MYCT1 MUTATED     0   6
  MYCT1 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCT1 MUTATED      0    6
  MYCT1 WILD-TYPE    4  304
                        clus
vv                       MYCT1 MUTATED MYCT1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(731) Variable = CDC6 MUTATION ANALYSIS
D731V1, survival
                sevent
clus2              0   1
  CDC6 MUTATED     3   4
  CDC6 WILD-TYPE 227 135
  CDC6 MUTATED CDC6 WILD-TYPE 
             7            362 
  CDC6 MUTATED CDC6 WILD-TYPE 
             4            135 
$`CDC6 MUTATED`
TCGA-BR-4184 TCGA-BR-8284 TCGA-CD-8529 TCGA-CD-A487 TCGA-D7-6518 TCGA-EQ-8122 
        6.97         8.05        12.30        12.30        19.13         7.99 
TCGA-HJ-7597 
       26.47 

$`CDC6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
          6.97           0.00 
  CDC6 MUTATED CDC6 WILD-TYPE 
         26.47         122.30 
  CDC6 MUTATED CDC6 WILD-TYPE 
         12.30          14.45 
[1] "7.0 - 26.5 (12.3)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "2"  
D731V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDC6 MUTATED         0        0        1        0         0         3
  CDC6 WILD-TYPE       2       15       39       30        37        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC6 MUTATED           0          2          0          1        1
  CDC6 WILD-TYPE         3         68         53         31       37
D731V3, multiclass
            clus
vv           CDC6 MUTATED CDC6 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CDC6 MUTATED     0   2   3   3
  CDC6 WILD-TYPE  22  90 170  94
D731V4, multiclass
    clus
vv   CDC6 MUTATED CDC6 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            3            170
  T4            3             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
  CDC6 MUTATED     3   3   0   2
  CDC6 WILD-TYPE 115 101  77  75
D731V5, multiclass
    clus
vv   CDC6 MUTATED CDC6 WILD-TYPE
  N0            3            115
  N1            3            101
  N2            0             77
  N3            2             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"
D731V6, binary
                cls
clus               0   1
  CDC6 MUTATED     4   1
  CDC6 WILD-TYPE 342  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      4    1
  CDC6 WILD-TYPE  342   28
   clus
vv  CDC6 MUTATED CDC6 WILD-TYPE
  0            4            342
  1            1             28
[1] 2 2
[1] FALSE
D731V7, binary
                cls
clus               0   1
  CDC6 MUTATED     3   5
  CDC6 WILD-TYPE 142 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      3    5
  CDC6 WILD-TYPE  142  243
        clus
vv       CDC6 MUTATED CDC6 WILD-TYPE
  FEMALE            3            142
  MALE              5            243
[1] 2 2
[1] FALSE
D731V8, binary
                cls
clus               0   1
  CDC6 MUTATED     6   2
  CDC6 WILD-TYPE 286  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      6    2
  CDC6 WILD-TYPE  286   57
     clus
vv    CDC6 MUTATED CDC6 WILD-TYPE
  NO             6            286
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CDC6 MUTATED                                          1
  CDC6 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CDC6 MUTATED                                       2
  CDC6 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDC6 MUTATED                                                        1
  CDC6 WILD-TYPE                                                    157
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CDC6 MUTATED                                                   1
  CDC6 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDC6 MUTATED                                                                   3
  CDC6 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CDC6 MUTATED                                                    0
  CDC6 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CDC6 MUTATED                                                  0
  CDC6 WILD-TYPE                                               61
D731V9, multiclass
                                                                   clus
vv                                                                  CDC6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  CDC6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CDC6 MUTATED     5   1   0   1
  CDC6 WILD-TYPE 306  13  15  23
D731V10, multiclass
    clus
vv   CDC6 MUTATED CDC6 WILD-TYPE
  R0            5            306
  R1            1             13
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D731V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CDC6 MUTATED       2                         0
  CDC6 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDC6 MUTATED                                           0     6
  CDC6 WILD-TYPE                                         1   237
D731V12, multiclass
                                           clus
vv                                          CDC6 MUTATED CDC6 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D731V13, binary
                cls
clus               0   1
  CDC6 MUTATED     0   8
  CDC6 WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      0    8
  CDC6 WILD-TYPE    4  302
                        clus
vv                       CDC6 MUTATED CDC6 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(732) Variable = CDX2 MUTATION ANALYSIS
D732V1, survival
                sevent
clus2              0   1
  CDX2 MUTATED     3   0
  CDX2 WILD-TYPE 227 139
  CDX2 MUTATED CDX2 WILD-TYPE 
             3            366 
  CDX2 MUTATED CDX2 WILD-TYPE 
             0            139 
$`CDX2 MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-6452 
       26.70        19.56        34.68 

$`CDX2 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        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-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-F1-6874 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 

  CDX2 MUTATED CDX2 WILD-TYPE 
         19.56           0.00 
  CDX2 MUTATED CDX2 WILD-TYPE 
         34.68         122.30 
  CDX2 MUTATED CDX2 WILD-TYPE 
         26.70          14.12 
[1] "19.6 - 34.7 (26.7)" "0.0 - 122.3 (14.1)"
[1] "hr="     "9100000"
D732V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDX2 MUTATED         0        0        0        0         1         1
  CDX2 WILD-TYPE       2       15       40       30        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDX2 MUTATED           0          0          0          1        1
  CDX2 WILD-TYPE         3         70         53         31       37
D732V3, multiclass
            clus
vv           CDX2 MUTATED CDX2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CDX2 MUTATED     0   0   1   3
  CDX2 WILD-TYPE  22  92 172  94
D732V4, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  T1            0             22
  T2            0             92
  T3            1            172
  T4            3             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
  CDX2 MUTATED     2   0   1   1
  CDX2 WILD-TYPE 116 104  76  76
D732V5, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  N0            2            116
  N1            0            104
  N2            1             76
  N3            1             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"
D732V6, binary
                cls
clus               0   1
  CDX2 MUTATED     4   0
  CDX2 WILD-TYPE 342  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      4    0
  CDX2 WILD-TYPE  342   29
   clus
vv  CDX2 MUTATED CDX2 WILD-TYPE
  0            4            342
  1            0             29
[1] 2 2
[1] FALSE
D732V7, binary
                cls
clus               0   1
  CDX2 MUTATED     3   1
  CDX2 WILD-TYPE 142 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      3    1
  CDX2 WILD-TYPE  142  247
        clus
vv       CDX2 MUTATED CDX2 WILD-TYPE
  FEMALE            3            142
  MALE              1            247
[1] 2 2
[1] FALSE
D732V8, binary
                cls
clus               0   1
  CDX2 MUTATED     3   0
  CDX2 WILD-TYPE 289  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      3    0
  CDX2 WILD-TYPE  289   59
     clus
vv    CDX2 MUTATED CDX2 WILD-TYPE
  NO             3            289
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CDX2 MUTATED                                          0
  CDX2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CDX2 MUTATED                                       2
  CDX2 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDX2 MUTATED                                                        2
  CDX2 WILD-TYPE                                                    156
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CDX2 MUTATED                                                   0
  CDX2 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDX2 MUTATED                                                                   0
  CDX2 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CDX2 MUTATED                                                    0
  CDX2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CDX2 MUTATED                                                  0
  CDX2 WILD-TYPE                                               61
D732V9, multiclass
                                                                   clus
vv                                                                  CDX2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  CDX2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CDX2 MUTATED     2   0   0   1
  CDX2 WILD-TYPE 309  14  15  23
D732V10, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  R0            2            309
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D732V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CDX2 MUTATED       0                         0
  CDX2 WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDX2 MUTATED                                           0     4
  CDX2 WILD-TYPE                                         1   239
D732V12, multiclass
                                           clus
vv                                          CDX2 MUTATED CDX2 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D732V13, binary
                cls
clus               0   1
  CDX2 MUTATED     0   4
  CDX2 WILD-TYPE   4 306
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      0    4
  CDX2 WILD-TYPE    4  306
                        clus
vv                       CDX2 MUTATED CDX2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            4            306
[1] 2 2
[1] FALSE

Clustering(733) Variable = EFHA1 MUTATION ANALYSIS
D733V1, survival
                 sevent
clus2               0   1
  EFHA1 MUTATED    11   2
  EFHA1 WILD-TYPE 219 137
  EFHA1 MUTATED EFHA1 WILD-TYPE 
             13             356 
  EFHA1 MUTATED EFHA1 WILD-TYPE 
              2             137 
$`EFHA1 MUTATED`
TCGA-BR-4257 TCGA-BR-7707 TCGA-BR-8360 TCGA-CG-5721 TCGA-F1-A448 TCGA-HF-A5NB 
        9.67        35.84         6.18         6.02        21.27        30.51 
TCGA-HU-8604 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4H4 TCGA-MX-A5UJ TCGA-R5-A7ZI 
       22.82        29.98         0.10        23.84        19.73        74.53 
TCGA-VQ-A8P2 
       38.14 

$`EFHA1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  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           14.07 
[1] "0.1 - 74.5 (22.8)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.2"
D733V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EFHA1 MUTATED         0        0        2        0         3         1
  EFHA1 WILD-TYPE       2       15       38       30        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFHA1 MUTATED           0          2          1          2        2
  EFHA1 WILD-TYPE         3         68         52         30       36
D733V3, multiclass
            clus
vv           EFHA1 MUTATED EFHA1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EFHA1 MUTATED     0   4   4   5
  EFHA1 WILD-TYPE  22  88 169  92
D733V4, multiclass
    clus
vv   EFHA1 MUTATED EFHA1 WILD-TYPE
  T1             0              22
  T2             4              88
  T3             4             169
  T4             5              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
  EFHA1 MUTATED     4   4   3   2
  EFHA1 WILD-TYPE 114 100  74  75
D733V5, multiclass
    clus
vv   EFHA1 MUTATED EFHA1 WILD-TYPE
  N0             4             114
  N1             4             100
  N2             3              74
  N3             2              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"
D733V6, binary
                 cls
clus                0   1
  EFHA1 MUTATED    13   1
  EFHA1 WILD-TYPE 333  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA1 MUTATED     13    1
  EFHA1 WILD-TYPE  333   28
   clus
vv  EFHA1 MUTATED EFHA1 WILD-TYPE
  0            13             333
  1             1              28
[1] 2 2
[1] FALSE
D733V7, binary
                 cls
clus                0   1
  EFHA1 MUTATED     7   7
  EFHA1 WILD-TYPE 138 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA1 MUTATED      7    7
  EFHA1 WILD-TYPE  138  241
        clus
vv       EFHA1 MUTATED EFHA1 WILD-TYPE
  FEMALE             7             138
  MALE               7             241
[1] 2 2
[1] FALSE
D733V8, binary
                 cls
clus                0   1
  EFHA1 MUTATED    10   3
  EFHA1 WILD-TYPE 282  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA1 MUTATED     10    3
  EFHA1 WILD-TYPE  282   56
     clus
vv    EFHA1 MUTATED EFHA1 WILD-TYPE
  NO             10             282
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EFHA1 MUTATED                                          0
  EFHA1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EFHA1 MUTATED                                       1
  EFHA1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EFHA1 MUTATED                                                        2
  EFHA1 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EFHA1 MUTATED                                                   3
  EFHA1 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EFHA1 MUTATED                                                                   3
  EFHA1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EFHA1 MUTATED                                                    0
  EFHA1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EFHA1 MUTATED                                                  5
  EFHA1 WILD-TYPE                                               56
D733V9, multiclass
                                                                   clus
vv                                                                  EFHA1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              5
                                                                   clus
vv                                                                  EFHA1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EFHA1 MUTATED    12   1   0   1
  EFHA1 WILD-TYPE 299  13  15  23
D733V10, multiclass
    clus
vv   EFHA1 MUTATED EFHA1 WILD-TYPE
  R0            12             299
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D733V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EFHA1 MUTATED       4                         0
  EFHA1 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EFHA1 MUTATED                                           0     7
  EFHA1 WILD-TYPE                                         1   236
D733V12, multiclass
                                           clus
vv                                          EFHA1 MUTATED EFHA1 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D733V13, binary
                 cls
clus                0   1
  EFHA1 MUTATED     2   8
  EFHA1 WILD-TYPE   2 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHA1 MUTATED      2    8
  EFHA1 WILD-TYPE    2  302
                        clus
vv                       EFHA1 MUTATED EFHA1 WILD-TYPE
  HISPANIC OR LATINO                 2               2
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(734) Variable = GPR124 MUTATION ANALYSIS
D734V1, survival
                  sevent
clus2                0   1
  GPR124 MUTATED    12   3
  GPR124 WILD-TYPE 218 136
  GPR124 MUTATED GPR124 WILD-TYPE 
              15              354 
  GPR124 MUTATED GPR124 WILD-TYPE 
               3              136 
$`GPR124 MUTATED`
TCGA-B7-A5TI TCGA-BR-4256 TCGA-BR-6458 TCGA-BR-8360 TCGA-BR-8372 TCGA-CD-8529 
       19.56         9.34        19.33         6.18        31.27        12.30 
TCGA-CD-8531 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5723 TCGA-F1-6874 TCGA-F1-A448 
       12.59         6.58         6.02       105.07        14.47        21.27 
TCGA-HF-A5NB TCGA-MX-A5UJ TCGA-VQ-A8P2 
       30.51        19.73        38.14 

$`GPR124 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-8532 TCGA-CD-8533 TCGA-CD-8534 
        7.17        12.33        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-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-F1-6875 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-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 

  GPR124 MUTATED GPR124 WILD-TYPE 
            6.02             0.00 
  GPR124 MUTATED GPR124 WILD-TYPE 
          105.07           122.30 
  GPR124 MUTATED GPR124 WILD-TYPE 
           19.33            14.12 
[1] "6.0 - 105.1 (19.3)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.2"
D734V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR124 MUTATED         0        0        1        1         2         1
  GPR124 WILD-TYPE       2       15       39       29        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR124 MUTATED           0          4          1          3        2
  GPR124 WILD-TYPE         3         66         52         29       36
D734V3, multiclass
            clus
vv           GPR124 MUTATED GPR124 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              1               52
  STAGE IIIC              3               29
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR124 MUTATED     1   2   6   7
  GPR124 WILD-TYPE  21  90 167  90
D734V4, multiclass
    clus
vv   GPR124 MUTATED GPR124 WILD-TYPE
  T1              1               21
  T2              2               90
  T3              6              167
  T4              7               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
  GPR124 MUTATED     5   6   1   4
  GPR124 WILD-TYPE 113  98  76  73
D734V5, multiclass
    clus
vv   GPR124 MUTATED GPR124 WILD-TYPE
  N0              5              113
  N1              6               98
  N2              1               76
  N3              4               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"
D734V6, binary
                  cls
clus                 0   1
  GPR124 MUTATED    16   1
  GPR124 WILD-TYPE 330  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR124 MUTATED     16    1
  GPR124 WILD-TYPE  330   28
   clus
vv  GPR124 MUTATED GPR124 WILD-TYPE
  0             16              330
  1              1               28
[1] 2 2
[1] FALSE
D734V7, binary
                  cls
clus                 0   1
  GPR124 MUTATED     6  11
  GPR124 WILD-TYPE 139 237
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR124 MUTATED      6   11
  GPR124 WILD-TYPE  139  237
        clus
vv       GPR124 MUTATED GPR124 WILD-TYPE
  FEMALE              6              139
  MALE               11              237
[1] 2 2
[1] FALSE
D734V8, binary
                  cls
clus                 0   1
  GPR124 MUTATED    10   5
  GPR124 WILD-TYPE 282  54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR124 MUTATED     10    5
  GPR124 WILD-TYPE  282   54
     clus
vv    GPR124 MUTATED GPR124 WILD-TYPE
  NO              10              282
  YES              5               54
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GPR124 MUTATED                                          0
  GPR124 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GPR124 MUTATED                                       3
  GPR124 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR124 MUTATED                                                        6
  GPR124 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GPR124 MUTATED                                                   4
  GPR124 WILD-TYPE                                                17
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR124 MUTATED                                                                   3
  GPR124 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GPR124 MUTATED                                                    0
  GPR124 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GPR124 MUTATED                                                  1
  GPR124 WILD-TYPE                                               60
D734V9, multiclass
                                                                   clus
vv                                                                  GPR124 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  GPR124 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR124 MUTATED    11   1   0   3
  GPR124 WILD-TYPE 300  13  15  21
D734V10, multiclass
    clus
vv   GPR124 MUTATED GPR124 WILD-TYPE
  R0             11              300
  R1              1               13
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D734V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GPR124 MUTATED       3                         0
  GPR124 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR124 MUTATED                                           0    11
  GPR124 WILD-TYPE                                         1   232
D734V12, multiclass
                                           clus
vv                                          GPR124 MUTATED GPR124 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D734V13, binary
                  cls
clus                 0   1
  GPR124 MUTATED     1  12
  GPR124 WILD-TYPE   3 298
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR124 MUTATED      1   12
  GPR124 WILD-TYPE    3  298
                        clus
vv                       GPR124 MUTATED GPR124 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             12              298
[1] 2 2
[1] FALSE

Clustering(735) Variable = TEX15 MUTATION ANALYSIS
D735V1, survival
                 sevent
clus2               0   1
  TEX15 MUTATED    16   5
  TEX15 WILD-TYPE 214 134
  TEX15 MUTATED TEX15 WILD-TYPE 
             21             348 
  TEX15 MUTATED TEX15 WILD-TYPE 
              5             134 
$`TEX15 MUTATED`
TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8060 
       21.99        22.98        16.24        26.70        34.68        11.44 
TCGA-BR-8680 TCGA-BR-A4CQ TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-4462 
       31.96        34.98        12.43        11.77        15.95         0.00 
TCGA-D7-A6EY TCGA-F1-6874 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4H4 
       11.44        14.47        22.32        22.68        29.98        23.84 
TCGA-MX-A5UJ TCGA-VQ-A8P2 TCGA-VQ-AA68 
       19.73        38.14        43.66 

$`TEX15 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-B7-5818 
       47.05        79.07         0.23        20.15         9.86        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-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-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-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-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-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-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-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-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-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 

  TEX15 MUTATED TEX15 WILD-TYPE 
            0.0             0.1 
  TEX15 MUTATED TEX15 WILD-TYPE 
          43.66          122.30 
  TEX15 MUTATED TEX15 WILD-TYPE 
         22.320          14.025 
[1] "0.0 - 43.7 (22.3)"  "0.1 - 122.3 (14.0)"
[1] "hr=" "2.1"
D735V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TEX15 MUTATED         0        0        2        2         3         7
  TEX15 WILD-TYPE       2       15       38       28        34        45
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TEX15 MUTATED           0          5          2          1        3
  TEX15 WILD-TYPE         3         65         51         31       35
D735V3, multiclass
            clus
vv           TEX15 MUTATED TEX15 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               2              28
  STAGE IIA              3              34
  STAGE IIB              7              45
  STAGE III              0               3
  STAGE IIIA             5              65
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TEX15 MUTATED     0   7   9  10
  TEX15 WILD-TYPE  22  85 164  87
D735V4, multiclass
    clus
vv   TEX15 MUTATED TEX15 WILD-TYPE
  T1             0              22
  T2             7              85
  T3             9             164
  T4            10              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
  TEX15 MUTATED     9   9   4   3
  TEX15 WILD-TYPE 109  95  73  74
D735V5, multiclass
    clus
vv   TEX15 MUTATED TEX15 WILD-TYPE
  N0             9             109
  N1             9              95
  N2             4              73
  N3             3              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"
D735V6, binary
                 cls
clus                0   1
  TEX15 MUTATED    22   3
  TEX15 WILD-TYPE 324  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX15 MUTATED     22    3
  TEX15 WILD-TYPE  324   26
   clus
vv  TEX15 MUTATED TEX15 WILD-TYPE
  0            22             324
  1             3              26
[1] 2 2
[1] FALSE
D735V7, binary
                 cls
clus                0   1
  TEX15 MUTATED    15  12
  TEX15 WILD-TYPE 130 236
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX15 MUTATED     15   12
  TEX15 WILD-TYPE  130  236
        clus
vv       TEX15 MUTATED TEX15 WILD-TYPE
  FEMALE            15             130
  MALE              12             236
[1] 2 2
[1] FALSE
D735V8, binary
                 cls
clus                0   1
  TEX15 MUTATED    18   4
  TEX15 WILD-TYPE 274  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX15 MUTATED     18    4
  TEX15 WILD-TYPE  274   55
     clus
vv    TEX15 MUTATED TEX15 WILD-TYPE
  NO             18             274
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TEX15 MUTATED                                          0
  TEX15 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TEX15 MUTATED                                       4
  TEX15 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TEX15 MUTATED                                                       11
  TEX15 WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TEX15 MUTATED                                                   1
  TEX15 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TEX15 MUTATED                                                                   3
  TEX15 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TEX15 MUTATED                                                    0
  TEX15 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TEX15 MUTATED                                                  6
  TEX15 WILD-TYPE                                               55
D735V9, multiclass
                                                                   clus
vv                                                                  TEX15 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              6
                                                                   clus
vv                                                                  TEX15 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TEX15 MUTATED    20   0   2   3
  TEX15 WILD-TYPE 291  14  13  21
D735V10, multiclass
    clus
vv   TEX15 MUTATED TEX15 WILD-TYPE
  R0            20             291
  R1             0              14
  R2             2              13
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D735V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TEX15 MUTATED       7                         0
  TEX15 WILD-TYPE    80                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TEX15 MUTATED                                           0    15
  TEX15 WILD-TYPE                                         1   228
D735V12, multiclass
                                           clus
vv                                          TEX15 MUTATED TEX15 WILD-TYPE
  ASIAN                                                 7              80
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D735V13, binary
                 cls
clus                0   1
  TEX15 MUTATED     0  20
  TEX15 WILD-TYPE   4 290
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX15 MUTATED      0   20
  TEX15 WILD-TYPE    4  290
                        clus
vv                       TEX15 MUTATED TEX15 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            20             290
[1] 2 2
[1] FALSE

Clustering(736) Variable = CD33 MUTATION ANALYSIS
D736V1, survival
                sevent
clus2              0   1
  CD33 MUTATED     4   4
  CD33 WILD-TYPE 226 135
  CD33 MUTATED CD33 WILD-TYPE 
             8            361 
  CD33 MUTATED CD33 WILD-TYPE 
             4            135 
$`CD33 MUTATED`
TCGA-BR-6452 TCGA-BR-7723 TCGA-BR-8373 TCGA-BR-8589 TCGA-HU-A4GQ TCGA-IN-A6RL 
       34.68        28.73        14.79        27.12         0.10        13.35 
TCGA-RD-A7BT TCGA-VQ-AA6A 
        8.61        38.93 

$`CD33 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  CD33 MUTATED CD33 WILD-TYPE 
           0.1            0.0 
  CD33 MUTATED CD33 WILD-TYPE 
         38.93         122.30 
  CD33 MUTATED CD33 WILD-TYPE 
        20.955         14.170 
[1] "0.1 - 38.9 (21.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D736V2, 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       2       15       39       30        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CD33 MUTATED           0          2          2          2        1
  CD33 WILD-TYPE         3         68         51         30       37
D736V3, multiclass
            clus
vv           CD33 MUTATED CD33 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            2             51
  STAGE IIIC            2             30
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD33 MUTATED     0   2   3   4
  CD33 WILD-TYPE  22  90 170  93
D736V4, multiclass
    clus
vv   CD33 MUTATED CD33 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            3            170
  T4            4             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
  CD33 MUTATED     2   3   1   3
  CD33 WILD-TYPE 116 101  76  74
D736V5, multiclass
    clus
vv   CD33 MUTATED CD33 WILD-TYPE
  N0            2            116
  N1            3            101
  N2            1             76
  N3            3             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"
D736V6, binary
                cls
clus               0   1
  CD33 MUTATED     9   0
  CD33 WILD-TYPE 337  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD33 MUTATED      9    0
  CD33 WILD-TYPE  337   29
   clus
vv  CD33 MUTATED CD33 WILD-TYPE
  0            9            337
  1            0             29
[1] 2 2
[1] FALSE
D736V7, binary
                cls
clus               0   1
  CD33 MUTATED     2   7
  CD33 WILD-TYPE 143 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD33 MUTATED      2    7
  CD33 WILD-TYPE  143  241
        clus
vv       CD33 MUTATED CD33 WILD-TYPE
  FEMALE            2            143
  MALE              7            241
[1] 2 2
[1] FALSE
D736V8, binary
                cls
clus               0   1
  CD33 MUTATED     7   1
  CD33 WILD-TYPE 285  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD33 MUTATED      7    1
  CD33 WILD-TYPE  285   58
     clus
vv    CD33 MUTATED CD33 WILD-TYPE
  NO             7            285
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CD33 MUTATED                                          0
  CD33 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CD33 MUTATED                                       0
  CD33 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD33 MUTATED                                                        4
  CD33 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CD33 MUTATED                                                   0
  CD33 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD33 MUTATED                                                                   4
  CD33 WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CD33 MUTATED                                                    0
  CD33 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CD33 MUTATED                                                  1
  CD33 WILD-TYPE                                               60
D736V9, multiclass
                                                                   clus
vv                                                                  CD33 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  CD33 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CD33 MUTATED     8   0   1   0
  CD33 WILD-TYPE 303  14  14  24
D736V10, multiclass
    clus
vv   CD33 MUTATED CD33 WILD-TYPE
  R0            8            303
  R1            0             14
  R2            1             14
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D736V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CD33 MUTATED       1                         0
  CD33 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD33 MUTATED                                           1     6
  CD33 WILD-TYPE                                         0   237
D736V12, multiclass
                                           clus
vv                                          CD33 MUTATED CD33 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D736V13, binary
                cls
clus               0   1
  CD33 MUTATED     0   7
  CD33 WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD33 MUTATED      0    7
  CD33 WILD-TYPE    4  303
                        clus
vv                       CD33 MUTATED CD33 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(737) Variable = GIPC3 MUTATION ANALYSIS
D737V1, survival
                 sevent
clus2               0   1
  GIPC3 MUTATED     5   2
  GIPC3 WILD-TYPE 225 137
  GIPC3 MUTATED GIPC3 WILD-TYPE 
              7             362 
  GIPC3 MUTATED GIPC3 WILD-TYPE 
              2             137 
$`GIPC3 MUTATED`
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 TCGA-CD-A4MI TCGA-D7-A4YV TCGA-FP-A4BE 
       36.16        35.84        29.59        11.77         5.92        11.08 
TCGA-HF-A5NB 
       30.51 

$`GIPC3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  GIPC3 MUTATED GIPC3 WILD-TYPE 
           5.92            0.00 
  GIPC3 MUTATED GIPC3 WILD-TYPE 
          36.16          122.30 
  GIPC3 MUTATED GIPC3 WILD-TYPE 
          29.59           14.22 
[1] "5.9 - 36.2 (29.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.7"
D737V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GIPC3 MUTATED         0        1        1        0         1         2
  GIPC3 WILD-TYPE       2       14       39       30        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GIPC3 MUTATED           0          1          0          1        0
  GIPC3 WILD-TYPE         3         69         53         31       38
D737V3, multiclass
            clus
vv           GIPC3 MUTATED GIPC3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GIPC3 MUTATED     1   1   3   2
  GIPC3 WILD-TYPE  21  91 170  95
D737V4, multiclass
    clus
vv   GIPC3 MUTATED GIPC3 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             3             170
  T4             2              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
  GIPC3 MUTATED     4   2   0   1
  GIPC3 WILD-TYPE 114 102  77  76
D737V5, multiclass
    clus
vv   GIPC3 MUTATED GIPC3 WILD-TYPE
  N0             4             114
  N1             2             102
  N2             0              77
  N3             1              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"
D737V6, binary
                 cls
clus                0   1
  GIPC3 MUTATED     7   0
  GIPC3 WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GIPC3 MUTATED      7    0
  GIPC3 WILD-TYPE  339   29
   clus
vv  GIPC3 MUTATED GIPC3 WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D737V7, binary
                 cls
clus                0   1
  GIPC3 MUTATED     4   3
  GIPC3 WILD-TYPE 141 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GIPC3 MUTATED      4    3
  GIPC3 WILD-TYPE  141  245
        clus
vv       GIPC3 MUTATED GIPC3 WILD-TYPE
  FEMALE             4             141
  MALE               3             245
[1] 2 2
[1] FALSE
D737V8, binary
                 cls
clus                0   1
  GIPC3 MUTATED     5   2
  GIPC3 WILD-TYPE 287  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GIPC3 MUTATED      5    2
  GIPC3 WILD-TYPE  287   57
     clus
vv    GIPC3 MUTATED GIPC3 WILD-TYPE
  NO              5             287
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GIPC3 MUTATED                                          0
  GIPC3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GIPC3 MUTATED                                       0
  GIPC3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GIPC3 MUTATED                                                        4
  GIPC3 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GIPC3 MUTATED                                                   1
  GIPC3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GIPC3 MUTATED                                                                   0
  GIPC3 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GIPC3 MUTATED                                                    1
  GIPC3 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GIPC3 MUTATED                                                  1
  GIPC3 WILD-TYPE                                               60
D737V9, multiclass
                                                                   clus
vv                                                                  GIPC3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  GIPC3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GIPC3 MUTATED     5   1   0   0
  GIPC3 WILD-TYPE 306  13  15  24
D737V10, multiclass
    clus
vv   GIPC3 MUTATED GIPC3 WILD-TYPE
  R0             5             306
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D737V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GIPC3 MUTATED       1                         1
  GIPC3 WILD-TYPE    86                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GIPC3 MUTATED                                           0     4
  GIPC3 WILD-TYPE                                         1   239
D737V12, multiclass
                                           clus
vv                                          GIPC3 MUTATED GIPC3 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D737V13, binary
                 cls
clus                0   1
  GIPC3 MUTATED     0   6
  GIPC3 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GIPC3 MUTATED      0    6
  GIPC3 WILD-TYPE    4  304
                        clus
vv                       GIPC3 MUTATED GIPC3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(738) Variable = PRAMEF14 MUTATION ANALYSIS
D738V1, survival
                    sevent
clus2                  0   1
  PRAMEF14 MUTATED     2   2
  PRAMEF14 WILD-TYPE 228 137
  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
                 4                365 
  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
                 2                137 
$`PRAMEF14 MUTATED`
TCGA-BR-8284 TCGA-BR-8360 TCGA-CD-A48A TCGA-HU-A4GQ 
        8.05         6.18        12.43         0.10 

$`PRAMEF14 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A48C TCGA-CD-A4MG 
       12.43         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-D7-8573 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 

  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
               0.1                0.0 
  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
             12.43             122.30 
  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE 
             7.115             14.470 
[1] "0.1 - 12.4 (7.1)"   "0.0 - 122.3 (14.5)"
[1] "hr=" "3.7"
D738V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRAMEF14 MUTATED         1        0        0        0         2         0
  PRAMEF14 WILD-TYPE       1       15       40       30        35        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRAMEF14 MUTATED           0          0          0          2        0
  PRAMEF14 WILD-TYPE         3         70         53         30       38
D738V3, multiclass
            clus
vv           PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 2                 35
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                0                 53
  STAGE IIIC                2                 30
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PRAMEF14 MUTATED     1   0   2   2
  PRAMEF14 WILD-TYPE  21  92 171  95
D738V4, multiclass
    clus
vv   PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  T1                1                 21
  T2                0                 92
  T3                2                171
  T4                2                 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
  PRAMEF14 MUTATED     2   1   1   1
  PRAMEF14 WILD-TYPE 116 103  76  76
D738V5, multiclass
    clus
vv   PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  N0                2                116
  N1                1                103
  N2                1                 76
  N3                1                 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"
D738V6, binary
                    cls
clus                   0   1
  PRAMEF14 MUTATED     4   0
  PRAMEF14 WILD-TYPE 342  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF14 MUTATED      4    0
  PRAMEF14 WILD-TYPE  342   29
   clus
vv  PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  0                4                342
  1                0                 29
[1] 2 2
[1] FALSE
D738V7, binary
                    cls
clus                   0   1
  PRAMEF14 MUTATED     1   4
  PRAMEF14 WILD-TYPE 144 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF14 MUTATED      1    4
  PRAMEF14 WILD-TYPE  144  244
        clus
vv       PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  FEMALE                1                144
  MALE                  4                244
[1] 2 2
[1] FALSE
D738V8, binary
                    cls
clus                   0   1
  PRAMEF14 MUTATED     4   1
  PRAMEF14 WILD-TYPE 288  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF14 MUTATED      4    1
  PRAMEF14 WILD-TYPE  288   58
     clus
vv    PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  NO                 4                288
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PRAMEF14 MUTATED                                          0
  PRAMEF14 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PRAMEF14 MUTATED                                       0
  PRAMEF14 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRAMEF14 MUTATED                                                        2
  PRAMEF14 WILD-TYPE                                                    156
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PRAMEF14 MUTATED                                                   0
  PRAMEF14 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRAMEF14 MUTATED                                                                   2
  PRAMEF14 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PRAMEF14 MUTATED                                                    0
  PRAMEF14 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PRAMEF14 MUTATED                                                  1
  PRAMEF14 WILD-TYPE                                               60
D738V9, multiclass
                                                                   clus
vv                                                                  PRAMEF14 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  PRAMEF14 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  PRAMEF14 MUTATED     4   0   0   0
  PRAMEF14 WILD-TYPE 307  14  15  24
D738V10, multiclass
    clus
vv   PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  R0                4                307
  R1                0                 14
  R2                0                 15
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D738V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PRAMEF14 MUTATED       2                         1
  PRAMEF14 WILD-TYPE    85                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRAMEF14 MUTATED                                           0     2
  PRAMEF14 WILD-TYPE                                         1   241
D738V12, multiclass
                                           clus
vv                                          PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    2                241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D738V13, binary
                    cls
clus                   0   1
  PRAMEF14 MUTATED     0   5
  PRAMEF14 WILD-TYPE   4 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF14 MUTATED      0    5
  PRAMEF14 WILD-TYPE    4  305
                        clus
vv                       PRAMEF14 MUTATED PRAMEF14 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                5                305
[1] 2 2
[1] FALSE

Clustering(739) Variable = PYGO2 MUTATION ANALYSIS
D739V1, survival
                 sevent
clus2               0   1
  PYGO2 MUTATED     7   1
  PYGO2 WILD-TYPE 223 138
  PYGO2 MUTATED PYGO2 WILD-TYPE 
              8             361 
  PYGO2 MUTATED PYGO2 WILD-TYPE 
              1             138 
$`PYGO2 MUTATED`
TCGA-B7-A5TJ TCGA-BR-6566 TCGA-BR-8081 TCGA-BR-8487 TCGA-D7-A6EY TCGA-F1-6874 
       11.01        32.78        32.25         1.12        11.44        14.47 
TCGA-HU-A4G8 TCGA-HU-A4H8 
       22.68        14.07 

$`PYGO2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15         9.86        26.70        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-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-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-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-F1-6875 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-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 

  PYGO2 MUTATED PYGO2 WILD-TYPE 
           1.12            0.00 
  PYGO2 MUTATED PYGO2 WILD-TYPE 
          32.78          122.30 
  PYGO2 MUTATED PYGO2 WILD-TYPE 
          14.27           14.27 
[1] "1.1 - 32.8 (14.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "3.1"
D739V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PYGO2 MUTATED         0        0        2        0         2         3
  PYGO2 WILD-TYPE       2       15       38       30        35        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PYGO2 MUTATED           0          0          1          0        0
  PYGO2 WILD-TYPE         3         70         52         32       38
D739V3, multiclass
            clus
vv           PYGO2 MUTATED PYGO2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PYGO2 MUTATED     1   1   4   2
  PYGO2 WILD-TYPE  21  91 169  95
D739V4, multiclass
    clus
vv   PYGO2 MUTATED PYGO2 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             4             169
  T4             2              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
  PYGO2 MUTATED     4   2   0   1
  PYGO2 WILD-TYPE 114 102  77  76
D739V5, multiclass
    clus
vv   PYGO2 MUTATED PYGO2 WILD-TYPE
  N0             4             114
  N1             2             102
  N2             0              77
  N3             1              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"
D739V6, binary
                 cls
clus                0   1
  PYGO2 MUTATED     8   0
  PYGO2 WILD-TYPE 338  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PYGO2 MUTATED      8    0
  PYGO2 WILD-TYPE  338   29
   clus
vv  PYGO2 MUTATED PYGO2 WILD-TYPE
  0             8             338
  1             0              29
[1] 2 2
[1] FALSE
D739V7, binary
                 cls
clus                0   1
  PYGO2 MUTATED     5   3
  PYGO2 WILD-TYPE 140 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PYGO2 MUTATED      5    3
  PYGO2 WILD-TYPE  140  245
        clus
vv       PYGO2 MUTATED PYGO2 WILD-TYPE
  FEMALE             5             140
  MALE               3             245
[1] 2 2
[1] FALSE
D739V8, binary
                 cls
clus                0   1
  PYGO2 MUTATED     8   0
  PYGO2 WILD-TYPE 284  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PYGO2 MUTATED      8    0
  PYGO2 WILD-TYPE  284   59
     clus
vv    PYGO2 MUTATED PYGO2 WILD-TYPE
  NO              8             284
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PYGO2 MUTATED                                          0
  PYGO2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PYGO2 MUTATED                                       1
  PYGO2 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PYGO2 MUTATED                                                        3
  PYGO2 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PYGO2 MUTATED                                                   0
  PYGO2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PYGO2 MUTATED                                                                   2
  PYGO2 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PYGO2 MUTATED                                                    0
  PYGO2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PYGO2 MUTATED                                                  2
  PYGO2 WILD-TYPE                                               59
D739V9, multiclass
                                                                   clus
vv                                                                  PYGO2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  PYGO2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PYGO2 MUTATED     6   0   0   0
  PYGO2 WILD-TYPE 305  14  15  24
D739V10, multiclass
    clus
vv   PYGO2 MUTATED PYGO2 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D739V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PYGO2 MUTATED       2                         0
  PYGO2 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PYGO2 MUTATED                                           0     6
  PYGO2 WILD-TYPE                                         1   237
D739V12, multiclass
                                           clus
vv                                          PYGO2 MUTATED PYGO2 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D739V13, binary
                 cls
clus                0   1
  PYGO2 MUTATED     0   8
  PYGO2 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PYGO2 MUTATED      0    8
  PYGO2 WILD-TYPE    4  302
                        clus
vv                       PYGO2 MUTATED PYGO2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(740) Variable = AVEN MUTATION ANALYSIS
D740V1, survival
                sevent
clus2              0   1
  AVEN MUTATED     5   2
  AVEN WILD-TYPE 225 137
  AVEN MUTATED AVEN WILD-TYPE 
             7            362 
  AVEN MUTATED AVEN WILD-TYPE 
             2            137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15         9.86        26.70        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-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-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-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-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        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 

  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          14.12 
[1] "9.7 - 38.1 (30.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D740V2, 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       2       14       39       30        37        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AVEN MUTATED           0          1          0          1        0
  AVEN WILD-TYPE         3         69         53         31       38
D740V3, multiclass
            clus
vv           AVEN MUTATED AVEN WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AVEN MUTATED     1   2   0   3
  AVEN WILD-TYPE  21  90 173  94
D740V4, multiclass
    clus
vv   AVEN MUTATED AVEN WILD-TYPE
  T1            1             21
  T2            2             90
  T3            0            173
  T4            3             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
  AVEN MUTATED     2   1   0   1
  AVEN WILD-TYPE 116 103  77  76
D740V5, multiclass
    clus
vv   AVEN MUTATED AVEN WILD-TYPE
  N0            2            116
  N1            1            103
  N2            0             77
  N3            1             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"
D740V6, binary
                cls
clus               0   1
  AVEN MUTATED     7   0
  AVEN WILD-TYPE 339  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  AVEN MUTATED      7    0
  AVEN WILD-TYPE  339   29
   clus
vv  AVEN MUTATED AVEN WILD-TYPE
  0            7            339
  1            0             29
[1] 2 2
[1] FALSE
D740V7, binary
                cls
clus               0   1
  AVEN MUTATED     4   3
  AVEN WILD-TYPE 141 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  AVEN MUTATED      4    3
  AVEN WILD-TYPE  141  245
        clus
vv       AVEN MUTATED AVEN WILD-TYPE
  FEMALE            4            141
  MALE              3            245
[1] 2 2
[1] FALSE
D740V8, binary
                cls
clus               0   1
  AVEN MUTATED     5   2
  AVEN WILD-TYPE 287  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  AVEN MUTATED      5    2
  AVEN WILD-TYPE  287   57
     clus
vv    AVEN MUTATED AVEN WILD-TYPE
  NO             5            287
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AVEN MUTATED                                          0
  AVEN WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AVEN MUTATED                                       0
  AVEN WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AVEN MUTATED                                                        3
  AVEN WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AVEN MUTATED                                                   2
  AVEN WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AVEN MUTATED                                                                   1
  AVEN WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AVEN MUTATED                                                    1
  AVEN WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AVEN MUTATED                                                  0
  AVEN WILD-TYPE                                               61
D740V9, multiclass
                                                                   clus
vv                                                                  AVEN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  AVEN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AVEN MUTATED     3   1   0   2
  AVEN WILD-TYPE 308  13  15  22
D740V10, multiclass
    clus
vv   AVEN MUTATED AVEN WILD-TYPE
  R0            3            308
  R1            1             13
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D740V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  AVEN MUTATED       1                         0
  AVEN WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AVEN MUTATED                                           0     5
  AVEN WILD-TYPE                                         1   238
D740V12, multiclass
                                           clus
vv                                          AVEN MUTATED AVEN WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D740V13, binary
                cls
clus               0   1
  AVEN MUTATED     0   5
  AVEN WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  AVEN MUTATED      0    5
  AVEN WILD-TYPE    4  305
                        clus
vv                       AVEN MUTATED AVEN WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(741) Variable = BAT4 MUTATION ANALYSIS
D741V1, survival
                sevent
clus2              0   1
  BAT4 MUTATED     2   3
  BAT4 WILD-TYPE 228 136
  BAT4 MUTATED BAT4 WILD-TYPE 
             5            364 
  BAT4 MUTATED BAT4 WILD-TYPE 
             3            136 
$`BAT4 MUTATED`
TCGA-BR-7707 TCGA-BR-8363 TCGA-BR-8370 TCGA-CD-A4MG TCGA-HU-A4GQ 
       35.84         0.26         3.32         6.58         0.10 

$`BAT4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  BAT4 MUTATED BAT4 WILD-TYPE 
           0.1            0.0 
  BAT4 MUTATED BAT4 WILD-TYPE 
         35.84         122.30 
  BAT4 MUTATED BAT4 WILD-TYPE 
          3.32          14.45 
[1] "0.1 - 35.8 (3.3)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "3.6"
D741V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BAT4 MUTATED         0        0        2        0         1         0
  BAT4 WILD-TYPE       2       15       38       30        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BAT4 MUTATED           0          0          1          1        0
  BAT4 WILD-TYPE         3         70         52         31       38
D741V3, multiclass
            clus
vv           BAT4 MUTATED BAT4 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BAT4 MUTATED     0   2   2   1
  BAT4 WILD-TYPE  22  90 171  96
D741V4, multiclass
    clus
vv   BAT4 MUTATED BAT4 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            2            171
  T4            1             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
  BAT4 MUTATED     3   0   1   1
  BAT4 WILD-TYPE 115 104  76  76
D741V5, multiclass
    clus
vv   BAT4 MUTATED BAT4 WILD-TYPE
  N0            3            115
  N1            0            104
  N2            1             76
  N3            1             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"
D741V6, binary
                cls
clus               0   1
  BAT4 MUTATED     5   0
  BAT4 WILD-TYPE 341  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT4 MUTATED      5    0
  BAT4 WILD-TYPE  341   29
   clus
vv  BAT4 MUTATED BAT4 WILD-TYPE
  0            5            341
  1            0             29
[1] 2 2
[1] FALSE
D741V7, binary
                cls
clus               0   1
  BAT4 MUTATED     2   3
  BAT4 WILD-TYPE 143 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT4 MUTATED      2    3
  BAT4 WILD-TYPE  143  245
        clus
vv       BAT4 MUTATED BAT4 WILD-TYPE
  FEMALE            2            143
  MALE              3            245
[1] 2 2
[1] FALSE
D741V8, binary
                cls
clus               0   1
  BAT4 MUTATED     5   0
  BAT4 WILD-TYPE 287  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT4 MUTATED      5    0
  BAT4 WILD-TYPE  287   59
     clus
vv    BAT4 MUTATED BAT4 WILD-TYPE
  NO             5            287
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BAT4 MUTATED                                          0
  BAT4 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BAT4 MUTATED                                       2
  BAT4 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BAT4 MUTATED                                                        2
  BAT4 WILD-TYPE                                                    156
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BAT4 MUTATED                                                   0
  BAT4 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BAT4 MUTATED                                                                   0
  BAT4 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BAT4 MUTATED                                                    0
  BAT4 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BAT4 MUTATED                                                  1
  BAT4 WILD-TYPE                                               60
D741V9, multiclass
                                                                   clus
vv                                                                  BAT4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  BAT4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BAT4 MUTATED     4   0   0   0
  BAT4 WILD-TYPE 307  14  15  24
D741V10, multiclass
    clus
vv   BAT4 MUTATED BAT4 WILD-TYPE
  R0            4            307
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D741V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BAT4 MUTATED       2                         0
  BAT4 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BAT4 MUTATED                                           0     3
  BAT4 WILD-TYPE                                         1   240
D741V12, multiclass
                                           clus
vv                                          BAT4 MUTATED BAT4 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D741V13, binary
                cls
clus               0   1
  BAT4 MUTATED     0   5
  BAT4 WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT4 MUTATED      0    5
  BAT4 WILD-TYPE    4  305
                        clus
vv                       BAT4 MUTATED BAT4 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(742) Variable = GPR1 MUTATION ANALYSIS
D742V1, survival
                sevent
clus2              0   1
  GPR1 MUTATED     4   2
  GPR1 WILD-TYPE 226 137
  GPR1 MUTATED GPR1 WILD-TYPE 
             6            363 
  GPR1 MUTATED GPR1 WILD-TYPE 
             2            137 
$`GPR1 MUTATED`
TCGA-BR-7707 TCGA-BR-8680 TCGA-CD-A4MG TCGA-D7-A6EY TCGA-HU-A4GU TCGA-MX-A5UJ 
       35.84        31.96         6.58        11.44         6.58        19.73 

$`GPR1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  GPR1 MUTATED GPR1 WILD-TYPE 
          6.58           0.00 
  GPR1 MUTATED GPR1 WILD-TYPE 
         35.84         122.30 
  GPR1 MUTATED GPR1 WILD-TYPE 
        15.585         14.270 
[1] "6.6 - 35.8 (15.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D742V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPR1 MUTATED         0        0        1        0         1         1
  GPR1 WILD-TYPE       2       15       39       30        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR1 MUTATED           0          1          1          0        1
  GPR1 WILD-TYPE         3         69         52         32       37
D742V3, multiclass
            clus
vv           GPR1 MUTATED GPR1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GPR1 MUTATED     0   1   4   1
  GPR1 WILD-TYPE  22  91 169  96
D742V4, multiclass
    clus
vv   GPR1 MUTATED GPR1 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            4            169
  T4            1             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
  GPR1 MUTATED     2   1   2   1
  GPR1 WILD-TYPE 116 103  75  76
D742V5, multiclass
    clus
vv   GPR1 MUTATED GPR1 WILD-TYPE
  N0            2            116
  N1            1            103
  N2            2             75
  N3            1             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"
D742V6, binary
                cls
clus               0   1
  GPR1 MUTATED     5   1
  GPR1 WILD-TYPE 341  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR1 MUTATED      5    1
  GPR1 WILD-TYPE  341   28
   clus
vv  GPR1 MUTATED GPR1 WILD-TYPE
  0            5            341
  1            1             28
[1] 2 2
[1] FALSE
D742V7, binary
                cls
clus               0   1
  GPR1 MUTATED     3   3
  GPR1 WILD-TYPE 142 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR1 MUTATED      3    3
  GPR1 WILD-TYPE  142  245
        clus
vv       GPR1 MUTATED GPR1 WILD-TYPE
  FEMALE            3            142
  MALE              3            245
[1] 2 2
[1] FALSE
D742V8, binary
                cls
clus               0   1
  GPR1 MUTATED     6   0
  GPR1 WILD-TYPE 286  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR1 MUTATED      6    0
  GPR1 WILD-TYPE  286   59
     clus
vv    GPR1 MUTATED GPR1 WILD-TYPE
  NO             6            286
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GPR1 MUTATED                                          0
  GPR1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GPR1 MUTATED                                       2
  GPR1 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR1 MUTATED                                                        1
  GPR1 WILD-TYPE                                                    157
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GPR1 MUTATED                                                   0
  GPR1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR1 MUTATED                                                                   0
  GPR1 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GPR1 MUTATED                                                    0
  GPR1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GPR1 MUTATED                                                  3
  GPR1 WILD-TYPE                                               58
D742V9, multiclass
                                                                   clus
vv                                                                  GPR1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  GPR1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GPR1 MUTATED     5   0   0   0
  GPR1 WILD-TYPE 306  14  15  24
D742V10, multiclass
    clus
vv   GPR1 MUTATED GPR1 WILD-TYPE
  R0            5            306
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D742V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GPR1 MUTATED       3                         0
  GPR1 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR1 MUTATED                                           0     3
  GPR1 WILD-TYPE                                         1   240
D742V12, multiclass
                                           clus
vv                                          GPR1 MUTATED GPR1 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D742V13, binary
                cls
clus               0   1
  GPR1 MUTATED     0   6
  GPR1 WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR1 MUTATED      0    6
  GPR1 WILD-TYPE    4  304
                        clus
vv                       GPR1 MUTATED GPR1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(743) Variable = KCTD9 MUTATION ANALYSIS
D743V1, survival
                 sevent
clus2               0   1
  KCTD9 MUTATED     8   1
  KCTD9 WILD-TYPE 222 138
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              9             360 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              1             138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  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           14.12 
[1] "3.3 - 22.7 (16.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.2"
D743V2, 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       2       15       40       28        37        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCTD9 MUTATED           0          1          2          2        2
  KCTD9 WILD-TYPE         3         69         51         30       36
D743V3, multiclass
            clus
vv           KCTD9 MUTATED KCTD9 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               2              28
  STAGE IIA              0              37
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCTD9 MUTATED     0   2   5   4
  KCTD9 WILD-TYPE  22  90 168  93
D743V4, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             5             168
  T4             4              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
  KCTD9 MUTATED     1   3   3   3
  KCTD9 WILD-TYPE 117 101  74  74
D743V5, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  N0             1             117
  N1             3             101
  N2             3              74
  N3             3              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"
D743V6, binary
                 cls
clus                0   1
  KCTD9 MUTATED    10   0
  KCTD9 WILD-TYPE 336  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED     10    0
  KCTD9 WILD-TYPE  336   29
   clus
vv  KCTD9 MUTATED KCTD9 WILD-TYPE
  0            10             336
  1             0              29
[1] 2 2
[1] FALSE
D743V7, binary
                 cls
clus                0   1
  KCTD9 MUTATED     5   6
  KCTD9 WILD-TYPE 140 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      5    6
  KCTD9 WILD-TYPE  140  242
        clus
vv       KCTD9 MUTATED KCTD9 WILD-TYPE
  FEMALE             5             140
  MALE               6             242
[1] 2 2
[1] FALSE
D743V8, binary
                 cls
clus                0   1
  KCTD9 MUTATED     9   0
  KCTD9 WILD-TYPE 283  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      9    0
  KCTD9 WILD-TYPE  283   59
     clus
vv    KCTD9 MUTATED KCTD9 WILD-TYPE
  NO              9             283
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KCTD9 MUTATED                                          0
  KCTD9 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KCTD9 MUTATED                                       4
  KCTD9 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCTD9 MUTATED                                                        4
  KCTD9 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KCTD9 MUTATED                                                   0
  KCTD9 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCTD9 MUTATED                                                                   2
  KCTD9 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KCTD9 MUTATED                                                    0
  KCTD9 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KCTD9 MUTATED                                                  1
  KCTD9 WILD-TYPE                                               60
D743V9, multiclass
                                                                   clus
vv                                                                  KCTD9 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  KCTD9 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCTD9 MUTATED     7   0   0   2
  KCTD9 WILD-TYPE 304  14  15  22
D743V10, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D743V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCTD9 MUTATED       3                         0
  KCTD9 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCTD9 MUTATED                                           0     5
  KCTD9 WILD-TYPE                                         1   238
D743V12, multiclass
                                           clus
vv                                          KCTD9 MUTATED KCTD9 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D743V13, binary
                 cls
clus                0   1
  KCTD9 MUTATED     0   8
  KCTD9 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      0    8
  KCTD9 WILD-TYPE    4  302
                        clus
vv                       KCTD9 MUTATED KCTD9 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(744) Variable = ZNF514 MUTATION ANALYSIS
D744V1, survival
                  sevent
clus2                0   1
  ZNF514 MUTATED     2   6
  ZNF514 WILD-TYPE 228 133
  ZNF514 MUTATED ZNF514 WILD-TYPE 
               8              361 
  ZNF514 MUTATED ZNF514 WILD-TYPE 
               6              133 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-4477 
       19.07        12.03         0.00         9.01        18.97        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-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-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 

  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           14.270 
[1] "6.6 - 34.7 (13.9)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2"  
D744V2, 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       2       14       40       30        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF514 MUTATED           0          1          1          0        2
  ZNF514 WILD-TYPE         3         69         52         32       36
D744V3, multiclass
            clus
vv           ZNF514 MUTATED ZNF514 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF514 MUTATED     1   0   5   1
  ZNF514 WILD-TYPE  21  92 168  96
D744V4, multiclass
    clus
vv   ZNF514 MUTATED ZNF514 WILD-TYPE
  T1              1               21
  T2              0               92
  T3              5              168
  T4              1               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
  ZNF514 MUTATED     3   2   2   1
  ZNF514 WILD-TYPE 115 102  75  76
D744V5, multiclass
    clus
vv   ZNF514 MUTATED ZNF514 WILD-TYPE
  N0              3              115
  N1              2              102
  N2              2               75
  N3              1               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"
D744V6, binary
                  cls
clus                 0   1
  ZNF514 MUTATED     7   1
  ZNF514 WILD-TYPE 339  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF514 MUTATED      7    1
  ZNF514 WILD-TYPE  339   28
   clus
vv  ZNF514 MUTATED ZNF514 WILD-TYPE
  0              7              339
  1              1               28
[1] 2 2
[1] FALSE
D744V7, binary
                  cls
clus                 0   1
  ZNF514 MUTATED     2   7
  ZNF514 WILD-TYPE 143 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF514 MUTATED      2    7
  ZNF514 WILD-TYPE  143  241
        clus
vv       ZNF514 MUTATED ZNF514 WILD-TYPE
  FEMALE              2              143
  MALE                7              241
[1] 2 2
[1] FALSE
D744V8, binary
                  cls
clus                 0   1
  ZNF514 MUTATED     5   1
  ZNF514 WILD-TYPE 287  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF514 MUTATED      5    1
  ZNF514 WILD-TYPE  287   58
     clus
vv    ZNF514 MUTATED ZNF514 WILD-TYPE
  NO               5              287
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF514 MUTATED                                          0
  ZNF514 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF514 MUTATED                                       1
  ZNF514 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF514 MUTATED                                                        4
  ZNF514 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF514 MUTATED                                                   0
  ZNF514 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF514 MUTATED                                                                   3
  ZNF514 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF514 MUTATED                                                    0
  ZNF514 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF514 MUTATED                                                  1
  ZNF514 WILD-TYPE                                               60
D744V9, multiclass
                                                                   clus
vv                                                                  ZNF514 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ZNF514 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF514 MUTATED     4   1   0   3
  ZNF514 WILD-TYPE 307  13  15  21
D744V10, multiclass
    clus
vv   ZNF514 MUTATED ZNF514 WILD-TYPE
  R0              4              307
  R1              1               13
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D744V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF514 MUTATED       2                         0
  ZNF514 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF514 MUTATED                                           0     5
  ZNF514 WILD-TYPE                                         1   238
D744V12, multiclass
                                           clus
vv                                          ZNF514 MUTATED ZNF514 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D744V13, binary
                  cls
clus                 0   1
  ZNF514 MUTATED     0   6
  ZNF514 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF514 MUTATED      0    6
  ZNF514 WILD-TYPE    4  304
                        clus
vv                       ZNF514 MUTATED ZNF514 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(745) Variable = AFP MUTATION ANALYSIS
D745V1, survival
               sevent
clus2             0   1
  AFP MUTATED     0   3
  AFP WILD-TYPE 230 136
  AFP MUTATED AFP WILD-TYPE 
            3           366 
  AFP MUTATED AFP WILD-TYPE 
            3           136 
$`AFP MUTATED`
TCGA-BR-4184 TCGA-CD-A4MI TCGA-R5-A7ZF 
        6.97        11.77         8.52 

$`AFP WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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         14.45 
[1] "7.0 - 11.8 (8.5)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "5.6"
D745V2, 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       2       15       40       30        37        51
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AFP MUTATED           0          2          0          0        1
  AFP WILD-TYPE         3         68         53         32       37
D745V3, multiclass
            clus
vv           AFP MUTATED AFP WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             0            40
  STAGE II             0            30
  STAGE IIA            0            37
  STAGE IIB            1            51
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           0            53
  STAGE IIIC           0            32
  STAGE IV             1            37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  AFP MUTATED     0   0   2   2
  AFP WILD-TYPE  22  92 171  95
D745V4, multiclass
    clus
vv   AFP MUTATED AFP WILD-TYPE
  T1           0            22
  T2           0            92
  T3           2           171
  T4           2            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
  AFP MUTATED     1   3   0   0
  AFP WILD-TYPE 117 101  77  77
D745V5, multiclass
    clus
vv   AFP MUTATED AFP WILD-TYPE
  N0           1           117
  N1           3           101
  N2           0            77
  N3           0            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"
D745V6, binary
               cls
clus              0   1
  AFP MUTATED     2   1
  AFP WILD-TYPE 344  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFP MUTATED      2    1
  AFP WILD-TYPE  344   28
   clus
vv  AFP MUTATED AFP WILD-TYPE
  0           2           344
  1           1            28
[1] 2 2
[1] FALSE
D745V7, binary
               cls
clus              0   1
  AFP MUTATED     1   3
  AFP WILD-TYPE 144 245
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFP MUTATED      1    3
  AFP WILD-TYPE  144  245
        clus
vv       AFP MUTATED AFP WILD-TYPE
  FEMALE           1           144
  MALE             3           245
[1] 2 2
[1] FALSE
D745V8, binary
               cls
clus              0   1
  AFP MUTATED     4   0
  AFP WILD-TYPE 288  59
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFP MUTATED      4    0
  AFP WILD-TYPE  288   59
     clus
vv    AFP MUTATED AFP WILD-TYPE
  NO            4           288
  YES           0            59
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AFP MUTATED                                          0
  AFP WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AFP MUTATED                                       0
  AFP WILD-TYPE                                    70
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AFP MUTATED                                                        2
  AFP WILD-TYPE                                                    156
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AFP MUTATED                                                   0
  AFP WILD-TYPE                                                21
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AFP MUTATED                                                                   1
  AFP WILD-TYPE                                                                67
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AFP MUTATED                                                    0
  AFP WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AFP MUTATED                                                  1
  AFP WILD-TYPE                                               60
D745V9, multiclass
                                                                   clus
vv                                                                  AFP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            1
                                                                   clus
vv                                                                  AFP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  AFP MUTATED     1   0   0   1
  AFP WILD-TYPE 310  14  15  23
D745V10, multiclass
[1] "Remove cluster labels:" "AFP MUTATED"           
clus
  AFP MUTATED AFP WILD-TYPE 
            2           362 
   TCGA-CG-4444    TCGA-CG-4460    TCGA-CG-4475    TCGA-CG-4476    TCGA-CG-5716 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-5727    TCGA-EQ-A4SO    TCGA-F1-6177    TCGA-FP-A8CX    TCGA-HF-7131 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-KB-A93G    TCGA-MX-A663    TCGA-B7-5816    TCGA-B7-5818    TCGA-BR-4183 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-4187    TCGA-BR-4188    TCGA-BR-4191    TCGA-BR-4201    TCGA-BR-4253 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-4255    TCGA-BR-4256    TCGA-BR-4257    TCGA-BR-4267    TCGA-BR-4279 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-4280    TCGA-BR-4292    TCGA-BR-4294    TCGA-BR-4357    TCGA-BR-4361 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-4362    TCGA-BR-4363    TCGA-BR-4366    TCGA-BR-4368    TCGA-BR-4369 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-4370    TCGA-BR-4371    TCGA-BR-6452    TCGA-BR-6453    TCGA-BR-6454 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6455    TCGA-BR-6456    TCGA-BR-6457    TCGA-BR-6458    TCGA-BR-6563 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6564    TCGA-BR-6565    TCGA-BR-6566    TCGA-BR-6705    TCGA-BR-6706 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6707    TCGA-BR-6709    TCGA-BR-6710    TCGA-BR-6801    TCGA-BR-6802 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6803    TCGA-BR-6852    TCGA-BR-7196    TCGA-BR-7197    TCGA-BR-7703 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-7704    TCGA-BR-7707    TCGA-BR-7715    TCGA-BR-7716    TCGA-BR-7717 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-7722    TCGA-BR-7723    TCGA-BR-7901    TCGA-BR-7957    TCGA-BR-7958 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-7959    TCGA-BR-8058    TCGA-BR-8059    TCGA-BR-8060    TCGA-BR-8077 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8078    TCGA-BR-8080    TCGA-BR-8081    TCGA-BR-8284    TCGA-BR-8285 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8286    TCGA-BR-8289    TCGA-BR-8291    TCGA-BR-8295    TCGA-BR-8297 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8360    TCGA-BR-8361    TCGA-BR-8363    TCGA-BR-8364    TCGA-BR-8365 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8366    TCGA-BR-8367    TCGA-BR-8368    TCGA-BR-8369    TCGA-BR-8370 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8371    TCGA-BR-8372    TCGA-BR-8373    TCGA-BR-8380    TCGA-BR-8381 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8382    TCGA-BR-8384    TCGA-BR-8483    TCGA-BR-8484    TCGA-BR-8485 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8486    TCGA-BR-8487    TCGA-BR-8588    TCGA-BR-8589    TCGA-BR-8590 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8591    TCGA-BR-8592    TCGA-BR-8676    TCGA-BR-8677    TCGA-BR-8678 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8679    TCGA-BR-8680    TCGA-BR-8682    TCGA-BR-8683    TCGA-BR-8686 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8687    TCGA-BR-8690    TCGA-BR-A44T    TCGA-BR-A44U    TCGA-BR-A452 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A453    TCGA-BR-A4CQ    TCGA-BR-A4CR    TCGA-BR-A4CS    TCGA-BR-A4IU 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4IV    TCGA-BR-A4IY    TCGA-BR-A4IZ    TCGA-BR-A4J1    TCGA-BR-A4J2 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4J4    TCGA-BR-A4J5    TCGA-BR-A4J6    TCGA-BR-A4J7    TCGA-BR-A4J8 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4PD    TCGA-BR-A4PE    TCGA-BR-A4PF    TCGA-BR-A4QI    TCGA-BR-A4QL 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4QM    TCGA-CD-5800    TCGA-CD-5801    TCGA-CD-5804    TCGA-CD-8524 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CD-8525    TCGA-CD-8526    TCGA-CD-8527    TCGA-CD-8528    TCGA-CD-8529 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CD-8530    TCGA-CD-8531    TCGA-CD-8532    TCGA-CD-8533    TCGA-CD-8534 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CD-8535    TCGA-CD-8536    TCGA-CD-A487    TCGA-CG-4300    TCGA-CG-4301 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4304    TCGA-CG-4305    TCGA-CG-4306    TCGA-CG-4436    TCGA-CG-4437 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4438    TCGA-CG-4440    TCGA-CG-4441    TCGA-CG-4442    TCGA-CG-4443 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4449    TCGA-CG-4455    TCGA-CG-4462    TCGA-CG-4465    TCGA-CG-4466 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4469    TCGA-CG-4474    TCGA-CG-4477    TCGA-CG-5717    TCGA-CG-5718 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-5719    TCGA-CG-5720    TCGA-CG-5721    TCGA-CG-5722    TCGA-CG-5723 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-5724    TCGA-CG-5725    TCGA-CG-5726    TCGA-CG-5728    TCGA-CG-5730 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-5732    TCGA-CG-5733    TCGA-CG-5734    TCGA-D7-5577    TCGA-D7-5578 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-5579    TCGA-D7-6518    TCGA-D7-6519    TCGA-D7-6520    TCGA-D7-6521 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-6522    TCGA-D7-6524    TCGA-D7-6525    TCGA-D7-6526    TCGA-D7-6527 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-6528    TCGA-D7-6815    TCGA-D7-6817    TCGA-D7-6818    TCGA-D7-6820 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-6822    TCGA-D7-8570    TCGA-D7-8572    TCGA-D7-8573    TCGA-D7-8574 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-8575    TCGA-D7-8576    TCGA-D7-8578    TCGA-D7-8579    TCGA-D7-A4YT 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-A4YU    TCGA-D7-A4YV    TCGA-D7-A4YX    TCGA-D7-A4YY    TCGA-D7-A4Z0 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-A6ET    TCGA-D7-A6EV    TCGA-D7-A6EX    TCGA-D7-A6EY    TCGA-D7-A6EZ 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-A6F0    TCGA-D7-A6F2    TCGA-D7-A747    TCGA-D7-A748    TCGA-D7-A74A 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-A74B    TCGA-EQ-5647    TCGA-F1-6874    TCGA-F1-6875    TCGA-F1-A448 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-F1-A72C    TCGA-FP-7735    TCGA-FP-7829    TCGA-FP-7998    TCGA-FP-8099 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-FP-8209    TCGA-FP-8211    TCGA-FP-8631    TCGA-FP-A4BE    TCGA-FP-A4BF 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-FP-A9TM    TCGA-HF-7132    TCGA-HF-7133    TCGA-HF-7134    TCGA-HF-7136 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HF-A5NB    TCGA-HJ-7597    TCGA-HU-8238    TCGA-HU-8243    TCGA-HU-8244 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-8249    TCGA-HU-8602    TCGA-HU-8604    TCGA-HU-8608    TCGA-HU-8610 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4G2    TCGA-HU-A4G3    TCGA-HU-A4G6    TCGA-HU-A4G9    TCGA-HU-A4GC 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4GD    TCGA-HU-A4GF    TCGA-HU-A4GH    TCGA-HU-A4GJ    TCGA-HU-A4GN 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4GP    TCGA-HU-A4GQ    TCGA-HU-A4GT    TCGA-HU-A4GU    TCGA-HU-A4GX 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4GY    TCGA-HU-A4H0    TCGA-HU-A4H2    TCGA-HU-A4H3    TCGA-HU-A4H4 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4H5    TCGA-HU-A4H6    TCGA-HU-A4H8    TCGA-HU-A4HB    TCGA-HU-A4HD 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-IN-7806    TCGA-IN-8462    TCGA-IN-8663    TCGA-IN-A6RI    TCGA-IN-A6RJ 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-IN-A6RL    TCGA-IN-A6RN    TCGA-IN-A6RO    TCGA-IN-A6RP    TCGA-IN-A6RR 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-IN-A6RS    TCGA-IN-A7NR    TCGA-IN-A7NT    TCGA-IN-A7NU    TCGA-IN-AB1V 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-IN-AB1X    TCGA-IP-7968    TCGA-KB-A6F5    TCGA-KB-A6F7    TCGA-KB-A93J 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-MX-A5UG    TCGA-MX-A5UJ    TCGA-R5-A7ZI    TCGA-RD-A7BS    TCGA-RD-A7BT 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-RD-A7BW    TCGA-RD-A7C1    TCGA-RD-A8MV    TCGA-RD-A8MW    TCGA-RD-A8N0 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-RD-A8N1    TCGA-RD-A8N2    TCGA-RD-A8N4    TCGA-RD-A8N5    TCGA-RD-A8N6 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-RD-A8N9    TCGA-SW-A7EA    TCGA-SW-A7EB    TCGA-VQ-A8DL    TCGA-VQ-A8DT 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-VQ-A8DU    TCGA-VQ-A8DV    TCGA-VQ-A8DZ    TCGA-VQ-A8E2    TCGA-VQ-A8E7 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-VQ-A8P2    TCGA-VQ-A8P3    TCGA-VQ-A8PE    TCGA-VQ-A8PK    TCGA-VQ-A8PM 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-VQ-A8PQ    TCGA-VQ-A91Q    TCGA-VQ-A91U    TCGA-VQ-A91V    TCGA-VQ-A92D 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-VQ-A94T    TCGA-VQ-AA64    TCGA-VQ-AA68    TCGA-VQ-AA69    TCGA-VQ-AA6A 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-VQ-AA6B    TCGA-VQ-AA6F    TCGA-VQ-AA6G    TCGA-VQ-AA6I    TCGA-VQ-AA6J 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-VQ-AA6K    TCGA-ZA-A8F6 
"AFP WILD-TYPE" "AFP WILD-TYPE" 
D745V11, continuous
[1] "Remove cluster labels:" "AFP MUTATED"           
clus
  AFP MUTATED AFP WILD-TYPE 
            2           341 
   TCGA-CG-4444    TCGA-CG-4460    TCGA-CG-4475    TCGA-CG-4476    TCGA-CG-5727 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-EQ-A4SO    TCGA-F1-6177    TCGA-FP-A8CX    TCGA-HF-7131    TCGA-KB-A93G 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-MX-A663    TCGA-B7-5816    TCGA-B7-A5TI    TCGA-BR-4183    TCGA-BR-4188 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-4191    TCGA-BR-4253    TCGA-BR-4255    TCGA-BR-4256    TCGA-BR-4267 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-4279    TCGA-BR-4280    TCGA-BR-4361    TCGA-BR-4362    TCGA-BR-4368 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6452    TCGA-BR-6453    TCGA-BR-6454    TCGA-BR-6455    TCGA-BR-6456 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6457    TCGA-BR-6458    TCGA-BR-6563    TCGA-BR-6564    TCGA-BR-6565 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6566    TCGA-BR-6705    TCGA-BR-6706    TCGA-BR-6707    TCGA-BR-6709 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-6710    TCGA-BR-6801    TCGA-BR-6802    TCGA-BR-6803    TCGA-BR-6852 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-7196    TCGA-BR-7197    TCGA-BR-7703    TCGA-BR-7704    TCGA-BR-7707 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-7715    TCGA-BR-7716    TCGA-BR-7717    TCGA-BR-7722    TCGA-BR-7723 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-7901    TCGA-BR-7957    TCGA-BR-7958    TCGA-BR-7959    TCGA-BR-8058 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8059    TCGA-BR-8060    TCGA-BR-8077    TCGA-BR-8078    TCGA-BR-8080 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8081    TCGA-BR-8284    TCGA-BR-8285    TCGA-BR-8286    TCGA-BR-8289 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8291    TCGA-BR-8295    TCGA-BR-8297    TCGA-BR-8360    TCGA-BR-8361 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8363    TCGA-BR-8364    TCGA-BR-8365    TCGA-BR-8366    TCGA-BR-8367 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8368    TCGA-BR-8369    TCGA-BR-8370    TCGA-BR-8371    TCGA-BR-8372 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8373    TCGA-BR-8380    TCGA-BR-8381    TCGA-BR-8382    TCGA-BR-8384 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8483    TCGA-BR-8484    TCGA-BR-8485    TCGA-BR-8486    TCGA-BR-8487 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8588    TCGA-BR-8589    TCGA-BR-8590    TCGA-BR-8591    TCGA-BR-8592 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8676    TCGA-BR-8677    TCGA-BR-8678    TCGA-BR-8679    TCGA-BR-8680 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-8682    TCGA-BR-8683    TCGA-BR-8686    TCGA-BR-8687    TCGA-BR-8690 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A44T    TCGA-BR-A44U    TCGA-BR-A452    TCGA-BR-A453    TCGA-BR-A4CQ 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4CR    TCGA-BR-A4CS    TCGA-BR-A4IU    TCGA-BR-A4IV    TCGA-BR-A4IY 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4IZ    TCGA-BR-A4J1    TCGA-BR-A4J2    TCGA-BR-A4J4    TCGA-BR-A4J5 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4J6    TCGA-BR-A4J8    TCGA-BR-A4PD    TCGA-BR-A4PE    TCGA-BR-A4PF 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-BR-A4QI    TCGA-BR-A4QL    TCGA-BR-A4QM    TCGA-CD-5804    TCGA-CD-8525 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CD-8526    TCGA-CD-8531    TCGA-CD-8535    TCGA-CD-A487    TCGA-CG-4301 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4304    TCGA-CG-4305    TCGA-CG-4436    TCGA-CG-4437    TCGA-CG-4438 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4440    TCGA-CG-4441    TCGA-CG-4442    TCGA-CG-4443    TCGA-CG-4449 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4455    TCGA-CG-4462    TCGA-CG-4465    TCGA-CG-4466    TCGA-CG-4469 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-4474    TCGA-CG-4477    TCGA-CG-5717    TCGA-CG-5718    TCGA-CG-5719 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-5720    TCGA-CG-5721    TCGA-CG-5722    TCGA-CG-5723    TCGA-CG-5724 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-5725    TCGA-CG-5726    TCGA-CG-5728    TCGA-CG-5730    TCGA-CG-5732 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-CG-5733    TCGA-CG-5734    TCGA-D7-5577    TCGA-D7-5578    TCGA-D7-5579 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-6518    TCGA-D7-6519    TCGA-D7-6520    TCGA-D7-6521    TCGA-D7-6522 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-6524    TCGA-D7-6525    TCGA-D7-6526    TCGA-D7-6527    TCGA-D7-6528 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-6815    TCGA-D7-6817    TCGA-D7-6818    TCGA-D7-6820    TCGA-D7-6822 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-8570    TCGA-D7-8572    TCGA-D7-8573    TCGA-D7-8574    TCGA-D7-8575 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-8576    TCGA-D7-8578    TCGA-D7-8579    TCGA-D7-A4YT    TCGA-D7-A4YU 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-A4YV    TCGA-D7-A4YX    TCGA-D7-A4YY    TCGA-D7-A4Z0    TCGA-D7-A6ET 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-A6EV    TCGA-D7-A6EX    TCGA-D7-A6EY    TCGA-D7-A6EZ    TCGA-D7-A6F0 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-D7-A6F2    TCGA-D7-A747    TCGA-D7-A748    TCGA-D7-A74A    TCGA-D7-A74B 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-EQ-5647    TCGA-EQ-8122    TCGA-F1-6874    TCGA-F1-6875    TCGA-F1-A448 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-F1-A72C    TCGA-FP-7735    TCGA-FP-7829    TCGA-FP-7916    TCGA-FP-7998 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-FP-8099    TCGA-FP-8209    TCGA-FP-8210    TCGA-FP-8211    TCGA-FP-8631 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-FP-A4BE    TCGA-FP-A4BF    TCGA-FP-A9TM    TCGA-HF-7132    TCGA-HF-7133 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HF-7134    TCGA-HF-7136    TCGA-HF-A5NB    TCGA-HJ-7597    TCGA-HU-8238 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-8243    TCGA-HU-8244    TCGA-HU-8249    TCGA-HU-8602    TCGA-HU-8604 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-8608    TCGA-HU-8610    TCGA-HU-A4G2    TCGA-HU-A4G3    TCGA-HU-A4G6 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4G8    TCGA-HU-A4G9    TCGA-HU-A4GC    TCGA-HU-A4GD    TCGA-HU-A4GF 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4GH    TCGA-HU-A4GJ    TCGA-HU-A4GN    TCGA-HU-A4GP    TCGA-HU-A4GQ 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4GT    TCGA-HU-A4GU    TCGA-HU-A4GX    TCGA-HU-A4GY    TCGA-HU-A4H0 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4H2    TCGA-HU-A4H3    TCGA-HU-A4H4    TCGA-HU-A4H5    TCGA-HU-A4H6 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-HU-A4H8    TCGA-HU-A4HB    TCGA-HU-A4HD    TCGA-IN-7806    TCGA-IN-7808 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-IN-8462    TCGA-IN-8663    TCGA-IN-A6RI    TCGA-IN-A6RJ    TCGA-IN-A6RL 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-IN-A6RN    TCGA-IN-A6RO    TCGA-IN-A6RP    TCGA-IN-A6RR    TCGA-IN-A6RS 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-IN-A7NR    TCGA-IN-A7NT    TCGA-IN-A7NU    TCGA-IN-AB1V    TCGA-IN-AB1X 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-IP-7968    TCGA-KB-A6F5    TCGA-KB-A6F7    TCGA-KB-A93J    TCGA-MX-A5UG 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-MX-A5UJ    TCGA-R5-A7ZI    TCGA-RD-A7BS    TCGA-RD-A7BT    TCGA-RD-A7BW 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-RD-A7C1    TCGA-RD-A8MV    TCGA-RD-A8MW    TCGA-RD-A8N0    TCGA-RD-A8N1 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-RD-A8N2    TCGA-RD-A8N4    TCGA-RD-A8N5    TCGA-RD-A8N6    TCGA-RD-A8N9 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-SW-A7EA    TCGA-SW-A7EB    TCGA-VQ-A8DL    TCGA-VQ-A8DT    TCGA-VQ-A8DU 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-VQ-A8DV    TCGA-VQ-A8DZ    TCGA-VQ-A8E2    TCGA-VQ-A8E7    TCGA-VQ-A8P2 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-VQ-A8P3    TCGA-VQ-A8PE    TCGA-VQ-A8PK    TCGA-VQ-A8PM    TCGA-VQ-A8PQ 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-VQ-A91Q    TCGA-VQ-A91U    TCGA-VQ-A91V    TCGA-VQ-A92D    TCGA-VQ-A94T 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-VQ-AA64    TCGA-VQ-AA68    TCGA-VQ-AA69    TCGA-VQ-AA6A    TCGA-VQ-AA6B 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-VQ-AA6F    TCGA-VQ-AA6G    TCGA-VQ-AA6I    TCGA-VQ-AA6J    TCGA-VQ-AA6K 
"AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" "AFP WILD-TYPE" 
   TCGA-ZA-A8F6 
"AFP WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  AFP MUTATED       1                         1
  AFP WILD-TYPE    86                         8
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AFP MUTATED                                           0     2
  AFP WILD-TYPE                                         1   241
D745V12, multiclass
                                           clus
vv                                          AFP MUTATED AFP WILD-TYPE
  ASIAN                                               1            86
  BLACK OR AFRICAN AMERICAN                           1             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               2           241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D745V13, binary
               cls
clus              0   1
  AFP MUTATED     0   4
  AFP WILD-TYPE   4 306
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFP MUTATED      0    4
  AFP WILD-TYPE    4  306
                        clus
vv                       AFP MUTATED AFP WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           4           306
[1] 2 2
[1] FALSE

Clustering(746) Variable = TRIOBP MUTATION ANALYSIS
D746V1, survival
                  sevent
clus2                0   1
  TRIOBP MUTATED    19   9
  TRIOBP WILD-TYPE 211 130
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              28              341 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
               9              130 
$`TRIOBP MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6801 
        6.97         9.34        34.68        32.78        25.61        40.21 
TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-5801 TCGA-CD-A4MG 
       29.59         1.12        31.96        16.14        13.18         6.58 
TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-6528 TCGA-D7-8572 TCGA-D7-A6EY TCGA-F1-6874 
        6.02        21.07        15.22        16.80        11.44        14.47 
TCGA-FP-7916 TCGA-FP-8631 TCGA-FP-A4BE TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-HU-A4H3 
       14.07         0.56        11.08        22.68        11.77        29.00 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-MX-A5UJ TCGA-VQ-A8P2 
       14.07        33.40        19.73        38.14 

$`TRIOBP WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-6706 TCGA-BR-6707 TCGA-BR-6709 
       39.12        26.10         9.17        18.05        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        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-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-5802 
       21.44         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-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-D7-6815 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-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-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF 
       22.29        17.06        59.54         5.03        13.58         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-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-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-A4HB TCGA-IN-7806 
       12.95        23.84        23.80        21.17        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-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 

  TRIOBP MUTATED TRIOBP WILD-TYPE 
            0.56             0.00 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
           40.21           122.30 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
           15.68            14.04 
[1] "0.6 - 40.2 (15.7)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.3"
D746V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIOBP MUTATED         0        1        3        0         6         3
  TRIOBP WILD-TYPE       2       14       37       30        31        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIOBP MUTATED           0          8          3          2        3
  TRIOBP WILD-TYPE         3         62         50         30       35
D746V3, multiclass
            clus
vv           TRIOBP MUTATED TRIOBP WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                3               37
  STAGE II                0               30
  STAGE IIA               6               31
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              8               62
  STAGE IIIB              3               50
  STAGE IIIC              2               30
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIOBP MUTATED     2   4  15   8
  TRIOBP WILD-TYPE  20  88 158  89
D746V4, multiclass
    clus
vv   TRIOBP MUTATED TRIOBP WILD-TYPE
  T1              2               20
  T2              4               88
  T3             15              158
  T4              8               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
  TRIOBP MUTATED    11   7   7   5
  TRIOBP WILD-TYPE 107  97  70  72
D746V5, multiclass
    clus
vv   TRIOBP MUTATED TRIOBP WILD-TYPE
  N0             11              107
  N1              7               97
  N2              7               70
  N3              5               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"
D746V6, binary
                  cls
clus                 0   1
  TRIOBP MUTATED    25   2
  TRIOBP WILD-TYPE 321  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED     25    2
  TRIOBP WILD-TYPE  321   27
   clus
vv  TRIOBP MUTATED TRIOBP WILD-TYPE
  0             25              321
  1              2               27
[1] 2 2
[1] FALSE
D746V7, binary
                  cls
clus                 0   1
  TRIOBP MUTATED    13  17
  TRIOBP WILD-TYPE 132 231
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED     13   17
  TRIOBP WILD-TYPE  132  231
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  FEMALE             13              132
  MALE               17              231
[1] 2 2
[1] FALSE
D746V8, binary
                  cls
clus                 0   1
  TRIOBP MUTATED    24   2
  TRIOBP WILD-TYPE 268  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED     24    2
  TRIOBP WILD-TYPE  268   57
     clus
vv    TRIOBP MUTATED TRIOBP WILD-TYPE
  NO              24              268
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TRIOBP MUTATED                                          0
  TRIOBP WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TRIOBP MUTATED                                       4
  TRIOBP WILD-TYPE                                    66
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRIOBP MUTATED                                                       14
  TRIOBP WILD-TYPE                                                    144
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TRIOBP MUTATED                                                   1
  TRIOBP WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRIOBP MUTATED                                                                   4
  TRIOBP WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TRIOBP MUTATED                                                    0
  TRIOBP WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TRIOBP MUTATED                                                  7
  TRIOBP WILD-TYPE                                               54
D746V9, multiclass
                                                                   clus
vv                                                                  TRIOBP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               7
                                                                   clus
vv                                                                  TRIOBP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIOBP MUTATED    23   0   1   3
  TRIOBP WILD-TYPE 288  14  14  21
D746V10, multiclass
    clus
vv   TRIOBP MUTATED TRIOBP WILD-TYPE
  R0             23              288
  R1              0               14
  R2              1               14
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D746V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TRIOBP MUTATED       9                         1
  TRIOBP WILD-TYPE    78                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRIOBP MUTATED                                           0    17
  TRIOBP WILD-TYPE                                         1   226
D746V12, multiclass
                                           clus
vv                                          TRIOBP MUTATED TRIOBP WILD-TYPE
  ASIAN                                                  9               78
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 17              226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D746V13, binary
                  cls
clus                 0   1
  TRIOBP MUTATED     0  26
  TRIOBP WILD-TYPE   4 284
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      0   26
  TRIOBP WILD-TYPE    4  284
                        clus
vv                       TRIOBP MUTATED TRIOBP WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             26              284
[1] 2 2
[1] FALSE

Clustering(747) Variable = CCAR1 MUTATION ANALYSIS
D747V1, survival
                 sevent
clus2               0   1
  CCAR1 MUTATED    12   5
  CCAR1 WILD-TYPE 218 134
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             17             352 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
              5             134 
$`CCAR1 MUTATED`
TCGA-BR-6452 TCGA-BR-8077 TCGA-BR-8366 TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-8683 
       34.68         0.69         0.95        25.05        31.96         9.86 
TCGA-BR-A44U TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CG-5721 TCGA-D7-8576 
       13.87        12.30        12.39        12.59         6.02        14.66 
TCGA-D7-A6EY TCGA-HF-7132 TCGA-HU-A4GT TCGA-R5-A7ZI TCGA-VQ-A8P2 
       11.44        77.29         6.51        74.53        38.14 

$`CCAR1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-8686 TCGA-BR-8687 
        7.53        26.73        24.79        32.58        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-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-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-D7-8578 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-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-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-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 

  CCAR1 MUTATED CCAR1 WILD-TYPE 
           0.69            0.00 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
          77.29          122.30 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
          12.59           14.45 
[1] "0.7 - 77.3 (12.6)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.4"
D747V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCAR1 MUTATED         0        1        1        2         3         0
  CCAR1 WILD-TYPE       2       14       39       28        34        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCAR1 MUTATED           0          2          5          1        4
  CCAR1 WILD-TYPE         3         68         48         31       34
D747V3, multiclass
            clus
vv           CCAR1 MUTATED CCAR1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              3              34
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             5              48
  STAGE IIIC             1              31
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CCAR1 MUTATED     1   2   8   8
  CCAR1 WILD-TYPE  21  90 165  89
D747V4, multiclass
    clus
vv   CCAR1 MUTATED CCAR1 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             8             165
  T4             8              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
  CCAR1 MUTATED     7   6   2   4
  CCAR1 WILD-TYPE 111  98  75  73
D747V5, multiclass
    clus
vv   CCAR1 MUTATED CCAR1 WILD-TYPE
  N0             7             111
  N1             6              98
  N2             2              75
  N3             4              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"
D747V6, binary
                 cls
clus                0   1
  CCAR1 MUTATED    16   3
  CCAR1 WILD-TYPE 330  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED     16    3
  CCAR1 WILD-TYPE  330   26
   clus
vv  CCAR1 MUTATED CCAR1 WILD-TYPE
  0            16             330
  1             3              26
[1] 2 2
[1] FALSE
D747V7, binary
                 cls
clus                0   1
  CCAR1 MUTATED     9  10
  CCAR1 WILD-TYPE 136 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED      9   10
  CCAR1 WILD-TYPE  136  238
        clus
vv       CCAR1 MUTATED CCAR1 WILD-TYPE
  FEMALE             9             136
  MALE              10             238
[1] 2 2
[1] FALSE
D747V8, binary
                 cls
clus                0   1
  CCAR1 MUTATED    11   6
  CCAR1 WILD-TYPE 281  53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED     11    6
  CCAR1 WILD-TYPE  281   53
     clus
vv    CCAR1 MUTATED CCAR1 WILD-TYPE
  NO             11             281
  YES             6              53
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CCAR1 MUTATED                                          0
  CCAR1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CCAR1 MUTATED                                       3
  CCAR1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCAR1 MUTATED                                                        5
  CCAR1 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CCAR1 MUTATED                                                   3
  CCAR1 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCAR1 MUTATED                                                                   3
  CCAR1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CCAR1 MUTATED                                                    0
  CCAR1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CCAR1 MUTATED                                                  5
  CCAR1 WILD-TYPE                                               56
D747V9, multiclass
                                                                   clus
vv                                                                  CCAR1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              5
                                                                   clus
vv                                                                  CCAR1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CCAR1 MUTATED    19   0   0   0
  CCAR1 WILD-TYPE 292  14  15  24
D747V10, multiclass
    clus
vv   CCAR1 MUTATED CCAR1 WILD-TYPE
  R0            19             292
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D747V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CCAR1 MUTATED       7                         0
  CCAR1 WILD-TYPE    80                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCAR1 MUTATED                                           0     9
  CCAR1 WILD-TYPE                                         1   234
D747V12, multiclass
                                           clus
vv                                          CCAR1 MUTATED CCAR1 WILD-TYPE
  ASIAN                                                 7              80
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D747V13, binary
                 cls
clus                0   1
  CCAR1 MUTATED     1  14
  CCAR1 WILD-TYPE   3 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED      1   14
  CCAR1 WILD-TYPE    3  296
                        clus
vv                       CCAR1 MUTATED CCAR1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(748) Variable = TMEM127 MUTATION ANALYSIS
D748V1, survival
                   sevent
clus2                 0   1
  TMEM127 MUTATED     5   0
  TMEM127 WILD-TYPE 225 139
  TMEM127 MUTATED TMEM127 WILD-TYPE 
                5               364 
  TMEM127 MUTATED TMEM127 WILD-TYPE 
                0               139 
$`TMEM127 MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-CD-8531 TCGA-HF-A5NB TCGA-R5-A7ZI 
       34.68        32.78        12.59        30.51        74.53 

$`TMEM127 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  TMEM127 MUTATED TMEM127 WILD-TYPE 
            12.59              0.00 
  TMEM127 MUTATED TMEM127 WILD-TYPE 
            74.53            122.30 
  TMEM127 MUTATED TMEM127 WILD-TYPE 
            32.78             14.12 
[1] "12.6 - 74.5 (32.8)" "0.0 - 122.3 (14.1)"
[1] "hr="     "9400000"
D748V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM127 MUTATED         0        0        0        0         2         0
  TMEM127 WILD-TYPE       2       15       40       30        35        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM127 MUTATED           0          1          0          1        1
  TMEM127 WILD-TYPE         3         69         53         31       37
D748V3, multiclass
            clus
vv           TMEM127 MUTATED TMEM127 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM127 MUTATED     0   0   3   2
  TMEM127 WILD-TYPE  22  92 170  95
D748V4, multiclass
    clus
vv   TMEM127 MUTATED TMEM127 WILD-TYPE
  T1               0                22
  T2               0                92
  T3               3               170
  T4               2                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
  TMEM127 MUTATED     2   2   0   1
  TMEM127 WILD-TYPE 116 102  77  76
D748V5, multiclass
    clus
vv   TMEM127 MUTATED TMEM127 WILD-TYPE
  N0               2               116
  N1               2               102
  N2               0                77
  N3               1                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"
D748V6, binary
                   cls
clus                  0   1
  TMEM127 MUTATED     4   1
  TMEM127 WILD-TYPE 342  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM127 MUTATED      4    1
  TMEM127 WILD-TYPE  342   28
   clus
vv  TMEM127 MUTATED TMEM127 WILD-TYPE
  0               4               342
  1               1                28
[1] 2 2
[1] FALSE
D748V7, binary
                   cls
clus                  0   1
  TMEM127 MUTATED     5   0
  TMEM127 WILD-TYPE 140 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM127 MUTATED      5    0
  TMEM127 WILD-TYPE  140  248
        clus
vv       TMEM127 MUTATED TMEM127 WILD-TYPE
  FEMALE               5               140
  MALE                 0               248
[1] 2 2
[1] FALSE
D748V8, binary
                   cls
clus                  0   1
  TMEM127 MUTATED     3   2
  TMEM127 WILD-TYPE 289  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM127 MUTATED      3    2
  TMEM127 WILD-TYPE  289   57
     clus
vv    TMEM127 MUTATED TMEM127 WILD-TYPE
  NO                3               289
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TMEM127 MUTATED                                          0
  TMEM127 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TMEM127 MUTATED                                       2
  TMEM127 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM127 MUTATED                                                        2
  TMEM127 WILD-TYPE                                                    156
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TMEM127 MUTATED                                                   1
  TMEM127 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM127 MUTATED                                                                   0
  TMEM127 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TMEM127 MUTATED                                                    0
  TMEM127 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TMEM127 MUTATED                                                  0
  TMEM127 WILD-TYPE                                               61
D748V9, multiclass
                                                                   clus
vv                                                                  TMEM127 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  TMEM127 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM127 MUTATED     4   1   0   0
  TMEM127 WILD-TYPE 307  13  15  24
D748V10, multiclass
    clus
vv   TMEM127 MUTATED TMEM127 WILD-TYPE
  R0               4               307
  R1               1                13
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D748V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM127 MUTATED       1                         0
  TMEM127 WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM127 MUTATED                                           0     3
  TMEM127 WILD-TYPE                                         1   240
D748V12, multiclass
                                           clus
vv                                          TMEM127 MUTATED TMEM127 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D748V13, binary
                   cls
clus                  0   1
  TMEM127 MUTATED     1   3
  TMEM127 WILD-TYPE   3 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM127 MUTATED      1    3
  TMEM127 WILD-TYPE    3  307
                        clus
vv                       TMEM127 MUTATED TMEM127 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               3               307
[1] 2 2
[1] FALSE

Clustering(749) Variable = ZNF142 MUTATION ANALYSIS
D749V1, survival
                  sevent
clus2                0   1
  ZNF142 MUTATED    11   7
  ZNF142 WILD-TYPE 219 132
  ZNF142 MUTATED ZNF142 WILD-TYPE 
              18              351 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
               7              132 
$`ZNF142 MUTATED`
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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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 

  ZNF142 MUTATED ZNF142 WILD-TYPE 
            1.02             0.00 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
            65.1            122.3 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
          21.025           14.040 
[1] "1.0 - 65.1 (21.0)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.2"
D749V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF142 MUTATED         1        0        2        2         2         2
  ZNF142 WILD-TYPE       1       15       38       28        35        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF142 MUTATED           2          3          1          2        2
  ZNF142 WILD-TYPE         1         67         52         30       36
D749V3, multiclass
            clus
vv           ZNF142 MUTATED ZNF142 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                2               28
  STAGE IIA               2               35
  STAGE IIB               2               50
  STAGE III               2                1
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              2               30
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF142 MUTATED     1   4   7   7
  ZNF142 WILD-TYPE  21  88 166  90
D749V4, multiclass
    clus
vv   ZNF142 MUTATED ZNF142 WILD-TYPE
  T1              1               21
  T2              4               88
  T3              7              166
  T4              7               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
  ZNF142 MUTATED     7   6   3   3
  ZNF142 WILD-TYPE 111  98  74  74
D749V5, multiclass
    clus
vv   ZNF142 MUTATED ZNF142 WILD-TYPE
  N0              7              111
  N1              6               98
  N2              3               74
  N3              3               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"
D749V6, binary
                  cls
clus                 0   1
  ZNF142 MUTATED    14   2
  ZNF142 WILD-TYPE 332  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED     14    2
  ZNF142 WILD-TYPE  332   27
   clus
vv  ZNF142 MUTATED ZNF142 WILD-TYPE
  0             14              332
  1              2               27
[1] 2 2
[1] FALSE
D749V7, binary
                  cls
clus                 0   1
  ZNF142 MUTATED     8  11
  ZNF142 WILD-TYPE 137 237
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED      8   11
  ZNF142 WILD-TYPE  137  237
        clus
vv       ZNF142 MUTATED ZNF142 WILD-TYPE
  FEMALE              8              137
  MALE               11              237
[1] 2 2
[1] FALSE
D749V8, binary
                  cls
clus                 0   1
  ZNF142 MUTATED    16   1
  ZNF142 WILD-TYPE 276  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED     16    1
  ZNF142 WILD-TYPE  276   58
     clus
vv    ZNF142 MUTATED ZNF142 WILD-TYPE
  NO              16              276
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF142 MUTATED                                          1
  ZNF142 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF142 MUTATED                                       3
  ZNF142 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF142 MUTATED                                                       10
  ZNF142 WILD-TYPE                                                    148
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF142 MUTATED                                                   1
  ZNF142 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF142 MUTATED                                                                   2
  ZNF142 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF142 MUTATED                                                    0
  ZNF142 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF142 MUTATED                                                  2
  ZNF142 WILD-TYPE                                               59
D749V9, multiclass
                                                                   clus
vv                                                                  ZNF142 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  ZNF142 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF142 MUTATED    15   0   1   2
  ZNF142 WILD-TYPE 296  14  14  22
D749V10, multiclass
    clus
vv   ZNF142 MUTATED ZNF142 WILD-TYPE
  R0             15              296
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D749V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF142 MUTATED       4                         1
  ZNF142 WILD-TYPE    83                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF142 MUTATED                                           0    11
  ZNF142 WILD-TYPE                                         1   232
D749V12, multiclass
                                           clus
vv                                          ZNF142 MUTATED ZNF142 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D749V13, binary
                  cls
clus                 0   1
  ZNF142 MUTATED     0  15
  ZNF142 WILD-TYPE   4 295
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED      0   15
  ZNF142 WILD-TYPE    4  295
                        clus
vv                       ZNF142 MUTATED ZNF142 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             15              295
[1] 2 2
[1] FALSE

Clustering(750) Variable = MRPS5 MUTATION ANALYSIS
D750V1, survival
                 sevent
clus2               0   1
  MRPS5 MUTATED     5   2
  MRPS5 WILD-TYPE 225 137
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              7             362 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              2             137 
$`MRPS5 MUTATED`
TCGA-BR-6452 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5723 TCGA-D7-A6EY TCGA-F1-A448 
       34.68        31.96         6.58       105.07        11.44        21.27 
TCGA-FP-A4BE 
       11.08 

$`MRPS5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  MRPS5 MUTATED MRPS5 WILD-TYPE 
           6.58            0.00 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
         105.07          122.30 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
          21.27           14.22 
[1] "6.6 - 105.1 (21.3)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.8"
D750V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MRPS5 MUTATED         0        0        0        1         3         0
  MRPS5 WILD-TYPE       2       15       40       29        34        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPS5 MUTATED           0          0          2          0        1
  MRPS5 WILD-TYPE         3         70         51         32       37
D750V3, multiclass
            clus
vv           MRPS5 MUTATED MRPS5 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             2              51
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MRPS5 MUTATED     0   1   5   1
  MRPS5 WILD-TYPE  22  91 168  96
D750V4, multiclass
    clus
vv   MRPS5 MUTATED MRPS5 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             5             168
  T4             1              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
  MRPS5 MUTATED     3   1   1   2
  MRPS5 WILD-TYPE 115 103  76  75
D750V5, multiclass
    clus
vv   MRPS5 MUTATED MRPS5 WILD-TYPE
  N0             3             115
  N1             1             103
  N2             1              76
  N3             2              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"
D750V6, binary
                 cls
clus                0   1
  MRPS5 MUTATED     6   1
  MRPS5 WILD-TYPE 340  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      6    1
  MRPS5 WILD-TYPE  340   28
   clus
vv  MRPS5 MUTATED MRPS5 WILD-TYPE
  0             6             340
  1             1              28
[1] 2 2
[1] FALSE
D750V7, binary
                 cls
clus                0   1
  MRPS5 MUTATED     2   5
  MRPS5 WILD-TYPE 143 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      2    5
  MRPS5 WILD-TYPE  143  243
        clus
vv       MRPS5 MUTATED MRPS5 WILD-TYPE
  FEMALE             2             143
  MALE               5             243
[1] 2 2
[1] FALSE
D750V8, binary
                 cls
clus                0   1
  MRPS5 MUTATED     5   2
  MRPS5 WILD-TYPE 287  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      5    2
  MRPS5 WILD-TYPE  287   57
     clus
vv    MRPS5 MUTATED MRPS5 WILD-TYPE
  NO              5             287
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MRPS5 MUTATED                                          0
  MRPS5 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MRPS5 MUTATED                                       1
  MRPS5 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MRPS5 MUTATED                                                        3
  MRPS5 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MRPS5 MUTATED                                                   1
  MRPS5 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MRPS5 MUTATED                                                                   0
  MRPS5 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MRPS5 MUTATED                                                    0
  MRPS5 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MRPS5 MUTATED                                                  2
  MRPS5 WILD-TYPE                                               59
D750V9, multiclass
                                                                   clus
vv                                                                  MRPS5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  MRPS5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MRPS5 MUTATED     6   0   0   0
  MRPS5 WILD-TYPE 305  14  15  24
D750V10, multiclass
    clus
vv   MRPS5 MUTATED MRPS5 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D750V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MRPS5 MUTATED       2                         1
  MRPS5 WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MRPS5 MUTATED                                           0     3
  MRPS5 WILD-TYPE                                         1   240
D750V12, multiclass
                                           clus
vv                                          MRPS5 MUTATED MRPS5 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D750V13, binary
                 cls
clus                0   1
  MRPS5 MUTATED     1   5
  MRPS5 WILD-TYPE   3 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      1    5
  MRPS5 WILD-TYPE    3  305
                        clus
vv                       MRPS5 MUTATED MRPS5 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(751) Variable = CEP250 MUTATION ANALYSIS
D751V1, survival
                  sevent
clus2                0   1
  CEP250 MUTATED    12   6
  CEP250 WILD-TYPE 218 133
  CEP250 MUTATED CEP250 WILD-TYPE 
              18              351 
  CEP250 MUTATED CEP250 WILD-TYPE 
               6              133 
$`CEP250 MUTATED`
TCGA-EQ-A4SO TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8372 
       16.24        19.56         6.97        36.16        35.84        31.27 
TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-4469 
       28.14        31.96        16.14         6.58         9.01         7.07 
TCGA-D7-8572 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-VQ-A8P2 
       16.80         0.10         6.58        20.25        23.84        38.14 

$`CEP250 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-4466 TCGA-CG-4477 
       29.98        19.07        12.03         0.00        18.97        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-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-A4GY 
       11.77        21.37        29.98         8.98         6.51         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-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 

  CEP250 MUTATED CEP250 WILD-TYPE 
             0.1              0.0 
  CEP250 MUTATED CEP250 WILD-TYPE 
           38.14           122.30 
  CEP250 MUTATED CEP250 WILD-TYPE 
           18.18            14.07 
[1] "0.1 - 38.1 (18.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D751V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CEP250 MUTATED         0        1        1        0         1         3
  CEP250 WILD-TYPE       2       14       39       30        36        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP250 MUTATED           0          3          2          5        3
  CEP250 WILD-TYPE         3         67         51         27       35
D751V3, multiclass
            clus
vv           CEP250 MUTATED CEP250 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              2               51
  STAGE IIIC              5               27
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CEP250 MUTATED     2   3   5  10
  CEP250 WILD-TYPE  20  89 168  87
D751V4, multiclass
    clus
vv   CEP250 MUTATED CEP250 WILD-TYPE
  T1              2               20
  T2              3               89
  T3              5              168
  T4             10               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
  CEP250 MUTATED     4   5   5   6
  CEP250 WILD-TYPE 114  99  72  71
D751V5, multiclass
    clus
vv   CEP250 MUTATED CEP250 WILD-TYPE
  N0              4              114
  N1              5               99
  N2              5               72
  N3              6               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"
D751V6, binary
                  cls
clus                 0   1
  CEP250 MUTATED    17   2
  CEP250 WILD-TYPE 329  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP250 MUTATED     17    2
  CEP250 WILD-TYPE  329   27
   clus
vv  CEP250 MUTATED CEP250 WILD-TYPE
  0             17              329
  1              2               27
[1] 2 2
[1] FALSE
D751V7, binary
                  cls
clus                 0   1
  CEP250 MUTATED     8  13
  CEP250 WILD-TYPE 137 235
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP250 MUTATED      8   13
  CEP250 WILD-TYPE  137  235
        clus
vv       CEP250 MUTATED CEP250 WILD-TYPE
  FEMALE              8              137
  MALE               13              235
[1] 2 2
[1] FALSE
D751V8, binary
                  cls
clus                 0   1
  CEP250 MUTATED    14   2
  CEP250 WILD-TYPE 278  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP250 MUTATED     14    2
  CEP250 WILD-TYPE  278   57
     clus
vv    CEP250 MUTATED CEP250 WILD-TYPE
  NO              14              278
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CEP250 MUTATED                                          0
  CEP250 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CEP250 MUTATED                                       5
  CEP250 WILD-TYPE                                    65
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CEP250 MUTATED                                                        9
  CEP250 WILD-TYPE                                                    149
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CEP250 MUTATED                                                   1
  CEP250 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CEP250 MUTATED                                                                   1
  CEP250 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CEP250 MUTATED                                                    1
  CEP250 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CEP250 MUTATED                                                  3
  CEP250 WILD-TYPE                                               58
D751V9, multiclass
                                                                   clus
vv                                                                  CEP250 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  CEP250 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CEP250 MUTATED    13   1   1   4
  CEP250 WILD-TYPE 298  13  14  20
D751V10, multiclass
    clus
vv   CEP250 MUTATED CEP250 WILD-TYPE
  R0             13              298
  R1              1               13
  R2              1               14
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D751V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CEP250 MUTATED       6                         0
  CEP250 WILD-TYPE    81                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CEP250 MUTATED                                           0    13
  CEP250 WILD-TYPE                                         1   230
D751V12, multiclass
                                           clus
vv                                          CEP250 MUTATED CEP250 WILD-TYPE
  ASIAN                                                  6               81
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D751V13, binary
                  cls
clus                 0   1
  CEP250 MUTATED     0  18
  CEP250 WILD-TYPE   4 292
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP250 MUTATED      0   18
  CEP250 WILD-TYPE    4  292
                        clus
vv                       CEP250 MUTATED CEP250 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             18              292
[1] 2 2
[1] FALSE

Clustering(752) Variable = ARMC4 MUTATION ANALYSIS
D752V1, survival
                 sevent
clus2               0   1
  ARMC4 MUTATED    12   6
  ARMC4 WILD-TYPE 218 133
  ARMC4 MUTATED ARMC4 WILD-TYPE 
             18             351 
  ARMC4 MUTATED ARMC4 WILD-TYPE 
              6             133 
$`ARMC4 MUTATED`
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-8078 TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8483 
        6.61        15.95        29.59         2.66        14.04         5.39 
TCGA-BR-8680 TCGA-CD-A4MG TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-HU-8602 TCGA-HU-A4GN 
       31.96         6.58         5.92        14.76        22.32        29.98 
TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-KB-A6F7 TCGA-MX-A5UJ TCGA-R5-A7ZE TCGA-VQ-A8P2 
        0.10        29.00        63.62        19.73        18.21        38.14 

$`ARMC4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-6455 TCGA-BR-6456 TCGA-BR-6457 
        6.18         9.57        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-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-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-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72        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-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-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-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-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-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-A93J 
       11.70        15.75        13.51         2.53         5.56        36.95 
TCGA-MX-A5UG TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR 
        3.72        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 

  ARMC4 MUTATED ARMC4 WILD-TYPE 
            0.1             0.0 
  ARMC4 MUTATED ARMC4 WILD-TYPE 
          63.62          122.30 
  ARMC4 MUTATED ARMC4 WILD-TYPE 
          17.08           14.07 
[1] "0.1 - 63.6 (17.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D752V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARMC4 MUTATED         0        0        1        0         3         4
  ARMC4 WILD-TYPE       2       15       39       30        34        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARMC4 MUTATED           1          4          1          2        2
  ARMC4 WILD-TYPE         2         66         52         30       36
D752V3, multiclass
            clus
vv           ARMC4 MUTATED ARMC4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              4              48
  STAGE III              1               2
  STAGE IIIA             4              66
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARMC4 MUTATED     1   4   6   7
  ARMC4 WILD-TYPE  21  88 167  90
D752V4, multiclass
    clus
vv   ARMC4 MUTATED ARMC4 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             6             167
  T4             7              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
  ARMC4 MUTATED     3   6   6   3
  ARMC4 WILD-TYPE 115  98  71  74
D752V5, multiclass
    clus
vv   ARMC4 MUTATED ARMC4 WILD-TYPE
  N0             3             115
  N1             6              98
  N2             6              71
  N3             3              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"
D752V6, binary
                 cls
clus                0   1
  ARMC4 MUTATED    16   2
  ARMC4 WILD-TYPE 330  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC4 MUTATED     16    2
  ARMC4 WILD-TYPE  330   27
   clus
vv  ARMC4 MUTATED ARMC4 WILD-TYPE
  0            16             330
  1             2              27
[1] 2 2
[1] FALSE
D752V7, binary
                 cls
clus                0   1
  ARMC4 MUTATED    10   8
  ARMC4 WILD-TYPE 135 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC4 MUTATED     10    8
  ARMC4 WILD-TYPE  135  240
        clus
vv       ARMC4 MUTATED ARMC4 WILD-TYPE
  FEMALE            10             135
  MALE               8             240
[1] 2 2
[1] FALSE
D752V8, binary
                 cls
clus                0   1
  ARMC4 MUTATED    14   3
  ARMC4 WILD-TYPE 278  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC4 MUTATED     14    3
  ARMC4 WILD-TYPE  278   56
     clus
vv    ARMC4 MUTATED ARMC4 WILD-TYPE
  NO             14             278
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARMC4 MUTATED                                          0
  ARMC4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARMC4 MUTATED                                       3
  ARMC4 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARMC4 MUTATED                                                        4
  ARMC4 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARMC4 MUTATED                                                   2
  ARMC4 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARMC4 MUTATED                                                                   3
  ARMC4 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARMC4 MUTATED                                                    0
  ARMC4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARMC4 MUTATED                                                  6
  ARMC4 WILD-TYPE                                               55
D752V9, multiclass
                                                                   clus
vv                                                                  ARMC4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              6
                                                                   clus
vv                                                                  ARMC4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ARMC4 MUTATED    15   0   0   1
  ARMC4 WILD-TYPE 296  14  15  23
D752V10, multiclass
    clus
vv   ARMC4 MUTATED ARMC4 WILD-TYPE
  R0            15             296
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D752V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ARMC4 MUTATED       6                         0
  ARMC4 WILD-TYPE    81                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARMC4 MUTATED                                           0    11
  ARMC4 WILD-TYPE                                         1   232
D752V12, multiclass
                                           clus
vv                                          ARMC4 MUTATED ARMC4 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D752V13, binary
                 cls
clus                0   1
  ARMC4 MUTATED     0  16
  ARMC4 WILD-TYPE   4 294
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC4 MUTATED      0   16
  ARMC4 WILD-TYPE    4  294
                        clus
vv                       ARMC4 MUTATED ARMC4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            16             294
[1] 2 2
[1] FALSE

Clustering(753) Variable = PCF11 MUTATION ANALYSIS
D753V1, survival
                 sevent
clus2               0   1
  PCF11 MUTATED    16   5
  PCF11 WILD-TYPE 214 134
  PCF11 MUTATED PCF11 WILD-TYPE 
             21             348 
  PCF11 MUTATED PCF11 WILD-TYPE 
              5             134 
$`PCF11 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8360 
       30.90        34.68        35.84        37.25         0.69         6.18 
TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5721 TCGA-D7-A6EX 
       31.96        11.77        15.95         1.02         6.02        11.31 
TCGA-D7-A6F0 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-A4G2 TCGA-HU-A4GQ TCGA-R5-A804 
       22.29        52.21        30.51        24.30         0.10         4.60 
TCGA-VQ-A8P2 TCGA-VQ-A92D TCGA-VQ-AA6B 
       38.14        66.81        32.94 

$`PCF11 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8059 TCGA-BR-8060 TCGA-BR-8078 
        9.07        29.56        33.21        14.43        11.44        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-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-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-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-A6F2 TCGA-D7-A747 
       26.43        11.24        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-HJ-7597 
       11.08         5.52         6.21        77.29        63.06        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-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76         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-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-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 

  PCF11 MUTATED PCF11 WILD-TYPE 
            0.1             0.0 
  PCF11 MUTATED PCF11 WILD-TYPE 
          66.81          122.30 
  PCF11 MUTATED PCF11 WILD-TYPE 
          24.30           14.07 
[1] "0.1 - 66.8 (24.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D753V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCF11 MUTATED         0        1        3        1         2         1
  PCF11 WILD-TYPE       2       14       37       29        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCF11 MUTATED           0          3          3          2        4
  PCF11 WILD-TYPE         3         67         50         30       34
D753V3, multiclass
            clus
vv           PCF11 MUTATED PCF11 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             3              50
  STAGE IIIC             2              30
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PCF11 MUTATED     1   5   9   7
  PCF11 WILD-TYPE  21  87 164  90
D753V4, multiclass
    clus
vv   PCF11 MUTATED PCF11 WILD-TYPE
  T1             1              21
  T2             5              87
  T3             9             164
  T4             7              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
  PCF11 MUTATED     6   6   7   1
  PCF11 WILD-TYPE 112  98  70  76
D753V5, multiclass
    clus
vv   PCF11 MUTATED PCF11 WILD-TYPE
  N0             6             112
  N1             6              98
  N2             7              70
  N3             1              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"
D753V6, binary
                 cls
clus                0   1
  PCF11 MUTATED    18   3
  PCF11 WILD-TYPE 328  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED     18    3
  PCF11 WILD-TYPE  328   26
   clus
vv  PCF11 MUTATED PCF11 WILD-TYPE
  0            18             328
  1             3              26
[1] 2 2
[1] FALSE
D753V7, binary
                 cls
clus                0   1
  PCF11 MUTATED     9  13
  PCF11 WILD-TYPE 136 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED      9   13
  PCF11 WILD-TYPE  136  235
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  FEMALE             9             136
  MALE              13             235
[1] 2 2
[1] FALSE
D753V8, binary
                 cls
clus                0   1
  PCF11 MUTATED    16   3
  PCF11 WILD-TYPE 276  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED     16    3
  PCF11 WILD-TYPE  276   56
     clus
vv    PCF11 MUTATED PCF11 WILD-TYPE
  NO             16             276
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PCF11 MUTATED                                          0
  PCF11 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PCF11 MUTATED                                       2
  PCF11 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PCF11 MUTATED                                                        8
  PCF11 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PCF11 MUTATED                                                   2
  PCF11 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PCF11 MUTATED                                                                   6
  PCF11 WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PCF11 MUTATED                                                    0
  PCF11 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PCF11 MUTATED                                                  4
  PCF11 WILD-TYPE                                               57
D753V9, multiclass
                                                                   clus
vv                                                                  PCF11 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  PCF11 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PCF11 MUTATED    16   1   1   2
  PCF11 WILD-TYPE 295  13  14  22
D753V10, multiclass
    clus
vv   PCF11 MUTATED PCF11 WILD-TYPE
  R0            16             295
  R1             1              13
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D753V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PCF11 MUTATED       4                         1
  PCF11 WILD-TYPE    83                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PCF11 MUTATED                                           0    12
  PCF11 WILD-TYPE                                         1   231
D753V12, multiclass
                                           clus
vv                                          PCF11 MUTATED PCF11 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D753V13, binary
                 cls
clus                0   1
  PCF11 MUTATED     0  14
  PCF11 WILD-TYPE   4 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED      0   14
  PCF11 WILD-TYPE    4  296
                        clus
vv                       PCF11 MUTATED PCF11 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(754) Variable = C2ORF76 MUTATION ANALYSIS
D754V1, survival
                   sevent
clus2                 0   1
  C2ORF76 MUTATED     2   1
  C2ORF76 WILD-TYPE 228 138
  C2ORF76 MUTATED C2ORF76 WILD-TYPE 
                3               366 
  C2ORF76 MUTATED C2ORF76 WILD-TYPE 
                1               138 
$`C2ORF76 MUTATED`
TCGA-BR-8591 TCGA-HU-A4GC TCGA-HU-A4GQ 
       28.14         3.25         0.10 

$`C2ORF76 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  C2ORF76 MUTATED C2ORF76 WILD-TYPE 
              0.1               0.0 
  C2ORF76 MUTATED C2ORF76 WILD-TYPE 
            28.14            122.30 
  C2ORF76 MUTATED C2ORF76 WILD-TYPE 
             3.25             14.35 
[1] "0.1 - 28.1 (3.2)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D754V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C2ORF76 MUTATED         0        0        0        0         0         0
  C2ORF76 WILD-TYPE       2       15       40       30        37        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C2ORF76 MUTATED           0          0          1          3        0
  C2ORF76 WILD-TYPE         3         70         52         29       38
D754V3, multiclass
            clus
vv           C2ORF76 MUTATED C2ORF76 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                0                37
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               1                52
  STAGE IIIC               3                29
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C2ORF76 MUTATED     0   0   0   4
  C2ORF76 WILD-TYPE  22  92 173  93
D754V4, multiclass
    clus
vv   C2ORF76 MUTATED C2ORF76 WILD-TYPE
  T1               0                22
  T2               0                92
  T3               0               173
  T4               4                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
  C2ORF76 MUTATED     0   0   2   2
  C2ORF76 WILD-TYPE 118 104  75  75
D754V5, multiclass
    clus
vv   C2ORF76 MUTATED C2ORF76 WILD-TYPE
  N0               0               118
  N1               0               104
  N2               2                75
  N3               2                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"
D754V6, binary
                   cls
clus                  0   1
  C2ORF76 MUTATED     4   0
  C2ORF76 WILD-TYPE 342  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF76 MUTATED      4    0
  C2ORF76 WILD-TYPE  342   29
   clus
vv  C2ORF76 MUTATED C2ORF76 WILD-TYPE
  0               4               342
  1               0                29
[1] 2 2
[1] FALSE
D754V7, binary
                   cls
clus                  0   1
  C2ORF76 MUTATED     0   4
  C2ORF76 WILD-TYPE 145 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF76 MUTATED      0    4
  C2ORF76 WILD-TYPE  145  244
        clus
vv       C2ORF76 MUTATED C2ORF76 WILD-TYPE
  FEMALE               0               145
  MALE                 4               244
[1] 2 2
[1] FALSE
D754V8, binary
                   cls
clus                  0   1
  C2ORF76 MUTATED     3   0
  C2ORF76 WILD-TYPE 289  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF76 MUTATED      3    0
  C2ORF76 WILD-TYPE  289   59
     clus
vv    C2ORF76 MUTATED C2ORF76 WILD-TYPE
  NO                3               289
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C2ORF76 MUTATED                                          0
  C2ORF76 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C2ORF76 MUTATED                                       2
  C2ORF76 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C2ORF76 MUTATED                                                        1
  C2ORF76 WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C2ORF76 MUTATED                                                   0
  C2ORF76 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C2ORF76 MUTATED                                                                   0
  C2ORF76 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C2ORF76 MUTATED                                                    0
  C2ORF76 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C2ORF76 MUTATED                                                  1
  C2ORF76 WILD-TYPE                                               60
D754V9, multiclass
                                                                   clus
vv                                                                  C2ORF76 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  C2ORF76 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C2ORF76 MUTATED     4   0   0   0
  C2ORF76 WILD-TYPE 307  14  15  24
D754V10, multiclass
    clus
vv   C2ORF76 MUTATED C2ORF76 WILD-TYPE
  R0               4               307
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D754V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C2ORF76 MUTATED       2                         0
  C2ORF76 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C2ORF76 MUTATED                                           0     1
  C2ORF76 WILD-TYPE                                         1   242
D754V12, multiclass
                                           clus
vv                                          C2ORF76 MUTATED C2ORF76 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   1               242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D754V13, binary
                   cls
clus                  0   1
  C2ORF76 MUTATED     0   3
  C2ORF76 WILD-TYPE   4 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF76 MUTATED      0    3
  C2ORF76 WILD-TYPE    4  307
                        clus
vv                       C2ORF76 MUTATED C2ORF76 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               3               307
[1] 2 2
[1] FALSE

Clustering(755) Variable = MBNL2 MUTATION ANALYSIS
D755V1, survival
                 sevent
clus2               0   1
  MBNL2 MUTATED     4   5
  MBNL2 WILD-TYPE 226 134
  MBNL2 MUTATED MBNL2 WILD-TYPE 
              9             360 
  MBNL2 MUTATED MBNL2 WILD-TYPE 
              5             134 
$`MBNL2 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-8487 TCGA-BR-8590 TCGA-D7-A4YV TCGA-D7-A6EV 
       21.99         6.97         1.12         9.34         5.92        11.24 
TCGA-HF-7132 TCGA-HU-A4GQ TCGA-HU-A4GU 
       77.29         0.10         6.58 

$`MBNL2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 
        9.21        20.22        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-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-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-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-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 

  MBNL2 MUTATED MBNL2 WILD-TYPE 
            0.1             0.0 
  MBNL2 MUTATED MBNL2 WILD-TYPE 
          77.29          122.30 
  MBNL2 MUTATED MBNL2 WILD-TYPE 
          6.970          14.565 
[1] "0.1 - 77.3 (7.0)"   "0.0 - 122.3 (14.6)"
[1] "hr=" "2.1"
D755V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MBNL2 MUTATED         0        0        0        1         1         3
  MBNL2 WILD-TYPE       2       15       40       29        36        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MBNL2 MUTATED           0          2          0          2        1
  MBNL2 WILD-TYPE         3         68         53         30       37
D755V3, multiclass
            clus
vv           MBNL2 MUTATED MBNL2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MBNL2 MUTATED     0   2   4   4
  MBNL2 WILD-TYPE  22  90 169  93
D755V4, multiclass
    clus
vv   MBNL2 MUTATED MBNL2 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             4             169
  T4             4              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
  MBNL2 MUTATED     2   5   3   0
  MBNL2 WILD-TYPE 116  99  74  77
D755V5, multiclass
    clus
vv   MBNL2 MUTATED MBNL2 WILD-TYPE
  N0             2             116
  N1             5              99
  N2             3              74
  N3             0              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"
D755V6, binary
                 cls
clus                0   1
  MBNL2 MUTATED     9   1
  MBNL2 WILD-TYPE 337  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MBNL2 MUTATED      9    1
  MBNL2 WILD-TYPE  337   28
   clus
vv  MBNL2 MUTATED MBNL2 WILD-TYPE
  0             9             337
  1             1              28
[1] 2 2
[1] FALSE
D755V7, binary
                 cls
clus                0   1
  MBNL2 MUTATED     6   5
  MBNL2 WILD-TYPE 139 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MBNL2 MUTATED      6    5
  MBNL2 WILD-TYPE  139  243
        clus
vv       MBNL2 MUTATED MBNL2 WILD-TYPE
  FEMALE             6             139
  MALE               5             243
[1] 2 2
[1] FALSE
D755V8, binary
                 cls
clus                0   1
  MBNL2 MUTATED     8   1
  MBNL2 WILD-TYPE 284  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MBNL2 MUTATED      8    1
  MBNL2 WILD-TYPE  284   58
     clus
vv    MBNL2 MUTATED MBNL2 WILD-TYPE
  NO              8             284
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MBNL2 MUTATED                                          0
  MBNL2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MBNL2 MUTATED                                       1
  MBNL2 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MBNL2 MUTATED                                                        6
  MBNL2 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MBNL2 MUTATED                                                   1
  MBNL2 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MBNL2 MUTATED                                                                   1
  MBNL2 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MBNL2 MUTATED                                                    0
  MBNL2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MBNL2 MUTATED                                                  2
  MBNL2 WILD-TYPE                                               59
D755V9, multiclass
                                                                   clus
vv                                                                  MBNL2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  MBNL2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MBNL2 MUTATED     7   0   1   3
  MBNL2 WILD-TYPE 304  14  14  21
D755V10, multiclass
    clus
vv   MBNL2 MUTATED MBNL2 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D755V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MBNL2 MUTATED       2                         0
  MBNL2 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MBNL2 MUTATED                                           0     7
  MBNL2 WILD-TYPE                                         1   236
D755V12, multiclass
                                           clus
vv                                          MBNL2 MUTATED MBNL2 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D755V13, binary
                 cls
clus                0   1
  MBNL2 MUTATED     0   9
  MBNL2 WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MBNL2 MUTATED      0    9
  MBNL2 WILD-TYPE    4  301
                        clus
vv                       MBNL2 MUTATED MBNL2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(756) Variable = ITGAE MUTATION ANALYSIS
D756V1, survival
                 sevent
clus2               0   1
  ITGAE MUTATED    11   4
  ITGAE WILD-TYPE 219 135
  ITGAE MUTATED ITGAE WILD-TYPE 
             15             354 
  ITGAE MUTATED ITGAE WILD-TYPE 
              4             135 
$`ITGAE MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8363 
       30.90        34.68        15.95        32.25         6.18         0.26 
TCGA-BR-8487 TCGA-BR-A4QL TCGA-CD-A48A TCGA-CG-5726 TCGA-FP-8211 TCGA-HU-A4GN 
        1.12        16.14        12.43        28.96        13.58        29.98 
TCGA-HU-A4GX TCGA-MX-A5UJ TCGA-VQ-A8P2 
       20.25        19.73        38.14 

$`ITGAE WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A48C TCGA-CD-A4MG 
       12.43         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-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-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-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 

  ITGAE MUTATED ITGAE WILD-TYPE 
           0.26            0.00 
  ITGAE MUTATED ITGAE WILD-TYPE 
          38.14          122.30 
  ITGAE MUTATED ITGAE WILD-TYPE 
          19.73           14.07 
[1] "0.3 - 38.1 (19.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D756V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITGAE MUTATED         0        1        1        0         6         2
  ITGAE WILD-TYPE       2       14       39       30        31        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ITGAE MUTATED           0          2          1          1        0
  ITGAE WILD-TYPE         3         68         52         31       38
D756V3, multiclass
            clus
vv           ITGAE MUTATED ITGAE WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              6              31
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGAE MUTATED     1   4   7   3
  ITGAE WILD-TYPE  21  88 166  94
D756V4, multiclass
    clus
vv   ITGAE MUTATED ITGAE WILD-TYPE
  T1             1              21
  T2             4              88
  T3             7             166
  T4             3              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
  ITGAE MUTATED     7   4   2   1
  ITGAE WILD-TYPE 111 100  75  76
D756V5, multiclass
    clus
vv   ITGAE MUTATED ITGAE WILD-TYPE
  N0             7             111
  N1             4             100
  N2             2              75
  N3             1              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"
D756V6, binary
                 cls
clus                0   1
  ITGAE MUTATED    14   0
  ITGAE WILD-TYPE 332  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAE MUTATED     14    0
  ITGAE WILD-TYPE  332   29
   clus
vv  ITGAE MUTATED ITGAE WILD-TYPE
  0            14             332
  1             0              29
[1] 2 2
[1] FALSE
D756V7, binary
                 cls
clus                0   1
  ITGAE MUTATED     8   7
  ITGAE WILD-TYPE 137 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAE MUTATED      8    7
  ITGAE WILD-TYPE  137  241
        clus
vv       ITGAE MUTATED ITGAE WILD-TYPE
  FEMALE             8             137
  MALE               7             241
[1] 2 2
[1] FALSE
D756V8, binary
                 cls
clus                0   1
  ITGAE MUTATED    11   3
  ITGAE WILD-TYPE 281  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAE MUTATED     11    3
  ITGAE WILD-TYPE  281   56
     clus
vv    ITGAE MUTATED ITGAE WILD-TYPE
  NO             11             281
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ITGAE MUTATED                                          0
  ITGAE WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ITGAE MUTATED                                       1
  ITGAE WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ITGAE MUTATED                                                        9
  ITGAE WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ITGAE MUTATED                                                   1
  ITGAE WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ITGAE MUTATED                                                                   2
  ITGAE WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ITGAE MUTATED                                                    0
  ITGAE WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ITGAE MUTATED                                                  2
  ITGAE WILD-TYPE                                               59
D756V9, multiclass
                                                                   clus
vv                                                                  ITGAE MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  ITGAE WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ITGAE MUTATED    12   1   0   1
  ITGAE WILD-TYPE 299  13  15  23
D756V10, multiclass
    clus
vv   ITGAE MUTATED ITGAE WILD-TYPE
  R0            12             299
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D756V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ITGAE MUTATED       3                         0
  ITGAE WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ITGAE MUTATED                                           0    11
  ITGAE WILD-TYPE                                         1   232
D756V12, multiclass
                                           clus
vv                                          ITGAE MUTATED ITGAE WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D756V13, binary
                 cls
clus                0   1
  ITGAE MUTATED     0  13
  ITGAE WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAE MUTATED      0   13
  ITGAE WILD-TYPE    4  297
                        clus
vv                       ITGAE MUTATED ITGAE WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(757) Variable = KIF6 MUTATION ANALYSIS
D757V1, survival
                sevent
clus2              0   1
  KIF6 MUTATED     6   5
  KIF6 WILD-TYPE 224 134
  KIF6 MUTATED KIF6 WILD-TYPE 
            11            358 
  KIF6 MUTATED KIF6 WILD-TYPE 
             5            134 
$`KIF6 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-4257 TCGA-BR-4267 TCGA-BR-4279 
       18.35        30.90         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-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-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-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-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-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-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-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 

  KIF6 MUTATED KIF6 WILD-TYPE 
          4.08           0.00 
  KIF6 MUTATED KIF6 WILD-TYPE 
         45.67         122.30 
  KIF6 MUTATED KIF6 WILD-TYPE 
         11.77          14.35 
[1] "4.1 - 45.7 (11.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D757V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIF6 MUTATED         0        0        1        0         2         0
  KIF6 WILD-TYPE       2       15       39       30        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF6 MUTATED           0          2          3          1        1
  KIF6 WILD-TYPE         3         68         50         31       37
D757V3, multiclass
            clus
vv           KIF6 MUTATED KIF6 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            3             50
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KIF6 MUTATED     0   1   7   2
  KIF6 WILD-TYPE  22  91 166  95
D757V4, multiclass
    clus
vv   KIF6 MUTATED KIF6 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            7            166
  T4            2             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
  KIF6 MUTATED     3   5   3   1
  KIF6 WILD-TYPE 115  99  74  76
D757V5, multiclass
    clus
vv   KIF6 MUTATED KIF6 WILD-TYPE
  N0            3            115
  N1            5             99
  N2            3             74
  N3            1             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"
D757V6, binary
                cls
clus               0   1
  KIF6 MUTATED    11   1
  KIF6 WILD-TYPE 335  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  KIF6 MUTATED     11    1
  KIF6 WILD-TYPE  335   28
   clus
vv  KIF6 MUTATED KIF6 WILD-TYPE
  0           11            335
  1            1             28
[1] 2 2
[1] FALSE
D757V7, binary
                cls
clus               0   1
  KIF6 MUTATED     6   6
  KIF6 WILD-TYPE 139 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  KIF6 MUTATED      6    6
  KIF6 WILD-TYPE  139  242
        clus
vv       KIF6 MUTATED KIF6 WILD-TYPE
  FEMALE            6            139
  MALE              6            242
[1] 2 2
[1] FALSE
D757V8, binary
                cls
clus               0   1
  KIF6 MUTATED     9   2
  KIF6 WILD-TYPE 283  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  KIF6 MUTATED      9    2
  KIF6 WILD-TYPE  283   57
     clus
vv    KIF6 MUTATED KIF6 WILD-TYPE
  NO             9            283
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIF6 MUTATED                                          0
  KIF6 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIF6 MUTATED                                       1
  KIF6 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIF6 MUTATED                                                        7
  KIF6 WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIF6 MUTATED                                                   0
  KIF6 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIF6 MUTATED                                                                   0
  KIF6 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIF6 MUTATED                                                    0
  KIF6 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIF6 MUTATED                                                  4
  KIF6 WILD-TYPE                                               57
D757V9, multiclass
                                                                   clus
vv                                                                  KIF6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  KIF6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KIF6 MUTATED     7   0   0   3
  KIF6 WILD-TYPE 304  14  15  21
D757V10, multiclass
    clus
vv   KIF6 MUTATED KIF6 WILD-TYPE
  R0            7            304
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D757V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  KIF6 MUTATED       3                         1
  KIF6 WILD-TYPE    84                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIF6 MUTATED                                           0     8
  KIF6 WILD-TYPE                                         1   235
D757V12, multiclass
                                           clus
vv                                          KIF6 MUTATED KIF6 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D757V13, binary
                cls
clus               0   1
  KIF6 MUTATED     1  10
  KIF6 WILD-TYPE   3 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  KIF6 MUTATED      1   10
  KIF6 WILD-TYPE    3  300
                        clus
vv                       KIF6 MUTATED KIF6 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           10            300
[1] 2 2
[1] FALSE

Clustering(758) Variable = TNFSF13 MUTATION ANALYSIS
D758V1, survival
                   sevent
clus2                 0   1
  TNFSF13 MUTATED     3   0
  TNFSF13 WILD-TYPE 227 139
  TNFSF13 MUTATED TNFSF13 WILD-TYPE 
                3               366 
  TNFSF13 MUTATED TNFSF13 WILD-TYPE 
                0               139 
$`TNFSF13 MUTATED`
TCGA-B7-5816 TCGA-CG-5723 TCGA-HU-A4G8 
       26.70       105.07        22.68 

$`TNFSF13 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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 

  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             14.12 
[1] "22.7 - 105.1 (26.7)" "0.0 - 122.3 (14.1)" 
[1] "hr="     "9300000"
D758V2, 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       2       15       40       29        37        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFSF13 MUTATED           0          0          0          0        0
  TNFSF13 WILD-TYPE         3         70         53         32       38
D758V3, multiclass
            clus
vv           TNFSF13 MUTATED TNFSF13 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 1                29
  STAGE IIA                0                37
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TNFSF13 MUTATED     0   1   1   1
  TNFSF13 WILD-TYPE  22  91 172  96
D758V4, multiclass
    clus
vv   TNFSF13 MUTATED TNFSF13 WILD-TYPE
  T1               0                22
  T2               1                91
  T3               1               172
  T4               1                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
  TNFSF13 MUTATED     1   2   0   0
  TNFSF13 WILD-TYPE 117 102  77  77
D758V5, multiclass
    clus
vv   TNFSF13 MUTATED TNFSF13 WILD-TYPE
  N0               1               117
  N1               2               102
  N2               0                77
  N3               0                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"
D758V6, binary
                   cls
clus                  0   1
  TNFSF13 MUTATED     3   0
  TNFSF13 WILD-TYPE 343  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF13 MUTATED      3    0
  TNFSF13 WILD-TYPE  343   29
   clus
vv  TNFSF13 MUTATED TNFSF13 WILD-TYPE
  0               3               343
  1               0                29
[1] 2 2
[1] FALSE
D758V7, binary
                   cls
clus                  0   1
  TNFSF13 MUTATED     2   1
  TNFSF13 WILD-TYPE 143 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF13 MUTATED      2    1
  TNFSF13 WILD-TYPE  143  247
        clus
vv       TNFSF13 MUTATED TNFSF13 WILD-TYPE
  FEMALE               2               143
  MALE                 1               247
[1] 2 2
[1] FALSE
D758V8, binary
                   cls
clus                  0   1
  TNFSF13 MUTATED     3   0
  TNFSF13 WILD-TYPE 289  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF13 MUTATED      3    0
  TNFSF13 WILD-TYPE  289   59
     clus
vv    TNFSF13 MUTATED TNFSF13 WILD-TYPE
  NO                3               289
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TNFSF13 MUTATED                                          0
  TNFSF13 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TNFSF13 MUTATED                                       2
  TNFSF13 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNFSF13 MUTATED                                                        1
  TNFSF13 WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TNFSF13 MUTATED                                                   0
  TNFSF13 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNFSF13 MUTATED                                                                   0
  TNFSF13 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TNFSF13 MUTATED                                                    0
  TNFSF13 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TNFSF13 MUTATED                                                  0
  TNFSF13 WILD-TYPE                                               61
D758V9, multiclass
                                                                   clus
vv                                                                  TNFSF13 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  TNFSF13 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TNFSF13 MUTATED     2   0   0   0
  TNFSF13 WILD-TYPE 309  14  15  24
D758V10, multiclass
[1] "Remove cluster labels:" "TNFSF13 MUTATED"       
clus
  TNFSF13 MUTATED TNFSF13 WILD-TYPE 
                2               362 
       TCGA-CG-4444        TCGA-CG-4460        TCGA-CG-4475        TCGA-CG-4476 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5727        TCGA-EQ-A4SO        TCGA-F1-6177 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-FP-A8CX        TCGA-HF-7131        TCGA-KB-A93G        TCGA-MX-A663 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184        TCGA-BR-4187 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4363 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4368        TCGA-BR-4369        TCGA-BR-4370 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4371        TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958        TCGA-BR-7959 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8058        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8297        TCGA-BR-8360        TCGA-BR-8361 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8363        TCGA-BR-8364        TCGA-BR-8365        TCGA-BR-8366 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8367        TCGA-BR-8368        TCGA-BR-8369        TCGA-BR-8370 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8371        TCGA-BR-8372        TCGA-BR-8373        TCGA-BR-8380 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8381        TCGA-BR-8382        TCGA-BR-8384        TCGA-BR-8483 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8484        TCGA-BR-8485        TCGA-BR-8486        TCGA-BR-8487 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8588        TCGA-BR-8589        TCGA-BR-8590        TCGA-BR-8591 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-8676        TCGA-BR-8677        TCGA-BR-8678 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8679        TCGA-BR-8680        TCGA-BR-8682        TCGA-BR-8683 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8686        TCGA-BR-8687        TCGA-BR-8690        TCGA-BR-A44T 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A44U        TCGA-BR-A452        TCGA-BR-A453        TCGA-BR-A4CQ 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4CR        TCGA-BR-A4CS        TCGA-BR-A4IU        TCGA-BR-A4IV 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4IY        TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4J4        TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J7 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4J8        TCGA-BR-A4PD        TCGA-BR-A4PE        TCGA-BR-A4PF 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-BR-A4QM        TCGA-CD-5800 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5804        TCGA-CD-8524        TCGA-CD-8525 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-8526        TCGA-CD-8527        TCGA-CD-8528        TCGA-CD-8529 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-8530        TCGA-CD-8531        TCGA-CD-8532        TCGA-CD-8533 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-8534        TCGA-CD-8535        TCGA-CD-8536        TCGA-CD-A487 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4462        TCGA-CG-4465 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4477 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5724        TCGA-CG-5725 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-8570        TCGA-D7-8572        TCGA-D7-8573        TCGA-D7-8574 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-8575        TCGA-D7-8576        TCGA-D7-8578        TCGA-D7-8579 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-A4YT        TCGA-D7-A4YU        TCGA-D7-A4YV        TCGA-D7-A4YX 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-A4YY        TCGA-D7-A4Z0        TCGA-D7-A6ET        TCGA-D7-A6EV 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-A6EX        TCGA-D7-A6EY        TCGA-D7-A6EZ        TCGA-D7-A6F0 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-A6F2        TCGA-D7-A747        TCGA-D7-A748        TCGA-D7-A74A 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-A74B        TCGA-EQ-5647        TCGA-F1-6874        TCGA-F1-6875 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-F1-A448        TCGA-F1-A72C        TCGA-FP-7735        TCGA-FP-7829 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        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-HF-7132        TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HF-A5NB        TCGA-HJ-7597        TCGA-HU-8238        TCGA-HU-8243 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-8244        TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-8608        TCGA-HU-8610        TCGA-HU-A4G2        TCGA-HU-A4G3 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4G6        TCGA-HU-A4G9        TCGA-HU-A4GC        TCGA-HU-A4GD 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4GF        TCGA-HU-A4GH        TCGA-HU-A4GJ        TCGA-HU-A4GN 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4GP        TCGA-HU-A4GQ        TCGA-HU-A4GT        TCGA-HU-A4GU 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4GX        TCGA-HU-A4GY        TCGA-HU-A4H0        TCGA-HU-A4H2 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4H3        TCGA-HU-A4H4        TCGA-HU-A4H5        TCGA-HU-A4H6 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4H8        TCGA-HU-A4HB        TCGA-HU-A4HD        TCGA-IN-7806 
"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-A6F5        TCGA-KB-A6F7        TCGA-KB-A93J        TCGA-MX-A5UG 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-MX-A5UJ        TCGA-R5-A7ZI        TCGA-RD-A7BS        TCGA-RD-A7BT 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-RD-A7BW        TCGA-RD-A7C1        TCGA-RD-A8MV        TCGA-RD-A8MW 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-RD-A8N0        TCGA-RD-A8N1        TCGA-RD-A8N2        TCGA-RD-A8N4 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-RD-A8N5        TCGA-RD-A8N6        TCGA-RD-A8N9        TCGA-SW-A7EA 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-SW-A7EB        TCGA-VQ-A8DL        TCGA-VQ-A8DT        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-A91Q        TCGA-VQ-A91U 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-A91V        TCGA-VQ-A92D        TCGA-VQ-A94T        TCGA-VQ-AA64 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-AA68        TCGA-VQ-AA69        TCGA-VQ-AA6A        TCGA-VQ-AA6B 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-AA6F        TCGA-VQ-AA6G        TCGA-VQ-AA6I        TCGA-VQ-AA6J 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-AA6K        TCGA-ZA-A8F6 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
D758V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TNFSF13 MUTATED       1                         0
  TNFSF13 WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNFSF13 MUTATED                                           0     1
  TNFSF13 WILD-TYPE                                         1   242
D758V12, multiclass
[1] "Remove cluster labels:" "TNFSF13 MUTATED"       
clus
  TNFSF13 MUTATED TNFSF13 WILD-TYPE 
                2               338 
       TCGA-EQ-A4SO        TCGA-F1-6177        TCGA-FP-A8CX        TCGA-KB-A93G 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-MX-A663        TCGA-B7-5818        TCGA-B7-A5TI        TCGA-B7-A5TJ 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-B7-A5TK        TCGA-B7-A5TN        TCGA-BR-4183        TCGA-BR-4184 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4368        TCGA-BR-4369 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452        TCGA-BR-6453 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-7959        TCGA-BR-8058        TCGA-BR-8059        TCGA-BR-8060 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8297        TCGA-BR-8360 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8361        TCGA-BR-8363        TCGA-BR-8364        TCGA-BR-8365 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8366        TCGA-BR-8367        TCGA-BR-8368        TCGA-BR-8369 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8370        TCGA-BR-8371        TCGA-BR-8372        TCGA-BR-8373 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8380        TCGA-BR-8381        TCGA-BR-8382        TCGA-BR-8384 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8483        TCGA-BR-8484        TCGA-BR-8485        TCGA-BR-8486 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8487        TCGA-BR-8588        TCGA-BR-8589        TCGA-BR-8590 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8591        TCGA-BR-8592        TCGA-BR-8676        TCGA-BR-8677 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8678        TCGA-BR-8679        TCGA-BR-8680        TCGA-BR-8682 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-8683        TCGA-BR-8686        TCGA-BR-8687        TCGA-BR-8690 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A44T        TCGA-BR-A44U        TCGA-BR-A452        TCGA-BR-A453 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4CQ        TCGA-BR-A4CR        TCGA-BR-A4CS        TCGA-BR-A4IU 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ        TCGA-BR-A4J1 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J5        TCGA-BR-A4J6 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4J7        TCGA-BR-A4J8        TCGA-BR-A4PD        TCGA-BR-A4PE 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-BR-A4QM 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804        TCGA-CD-5813 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-8524        TCGA-CD-8525        TCGA-CD-8526        TCGA-CD-8527 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-8528        TCGA-CD-8529        TCGA-CD-8530        TCGA-CD-8531 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-8532        TCGA-CD-8533        TCGA-CD-8534        TCGA-CD-8535 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-8536        TCGA-CD-A486        TCGA-CD-A487        TCGA-CD-A489 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-A48A        TCGA-CD-A48C        TCGA-CD-A4MG        TCGA-CD-A4MH 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-CD-A4MI        TCGA-CD-A4MJ        TCGA-D7-5577        TCGA-D7-5578 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-8570        TCGA-D7-8572        TCGA-D7-8573        TCGA-D7-8574 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-8575        TCGA-D7-8576        TCGA-D7-8578        TCGA-D7-8579 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-A4YT        TCGA-D7-A4YU        TCGA-D7-A4YV        TCGA-D7-A4YX 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-A4YY        TCGA-D7-A4Z0        TCGA-D7-A6ET        TCGA-D7-A6EV 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-A6EX        TCGA-D7-A6EY        TCGA-D7-A6EZ        TCGA-D7-A6F0 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-A6F2        TCGA-D7-A747        TCGA-D7-A748        TCGA-D7-A74A 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-D7-A74B        TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6874 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-F1-6875        TCGA-F1-A448        TCGA-F1-A72C        TCGA-FP-7735 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-FP-A4BE        TCGA-FP-A4BF        TCGA-FP-A9TM        TCGA-HJ-7597 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-8238        TCGA-HU-8243        TCGA-HU-8244        TCGA-HU-8249 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-8602        TCGA-HU-8604        TCGA-HU-8608        TCGA-HU-8610 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4G2        TCGA-HU-A4G3        TCGA-HU-A4G6        TCGA-HU-A4G9 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4GC        TCGA-HU-A4GD        TCGA-HU-A4GF        TCGA-HU-A4GH 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4GJ        TCGA-HU-A4GN        TCGA-HU-A4GP        TCGA-HU-A4GQ 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4GT        TCGA-HU-A4GU        TCGA-HU-A4GX        TCGA-HU-A4GY 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4H0        TCGA-HU-A4H2        TCGA-HU-A4H3        TCGA-HU-A4H4 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4H5        TCGA-HU-A4H6        TCGA-HU-A4H8        TCGA-HU-A4HB 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-HU-A4HD        TCGA-IN-7806        TCGA-IN-7808        TCGA-IN-8462 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-IN-8663        TCGA-IN-A6RI        TCGA-IN-A6RJ        TCGA-IN-A6RL 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-IN-A6RN        TCGA-IN-A6RO        TCGA-IN-A6RP        TCGA-IN-A6RR 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-IN-A6RS        TCGA-IN-A7NR        TCGA-IN-A7NT        TCGA-IN-A7NU 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-IN-AB1V        TCGA-IN-AB1X        TCGA-IP-7968        TCGA-KB-A93J 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-MX-A5UG        TCGA-MX-A5UJ        TCGA-MX-A666        TCGA-R5-A7O7 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-R5-A7ZE        TCGA-R5-A7ZF        TCGA-R5-A7ZI        TCGA-R5-A7ZR 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-R5-A804        TCGA-R5-A805        TCGA-RD-A7BS        TCGA-RD-A7BT 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-RD-A7BW        TCGA-RD-A7C1        TCGA-RD-A8MV        TCGA-RD-A8MW 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-RD-A8N0        TCGA-RD-A8N1        TCGA-RD-A8N2        TCGA-RD-A8N4 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-RD-A8N5        TCGA-RD-A8N6        TCGA-RD-A8N9        TCGA-SW-A7EA 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-SW-A7EB        TCGA-VQ-A8DL        TCGA-VQ-A8DU        TCGA-VQ-A8DV 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-A8DZ        TCGA-VQ-A8E2        TCGA-VQ-A8E7        TCGA-VQ-A8P2 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-A8P3        TCGA-VQ-A8PE        TCGA-VQ-A8PK        TCGA-VQ-A8PM 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-A8PQ        TCGA-VQ-A91U        TCGA-VQ-A92D        TCGA-VQ-AA64 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-AA68        TCGA-VQ-AA69        TCGA-VQ-AA6A        TCGA-VQ-AA6B 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-AA6F        TCGA-VQ-AA6G        TCGA-VQ-AA6I        TCGA-VQ-AA6J 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
       TCGA-VQ-AA6K        TCGA-ZA-A8F6 
"TNFSF13 WILD-TYPE" "TNFSF13 WILD-TYPE" 
D758V13, binary
                   cls
clus                  0   1
  TNFSF13 MUTATED     0   2
  TNFSF13 WILD-TYPE   4 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFSF13 MUTATED      0    2
  TNFSF13 WILD-TYPE    4  308
                        clus
vv                       TNFSF13 MUTATED TNFSF13 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               2               308
[1] 2 2
[1] FALSE

Clustering(759) Variable = CASKIN2 MUTATION ANALYSIS
D759V1, survival
                   sevent
clus2                 0   1
  CASKIN2 MUTATED     8   5
  CASKIN2 WILD-TYPE 222 134
  CASKIN2 MUTATED CASKIN2 WILD-TYPE 
               13               356 
  CASKIN2 MUTATED CASKIN2 WILD-TYPE 
                5               134 
$`CASKIN2 MUTATED`
TCGA-BR-6852 TCGA-BR-8059 TCGA-BR-8591 TCGA-CG-4441 TCGA-CG-5718 TCGA-CG-5725 
       44.94        14.43        28.14        14.01        36.00        15.02 
TCGA-D7-5578 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-IN-AB1X TCGA-VQ-A8PM 
       12.66        30.51        22.32        22.68        13.51         1.87 
TCGA-VQ-AA6J 
       27.55 

$`CASKIN2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-D7-5579 TCGA-D7-6518 
       69.04        21.07         7.99        25.71        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-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-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-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-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-AA6K TCGA-ZA-A8F6 
       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 
            22.32             14.07 
[1] "1.9 - 44.9 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D759V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CASKIN2 MUTATED         1        0        1        1         2         2
  CASKIN2 WILD-TYPE       1       15       39       29        35        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASKIN2 MUTATED           1          2          1          2        1
  CASKIN2 WILD-TYPE         2         68         52         30       37
D759V3, multiclass
            clus
vv           CASKIN2 MUTATED CASKIN2 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                2                35
  STAGE IIB                2                50
  STAGE III                1                 2
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               2                30
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CASKIN2 MUTATED     1   3   5   6
  CASKIN2 WILD-TYPE  21  89 168  91
D759V4, multiclass
    clus
vv   CASKIN2 MUTATED CASKIN2 WILD-TYPE
  T1               1                21
  T2               3                89
  T3               5               168
  T4               6                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
  CASKIN2 MUTATED     4   4   3   3
  CASKIN2 WILD-TYPE 114 100  74  74
D759V5, multiclass
    clus
vv   CASKIN2 MUTATED CASKIN2 WILD-TYPE
  N0               4               114
  N1               4               100
  N2               3                74
  N3               3                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"
D759V6, binary
                   cls
clus                  0   1
  CASKIN2 MUTATED    13   0
  CASKIN2 WILD-TYPE 333  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CASKIN2 MUTATED     13    0
  CASKIN2 WILD-TYPE  333   29
   clus
vv  CASKIN2 MUTATED CASKIN2 WILD-TYPE
  0              13               333
  1               0                29
[1] 2 2
[1] FALSE
D759V7, binary
                   cls
clus                  0   1
  CASKIN2 MUTATED     7   8
  CASKIN2 WILD-TYPE 138 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CASKIN2 MUTATED      7    8
  CASKIN2 WILD-TYPE  138  240
        clus
vv       CASKIN2 MUTATED CASKIN2 WILD-TYPE
  FEMALE               7               138
  MALE                 8               240
[1] 2 2
[1] FALSE
D759V8, binary
                   cls
clus                  0   1
  CASKIN2 MUTATED    12   1
  CASKIN2 WILD-TYPE 280  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CASKIN2 MUTATED     12    1
  CASKIN2 WILD-TYPE  280   58
     clus
vv    CASKIN2 MUTATED CASKIN2 WILD-TYPE
  NO               12               280
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CASKIN2 MUTATED                                          1
  CASKIN2 WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CASKIN2 MUTATED                                       2
  CASKIN2 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CASKIN2 MUTATED                                                        6
  CASKIN2 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CASKIN2 MUTATED                                                   1
  CASKIN2 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CASKIN2 MUTATED                                                                   4
  CASKIN2 WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CASKIN2 MUTATED                                                    0
  CASKIN2 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CASKIN2 MUTATED                                                  1
  CASKIN2 WILD-TYPE                                               60
D759V9, multiclass
                                                                   clus
vv                                                                  CASKIN2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  CASKIN2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CASKIN2 MUTATED    12   1   0   1
  CASKIN2 WILD-TYPE 299  13  15  23
D759V10, multiclass
    clus
vv   CASKIN2 MUTATED CASKIN2 WILD-TYPE
  R0              12               299
  R1               1                13
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D759V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CASKIN2 MUTATED       2                         2
  CASKIN2 WILD-TYPE    85                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CASKIN2 MUTATED                                           0     7
  CASKIN2 WILD-TYPE                                         1   236
D759V12, multiclass
                                           clus
vv                                          CASKIN2 MUTATED CASKIN2 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               2                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D759V13, binary
                   cls
clus                  0   1
  CASKIN2 MUTATED     0   9
  CASKIN2 WILD-TYPE   4 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CASKIN2 MUTATED      0    9
  CASKIN2 WILD-TYPE    4  301
                        clus
vv                       CASKIN2 MUTATED CASKIN2 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               9               301
[1] 2 2
[1] FALSE

Clustering(760) Variable = ALPK1 MUTATION ANALYSIS
D760V1, survival
                 sevent
clus2               0   1
  ALPK1 MUTATED    13   5
  ALPK1 WILD-TYPE 217 134
  ALPK1 MUTATED ALPK1 WILD-TYPE 
             18             351 
  ALPK1 MUTATED ALPK1 WILD-TYPE 
              5             134 
$`ALPK1 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8361 
       26.70        30.90        34.68        44.94        32.25        31.10 
TCGA-BR-8487 TCGA-CD-8531 TCGA-CD-A48C TCGA-CG-5728 TCGA-D7-A4YV TCGA-D7-A6EY 
        1.12        12.59        11.61        65.10         5.92        11.44 
TCGA-F1-A448 TCGA-HF-7134 TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-VQ-A8P2 
       21.27        52.21         8.98         0.10        20.25        38.14 

$`ALPK1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       21.37        29.98         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 

  ALPK1 MUTATED ALPK1 WILD-TYPE 
            0.1             0.0 
  ALPK1 MUTATED ALPK1 WILD-TYPE 
           65.1           122.3 
  ALPK1 MUTATED ALPK1 WILD-TYPE 
         23.985          14.070 
[1] "0.1 - 65.1 (24.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D760V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ALPK1 MUTATED         1        1        1        0         4         4
  ALPK1 WILD-TYPE       1       14       39       30        33        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ALPK1 MUTATED           0          2          2          3        0
  ALPK1 WILD-TYPE         3         68         51         29       38
D760V3, multiclass
            clus
vv           ALPK1 MUTATED ALPK1 WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              4              33
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             3              29
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALPK1 MUTATED     2   3   8   6
  ALPK1 WILD-TYPE  20  89 165  91
D760V4, multiclass
    clus
vv   ALPK1 MUTATED ALPK1 WILD-TYPE
  T1             2              20
  T2             3              89
  T3             8             165
  T4             6              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
  ALPK1 MUTATED     7   6   3   2
  ALPK1 WILD-TYPE 111  98  74  75
D760V5, multiclass
    clus
vv   ALPK1 MUTATED ALPK1 WILD-TYPE
  N0             7             111
  N1             6              98
  N2             3              74
  N3             2              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"
D760V6, binary
                 cls
clus                0   1
  ALPK1 MUTATED    18   0
  ALPK1 WILD-TYPE 328  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK1 MUTATED     18    0
  ALPK1 WILD-TYPE  328   29
   clus
vv  ALPK1 MUTATED ALPK1 WILD-TYPE
  0            18             328
  1             0              29
[1] 2 2
[1] FALSE
D760V7, binary
                 cls
clus                0   1
  ALPK1 MUTATED    14   5
  ALPK1 WILD-TYPE 131 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK1 MUTATED     14    5
  ALPK1 WILD-TYPE  131  243
        clus
vv       ALPK1 MUTATED ALPK1 WILD-TYPE
  FEMALE            14             131
  MALE               5             243
[1] 2 2
[1] FALSE
D760V8, binary
                 cls
clus                0   1
  ALPK1 MUTATED    15   3
  ALPK1 WILD-TYPE 277  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK1 MUTATED     15    3
  ALPK1 WILD-TYPE  277   56
     clus
vv    ALPK1 MUTATED ALPK1 WILD-TYPE
  NO             15             277
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ALPK1 MUTATED                                          0
  ALPK1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ALPK1 MUTATED                                       4
  ALPK1 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ALPK1 MUTATED                                                        8
  ALPK1 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ALPK1 MUTATED                                                   2
  ALPK1 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ALPK1 MUTATED                                                                   2
  ALPK1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ALPK1 MUTATED                                                    0
  ALPK1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ALPK1 MUTATED                                                  3
  ALPK1 WILD-TYPE                                               58
D760V9, multiclass
                                                                   clus
vv                                                                  ALPK1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  ALPK1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ALPK1 MUTATED    17   0   0   1
  ALPK1 WILD-TYPE 294  14  15  23
D760V10, multiclass
    clus
vv   ALPK1 MUTATED ALPK1 WILD-TYPE
  R0            17             294
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D760V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ALPK1 MUTATED       5                         1
  ALPK1 WILD-TYPE    82                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ALPK1 MUTATED                                           0    11
  ALPK1 WILD-TYPE                                         1   232
D760V12, multiclass
                                           clus
vv                                          ALPK1 MUTATED ALPK1 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D760V13, binary
                 cls
clus                0   1
  ALPK1 MUTATED     1  15
  ALPK1 WILD-TYPE   3 295
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK1 MUTATED      1   15
  ALPK1 WILD-TYPE    3  295
                        clus
vv                       ALPK1 MUTATED ALPK1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            15             295
[1] 2 2
[1] FALSE

Clustering(761) Variable = SUCLG2 MUTATION ANALYSIS
D761V1, survival
                  sevent
clus2                0   1
  SUCLG2 MUTATED     2   3
  SUCLG2 WILD-TYPE 228 136
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
               5              364 
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
               3              136 
$`SUCLG2 MUTATED`
TCGA-CG-4460 TCGA-BR-A4QL TCGA-CG-5723 TCGA-D7-A6EY TCGA-HU-A4H8 
       21.99        16.14       105.07        11.44        14.07 

$`SUCLG2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
           11.44             0.00 
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
          105.07           122.30 
  SUCLG2 MUTATED SUCLG2 WILD-TYPE 
           16.14            14.22 
[1] "11.4 - 105.1 (16.1)" "0.0 - 122.3 (14.2)" 
[1] "hr=" "1.2"
D761V2, 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       1       15       39       29        37        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SUCLG2 MUTATED           0          1          2          0        1
  SUCLG2 WILD-TYPE         3         69         51         32       37
D761V3, multiclass
            clus
vv           SUCLG2 MUTATED SUCLG2 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               0               37
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              2               51
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SUCLG2 MUTATED     2   1   2   2
  SUCLG2 WILD-TYPE  20  91 171  95
D761V4, multiclass
    clus
vv   SUCLG2 MUTATED SUCLG2 WILD-TYPE
  T1              2               20
  T2              1               91
  T3              2              171
  T4              2               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
  SUCLG2 MUTATED     1   4   0   2
  SUCLG2 WILD-TYPE 117 100  77  75
D761V5, multiclass
    clus
vv   SUCLG2 MUTATED SUCLG2 WILD-TYPE
  N0              1              117
  N1              4              100
  N2              0               77
  N3              2               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"
D761V6, binary
                  cls
clus                 0   1
  SUCLG2 MUTATED     5   1
  SUCLG2 WILD-TYPE 341  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCLG2 MUTATED      5    1
  SUCLG2 WILD-TYPE  341   28
   clus
vv  SUCLG2 MUTATED SUCLG2 WILD-TYPE
  0              5              341
  1              1               28
[1] 2 2
[1] FALSE
D761V7, binary
                  cls
clus                 0   1
  SUCLG2 MUTATED     4   3
  SUCLG2 WILD-TYPE 141 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCLG2 MUTATED      4    3
  SUCLG2 WILD-TYPE  141  245
        clus
vv       SUCLG2 MUTATED SUCLG2 WILD-TYPE
  FEMALE              4              141
  MALE                3              245
[1] 2 2
[1] FALSE
D761V8, binary
                  cls
clus                 0   1
  SUCLG2 MUTATED     6   0
  SUCLG2 WILD-TYPE 286  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCLG2 MUTATED      6    0
  SUCLG2 WILD-TYPE  286   59
     clus
vv    SUCLG2 MUTATED SUCLG2 WILD-TYPE
  NO               6              286
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SUCLG2 MUTATED                                          0
  SUCLG2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SUCLG2 MUTATED                                       0
  SUCLG2 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SUCLG2 MUTATED                                                        4
  SUCLG2 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SUCLG2 MUTATED                                                   0
  SUCLG2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SUCLG2 MUTATED                                                                   1
  SUCLG2 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SUCLG2 MUTATED                                                    0
  SUCLG2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SUCLG2 MUTATED                                                  2
  SUCLG2 WILD-TYPE                                               59
D761V9, multiclass
                                                                   clus
vv                                                                  SUCLG2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  SUCLG2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SUCLG2 MUTATED     5   0   1   1
  SUCLG2 WILD-TYPE 306  14  14  23
D761V10, multiclass
    clus
vv   SUCLG2 MUTATED SUCLG2 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D761V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SUCLG2 MUTATED       1                         1
  SUCLG2 WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SUCLG2 MUTATED                                           0     3
  SUCLG2 WILD-TYPE                                         1   240
D761V12, multiclass
                                           clus
vv                                          SUCLG2 MUTATED SUCLG2 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D761V13, binary
                  cls
clus                 0   1
  SUCLG2 MUTATED     0   5
  SUCLG2 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCLG2 MUTATED      0    5
  SUCLG2 WILD-TYPE    4  305
                        clus
vv                       SUCLG2 MUTATED SUCLG2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(762) Variable = NOS1 MUTATION ANALYSIS
D762V1, survival
                sevent
clus2              0   1
  NOS1 MUTATED    19   8
  NOS1 WILD-TYPE 211 131
  NOS1 MUTATED NOS1 WILD-TYPE 
            27            342 
  NOS1 MUTATED NOS1 WILD-TYPE 
             8            131 
$`NOS1 MUTATED`
TCGA-CG-4460 TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8078 TCGA-BR-8361 
       21.99        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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        26.70        11.70        19.56         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-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-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-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-8686 TCGA-BR-8687 
        7.53        26.73        24.79        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-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17        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-D7-5578 
       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-D7-8578 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-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-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       22.68         3.25        22.75        25.81        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-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-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 

  NOS1 MUTATED NOS1 WILD-TYPE 
          0.53           0.00 
  NOS1 MUTATED NOS1 WILD-TYPE 
        105.07         122.30 
  NOS1 MUTATED NOS1 WILD-TYPE 
         21.99          14.04 
[1] "0.5 - 105.1 (22.0)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.6"
D762V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOS1 MUTATED         0        2        3        1         1         4
  NOS1 WILD-TYPE       2       13       37       29        36        48
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOS1 MUTATED           0          4          6          3        5
  NOS1 WILD-TYPE         3         66         47         29       33
D762V3, multiclass
            clus
vv           NOS1 MUTATED NOS1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              2             13
  STAGE IB              3             37
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             4             48
  STAGE III             0              3
  STAGE IIIA            4             66
  STAGE IIIB            6             47
  STAGE IIIC            3             29
  STAGE IV              5             33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOS1 MUTATED     4   5   6  16
  NOS1 WILD-TYPE  18  87 167  81
D762V4, multiclass
    clus
vv   NOS1 MUTATED NOS1 WILD-TYPE
  T1            4             18
  T2            5             87
  T3            6            167
  T4           16             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"
                vv
clus              N0  N1  N2  N3
  NOS1 MUTATED     8   9   5   6
  NOS1 WILD-TYPE 110  95  72  71
D762V5, multiclass
    clus
vv   NOS1 MUTATED NOS1 WILD-TYPE
  N0            8            110
  N1            9             95
  N2            5             72
  N3            6             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"
D762V6, binary
                cls
clus               0   1
  NOS1 MUTATED    27   3
  NOS1 WILD-TYPE 319  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS1 MUTATED     27    3
  NOS1 WILD-TYPE  319   26
   clus
vv  NOS1 MUTATED NOS1 WILD-TYPE
  0           27            319
  1            3             26
[1] 2 2
[1] FALSE
D762V7, binary
                cls
clus               0   1
  NOS1 MUTATED    16  15
  NOS1 WILD-TYPE 129 233
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS1 MUTATED     16   15
  NOS1 WILD-TYPE  129  233
        clus
vv       NOS1 MUTATED NOS1 WILD-TYPE
  FEMALE           16            129
  MALE             15            233
[1] 2 2
[1] FALSE
D762V8, binary
                cls
clus               0   1
  NOS1 MUTATED    25   1
  NOS1 WILD-TYPE 267  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS1 MUTATED     25    1
  NOS1 WILD-TYPE  267   58
     clus
vv    NOS1 MUTATED NOS1 WILD-TYPE
  NO            25            267
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NOS1 MUTATED                                          0
  NOS1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NOS1 MUTATED                                       4
  NOS1 WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NOS1 MUTATED                                                       14
  NOS1 WILD-TYPE                                                    144
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NOS1 MUTATED                                                   1
  NOS1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NOS1 MUTATED                                                                   4
  NOS1 WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NOS1 MUTATED                                                    0
  NOS1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NOS1 MUTATED                                                  8
  NOS1 WILD-TYPE                                               53
D762V9, multiclass
                                                                   clus
vv                                                                  NOS1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             8
                                                                   clus
vv                                                                  NOS1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              53
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NOS1 MUTATED    24   0   1   5
  NOS1 WILD-TYPE 287  14  14  19
D762V10, multiclass
    clus
vv   NOS1 MUTATED NOS1 WILD-TYPE
  R0           24            287
  R1            0             14
  R2            1             14
  RX            5             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D762V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NOS1 MUTATED       8                         0
  NOS1 WILD-TYPE    79                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOS1 MUTATED                                           0    19
  NOS1 WILD-TYPE                                         1   224
D762V12, multiclass
                                           clus
vv                                          NOS1 MUTATED NOS1 WILD-TYPE
  ASIAN                                                8             79
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               19            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D762V13, binary
                cls
clus               0   1
  NOS1 MUTATED     1  25
  NOS1 WILD-TYPE   3 285
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS1 MUTATED      1   25
  NOS1 WILD-TYPE    3  285
                        clus
vv                       NOS1 MUTATED NOS1 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           25            285
[1] 2 2
[1] FALSE

Clustering(763) Variable = SLA MUTATION ANALYSIS
D763V1, survival
               sevent
clus2             0   1
  SLA MUTATED     5   1
  SLA WILD-TYPE 225 138
  SLA MUTATED SLA WILD-TYPE 
            6           363 
  SLA MUTATED SLA WILD-TYPE 
            1           138 
$`SLA MUTATED`
TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 TCGA-CG-5728 TCGA-D7-A6EY TCGA-HU-8602 
       34.68        35.84         1.12        65.10        11.44        22.32 

$`SLA WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  SLA MUTATED SLA WILD-TYPE 
         1.12          0.00 
  SLA MUTATED SLA WILD-TYPE 
         65.1         122.3 
  SLA MUTATED SLA WILD-TYPE 
        28.50         14.17 
[1] "1.1 - 65.1 (28.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3.1"
D763V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLA MUTATED         0        0        2        0         2         1
  SLA WILD-TYPE       2       15       38       30        35        51
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLA MUTATED           0          0          1          0        0
  SLA WILD-TYPE         3         70         52         32       38
D763V3, multiclass
            clus
vv           SLA MUTATED SLA WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             2            38
  STAGE II             0            30
  STAGE IIA            2            35
  STAGE IIB            1            51
  STAGE III            0             3
  STAGE IIIA           0            70
  STAGE IIIB           1            52
  STAGE IIIC           0            32
  STAGE IV             0            38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SLA MUTATED     0   2   3   1
  SLA WILD-TYPE  22  90 170  96
D763V4, multiclass
    clus
vv   SLA MUTATED SLA WILD-TYPE
  T1           0            22
  T2           2            90
  T3           3           170
  T4           1            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
  SLA MUTATED     5   0   0   1
  SLA WILD-TYPE 113 104  77  76
D763V5, multiclass
    clus
vv   SLA MUTATED SLA WILD-TYPE
  N0           5           113
  N1           0           104
  N2           0            77
  N3           1            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"
D763V6, binary
               cls
clus              0   1
  SLA MUTATED     6   0
  SLA WILD-TYPE 340  29
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLA MUTATED      6    0
  SLA WILD-TYPE  340   29
   clus
vv  SLA MUTATED SLA WILD-TYPE
  0           6           340
  1           0            29
[1] 2 2
[1] FALSE
D763V7, binary
               cls
clus              0   1
  SLA MUTATED     6   0
  SLA WILD-TYPE 139 248
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLA MUTATED      6    0
  SLA WILD-TYPE  139  248
        clus
vv       SLA MUTATED SLA WILD-TYPE
  FEMALE           6           139
  MALE             0           248
[1] 2 2
[1] FALSE
D763V8, binary
               cls
clus              0   1
  SLA MUTATED     5   0
  SLA WILD-TYPE 287  59
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLA MUTATED      5    0
  SLA WILD-TYPE  287   59
     clus
vv    SLA MUTATED SLA WILD-TYPE
  NO            5           287
  YES           0            59
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLA MUTATED                                          0
  SLA WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLA MUTATED                                       1
  SLA WILD-TYPE                                    69
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLA MUTATED                                                        3
  SLA WILD-TYPE                                                    155
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLA MUTATED                                                   0
  SLA WILD-TYPE                                                21
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLA MUTATED                                                                   1
  SLA WILD-TYPE                                                                67
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLA MUTATED                                                    0
  SLA WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLA MUTATED                                                  1
  SLA WILD-TYPE                                               60
D763V9, multiclass
                                                                   clus
vv                                                                  SLA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            1
                                                                   clus
vv                                                                  SLA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  SLA MUTATED     6   0   0   0
  SLA WILD-TYPE 305  14  15  24
D763V10, multiclass
    clus
vv   SLA MUTATED SLA WILD-TYPE
  R0           6           305
  R1           0            14
  R2           0            15
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D763V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  SLA MUTATED       1                         0
  SLA WILD-TYPE    86                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLA MUTATED                                           0     4
  SLA WILD-TYPE                                         1   239
D763V12, multiclass
                                           clus
vv                                          SLA MUTATED SLA WILD-TYPE
  ASIAN                                               1            86
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               4           239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D763V13, binary
               cls
clus              0   1
  SLA MUTATED     0   5
  SLA WILD-TYPE   4 305
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLA MUTATED      0    5
  SLA WILD-TYPE    4  305
                        clus
vv                       SLA MUTATED SLA WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           5           305
[1] 2 2
[1] FALSE

Clustering(764) Variable = C9ORF98 MUTATION ANALYSIS
D764V1, survival
                   sevent
clus2                 0   1
  C9ORF98 MUTATED     7   1
  C9ORF98 WILD-TYPE 223 138
  C9ORF98 MUTATED C9ORF98 WILD-TYPE 
                8               361 
  C9ORF98 MUTATED C9ORF98 WILD-TYPE 
                1               138 
$`C9ORF98 MUTATED`
TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-8535 TCGA-CD-8536 TCGA-CG-4306 TCGA-CG-5723 
        1.12        28.14        12.82        12.43         1.02       105.07 
TCGA-HU-A4G9 TCGA-HU-A4H8 
       24.20        14.07 

$`C9ORF98 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-A486 
       12.39        12.59        11.64        15.39        12.07         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-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-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 

  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            14.430 
[1] "1.0 - 105.1 (13.4)" "0.0 - 122.3 (14.4)"
[1] "hr=" "3.3"
D764V2, 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       2       14       39       28        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF98 MUTATED           0          1          0          1        1
  C9ORF98 WILD-TYPE         3         69         53         31       37
D764V3, multiclass
            clus
vv           C9ORF98 MUTATED C9ORF98 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 2                28
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C9ORF98 MUTATED     2   1   5   1
  C9ORF98 WILD-TYPE  20  91 168  96
D764V4, multiclass
    clus
vv   C9ORF98 MUTATED C9ORF98 WILD-TYPE
  T1               2                20
  T2               1                91
  T3               5               168
  T4               1                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
  C9ORF98 MUTATED     3   4   1   1
  C9ORF98 WILD-TYPE 115 100  76  76
D764V5, multiclass
    clus
vv   C9ORF98 MUTATED C9ORF98 WILD-TYPE
  N0               3               115
  N1               4               100
  N2               1                76
  N3               1                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"
D764V6, binary
                   cls
clus                  0   1
  C9ORF98 MUTATED     8   1
  C9ORF98 WILD-TYPE 338  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF98 MUTATED      8    1
  C9ORF98 WILD-TYPE  338   28
   clus
vv  C9ORF98 MUTATED C9ORF98 WILD-TYPE
  0               8               338
  1               1                28
[1] 2 2
[1] FALSE
D764V7, binary
                   cls
clus                  0   1
  C9ORF98 MUTATED     4   6
  C9ORF98 WILD-TYPE 141 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF98 MUTATED      4    6
  C9ORF98 WILD-TYPE  141  242
        clus
vv       C9ORF98 MUTATED C9ORF98 WILD-TYPE
  FEMALE               4               141
  MALE                 6               242
[1] 2 2
[1] FALSE
D764V8, binary
                   cls
clus                  0   1
  C9ORF98 MUTATED     7   0
  C9ORF98 WILD-TYPE 285  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF98 MUTATED      7    0
  C9ORF98 WILD-TYPE  285   59
     clus
vv    C9ORF98 MUTATED C9ORF98 WILD-TYPE
  NO                7               285
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C9ORF98 MUTATED                                          0
  C9ORF98 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C9ORF98 MUTATED                                       0
  C9ORF98 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C9ORF98 MUTATED                                                        8
  C9ORF98 WILD-TYPE                                                    150
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C9ORF98 MUTATED                                                   0
  C9ORF98 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C9ORF98 MUTATED                                                                   0
  C9ORF98 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C9ORF98 MUTATED                                                    0
  C9ORF98 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C9ORF98 MUTATED                                                  2
  C9ORF98 WILD-TYPE                                               59
D764V9, multiclass
                                                                   clus
vv                                                                  C9ORF98 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  C9ORF98 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C9ORF98 MUTATED     7   0   1   2
  C9ORF98 WILD-TYPE 304  14  14  22
D764V10, multiclass
    clus
vv   C9ORF98 MUTATED C9ORF98 WILD-TYPE
  R0               7               304
  R1               0                14
  R2               1                14
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D764V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C9ORF98 MUTATED       4                         0
  C9ORF98 WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C9ORF98 MUTATED                                           0     4
  C9ORF98 WILD-TYPE                                         1   239
D764V12, multiclass
                                           clus
vv                                          C9ORF98 MUTATED C9ORF98 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D764V13, binary
                   cls
clus                  0   1
  C9ORF98 MUTATED     0   8
  C9ORF98 WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF98 MUTATED      0    8
  C9ORF98 WILD-TYPE    4  302
                        clus
vv                       C9ORF98 MUTATED C9ORF98 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(765) Variable = TOPBP1 MUTATION ANALYSIS
D765V1, survival
                  sevent
clus2                0   1
  TOPBP1 MUTATED     9   4
  TOPBP1 WILD-TYPE 221 135
  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
              13              356 
  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
               4              135 
$`TOPBP1 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-5718 TCGA-CG-5719 
        9.01        18.97         7.07        30.97        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-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-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-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 

  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
            4.31             0.00 
  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
           34.68           122.30 
  TOPBP1 MUTATED TOPBP1 WILD-TYPE 
           12.43            14.45 
[1] "4.3 - 34.7 (12.4)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1"  
D765V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TOPBP1 MUTATED         0        0        2        3         2         3
  TOPBP1 WILD-TYPE       2       15       38       27        35        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TOPBP1 MUTATED           0          2          2          0        0
  TOPBP1 WILD-TYPE         3         68         51         32       38
D765V3, multiclass
            clus
vv           TOPBP1 MUTATED TOPBP1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                3               27
  STAGE IIA               2               35
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              2               51
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TOPBP1 MUTATED     1   6   6   2
  TOPBP1 WILD-TYPE  21  86 167  95
D765V4, multiclass
    clus
vv   TOPBP1 MUTATED TOPBP1 WILD-TYPE
  T1              1               21
  T2              6               86
  T3              6              167
  T4              2               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
  TOPBP1 MUTATED     6   5   2   1
  TOPBP1 WILD-TYPE 112  99  75  76
D765V5, multiclass
    clus
vv   TOPBP1 MUTATED TOPBP1 WILD-TYPE
  N0              6              112
  N1              5               99
  N2              2               75
  N3              1               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"
D765V6, binary
                  cls
clus                 0   1
  TOPBP1 MUTATED    15   0
  TOPBP1 WILD-TYPE 331  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TOPBP1 MUTATED     15    0
  TOPBP1 WILD-TYPE  331   29
   clus
vv  TOPBP1 MUTATED TOPBP1 WILD-TYPE
  0             15              331
  1              0               29
[1] 2 2
[1] FALSE
D765V7, binary
                  cls
clus                 0   1
  TOPBP1 MUTATED    11   5
  TOPBP1 WILD-TYPE 134 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TOPBP1 MUTATED     11    5
  TOPBP1 WILD-TYPE  134  243
        clus
vv       TOPBP1 MUTATED TOPBP1 WILD-TYPE
  FEMALE             11              134
  MALE                5              243
[1] 2 2
[1] FALSE
D765V8, binary
                  cls
clus                 0   1
  TOPBP1 MUTATED    13   0
  TOPBP1 WILD-TYPE 279  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TOPBP1 MUTATED     13    0
  TOPBP1 WILD-TYPE  279   59
     clus
vv    TOPBP1 MUTATED TOPBP1 WILD-TYPE
  NO              13              279
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TOPBP1 MUTATED                                          0
  TOPBP1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TOPBP1 MUTATED                                       1
  TOPBP1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TOPBP1 MUTATED                                                       13
  TOPBP1 WILD-TYPE                                                    145
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TOPBP1 MUTATED                                                   0
  TOPBP1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TOPBP1 MUTATED                                                                   0
  TOPBP1 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TOPBP1 MUTATED                                                    0
  TOPBP1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TOPBP1 MUTATED                                                  2
  TOPBP1 WILD-TYPE                                               59
D765V9, multiclass
                                                                   clus
vv                                                                  TOPBP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  TOPBP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TOPBP1 MUTATED    12   0   0   4
  TOPBP1 WILD-TYPE 299  14  15  20
D765V10, multiclass
    clus
vv   TOPBP1 MUTATED TOPBP1 WILD-TYPE
  R0             12              299
  R1              0               14
  R2              0               15
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D765V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TOPBP1 MUTATED       3                         0
  TOPBP1 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TOPBP1 MUTATED                                           0    11
  TOPBP1 WILD-TYPE                                         1   232
D765V12, multiclass
                                           clus
vv                                          TOPBP1 MUTATED TOPBP1 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D765V13, binary
                  cls
clus                 0   1
  TOPBP1 MUTATED     0  14
  TOPBP1 WILD-TYPE   4 296
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TOPBP1 MUTATED      0   14
  TOPBP1 WILD-TYPE    4  296
                        clus
vv                       TOPBP1 MUTATED TOPBP1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             14              296
[1] 2 2
[1] FALSE

Clustering(766) Variable = KCNH2 MUTATION ANALYSIS
D766V1, survival
                 sevent
clus2               0   1
  KCNH2 MUTATED     9   4
  KCNH2 WILD-TYPE 221 135
  KCNH2 MUTATED KCNH2 WILD-TYPE 
             13             356 
  KCNH2 MUTATED KCNH2 WILD-TYPE 
              4             135 
$`KCNH2 MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-8077 
       26.70        19.56         6.97        18.35         9.67         0.69 
TCGA-BR-8487 TCGA-CG-4469 TCGA-CG-5723 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GX 
        1.12         7.07       105.07        22.32        22.68        20.25 
TCGA-VQ-A8P2 
       38.14 

$`KCNH2 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        11.70        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-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-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-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-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-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-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-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 

  KCNH2 MUTATED KCNH2 WILD-TYPE 
           0.69            0.00 
  KCNH2 MUTATED KCNH2 WILD-TYPE 
         105.07          122.30 
  KCNH2 MUTATED KCNH2 WILD-TYPE 
          19.56           14.12 
[1] "0.7 - 105.1 (19.6)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D766V2, 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       2       15       40       29        36        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNH2 MUTATED           0          2          1          2        1
  KCNH2 WILD-TYPE         3         68         52         30       37
D766V3, multiclass
            clus
vv           KCNH2 MUTATED KCNH2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNH2 MUTATED     0   1   4   7
  KCNH2 WILD-TYPE  22  91 169  90
D766V4, multiclass
    clus
vv   KCNH2 MUTATED KCNH2 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             4             169
  T4             7              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
  KCNH2 MUTATED     4   6   1   2
  KCNH2 WILD-TYPE 114  98  76  75
D766V5, multiclass
    clus
vv   KCNH2 MUTATED KCNH2 WILD-TYPE
  N0             4             114
  N1             6              98
  N2             1              76
  N3             2              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"
D766V6, binary
                 cls
clus                0   1
  KCNH2 MUTATED    13   0
  KCNH2 WILD-TYPE 333  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH2 MUTATED     13    0
  KCNH2 WILD-TYPE  333   29
   clus
vv  KCNH2 MUTATED KCNH2 WILD-TYPE
  0            13             333
  1             0              29
[1] 2 2
[1] FALSE
D766V7, binary
                 cls
clus                0   1
  KCNH2 MUTATED     7   7
  KCNH2 WILD-TYPE 138 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH2 MUTATED      7    7
  KCNH2 WILD-TYPE  138  241
        clus
vv       KCNH2 MUTATED KCNH2 WILD-TYPE
  FEMALE             7             138
  MALE               7             241
[1] 2 2
[1] FALSE
D766V8, binary
                 cls
clus                0   1
  KCNH2 MUTATED    11   1
  KCNH2 WILD-TYPE 281  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH2 MUTATED     11    1
  KCNH2 WILD-TYPE  281   58
     clus
vv    KCNH2 MUTATED KCNH2 WILD-TYPE
  NO             11             281
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KCNH2 MUTATED                                          0
  KCNH2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KCNH2 MUTATED                                       5
  KCNH2 WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNH2 MUTATED                                                        5
  KCNH2 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KCNH2 MUTATED                                                   1
  KCNH2 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNH2 MUTATED                                                                   3
  KCNH2 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KCNH2 MUTATED                                                    0
  KCNH2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KCNH2 MUTATED                                                  0
  KCNH2 WILD-TYPE                                               61
D766V9, multiclass
                                                                   clus
vv                                                                  KCNH2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  KCNH2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCNH2 MUTATED     8   1   0   3
  KCNH2 WILD-TYPE 303  13  15  21
D766V10, multiclass
    clus
vv   KCNH2 MUTATED KCNH2 WILD-TYPE
  R0             8             303
  R1             1              13
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D766V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCNH2 MUTATED       3                         0
  KCNH2 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNH2 MUTATED                                           0     9
  KCNH2 WILD-TYPE                                         1   234
D766V12, multiclass
                                           clus
vv                                          KCNH2 MUTATED KCNH2 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D766V13, binary
                 cls
clus                0   1
  KCNH2 MUTATED     0  11
  KCNH2 WILD-TYPE   4 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH2 MUTATED      0   11
  KCNH2 WILD-TYPE    4  299
                        clus
vv                       KCNH2 MUTATED KCNH2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(767) Variable = FAHD2A MUTATION ANALYSIS
D767V1, survival
                  sevent
clus2                0   1
  FAHD2A MUTATED     3   4
  FAHD2A WILD-TYPE 227 135
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               7              362 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               4              135 
$`FAHD2A MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-8363 TCGA-BR-8487 TCGA-HU-A4G8 TCGA-HU-A4GQ 
       21.99         6.97         0.26         1.12        22.68         0.10 
TCGA-VQ-A8P2 
       38.14 

$`FAHD2A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  FAHD2A MUTATED FAHD2A WILD-TYPE 
             0.1              0.0 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
           38.14           122.30 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
            6.97            14.35 
[1] "0.1 - 38.1 (7.0)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "2.1"
D767V2, 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       2       15       39       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAHD2A MUTATED           0          3          0          1        1
  FAHD2A WILD-TYPE         3         67         53         31       37
D767V3, multiclass
            clus
vv           FAHD2A MUTATED FAHD2A WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAHD2A MUTATED     0   1   3   4
  FAHD2A WILD-TYPE  22  91 170  93
D767V4, multiclass
    clus
vv   FAHD2A MUTATED FAHD2A WILD-TYPE
  T1              0               22
  T2              1               91
  T3              3              170
  T4              4               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
  FAHD2A MUTATED     3   4   1   0
  FAHD2A WILD-TYPE 115 100  76  77
D767V5, multiclass
    clus
vv   FAHD2A MUTATED FAHD2A WILD-TYPE
  N0              3              115
  N1              4              100
  N2              1               76
  N3              0               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"
D767V6, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     6   1
  FAHD2A WILD-TYPE 340  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      6    1
  FAHD2A WILD-TYPE  340   28
   clus
vv  FAHD2A MUTATED FAHD2A WILD-TYPE
  0              6              340
  1              1               28
[1] 2 2
[1] FALSE
D767V7, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     5   3
  FAHD2A WILD-TYPE 140 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      5    3
  FAHD2A WILD-TYPE  140  245
        clus
vv       FAHD2A MUTATED FAHD2A WILD-TYPE
  FEMALE              5              140
  MALE                3              245
[1] 2 2
[1] FALSE
D767V8, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     6   1
  FAHD2A WILD-TYPE 286  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      6    1
  FAHD2A WILD-TYPE  286   58
     clus
vv    FAHD2A MUTATED FAHD2A WILD-TYPE
  NO               6              286
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAHD2A MUTATED                                          0
  FAHD2A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAHD2A MUTATED                                       1
  FAHD2A WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAHD2A MUTATED                                                        4
  FAHD2A WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAHD2A MUTATED                                                   1
  FAHD2A WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAHD2A MUTATED                                                                   1
  FAHD2A WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAHD2A MUTATED                                                    0
  FAHD2A WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAHD2A MUTATED                                                  1
  FAHD2A WILD-TYPE                                               60
D767V9, multiclass
                                                                   clus
vv                                                                  FAHD2A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  FAHD2A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAHD2A MUTATED     4   0   1   2
  FAHD2A WILD-TYPE 307  14  14  22
D767V10, multiclass
    clus
vv   FAHD2A MUTATED FAHD2A WILD-TYPE
  R0              4              307
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D767V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAHD2A MUTATED       2                         0
  FAHD2A WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAHD2A MUTATED                                           0     5
  FAHD2A WILD-TYPE                                         1   238
D767V12, multiclass
                                           clus
vv                                          FAHD2A MUTATED FAHD2A WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D767V13, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     0   6
  FAHD2A WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      0    6
  FAHD2A WILD-TYPE    4  304
                        clus
vv                       FAHD2A MUTATED FAHD2A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(768) Variable = PTPN3 MUTATION ANALYSIS
D768V1, survival
                 sevent
clus2               0   1
  PTPN3 MUTATED     6   6
  PTPN3 WILD-TYPE 224 133
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             12             357 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
              6             133 
$`PTPN3 MUTATED`
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8382 TCGA-D7-A4YV TCGA-F1-A448 
        9.34         9.67        34.68        25.05         5.92        21.27 
TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4GQ TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-VQ-A8PM 
       11.08        22.32         0.10        19.73        74.53         1.87 

$`PTPN3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
         15.405          14.270 
[1] "0.1 - 74.5 (15.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D768V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPN3 MUTATED         0        0        0        0         2         3
  PTPN3 WILD-TYPE       2       15       40       30        35        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN3 MUTATED           0          1          1          2        2
  PTPN3 WILD-TYPE         3         69         52         30       36
D768V3, multiclass
            clus
vv           PTPN3 MUTATED PTPN3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPN3 MUTATED     0   0   6   6
  PTPN3 WILD-TYPE  22  92 167  91
D768V4, multiclass
    clus
vv   PTPN3 MUTATED PTPN3 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             6             167
  T4             6              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
  PTPN3 MUTATED     4   3   2   3
  PTPN3 WILD-TYPE 114 101  75  74
D768V5, multiclass
    clus
vv   PTPN3 MUTATED PTPN3 WILD-TYPE
  N0             4             114
  N1             3             101
  N2             2              75
  N3             3              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"
D768V6, binary
                 cls
clus                0   1
  PTPN3 MUTATED    13   1
  PTPN3 WILD-TYPE 333  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED     13    1
  PTPN3 WILD-TYPE  333   28
   clus
vv  PTPN3 MUTATED PTPN3 WILD-TYPE
  0            13             333
  1             1              28
[1] 2 2
[1] FALSE
D768V7, binary
                 cls
clus                0   1
  PTPN3 MUTATED     9   6
  PTPN3 WILD-TYPE 136 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED      9    6
  PTPN3 WILD-TYPE  136  242
        clus
vv       PTPN3 MUTATED PTPN3 WILD-TYPE
  FEMALE             9             136
  MALE               6             242
[1] 2 2
[1] FALSE
D768V8, binary
                 cls
clus                0   1
  PTPN3 MUTATED    11   2
  PTPN3 WILD-TYPE 281  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED     11    2
  PTPN3 WILD-TYPE  281   57
     clus
vv    PTPN3 MUTATED PTPN3 WILD-TYPE
  NO             11             281
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PTPN3 MUTATED                                          1
  PTPN3 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PTPN3 MUTATED                                       2
  PTPN3 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTPN3 MUTATED                                                        7
  PTPN3 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PTPN3 MUTATED                                                   1
  PTPN3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTPN3 MUTATED                                                                   1
  PTPN3 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PTPN3 MUTATED                                                    0
  PTPN3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PTPN3 MUTATED                                                  3
  PTPN3 WILD-TYPE                                               58
D768V9, multiclass
                                                                   clus
vv                                                                  PTPN3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  PTPN3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTPN3 MUTATED    11   0   0   4
  PTPN3 WILD-TYPE 300  14  15  20
D768V10, multiclass
    clus
vv   PTPN3 MUTATED PTPN3 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D768V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PTPN3 MUTATED       2                         1
  PTPN3 WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPN3 MUTATED                                           0    12
  PTPN3 WILD-TYPE                                         1   231
D768V12, multiclass
                                           clus
vv                                          PTPN3 MUTATED PTPN3 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D768V13, binary
                 cls
clus                0   1
  PTPN3 MUTATED     2  12
  PTPN3 WILD-TYPE   2 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED      2   12
  PTPN3 WILD-TYPE    2  298
                        clus
vv                       PTPN3 MUTATED PTPN3 WILD-TYPE
  HISPANIC OR LATINO                 2               2
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(769) Variable = E2F5 MUTATION ANALYSIS
D769V1, survival
                sevent
clus2              0   1
  E2F5 MUTATED     2   1
  E2F5 WILD-TYPE 228 138
  E2F5 MUTATED E2F5 WILD-TYPE 
             3            366 
  E2F5 MUTATED E2F5 WILD-TYPE 
             1            138 
$`E2F5 MUTATED`
TCGA-D7-A6EX TCGA-HU-A4GQ TCGA-HU-A4H3 
       11.31         0.10        29.00 

$`E2F5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  E2F5 MUTATED E2F5 WILD-TYPE 
           0.1            0.0 
  E2F5 MUTATED E2F5 WILD-TYPE 
          29.0          122.3 
  E2F5 MUTATED E2F5 WILD-TYPE 
         11.31          14.35 
[1] "0.1 - 29.0 (11.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D769V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  E2F5 MUTATED         0        0        0        0         0         0
  E2F5 WILD-TYPE       2       15       40       30        37        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  E2F5 MUTATED           0          1          0          2        0
  E2F5 WILD-TYPE         3         69         53         30       38
D769V3, multiclass
            clus
vv           E2F5 MUTATED E2F5 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  E2F5 MUTATED     1   0   1   2
  E2F5 WILD-TYPE  21  92 172  95
D769V4, multiclass
    clus
vv   E2F5 MUTATED E2F5 WILD-TYPE
  T1            1             21
  T2            0             92
  T3            1            172
  T4            2             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
  E2F5 MUTATED     0   0   2   1
  E2F5 WILD-TYPE 118 104  75  76
D769V5, multiclass
    clus
vv   E2F5 MUTATED E2F5 WILD-TYPE
  N0            0            118
  N1            0            104
  N2            2             75
  N3            1             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"
D769V6, binary
                cls
clus               0   1
  E2F5 MUTATED     4   0
  E2F5 WILD-TYPE 342  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      4    0
  E2F5 WILD-TYPE  342   29
   clus
vv  E2F5 MUTATED E2F5 WILD-TYPE
  0            4            342
  1            0             29
[1] 2 2
[1] FALSE
D769V7, binary
                cls
clus               0   1
  E2F5 MUTATED     3   1
  E2F5 WILD-TYPE 142 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      3    1
  E2F5 WILD-TYPE  142  247
        clus
vv       E2F5 MUTATED E2F5 WILD-TYPE
  FEMALE            3            142
  MALE              1            247
[1] 2 2
[1] FALSE
D769V8, binary
                cls
clus               0   1
  E2F5 MUTATED     2   0
  E2F5 WILD-TYPE 290  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      2    0
  E2F5 WILD-TYPE  290   59
     clus
vv    E2F5 MUTATED E2F5 WILD-TYPE
  NO             2            290
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  E2F5 MUTATED                                          0
  E2F5 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  E2F5 MUTATED                                       1
  E2F5 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  E2F5 MUTATED                                                        1
  E2F5 WILD-TYPE                                                    157
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  E2F5 MUTATED                                                   0
  E2F5 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  E2F5 MUTATED                                                                   0
  E2F5 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  E2F5 MUTATED                                                    0
  E2F5 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  E2F5 MUTATED                                                  2
  E2F5 WILD-TYPE                                               59
D769V9, multiclass
                                                                   clus
vv                                                                  E2F5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  E2F5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  E2F5 MUTATED     3   0   0   1
  E2F5 WILD-TYPE 308  14  15  23
D769V10, multiclass
    clus
vv   E2F5 MUTATED E2F5 WILD-TYPE
  R0            3            308
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D769V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  E2F5 MUTATED       2                         0
  E2F5 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  E2F5 MUTATED                                           0     2
  E2F5 WILD-TYPE                                         1   241
D769V12, multiclass
                                           clus
vv                                          E2F5 MUTATED E2F5 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D769V13, binary
                cls
clus               0   1
  E2F5 MUTATED     0   4
  E2F5 WILD-TYPE   4 306
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      0    4
  E2F5 WILD-TYPE    4  306
                        clus
vv                       E2F5 MUTATED E2F5 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            4            306
[1] 2 2
[1] FALSE

Clustering(770) Variable = PABPC4 MUTATION ANALYSIS
D770V1, survival
                  sevent
clus2                0   1
  PABPC4 MUTATED     6   3
  PABPC4 WILD-TYPE 224 136
  PABPC4 MUTATED PABPC4 WILD-TYPE 
               9              360 
  PABPC4 MUTATED PABPC4 WILD-TYPE 
               3              136 
$`PABPC4 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8589 TCGA-CD-8536 
       21.99         6.97         0.26         1.12        27.12        12.43 
TCGA-CG-5721 TCGA-HF-7134 TCGA-HU-A4H4 
        6.02        52.21        23.84 

$`PABPC4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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 

  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            14.35 
[1] "0.3 - 52.2 (12.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D770V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PABPC4 MUTATED         0        1        1        1         1         1
  PABPC4 WILD-TYPE       2       14       39       29        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PABPC4 MUTATED           0          1          1          0        2
  PABPC4 WILD-TYPE         3         69         52         32       36
D770V3, multiclass
            clus
vv           PABPC4 MUTATED PABPC4 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PABPC4 MUTATED     1   2   3   3
  PABPC4 WILD-TYPE  21  90 170  94
D770V4, multiclass
    clus
vv   PABPC4 MUTATED PABPC4 WILD-TYPE
  T1              1               21
  T2              2               90
  T3              3              170
  T4              3               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
  PABPC4 MUTATED     4   4   1   0
  PABPC4 WILD-TYPE 114 100  76  77
D770V5, multiclass
    clus
vv   PABPC4 MUTATED PABPC4 WILD-TYPE
  N0              4              114
  N1              4              100
  N2              1               76
  N3              0               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"
D770V6, binary
                  cls
clus                 0   1
  PABPC4 MUTATED     7   1
  PABPC4 WILD-TYPE 339  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC4 MUTATED      7    1
  PABPC4 WILD-TYPE  339   28
   clus
vv  PABPC4 MUTATED PABPC4 WILD-TYPE
  0              7              339
  1              1               28
[1] 2 2
[1] FALSE
D770V7, binary
                  cls
clus                 0   1
  PABPC4 MUTATED     4   5
  PABPC4 WILD-TYPE 141 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC4 MUTATED      4    5
  PABPC4 WILD-TYPE  141  243
        clus
vv       PABPC4 MUTATED PABPC4 WILD-TYPE
  FEMALE              4              141
  MALE                5              243
[1] 2 2
[1] FALSE
D770V8, binary
                  cls
clus                 0   1
  PABPC4 MUTATED     9   0
  PABPC4 WILD-TYPE 283  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC4 MUTATED      9    0
  PABPC4 WILD-TYPE  283   59
     clus
vv    PABPC4 MUTATED PABPC4 WILD-TYPE
  NO               9              283
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PABPC4 MUTATED                                          0
  PABPC4 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PABPC4 MUTATED                                       0
  PABPC4 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PABPC4 MUTATED                                                        5
  PABPC4 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PABPC4 MUTATED                                                   0
  PABPC4 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PABPC4 MUTATED                                                                   3
  PABPC4 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PABPC4 MUTATED                                                    0
  PABPC4 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PABPC4 MUTATED                                                  1
  PABPC4 WILD-TYPE                                               60
D770V9, multiclass
                                                                   clus
vv                                                                  PABPC4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  PABPC4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PABPC4 MUTATED     7   0   1   1
  PABPC4 WILD-TYPE 304  14  14  23
D770V10, multiclass
    clus
vv   PABPC4 MUTATED PABPC4 WILD-TYPE
  R0              7              304
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D770V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PABPC4 MUTATED       2                         0
  PABPC4 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PABPC4 MUTATED                                           0     4
  PABPC4 WILD-TYPE                                         1   239
D770V12, multiclass
                                           clus
vv                                          PABPC4 MUTATED PABPC4 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D770V13, binary
                  cls
clus                 0   1
  PABPC4 MUTATED     0   6
  PABPC4 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC4 MUTATED      0    6
  PABPC4 WILD-TYPE    4  304
                        clus
vv                       PABPC4 MUTATED PABPC4 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(771) Variable = ERV3 MUTATION ANALYSIS
D771V1, survival
                sevent
clus2              0   1
  ERV3 MUTATED     2   3
  ERV3 WILD-TYPE 228 136
  ERV3 MUTATED ERV3 WILD-TYPE 
             5            364 
  ERV3 MUTATED ERV3 WILD-TYPE 
             3            136 
$`ERV3 MUTATED`
TCGA-BR-4256 TCGA-CD-8535 TCGA-D7-6818 TCGA-D7-A6EY TCGA-FP-A4BE 
        9.34        12.82        12.36        11.44        11.08 

$`ERV3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-6820 TCGA-D7-6822 
       10.26        15.22        15.98        12.79        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-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 

  ERV3 MUTATED ERV3 WILD-TYPE 
          9.34           0.00 
  ERV3 MUTATED ERV3 WILD-TYPE 
         12.82         122.30 
  ERV3 MUTATED ERV3 WILD-TYPE 
        11.440         14.565 
[1] "9.3 - 12.8 (11.4)"  "0.0 - 122.3 (14.6)"
[1] "hr=" "2.5"
D771V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ERV3 MUTATED         0        0        0        0         1         0
  ERV3 WILD-TYPE       2       15       40       30        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERV3 MUTATED           0          2          1          0        0
  ERV3 WILD-TYPE         3         68         52         32       38
D771V3, multiclass
            clus
vv           ERV3 MUTATED ERV3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ERV3 MUTATED     0   1   3   0
  ERV3 WILD-TYPE  22  91 170  97
D771V4, multiclass
    clus
vv   ERV3 MUTATED ERV3 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            3            170
  T4            0             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
  ERV3 MUTATED     1   2   0   2
  ERV3 WILD-TYPE 117 102  77  75
D771V5, multiclass
    clus
vv   ERV3 MUTATED ERV3 WILD-TYPE
  N0            1            117
  N1            2            102
  N2            0             77
  N3            2             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"
D771V6, binary
                cls
clus               0   1
  ERV3 MUTATED     5   0
  ERV3 WILD-TYPE 341  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERV3 MUTATED      5    0
  ERV3 WILD-TYPE  341   29
   clus
vv  ERV3 MUTATED ERV3 WILD-TYPE
  0            5            341
  1            0             29
[1] 2 2
[1] FALSE
D771V7, binary
                cls
clus               0   1
  ERV3 MUTATED     1   4
  ERV3 WILD-TYPE 144 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERV3 MUTATED      1    4
  ERV3 WILD-TYPE  144  244
        clus
vv       ERV3 MUTATED ERV3 WILD-TYPE
  FEMALE            1            144
  MALE              4            244
[1] 2 2
[1] FALSE
D771V8, binary
                cls
clus               0   1
  ERV3 MUTATED     3   2
  ERV3 WILD-TYPE 289  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERV3 MUTATED      3    2
  ERV3 WILD-TYPE  289   57
     clus
vv    ERV3 MUTATED ERV3 WILD-TYPE
  NO             3            289
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ERV3 MUTATED                                          0
  ERV3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ERV3 MUTATED                                       1
  ERV3 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ERV3 MUTATED                                                        3
  ERV3 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ERV3 MUTATED                                                   0
  ERV3 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ERV3 MUTATED                                                                   0
  ERV3 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ERV3 MUTATED                                                    0
  ERV3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ERV3 MUTATED                                                  1
  ERV3 WILD-TYPE                                               60
D771V9, multiclass
                                                                   clus
vv                                                                  ERV3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  ERV3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ERV3 MUTATED     4   0   0   1
  ERV3 WILD-TYPE 307  14  15  23
D771V10, multiclass
    clus
vv   ERV3 MUTATED ERV3 WILD-TYPE
  R0            4            307
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D771V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ERV3 MUTATED       1                         1
  ERV3 WILD-TYPE    86                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ERV3 MUTATED                                           0     3
  ERV3 WILD-TYPE                                         1   240
D771V12, multiclass
                                           clus
vv                                          ERV3 MUTATED ERV3 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D771V13, binary
                cls
clus               0   1
  ERV3 MUTATED     0   5
  ERV3 WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERV3 MUTATED      0    5
  ERV3 WILD-TYPE    4  305
                        clus
vv                       ERV3 MUTATED ERV3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(772) Variable = SLC39A8 MUTATION ANALYSIS
D772V1, survival
                   sevent
clus2                 0   1
  SLC39A8 MUTATED     3   4
  SLC39A8 WILD-TYPE 227 135
  SLC39A8 MUTATED SLC39A8 WILD-TYPE 
                7               362 
  SLC39A8 MUTATED SLC39A8 WILD-TYPE 
                4               135 
$`SLC39A8 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-A4QL TCGA-CG-5733 TCGA-D7-A6F0 TCGA-VQ-A8P2 
        6.97        34.68        16.14        21.07        22.29        38.14 
TCGA-VQ-AA6I 
       16.14 

$`SLC39A8 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-AA6J 
       28.41        38.93        32.94        54.12        26.04        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  SLC39A8 MUTATED SLC39A8 WILD-TYPE 
             6.97              0.00 
  SLC39A8 MUTATED SLC39A8 WILD-TYPE 
            38.14            122.30 
  SLC39A8 MUTATED SLC39A8 WILD-TYPE 
            21.07             14.07 
[1] "7.0 - 38.1 (21.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D772V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC39A8 MUTATED         0        0        1        0         1         0
  SLC39A8 WILD-TYPE       2       15       39       30        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC39A8 MUTATED           0          3          2          0        0
  SLC39A8 WILD-TYPE         3         67         51         32       38
D772V3, multiclass
            clus
vv           SLC39A8 MUTATED SLC39A8 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               3                67
  STAGE IIIB               2                51
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC39A8 MUTATED     0   2   4   1
  SLC39A8 WILD-TYPE  22  90 169  96
D772V4, multiclass
    clus
vv   SLC39A8 MUTATED SLC39A8 WILD-TYPE
  T1               0                22
  T2               2                90
  T3               4               169
  T4               1                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
  SLC39A8 MUTATED     2   2   1   2
  SLC39A8 WILD-TYPE 116 102  76  75
D772V5, multiclass
    clus
vv   SLC39A8 MUTATED SLC39A8 WILD-TYPE
  N0               2               116
  N1               2               102
  N2               1                76
  N3               2                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"
D772V6, binary
                   cls
clus                  0   1
  SLC39A8 MUTATED     6   0
  SLC39A8 WILD-TYPE 340  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A8 MUTATED      6    0
  SLC39A8 WILD-TYPE  340   29
   clus
vv  SLC39A8 MUTATED SLC39A8 WILD-TYPE
  0               6               340
  1               0                29
[1] 2 2
[1] FALSE
D772V7, binary
                   cls
clus                  0   1
  SLC39A8 MUTATED     4   3
  SLC39A8 WILD-TYPE 141 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A8 MUTATED      4    3
  SLC39A8 WILD-TYPE  141  245
        clus
vv       SLC39A8 MUTATED SLC39A8 WILD-TYPE
  FEMALE               4               141
  MALE                 3               245
[1] 2 2
[1] FALSE
D772V8, binary
                   cls
clus                  0   1
  SLC39A8 MUTATED     6   1
  SLC39A8 WILD-TYPE 286  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A8 MUTATED      6    1
  SLC39A8 WILD-TYPE  286   58
     clus
vv    SLC39A8 MUTATED SLC39A8 WILD-TYPE
  NO                6               286
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC39A8 MUTATED                                          0
  SLC39A8 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC39A8 MUTATED                                       0
  SLC39A8 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC39A8 MUTATED                                                        3
  SLC39A8 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC39A8 MUTATED                                                   1
  SLC39A8 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC39A8 MUTATED                                                                   3
  SLC39A8 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC39A8 MUTATED                                                    0
  SLC39A8 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC39A8 MUTATED                                                  0
  SLC39A8 WILD-TYPE                                               61
D772V9, multiclass
                                                                   clus
vv                                                                  SLC39A8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  SLC39A8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC39A8 MUTATED     6   0   0   1
  SLC39A8 WILD-TYPE 305  14  15  23
D772V10, multiclass
    clus
vv   SLC39A8 MUTATED SLC39A8 WILD-TYPE
  R0               6               305
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D772V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC39A8 MUTATED       0                         0
  SLC39A8 WILD-TYPE    87                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC39A8 MUTATED                                           0     6
  SLC39A8 WILD-TYPE                                         1   237
D772V12, multiclass
                                           clus
vv                                          SLC39A8 MUTATED SLC39A8 WILD-TYPE
  ASIAN                                                   0                87
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D772V13, binary
                   cls
clus                  0   1
  SLC39A8 MUTATED     0   4
  SLC39A8 WILD-TYPE   4 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A8 MUTATED      0    4
  SLC39A8 WILD-TYPE    4  306
                        clus
vv                       SLC39A8 MUTATED SLC39A8 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4               306
[1] 2 2
[1] FALSE

Clustering(773) Variable = RIMKLB MUTATION ANALYSIS
D773V1, survival
                  sevent
clus2                0   1
  RIMKLB MUTATED     6   4
  RIMKLB WILD-TYPE 224 135
  RIMKLB MUTATED RIMKLB WILD-TYPE 
              10              359 
  RIMKLB MUTATED RIMKLB WILD-TYPE 
               4              135 
$`RIMKLB MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-D7-A4YV TCGA-D7-A6EY 
       26.70         6.97        30.90        34.68         5.92        11.44 
TCGA-HF-A5NB TCGA-HU-A4G9 TCGA-HU-A4H4 TCGA-VQ-A8P2 
       30.51        24.20        23.84        38.14 

$`RIMKLB WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  RIMKLB MUTATED RIMKLB WILD-TYPE 
            5.92             0.00 
  RIMKLB MUTATED RIMKLB WILD-TYPE 
           38.14           122.30 
  RIMKLB MUTATED RIMKLB WILD-TYPE 
           25.45            14.07 
[1] "5.9 - 38.1 (25.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D773V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RIMKLB MUTATED         0        1        1        0         1         3
  RIMKLB WILD-TYPE       2       14       39       30        36        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RIMKLB MUTATED           0          2          1          1        0
  RIMKLB WILD-TYPE         3         68         52         31       38
D773V3, multiclass
            clus
vv           RIMKLB MUTATED RIMKLB WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RIMKLB MUTATED     1   3   4   3
  RIMKLB WILD-TYPE  21  89 169  94
D773V4, multiclass
    clus
vv   RIMKLB MUTATED RIMKLB WILD-TYPE
  T1              1               21
  T2              3               89
  T3              4              169
  T4              3               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
  RIMKLB MUTATED     4   3   1   2
  RIMKLB WILD-TYPE 114 101  76  75
D773V5, multiclass
    clus
vv   RIMKLB MUTATED RIMKLB WILD-TYPE
  N0              4              114
  N1              3              101
  N2              1               76
  N3              2               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"
D773V6, binary
                  cls
clus                 0   1
  RIMKLB MUTATED    10   0
  RIMKLB WILD-TYPE 336  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMKLB MUTATED     10    0
  RIMKLB WILD-TYPE  336   29
   clus
vv  RIMKLB MUTATED RIMKLB WILD-TYPE
  0             10              336
  1              0               29
[1] 2 2
[1] FALSE
D773V7, binary
                  cls
clus                 0   1
  RIMKLB MUTATED     8   3
  RIMKLB WILD-TYPE 137 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMKLB MUTATED      8    3
  RIMKLB WILD-TYPE  137  245
        clus
vv       RIMKLB MUTATED RIMKLB WILD-TYPE
  FEMALE              8              137
  MALE                3              245
[1] 2 2
[1] FALSE
D773V8, binary
                  cls
clus                 0   1
  RIMKLB MUTATED     8   2
  RIMKLB WILD-TYPE 284  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMKLB MUTATED      8    2
  RIMKLB WILD-TYPE  284   57
     clus
vv    RIMKLB MUTATED RIMKLB WILD-TYPE
  NO               8              284
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RIMKLB MUTATED                                          0
  RIMKLB WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RIMKLB MUTATED                                       1
  RIMKLB WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RIMKLB MUTATED                                                        3
  RIMKLB WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RIMKLB MUTATED                                                   2
  RIMKLB WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RIMKLB MUTATED                                                                   1
  RIMKLB WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RIMKLB MUTATED                                                    0
  RIMKLB WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RIMKLB MUTATED                                                  4
  RIMKLB WILD-TYPE                                               57
D773V9, multiclass
                                                                   clus
vv                                                                  RIMKLB MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  RIMKLB WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RIMKLB MUTATED     8   1   0   2
  RIMKLB WILD-TYPE 303  13  15  22
D773V10, multiclass
    clus
vv   RIMKLB MUTATED RIMKLB WILD-TYPE
  R0              8              303
  R1              1               13
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D773V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RIMKLB MUTATED       2                         0
  RIMKLB WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RIMKLB MUTATED                                           0     7
  RIMKLB WILD-TYPE                                         1   236
D773V12, multiclass
                                           clus
vv                                          RIMKLB MUTATED RIMKLB WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D773V13, binary
                  cls
clus                 0   1
  RIMKLB MUTATED     0   8
  RIMKLB WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMKLB MUTATED      0    8
  RIMKLB WILD-TYPE    4  302
                        clus
vv                       RIMKLB MUTATED RIMKLB WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(774) Variable = UGT1A4 MUTATION ANALYSIS
D774V1, survival
                  sevent
clus2                0   1
  UGT1A4 MUTATED     6   4
  UGT1A4 WILD-TYPE 224 135
  UGT1A4 MUTATED UGT1A4 WILD-TYPE 
              10              359 
  UGT1A4 MUTATED UGT1A4 WILD-TYPE 
               4              135 
$`UGT1A4 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8059 TCGA-CD-8536 TCGA-D7-A4YT TCGA-D7-A4YV 
        6.97        34.68        14.43        12.43        14.27         5.92 
TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-VQ-A8DU TCGA-VQ-A8P2 
        6.51        29.00         5.46        38.14 

$`UGT1A4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-A4YU TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91        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-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-A8DV TCGA-VQ-A8DZ 
       19.04         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-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 

  UGT1A4 MUTATED UGT1A4 WILD-TYPE 
            5.46             0.00 
  UGT1A4 MUTATED UGT1A4 WILD-TYPE 
           38.14           122.30 
  UGT1A4 MUTATED UGT1A4 WILD-TYPE 
           13.35            14.47 
[1] "5.5 - 38.1 (13.3)"  "0.0 - 122.3 (14.5)"
[1] "hr=" "1.2"
D774V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UGT1A4 MUTATED         0        0        0        1         2         1
  UGT1A4 WILD-TYPE       2       15       40       29        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT1A4 MUTATED           1          4          0          1        0
  UGT1A4 WILD-TYPE         2         66         53         31       38
D774V3, multiclass
            clus
vv           UGT1A4 MUTATED UGT1A4 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               1                2
  STAGE IIIA              4               66
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UGT1A4 MUTATED     0   1   6   3
  UGT1A4 WILD-TYPE  22  91 167  94
D774V4, multiclass
    clus
vv   UGT1A4 MUTATED UGT1A4 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              6              167
  T4              3               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
  UGT1A4 MUTATED     3   4   1   2
  UGT1A4 WILD-TYPE 115 100  76  75
D774V5, multiclass
    clus
vv   UGT1A4 MUTATED UGT1A4 WILD-TYPE
  N0              3              115
  N1              4              100
  N2              1               76
  N3              2               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"
D774V6, binary
                  cls
clus                 0   1
  UGT1A4 MUTATED     9   0
  UGT1A4 WILD-TYPE 337  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A4 MUTATED      9    0
  UGT1A4 WILD-TYPE  337   29
   clus
vv  UGT1A4 MUTATED UGT1A4 WILD-TYPE
  0              9              337
  1              0               29
[1] 2 2
[1] FALSE
D774V7, binary
                  cls
clus                 0   1
  UGT1A4 MUTATED     4   6
  UGT1A4 WILD-TYPE 141 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A4 MUTATED      4    6
  UGT1A4 WILD-TYPE  141  242
        clus
vv       UGT1A4 MUTATED UGT1A4 WILD-TYPE
  FEMALE              4              141
  MALE                6              242
[1] 2 2
[1] FALSE
D774V8, binary
                  cls
clus                 0   1
  UGT1A4 MUTATED     8   1
  UGT1A4 WILD-TYPE 284  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A4 MUTATED      8    1
  UGT1A4 WILD-TYPE  284   58
     clus
vv    UGT1A4 MUTATED UGT1A4 WILD-TYPE
  NO               8              284
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  UGT1A4 MUTATED                                          0
  UGT1A4 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  UGT1A4 MUTATED                                       1
  UGT1A4 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UGT1A4 MUTATED                                                        3
  UGT1A4 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  UGT1A4 MUTATED                                                   1
  UGT1A4 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UGT1A4 MUTATED                                                                   1
  UGT1A4 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  UGT1A4 MUTATED                                                    0
  UGT1A4 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  UGT1A4 MUTATED                                                  4
  UGT1A4 WILD-TYPE                                               57
D774V9, multiclass
                                                                   clus
vv                                                                  UGT1A4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  UGT1A4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  UGT1A4 MUTATED     9   0   0   1
  UGT1A4 WILD-TYPE 302  14  15  23
D774V10, multiclass
    clus
vv   UGT1A4 MUTATED UGT1A4 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D774V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  UGT1A4 MUTATED       3                         0
  UGT1A4 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UGT1A4 MUTATED                                           0     7
  UGT1A4 WILD-TYPE                                         1   236
D774V12, multiclass
                                           clus
vv                                          UGT1A4 MUTATED UGT1A4 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D774V13, binary
                  cls
clus                 0   1
  UGT1A4 MUTATED     0   8
  UGT1A4 WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A4 MUTATED      0    8
  UGT1A4 WILD-TYPE    4  302
                        clus
vv                       UGT1A4 MUTATED UGT1A4 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(775) Variable = PLA2G15 MUTATION ANALYSIS
D775V1, survival
                   sevent
clus2                 0   1
  PLA2G15 MUTATED     5   4
  PLA2G15 WILD-TYPE 225 135
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                9               360 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                4               135 
$`PLA2G15 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6802 TCGA-BR-8360 TCGA-CD-A4MJ TCGA-CG-5726 
        6.97         6.61        30.90         6.18        12.62        28.96 
TCGA-HF-7132 TCGA-HU-A4GH TCGA-HU-A4GQ 
       77.29        11.77         0.10 

$`PLA2G15 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
              0.1               0.0 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
            77.29            122.30 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
            11.77             14.45 
[1] "0.1 - 77.3 (11.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D775V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLA2G15 MUTATED         0        2        2        1         1         0
  PLA2G15 WILD-TYPE       2       13       38       29        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLA2G15 MUTATED           1          2          0          1        0
  PLA2G15 WILD-TYPE         2         68         53         31       38
D775V3, multiclass
            clus
vv           PLA2G15 MUTATED PLA2G15 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                13
  STAGE IB                 2                38
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                1                 2
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLA2G15 MUTATED     2   4   3   1
  PLA2G15 WILD-TYPE  20  88 170  96
D775V4, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  T1               2                20
  T2               4                88
  T3               3               170
  T4               1                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
  PLA2G15 MUTATED     5   3   2   0
  PLA2G15 WILD-TYPE 113 101  75  77
D775V5, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  N0               5               113
  N1               3               101
  N2               2                75
  N3               0                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"
D775V6, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     9   0
  PLA2G15 WILD-TYPE 337  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      9    0
  PLA2G15 WILD-TYPE  337   29
   clus
vv  PLA2G15 MUTATED PLA2G15 WILD-TYPE
  0               9               337
  1               0                29
[1] 2 2
[1] FALSE
D775V7, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     1   9
  PLA2G15 WILD-TYPE 144 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      1    9
  PLA2G15 WILD-TYPE  144  239
        clus
vv       PLA2G15 MUTATED PLA2G15 WILD-TYPE
  FEMALE               1               144
  MALE                 9               239
[1] 2 2
[1] FALSE
D775V8, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     7   1
  PLA2G15 WILD-TYPE 285  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      7    1
  PLA2G15 WILD-TYPE  285   58
     clus
vv    PLA2G15 MUTATED PLA2G15 WILD-TYPE
  NO                7               285
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PLA2G15 MUTATED                                          0
  PLA2G15 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PLA2G15 MUTATED                                       0
  PLA2G15 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLA2G15 MUTATED                                                        4
  PLA2G15 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PLA2G15 MUTATED                                                   1
  PLA2G15 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLA2G15 MUTATED                                                                   3
  PLA2G15 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PLA2G15 MUTATED                                                    0
  PLA2G15 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PLA2G15 MUTATED                                                  2
  PLA2G15 WILD-TYPE                                               59
D775V9, multiclass
                                                                   clus
vv                                                                  PLA2G15 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  PLA2G15 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PLA2G15 MUTATED     7   0   0   2
  PLA2G15 WILD-TYPE 304  14  15  22
D775V10, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  R0               7               304
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D775V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PLA2G15 MUTATED       3                         0
  PLA2G15 WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLA2G15 MUTATED                                           0     4
  PLA2G15 WILD-TYPE                                         1   239
D775V12, multiclass
                                           clus
vv                                          PLA2G15 MUTATED PLA2G15 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D775V13, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     0   7
  PLA2G15 WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      0    7
  PLA2G15 WILD-TYPE    4  303
                        clus
vv                       PLA2G15 MUTATED PLA2G15 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(776) Variable = MNS1 MUTATION ANALYSIS
D776V1, survival
                sevent
clus2              0   1
  MNS1 MUTATED     4   3
  MNS1 WILD-TYPE 226 136
  MNS1 MUTATED MNS1 WILD-TYPE 
             7            362 
  MNS1 MUTATED MNS1 WILD-TYPE 
             3            136 
$`MNS1 MUTATED`
TCGA-B7-5818 TCGA-BR-8078 TCGA-BR-8382 TCGA-FP-7998 TCGA-HJ-7597 TCGA-IN-7808 
       11.70        29.59        25.05        22.29        26.47         3.45 
TCGA-VQ-A8P2 
       38.14 

$`MNS1 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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 

  MNS1 MUTATED MNS1 WILD-TYPE 
          3.45           0.00 
  MNS1 MUTATED MNS1 WILD-TYPE 
         38.14         122.30 
  MNS1 MUTATED MNS1 WILD-TYPE 
         25.05          14.12 
[1] "3.5 - 38.1 (25.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D776V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MNS1 MUTATED         0        0        2        0         1         1
  MNS1 WILD-TYPE       2       15       38       30        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MNS1 MUTATED           0          1          0          2        0
  MNS1 WILD-TYPE         3         69         53         30       38
D776V3, multiclass
            clus
vv           MNS1 MUTATED MNS1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MNS1 MUTATED     0   2   2   4
  MNS1 WILD-TYPE  22  90 171  93
D776V4, multiclass
    clus
vv   MNS1 MUTATED MNS1 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            2            171
  T4            4             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
  MNS1 MUTATED     4   1   0   3
  MNS1 WILD-TYPE 114 103  77  74
D776V5, multiclass
    clus
vv   MNS1 MUTATED MNS1 WILD-TYPE
  N0            4            114
  N1            1            103
  N2            0             77
  N3            3             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"
D776V6, binary
                cls
clus               0   1
  MNS1 MUTATED     5   1
  MNS1 WILD-TYPE 341  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MNS1 MUTATED      5    1
  MNS1 WILD-TYPE  341   28
   clus
vv  MNS1 MUTATED MNS1 WILD-TYPE
  0            5            341
  1            1             28
[1] 2 2
[1] FALSE
D776V7, binary
                cls
clus               0   1
  MNS1 MUTATED     3   5
  MNS1 WILD-TYPE 142 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  MNS1 MUTATED      3    5
  MNS1 WILD-TYPE  142  243
        clus
vv       MNS1 MUTATED MNS1 WILD-TYPE
  FEMALE            3            142
  MALE              5            243
[1] 2 2
[1] FALSE
D776V8, binary
                cls
clus               0   1
  MNS1 MUTATED     6   1
  MNS1 WILD-TYPE 286  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  MNS1 MUTATED      6    1
  MNS1 WILD-TYPE  286   58
     clus
vv    MNS1 MUTATED MNS1 WILD-TYPE
  NO             6            286
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MNS1 MUTATED                                          1
  MNS1 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MNS1 MUTATED                                       3
  MNS1 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MNS1 MUTATED                                                        3
  MNS1 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MNS1 MUTATED                                                   1
  MNS1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MNS1 MUTATED                                                                   0
  MNS1 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MNS1 MUTATED                                                    0
  MNS1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MNS1 MUTATED                                                  0
  MNS1 WILD-TYPE                                               61
D776V9, multiclass
                                                                   clus
vv                                                                  MNS1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  MNS1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MNS1 MUTATED     7   0   0   0
  MNS1 WILD-TYPE 304  14  15  24
D776V10, multiclass
    clus
vv   MNS1 MUTATED MNS1 WILD-TYPE
  R0            7            304
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D776V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MNS1 MUTATED       0                         0
  MNS1 WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MNS1 MUTATED                                           0     8
  MNS1 WILD-TYPE                                         1   235
D776V12, multiclass
                                           clus
vv                                          MNS1 MUTATED MNS1 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D776V13, binary
                cls
clus               0   1
  MNS1 MUTATED     1   6
  MNS1 WILD-TYPE   3 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  MNS1 MUTATED      1    6
  MNS1 WILD-TYPE    3  304
                        clus
vv                       MNS1 MUTATED MNS1 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(777) Variable = ZNF800 MUTATION ANALYSIS
D777V1, survival
                  sevent
clus2                0   1
  ZNF800 MUTATED     7   2
  ZNF800 WILD-TYPE 223 137
  ZNF800 MUTATED ZNF800 WILD-TYPE 
               9              360 
  ZNF800 MUTATED ZNF800 WILD-TYPE 
               2              137 
$`ZNF800 MUTATED`
TCGA-BR-4184 TCGA-BR-8081 TCGA-CG-4305 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-A6F0 
        6.97        32.25        15.95       105.07        28.96        22.29 
TCGA-HU-A4G8 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       22.68        19.73        38.14 

$`ZNF800 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  ZNF800 MUTATED ZNF800 WILD-TYPE 
            6.97             0.00 
  ZNF800 MUTATED ZNF800 WILD-TYPE 
          105.07           122.30 
  ZNF800 MUTATED ZNF800 WILD-TYPE 
          22.680           14.055 
[1] "7.0 - 105.1 (22.7)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.7"
D777V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF800 MUTATED         0        1        1        2         0         2
  ZNF800 WILD-TYPE       2       14       39       28        37        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF800 MUTATED           0          4          0          0        1
  ZNF800 WILD-TYPE         3         66         53         32       37
D777V3, multiclass
            clus
vv           ZNF800 MUTATED ZNF800 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               0               37
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF800 MUTATED     1   3   3   4
  ZNF800 WILD-TYPE  21  89 170  93
D777V4, multiclass
    clus
vv   ZNF800 MUTATED ZNF800 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              3              170
  T4              4               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
  ZNF800 MUTATED     4   5   2   0
  ZNF800 WILD-TYPE 114  99  75  77
D777V5, multiclass
    clus
vv   ZNF800 MUTATED ZNF800 WILD-TYPE
  N0              4              114
  N1              5               99
  N2              2               75
  N3              0               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"
D777V6, binary
                  cls
clus                 0   1
  ZNF800 MUTATED    11   0
  ZNF800 WILD-TYPE 335  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF800 MUTATED     11    0
  ZNF800 WILD-TYPE  335   29
   clus
vv  ZNF800 MUTATED ZNF800 WILD-TYPE
  0             11              335
  1              0               29
[1] 2 2
[1] FALSE
D777V7, binary
                  cls
clus                 0   1
  ZNF800 MUTATED     7   5
  ZNF800 WILD-TYPE 138 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF800 MUTATED      7    5
  ZNF800 WILD-TYPE  138  243
        clus
vv       ZNF800 MUTATED ZNF800 WILD-TYPE
  FEMALE              7              138
  MALE                5              243
[1] 2 2
[1] FALSE
D777V8, binary
                  cls
clus                 0   1
  ZNF800 MUTATED     7   1
  ZNF800 WILD-TYPE 285  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF800 MUTATED      7    1
  ZNF800 WILD-TYPE  285   58
     clus
vv    ZNF800 MUTATED ZNF800 WILD-TYPE
  NO               7              285
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF800 MUTATED                                          0
  ZNF800 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF800 MUTATED                                       1
  ZNF800 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF800 MUTATED                                                        7
  ZNF800 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF800 MUTATED                                                   1
  ZNF800 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF800 MUTATED                                                                   2
  ZNF800 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF800 MUTATED                                                    0
  ZNF800 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF800 MUTATED                                                  1
  ZNF800 WILD-TYPE                                               60
D777V9, multiclass
                                                                   clus
vv                                                                  ZNF800 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ZNF800 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF800 MUTATED     7   0   0   4
  ZNF800 WILD-TYPE 304  14  15  20
D777V10, multiclass
    clus
vv   ZNF800 MUTATED ZNF800 WILD-TYPE
  R0              7              304
  R1              0               14
  R2              0               15
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D777V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF800 MUTATED       1                         0
  ZNF800 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF800 MUTATED                                           0     8
  ZNF800 WILD-TYPE                                         1   235
D777V12, multiclass
                                           clus
vv                                          ZNF800 MUTATED ZNF800 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D777V13, binary
                  cls
clus                 0   1
  ZNF800 MUTATED     0   8
  ZNF800 WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF800 MUTATED      0    8
  ZNF800 WILD-TYPE    4  302
                        clus
vv                       ZNF800 MUTATED ZNF800 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(778) Variable = PHACTR2 MUTATION ANALYSIS
D778V1, survival
                   sevent
clus2                 0   1
  PHACTR2 MUTATED    11   4
  PHACTR2 WILD-TYPE 219 135
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
               15               354 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
                4               135 
$`PHACTR2 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-8373 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 
       21.99        34.68        14.79         1.12        28.14        31.96 
TCGA-BR-8682 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-A4MJ TCGA-D7-A6EY TCGA-HU-8602 
       32.58        20.42         1.15        12.62        11.44        22.32 
TCGA-HU-A4GQ TCGA-VQ-A8P2 TCGA-VQ-A8PE 
        0.10        38.14        22.19 

$`PHACTR2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       26.73        24.79         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-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-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-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 

  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
              0.1               0.0 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
            38.14            122.30 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
            21.99             14.07 
[1] "0.1 - 38.1 (22.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D778V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHACTR2 MUTATED         0        0        2        0         2         2
  PHACTR2 WILD-TYPE       2       15       38       30        35        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHACTR2 MUTATED           0          2          3          2        2
  PHACTR2 WILD-TYPE         3         68         50         30       36
D778V3, multiclass
            clus
vv           PHACTR2 MUTATED PHACTR2 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               3                50
  STAGE IIIC               2                30
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PHACTR2 MUTATED     0   2   4   9
  PHACTR2 WILD-TYPE  22  90 169  88
D778V4, multiclass
    clus
vv   PHACTR2 MUTATED PHACTR2 WILD-TYPE
  T1               0                22
  T2               2                90
  T3               4               169
  T4               9                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
  PHACTR2 MUTATED     6   3   3   3
  PHACTR2 WILD-TYPE 112 101  74  74
D778V5, multiclass
    clus
vv   PHACTR2 MUTATED PHACTR2 WILD-TYPE
  N0               6               112
  N1               3               101
  N2               3                74
  N3               3                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"
D778V6, binary
                   cls
clus                  0   1
  PHACTR2 MUTATED    13   2
  PHACTR2 WILD-TYPE 333  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED     13    2
  PHACTR2 WILD-TYPE  333   27
   clus
vv  PHACTR2 MUTATED PHACTR2 WILD-TYPE
  0              13               333
  1               2                27
[1] 2 2
[1] FALSE
D778V7, binary
                   cls
clus                  0   1
  PHACTR2 MUTATED     7   8
  PHACTR2 WILD-TYPE 138 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED      7    8
  PHACTR2 WILD-TYPE  138  240
        clus
vv       PHACTR2 MUTATED PHACTR2 WILD-TYPE
  FEMALE               7               138
  MALE                 8               240
[1] 2 2
[1] FALSE
D778V8, binary
                   cls
clus                  0   1
  PHACTR2 MUTATED    14   1
  PHACTR2 WILD-TYPE 278  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED     14    1
  PHACTR2 WILD-TYPE  278   58
     clus
vv    PHACTR2 MUTATED PHACTR2 WILD-TYPE
  NO               14               278
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PHACTR2 MUTATED                                          0
  PHACTR2 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PHACTR2 MUTATED                                       1
  PHACTR2 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PHACTR2 MUTATED                                                        6
  PHACTR2 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PHACTR2 MUTATED                                                   2
  PHACTR2 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PHACTR2 MUTATED                                                                   2
  PHACTR2 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PHACTR2 MUTATED                                                    0
  PHACTR2 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PHACTR2 MUTATED                                                  4
  PHACTR2 WILD-TYPE                                               57
D778V9, multiclass
                                                                   clus
vv                                                                  PHACTR2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                4
                                                                   clus
vv                                                                  PHACTR2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PHACTR2 MUTATED    13   0   1   0
  PHACTR2 WILD-TYPE 298  14  14  24
D778V10, multiclass
    clus
vv   PHACTR2 MUTATED PHACTR2 WILD-TYPE
  R0              13               298
  R1               0                14
  R2               1                14
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D778V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PHACTR2 MUTATED       5                         0
  PHACTR2 WILD-TYPE    82                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PHACTR2 MUTATED                                           0     9
  PHACTR2 WILD-TYPE                                         1   234
D778V12, multiclass
                                           clus
vv                                          PHACTR2 MUTATED PHACTR2 WILD-TYPE
  ASIAN                                                   5                82
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D778V13, binary
                   cls
clus                  0   1
  PHACTR2 MUTATED     0  12
  PHACTR2 WILD-TYPE   4 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED      0   12
  PHACTR2 WILD-TYPE    4  298
                        clus
vv                       PHACTR2 MUTATED PHACTR2 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              12               298
[1] 2 2
[1] FALSE

Clustering(779) Variable = PLK2 MUTATION ANALYSIS
D779V1, survival
                sevent
clus2              0   1
  PLK2 MUTATED     5   2
  PLK2 WILD-TYPE 225 137
  PLK2 MUTATED PLK2 WILD-TYPE 
             7            362 
  PLK2 MUTATED PLK2 WILD-TYPE 
             2            137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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          14.12 
[1] "1.1 - 66.8 (19.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D779V2, 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       2       15       39       30        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLK2 MUTATED           0          1          1          1        1
  PLK2 WILD-TYPE         3         69         52         31       37
D779V3, multiclass
            clus
vv           PLK2 MUTATED PLK2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PLK2 MUTATED     0   1   4   2
  PLK2 WILD-TYPE  22  91 169  95
D779V4, multiclass
    clus
vv   PLK2 MUTATED PLK2 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            4            169
  T4            2             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
  PLK2 MUTATED     3   0   2   2
  PLK2 WILD-TYPE 115 104  75  75
D779V5, multiclass
    clus
vv   PLK2 MUTATED PLK2 WILD-TYPE
  N0            3            115
  N1            0            104
  N2            2             75
  N3            2             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"
D779V6, binary
                cls
clus               0   1
  PLK2 MUTATED     7   1
  PLK2 WILD-TYPE 339  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      7    1
  PLK2 WILD-TYPE  339   28
   clus
vv  PLK2 MUTATED PLK2 WILD-TYPE
  0            7            339
  1            1             28
[1] 2 2
[1] FALSE
D779V7, binary
                cls
clus               0   1
  PLK2 MUTATED     5   3
  PLK2 WILD-TYPE 140 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      5    3
  PLK2 WILD-TYPE  140  245
        clus
vv       PLK2 MUTATED PLK2 WILD-TYPE
  FEMALE            5            140
  MALE              3            245
[1] 2 2
[1] FALSE
D779V8, binary
                cls
clus               0   1
  PLK2 MUTATED     6   0
  PLK2 WILD-TYPE 286  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      6    0
  PLK2 WILD-TYPE  286   59
     clus
vv    PLK2 MUTATED PLK2 WILD-TYPE
  NO             6            286
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PLK2 MUTATED                                          0
  PLK2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PLK2 MUTATED                                       2
  PLK2 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLK2 MUTATED                                                        3
  PLK2 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PLK2 MUTATED                                                   0
  PLK2 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLK2 MUTATED                                                                   0
  PLK2 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PLK2 MUTATED                                                    0
  PLK2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PLK2 MUTATED                                                  3
  PLK2 WILD-TYPE                                               58
D779V9, multiclass
                                                                   clus
vv                                                                  PLK2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  PLK2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PLK2 MUTATED     6   0   0   1
  PLK2 WILD-TYPE 305  14  15  23
D779V10, multiclass
    clus
vv   PLK2 MUTATED PLK2 WILD-TYPE
  R0            6            305
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D779V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PLK2 MUTATED       3                         0
  PLK2 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLK2 MUTATED                                           0     5
  PLK2 WILD-TYPE                                         1   238
D779V12, multiclass
                                           clus
vv                                          PLK2 MUTATED PLK2 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D779V13, binary
                cls
clus               0   1
  PLK2 MUTATED     0   7
  PLK2 WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      0    7
  PLK2 WILD-TYPE    4  303
                        clus
vv                       PLK2 MUTATED PLK2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(780) Variable = SERPINB7 MUTATION ANALYSIS
D780V1, survival
                    sevent
clus2                  0   1
  SERPINB7 MUTATED     3   3
  SERPINB7 WILD-TYPE 227 136
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 6                363 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 3                136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58        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-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-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-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-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 

  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             14.430 
[1] "1.5 - 34.7 (10.9)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.7"
D780V2, 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       2       15       40       29        35        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB7 MUTATED           0          0          1          1        0
  SERPINB7 WILD-TYPE         3         70         52         31       38
D780V3, multiclass
            clus
vv           SERPINB7 MUTATED SERPINB7 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  1                 29
  STAGE IIA                 2                 35
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                1                 52
  STAGE IIIC                1                 31
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SERPINB7 MUTATED     0   1   2   3
  SERPINB7 WILD-TYPE  22  91 171  94
D780V4, multiclass
    clus
vv   SERPINB7 MUTATED SERPINB7 WILD-TYPE
  T1                0                 22
  T2                1                 91
  T3                2                171
  T4                3                 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
  SERPINB7 MUTATED     3   1   1   1
  SERPINB7 WILD-TYPE 115 103  76  76
D780V5, multiclass
    clus
vv   SERPINB7 MUTATED SERPINB7 WILD-TYPE
  N0                3                115
  N1                1                103
  N2                1                 76
  N3                1                 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"
D780V6, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     6   0
  SERPINB7 WILD-TYPE 340  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      6    0
  SERPINB7 WILD-TYPE  340   29
   clus
vv  SERPINB7 MUTATED SERPINB7 WILD-TYPE
  0                6                340
  1                0                 29
[1] 2 2
[1] FALSE
D780V7, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     2   4
  SERPINB7 WILD-TYPE 143 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      2    4
  SERPINB7 WILD-TYPE  143  244
        clus
vv       SERPINB7 MUTATED SERPINB7 WILD-TYPE
  FEMALE                2                143
  MALE                  4                244
[1] 2 2
[1] FALSE
D780V8, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     6   0
  SERPINB7 WILD-TYPE 286  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      6    0
  SERPINB7 WILD-TYPE  286   59
     clus
vv    SERPINB7 MUTATED SERPINB7 WILD-TYPE
  NO                 6                286
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SERPINB7 MUTATED                                          0
  SERPINB7 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SERPINB7 MUTATED                                       1
  SERPINB7 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SERPINB7 MUTATED                                                        3
  SERPINB7 WILD-TYPE                                                    155
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SERPINB7 MUTATED                                                   1
  SERPINB7 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SERPINB7 MUTATED                                                                   0
  SERPINB7 WILD-TYPE                                                                68
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SERPINB7 MUTATED                                                    0
  SERPINB7 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SERPINB7 MUTATED                                                  1
  SERPINB7 WILD-TYPE                                               60
D780V9, multiclass
                                                                   clus
vv                                                                  SERPINB7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  SERPINB7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SERPINB7 MUTATED     5   0   0   0
  SERPINB7 WILD-TYPE 306  14  15  24
D780V10, multiclass
    clus
vv   SERPINB7 MUTATED SERPINB7 WILD-TYPE
  R0                5                306
  R1                0                 14
  R2                0                 15
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D780V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SERPINB7 MUTATED       2                         0
  SERPINB7 WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SERPINB7 MUTATED                                           0     3
  SERPINB7 WILD-TYPE                                         1   240
D780V12, multiclass
                                           clus
vv                                          SERPINB7 MUTATED SERPINB7 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D780V13, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     0   5
  SERPINB7 WILD-TYPE   4 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      0    5
  SERPINB7 WILD-TYPE    4  305
                        clus
vv                       SERPINB7 MUTATED SERPINB7 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                5                305
[1] 2 2
[1] FALSE

Clustering(781) Variable = ZNF295 MUTATION ANALYSIS
D781V1, survival
                  sevent
clus2                0   1
  ZNF295 MUTATED     8   6
  ZNF295 WILD-TYPE 222 133
  ZNF295 MUTATED ZNF295 WILD-TYPE 
              14              355 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
               6              133 
$`ZNF295 MUTATED`
TCGA-CG-4460 TCGA-CG-5727 TCGA-B7-5816 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8363 
       21.99        79.07        26.70         9.34        34.68         0.26 
TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MI TCGA-CG-5728 TCGA-CG-5733 TCGA-HF-7132 
       16.14        12.43        11.77        65.10        21.07        77.29 
TCGA-HU-A4H6 TCGA-SW-A7EA 
       21.17        19.04 

$`ZNF295 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       47.05        22.98        16.24         0.23        20.15         9.86 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-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-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-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-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-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-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-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-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 

  ZNF295 MUTATED ZNF295 WILD-TYPE 
            0.26             0.00 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
           79.07           122.30 
  ZNF295 MUTATED ZNF295 WILD-TYPE 
           21.12            14.07 
[1] "0.3 - 79.1 (21.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D781V2, 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       1       15       37       27        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF295 MUTATED           0          4          1          0        1
  ZNF295 WILD-TYPE         3         66         52         32       37
D781V3, multiclass
            clus
vv           ZNF295 MUTATED ZNF295 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                3               27
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF295 MUTATED     1   5   6   3
  ZNF295 WILD-TYPE  21  87 167  94
D781V4, multiclass
    clus
vv   ZNF295 MUTATED ZNF295 WILD-TYPE
  T1              1               21
  T2              5               87
  T3              6              167
  T4              3               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
  ZNF295 MUTATED     8   6   2   1
  ZNF295 WILD-TYPE 110  98  75  76
D781V5, multiclass
    clus
vv   ZNF295 MUTATED ZNF295 WILD-TYPE
  N0              8              110
  N1              6               98
  N2              2               75
  N3              1               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"
D781V6, binary
                  cls
clus                 0   1
  ZNF295 MUTATED    16   1
  ZNF295 WILD-TYPE 330  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF295 MUTATED     16    1
  ZNF295 WILD-TYPE  330   28
   clus
vv  ZNF295 MUTATED ZNF295 WILD-TYPE
  0             16              330
  1              1               28
[1] 2 2
[1] FALSE
D781V7, binary
                  cls
clus                 0   1
  ZNF295 MUTATED    12   6
  ZNF295 WILD-TYPE 133 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF295 MUTATED     12    6
  ZNF295 WILD-TYPE  133  242
        clus
vv       ZNF295 MUTATED ZNF295 WILD-TYPE
  FEMALE             12              133
  MALE                6              242
[1] 2 2
[1] FALSE
D781V8, binary
                  cls
clus                 0   1
  ZNF295 MUTATED    13   1
  ZNF295 WILD-TYPE 279  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF295 MUTATED     13    1
  ZNF295 WILD-TYPE  279   58
     clus
vv    ZNF295 MUTATED ZNF295 WILD-TYPE
  NO              13              279
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF295 MUTATED                                          0
  ZNF295 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF295 MUTATED                                       2
  ZNF295 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF295 MUTATED                                                       10
  ZNF295 WILD-TYPE                                                    148
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF295 MUTATED                                                   1
  ZNF295 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF295 MUTATED                                                                   4
  ZNF295 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF295 MUTATED                                                    0
  ZNF295 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF295 MUTATED                                                  1
  ZNF295 WILD-TYPE                                               60
D781V9, multiclass
                                                                   clus
vv                                                                  ZNF295 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ZNF295 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF295 MUTATED    12   0   1   4
  ZNF295 WILD-TYPE 299  14  14  20
D781V10, multiclass
    clus
vv   ZNF295 MUTATED ZNF295 WILD-TYPE
  R0             12              299
  R1              0               14
  R2              1               14
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D781V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF295 MUTATED       3                         1
  ZNF295 WILD-TYPE    84                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF295 MUTATED                                           0     9
  ZNF295 WILD-TYPE                                         1   234
D781V12, multiclass
                                           clus
vv                                          ZNF295 MUTATED ZNF295 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D781V13, binary
                  cls
clus                 0   1
  ZNF295 MUTATED     0  13
  ZNF295 WILD-TYPE   4 297
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF295 MUTATED      0   13
  ZNF295 WILD-TYPE    4  297
                        clus
vv                       ZNF295 MUTATED ZNF295 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             13              297
[1] 2 2
[1] FALSE

Clustering(782) Variable = RINT1 MUTATION ANALYSIS
D782V1, survival
                 sevent
clus2               0   1
  RINT1 MUTATED     2   3
  RINT1 WILD-TYPE 228 136
  RINT1 MUTATED RINT1 WILD-TYPE 
              5             364 
  RINT1 MUTATED RINT1 WILD-TYPE 
              3             136 
$`RINT1 MUTATED`
TCGA-BR-6709 TCGA-BR-8078 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5726 
       12.16        29.59        31.96         6.58        28.96 

$`RINT1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-6710 TCGA-BR-6801 
       32.78        25.61        18.05        19.89         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-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-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 

  RINT1 MUTATED RINT1 WILD-TYPE 
           6.58            0.00 
  RINT1 MUTATED RINT1 WILD-TYPE 
          31.96          122.30 
  RINT1 MUTATED RINT1 WILD-TYPE 
          28.96           14.22 
[1] "6.6 - 32.0 (29.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D782V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RINT1 MUTATED         1        2        0        0         1         1
  RINT1 WILD-TYPE       1       13       40       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RINT1 MUTATED           0          0          1          0        1
  RINT1 WILD-TYPE         3         70         52         32       37
D782V3, multiclass
            clus
vv           RINT1 MUTATED RINT1 WILD-TYPE
  STAGE I                1               1
  STAGE IA               2              13
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RINT1 MUTATED     3   0   2   2
  RINT1 WILD-TYPE  19  92 171  95
D782V4, multiclass
    clus
vv   RINT1 MUTATED RINT1 WILD-TYPE
  T1             3              19
  T2             0              92
  T3             2             171
  T4             2              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
  RINT1 MUTATED     4   1   1   1
  RINT1 WILD-TYPE 114 103  76  76
D782V5, multiclass
    clus
vv   RINT1 MUTATED RINT1 WILD-TYPE
  N0             4             114
  N1             1             103
  N2             1              76
  N3             1              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"
D782V6, binary
                 cls
clus                0   1
  RINT1 MUTATED     5   1
  RINT1 WILD-TYPE 341  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RINT1 MUTATED      5    1
  RINT1 WILD-TYPE  341   28
   clus
vv  RINT1 MUTATED RINT1 WILD-TYPE
  0             5             341
  1             1              28
[1] 2 2
[1] FALSE
D782V7, binary
                 cls
clus                0   1
  RINT1 MUTATED     2   5
  RINT1 WILD-TYPE 143 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RINT1 MUTATED      2    5
  RINT1 WILD-TYPE  143  243
        clus
vv       RINT1 MUTATED RINT1 WILD-TYPE
  FEMALE             2             143
  MALE               5             243
[1] 2 2
[1] FALSE
D782V8, binary
                 cls
clus                0   1
  RINT1 MUTATED     5   1
  RINT1 WILD-TYPE 287  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RINT1 MUTATED      5    1
  RINT1 WILD-TYPE  287   58
     clus
vv    RINT1 MUTATED RINT1 WILD-TYPE
  NO              5             287
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RINT1 MUTATED                                          0
  RINT1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RINT1 MUTATED                                       1
  RINT1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RINT1 MUTATED                                                        4
  RINT1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RINT1 MUTATED                                                   0
  RINT1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RINT1 MUTATED                                                                   1
  RINT1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RINT1 MUTATED                                                    0
  RINT1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RINT1 MUTATED                                                  1
  RINT1 WILD-TYPE                                               60
D782V9, multiclass
                                                                   clus
vv                                                                  RINT1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  RINT1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RINT1 MUTATED     5   1   0   0
  RINT1 WILD-TYPE 306  13  15  24
D782V10, multiclass
    clus
vv   RINT1 MUTATED RINT1 WILD-TYPE
  R0             5             306
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D782V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RINT1 MUTATED       3                         1
  RINT1 WILD-TYPE    84                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RINT1 MUTATED                                           0     2
  RINT1 WILD-TYPE                                         1   241
D782V12, multiclass
                                           clus
vv                                          RINT1 MUTATED RINT1 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D782V13, binary
                 cls
clus                0   1
  RINT1 MUTATED     0   6
  RINT1 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RINT1 MUTATED      0    6
  RINT1 WILD-TYPE    4  304
                        clus
vv                       RINT1 MUTATED RINT1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(783) Variable = PDS5B MUTATION ANALYSIS
D783V1, survival
                 sevent
clus2               0   1
  PDS5B MUTATED    12   5
  PDS5B WILD-TYPE 218 134
  PDS5B MUTATED PDS5B WILD-TYPE 
             17             352 
  PDS5B MUTATED PDS5B WILD-TYPE 
              5             134 
$`PDS5B MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-8360 TCGA-BR-8680 
       21.99        26.70         6.97         9.34         6.18        31.96 
TCGA-CD-A4MG TCGA-CG-5723 TCGA-D7-A4YY TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GQ 
        6.58       105.07        13.78        22.32        24.20         0.10 
TCGA-HU-A4GU TCGA-HU-A4H6 TCGA-R5-A7ZI TCGA-SW-A7EA TCGA-VQ-A8P2 
        6.58        21.17        74.53        19.04        38.14 

$`PDS5B WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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-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-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 

  PDS5B MUTATED PDS5B WILD-TYPE 
            0.1             0.0 
  PDS5B MUTATED PDS5B WILD-TYPE 
         105.07          122.30 
  PDS5B MUTATED PDS5B WILD-TYPE 
          21.17           14.12 
[1] "0.1 - 105.1 (21.2)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D783V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PDS5B MUTATED         0        2        1        1         2         3
  PDS5B WILD-TYPE       2       13       39       29        35        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PDS5B MUTATED           0          3          1          1        4
  PDS5B WILD-TYPE         3         67         52         31       34
D783V3, multiclass
            clus
vv           PDS5B MUTATED PDS5B WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PDS5B MUTATED     2   2   6   8
  PDS5B WILD-TYPE  20  90 167  89
D783V4, multiclass
    clus
vv   PDS5B MUTATED PDS5B WILD-TYPE
  T1             2              20
  T2             2              90
  T3             6             167
  T4             8              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
  PDS5B MUTATED     7   7   4   1
  PDS5B WILD-TYPE 111  97  73  76
D783V5, multiclass
    clus
vv   PDS5B MUTATED PDS5B WILD-TYPE
  N0             7             111
  N1             7              97
  N2             4              73
  N3             1              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"
D783V6, binary
                 cls
clus                0   1
  PDS5B MUTATED    15   3
  PDS5B WILD-TYPE 331  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5B MUTATED     15    3
  PDS5B WILD-TYPE  331   26
   clus
vv  PDS5B MUTATED PDS5B WILD-TYPE
  0            15             331
  1             3              26
[1] 2 2
[1] FALSE
D783V7, binary
                 cls
clus                0   1
  PDS5B MUTATED     8  11
  PDS5B WILD-TYPE 137 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5B MUTATED      8   11
  PDS5B WILD-TYPE  137  237
        clus
vv       PDS5B MUTATED PDS5B WILD-TYPE
  FEMALE             8             137
  MALE              11             237
[1] 2 2
[1] FALSE
D783V8, binary
                 cls
clus                0   1
  PDS5B MUTATED    15   3
  PDS5B WILD-TYPE 277  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5B MUTATED     15    3
  PDS5B WILD-TYPE  277   56
     clus
vv    PDS5B MUTATED PDS5B WILD-TYPE
  NO             15             277
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PDS5B MUTATED                                          0
  PDS5B WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PDS5B MUTATED                                       6
  PDS5B WILD-TYPE                                    64
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PDS5B MUTATED                                                        6
  PDS5B WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PDS5B MUTATED                                                   1
  PDS5B WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PDS5B MUTATED                                                                   2
  PDS5B WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PDS5B MUTATED                                                    0
  PDS5B WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PDS5B MUTATED                                                  4
  PDS5B WILD-TYPE                                               57
D783V9, multiclass
                                                                   clus
vv                                                                  PDS5B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  PDS5B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PDS5B MUTATED    14   0   1   3
  PDS5B WILD-TYPE 297  14  14  21
D783V10, multiclass
    clus
vv   PDS5B MUTATED PDS5B WILD-TYPE
  R0            14             297
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D783V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PDS5B MUTATED       8                         0
  PDS5B WILD-TYPE    79                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PDS5B MUTATED                                           0     9
  PDS5B WILD-TYPE                                         1   234
D783V12, multiclass
                                           clus
vv                                          PDS5B MUTATED PDS5B WILD-TYPE
  ASIAN                                                 8              79
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D783V13, binary
                 cls
clus                0   1
  PDS5B MUTATED     1  15
  PDS5B WILD-TYPE   3 295
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDS5B MUTATED      1   15
  PDS5B WILD-TYPE    3  295
                        clus
vv                       PDS5B MUTATED PDS5B WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            15             295
[1] 2 2
[1] FALSE

Clustering(784) Variable = YBX2 MUTATION ANALYSIS
D784V1, survival
                sevent
clus2              0   1
  YBX2 MUTATED     4   2
  YBX2 WILD-TYPE 226 137
  YBX2 MUTATED YBX2 WILD-TYPE 
             6            363 
  YBX2 MUTATED YBX2 WILD-TYPE 
             2            137 
$`YBX2 MUTATED`
TCGA-B7-A5TI TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-A4QL TCGA-CG-4465 TCGA-HU-A4H4 
       19.56        34.68         4.31        16.14         9.01        23.84 

$`YBX2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  YBX2 MUTATED YBX2 WILD-TYPE 
          4.31           0.00 
  YBX2 MUTATED YBX2 WILD-TYPE 
         34.68         122.30 
  YBX2 MUTATED YBX2 WILD-TYPE 
         17.85          14.17 
[1] "4.3 - 34.7 (17.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D784V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  YBX2 MUTATED         0        0        1        0         1         1
  YBX2 WILD-TYPE       2       15       39       30        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  YBX2 MUTATED           0          0          1          1        1
  YBX2 WILD-TYPE         3         70         52         31       37
D784V3, multiclass
            clus
vv           YBX2 MUTATED YBX2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  YBX2 MUTATED     0   2   2   2
  YBX2 WILD-TYPE  22  90 171  95
D784V4, multiclass
    clus
vv   YBX2 MUTATED YBX2 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            2            171
  T4            2             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
  YBX2 MUTATED     2   0   1   3
  YBX2 WILD-TYPE 116 104  76  74
D784V5, multiclass
    clus
vv   YBX2 MUTATED YBX2 WILD-TYPE
  N0            2            116
  N1            0            104
  N2            1             76
  N3            3             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"
D784V6, binary
                cls
clus               0   1
  YBX2 MUTATED     5   1
  YBX2 WILD-TYPE 341  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  YBX2 MUTATED      5    1
  YBX2 WILD-TYPE  341   28
   clus
vv  YBX2 MUTATED YBX2 WILD-TYPE
  0            5            341
  1            1             28
[1] 2 2
[1] FALSE
D784V7, binary
                cls
clus               0   1
  YBX2 MUTATED     5   1
  YBX2 WILD-TYPE 140 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  YBX2 MUTATED      5    1
  YBX2 WILD-TYPE  140  247
        clus
vv       YBX2 MUTATED YBX2 WILD-TYPE
  FEMALE            5            140
  MALE              1            247
[1] 2 2
[1] FALSE
D784V8, binary
                cls
clus               0   1
  YBX2 MUTATED     5   0
  YBX2 WILD-TYPE 287  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  YBX2 MUTATED      5    0
  YBX2 WILD-TYPE  287   59
     clus
vv    YBX2 MUTATED YBX2 WILD-TYPE
  NO             5            287
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  YBX2 MUTATED                                          0
  YBX2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  YBX2 MUTATED                                       2
  YBX2 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  YBX2 MUTATED                                                        3
  YBX2 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  YBX2 MUTATED                                                   0
  YBX2 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  YBX2 MUTATED                                                                   0
  YBX2 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  YBX2 MUTATED                                                    0
  YBX2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  YBX2 MUTATED                                                  1
  YBX2 WILD-TYPE                                               60
D784V9, multiclass
                                                                   clus
vv                                                                  YBX2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  YBX2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  YBX2 MUTATED     4   0   1   0
  YBX2 WILD-TYPE 307  14  14  24
D784V10, multiclass
    clus
vv   YBX2 MUTATED YBX2 WILD-TYPE
  R0            4            307
  R1            0             14
  R2            1             14
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D784V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  YBX2 MUTATED       1                         0
  YBX2 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  YBX2 MUTATED                                           0     4
  YBX2 WILD-TYPE                                         1   239
D784V12, multiclass
                                           clus
vv                                          YBX2 MUTATED YBX2 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D784V13, binary
                cls
clus               0   1
  YBX2 MUTATED     0   5
  YBX2 WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  YBX2 MUTATED      0    5
  YBX2 WILD-TYPE    4  305
                        clus
vv                       YBX2 MUTATED YBX2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(785) Variable = CNOT6 MUTATION ANALYSIS
D785V1, survival
                 sevent
clus2               0   1
  CNOT6 MUTATED     4   2
  CNOT6 WILD-TYPE 226 137
  CNOT6 MUTATED CNOT6 WILD-TYPE 
              6             363 
  CNOT6 MUTATED CNOT6 WILD-TYPE 
              2             137 
$`CNOT6 MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-CG-5721 TCGA-CG-5728 TCGA-HJ-7597 TCGA-HU-A4GQ 
       26.70        19.56         6.02        65.10        26.47         0.10 

$`CNOT6 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        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-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-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-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 

  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          14.170 
[1] "0.1 - 65.1 (23.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D785V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNOT6 MUTATED         0        0        3        0         0         1
  CNOT6 WILD-TYPE       2       15       37       30        37        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNOT6 MUTATED           0          0          0          2        1
  CNOT6 WILD-TYPE         3         70         53         30       37
D785V3, multiclass
            clus
vv           CNOT6 MUTATED CNOT6 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CNOT6 MUTATED     1   3   0   4
  CNOT6 WILD-TYPE  21  89 173  93
D785V4, multiclass
    clus
vv   CNOT6 MUTATED CNOT6 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             0             173
  T4             4              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
  CNOT6 MUTATED     4   1   1   1
  CNOT6 WILD-TYPE 114 103  76  76
D785V5, multiclass
    clus
vv   CNOT6 MUTATED CNOT6 WILD-TYPE
  N0             4             114
  N1             1             103
  N2             1              76
  N3             1              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"
D785V6, binary
                 cls
clus                0   1
  CNOT6 MUTATED     7   0
  CNOT6 WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT6 MUTATED      7    0
  CNOT6 WILD-TYPE  339   29
   clus
vv  CNOT6 MUTATED CNOT6 WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D785V7, binary
                 cls
clus                0   1
  CNOT6 MUTATED     4   4
  CNOT6 WILD-TYPE 141 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT6 MUTATED      4    4
  CNOT6 WILD-TYPE  141  244
        clus
vv       CNOT6 MUTATED CNOT6 WILD-TYPE
  FEMALE             4             141
  MALE               4             244
[1] 2 2
[1] FALSE
D785V8, binary
                 cls
clus                0   1
  CNOT6 MUTATED     5   0
  CNOT6 WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT6 MUTATED      5    0
  CNOT6 WILD-TYPE  287   59
     clus
vv    CNOT6 MUTATED CNOT6 WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CNOT6 MUTATED                                          1
  CNOT6 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CNOT6 MUTATED                                       2
  CNOT6 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CNOT6 MUTATED                                                        1
  CNOT6 WILD-TYPE                                                    157
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CNOT6 MUTATED                                                   0
  CNOT6 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CNOT6 MUTATED                                                                   3
  CNOT6 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CNOT6 MUTATED                                                    0
  CNOT6 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CNOT6 MUTATED                                                  1
  CNOT6 WILD-TYPE                                               60
D785V9, multiclass
                                                                   clus
vv                                                                  CNOT6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  CNOT6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CNOT6 MUTATED     6   0   0   1
  CNOT6 WILD-TYPE 305  14  15  23
D785V10, multiclass
    clus
vv   CNOT6 MUTATED CNOT6 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D785V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CNOT6 MUTATED       1                         0
  CNOT6 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CNOT6 MUTATED                                           0     4
  CNOT6 WILD-TYPE                                         1   239
D785V12, multiclass
                                           clus
vv                                          CNOT6 MUTATED CNOT6 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D785V13, binary
                 cls
clus                0   1
  CNOT6 MUTATED     0   5
  CNOT6 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT6 MUTATED      0    5
  CNOT6 WILD-TYPE    4  305
                        clus
vv                       CNOT6 MUTATED CNOT6 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(786) Variable = ESRP1 MUTATION ANALYSIS
D786V1, survival
                 sevent
clus2               0   1
  ESRP1 MUTATED     4   4
  ESRP1 WILD-TYPE 226 135
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              8             361 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              4             135 
$`ESRP1 MUTATED`
TCGA-BR-4184 TCGA-BR-8363 TCGA-BR-8382 TCGA-CD-A4MG TCGA-CG-4477 TCGA-CG-5721 
        6.97         0.26        25.05         6.58        30.97         6.02 
TCGA-HU-A4H3 TCGA-VQ-AA6B 
       29.00        32.94 

$`ESRP1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
        7.07         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-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-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 

  ESRP1 MUTATED ESRP1 WILD-TYPE 
           0.26            0.00 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
          32.94          122.30 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
          16.01           14.27 
[1] "0.3 - 32.9 (16.0)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D786V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ESRP1 MUTATED         0        0        2        0         1         0
  ESRP1 WILD-TYPE       2       15       38       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ESRP1 MUTATED           0          1          1          2        1
  ESRP1 WILD-TYPE         3         69         52         30       37
D786V3, multiclass
            clus
vv           ESRP1 MUTATED ESRP1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ESRP1 MUTATED     1   2   3   3
  ESRP1 WILD-TYPE  21  90 170  94
D786V4, multiclass
    clus
vv   ESRP1 MUTATED ESRP1 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             3             170
  T4             3              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
  ESRP1 MUTATED     3   2   1   2
  ESRP1 WILD-TYPE 115 102  76  75
D786V5, multiclass
    clus
vv   ESRP1 MUTATED ESRP1 WILD-TYPE
  N0             3             115
  N1             2             102
  N2             1              76
  N3             2              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"
D786V6, binary
                 cls
clus                0   1
  ESRP1 MUTATED     8   0
  ESRP1 WILD-TYPE 338  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP1 MUTATED      8    0
  ESRP1 WILD-TYPE  338   29
   clus
vv  ESRP1 MUTATED ESRP1 WILD-TYPE
  0             8             338
  1             0              29
[1] 2 2
[1] FALSE
D786V7, binary
                 cls
clus                0   1
  ESRP1 MUTATED     5   4
  ESRP1 WILD-TYPE 140 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP1 MUTATED      5    4
  ESRP1 WILD-TYPE  140  244
        clus
vv       ESRP1 MUTATED ESRP1 WILD-TYPE
  FEMALE             5             140
  MALE               4             244
[1] 2 2
[1] FALSE
D786V8, binary
                 cls
clus                0   1
  ESRP1 MUTATED     5   2
  ESRP1 WILD-TYPE 287  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP1 MUTATED      5    2
  ESRP1 WILD-TYPE  287   57
     clus
vv    ESRP1 MUTATED ESRP1 WILD-TYPE
  NO              5             287
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ESRP1 MUTATED                                          0
  ESRP1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ESRP1 MUTATED                                       2
  ESRP1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ESRP1 MUTATED                                                        4
  ESRP1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ESRP1 MUTATED                                                   0
  ESRP1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ESRP1 MUTATED                                                                   3
  ESRP1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ESRP1 MUTATED                                                    0
  ESRP1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ESRP1 MUTATED                                                  0
  ESRP1 WILD-TYPE                                               61
D786V9, multiclass
                                                                   clus
vv                                                                  ESRP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  ESRP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ESRP1 MUTATED     6   0   0   2
  ESRP1 WILD-TYPE 305  14  15  22
D786V10, multiclass
    clus
vv   ESRP1 MUTATED ESRP1 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D786V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ESRP1 MUTATED       2                         0
  ESRP1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ESRP1 MUTATED                                           0     5
  ESRP1 WILD-TYPE                                         1   238
D786V12, multiclass
                                           clus
vv                                          ESRP1 MUTATED ESRP1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D786V13, binary
                 cls
clus                0   1
  ESRP1 MUTATED     0   6
  ESRP1 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP1 MUTATED      0    6
  ESRP1 WILD-TYPE    4  304
                        clus
vv                       ESRP1 MUTATED ESRP1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(787) Variable = LCE1A MUTATION ANALYSIS
D787V1, survival
                 sevent
clus2               0   1
  LCE1A MUTATED     2   2
  LCE1A WILD-TYPE 228 137
  LCE1A MUTATED LCE1A WILD-TYPE 
              4             365 
  LCE1A MUTATED LCE1A WILD-TYPE 
              2             137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
       13.87         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-D7-6518 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 

  LCE1A MUTATED LCE1A WILD-TYPE 
            7.4             0.0 
  LCE1A MUTATED LCE1A WILD-TYPE 
          20.65          122.30 
  LCE1A MUTATED LCE1A WILD-TYPE 
          10.98           14.27 
[1] "7.4 - 20.6 (11.0)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.8"
D787V2, 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       2       15       40       30        37        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LCE1A MUTATED           1          1          0          1        0
  LCE1A WILD-TYPE         2         69         53         31       38
D787V3, multiclass
            clus
vv           LCE1A MUTATED LCE1A WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LCE1A MUTATED     0   0   0   4
  LCE1A WILD-TYPE  22  92 173  93
D787V4, multiclass
    clus
vv   LCE1A MUTATED LCE1A WILD-TYPE
  T1             0              22
  T2             0              92
  T3             0             173
  T4             4              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
  LCE1A MUTATED     1   2   0   1
  LCE1A WILD-TYPE 117 102  77  76
D787V5, multiclass
    clus
vv   LCE1A MUTATED LCE1A WILD-TYPE
  N0             1             117
  N1             2             102
  N2             0              77
  N3             1              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"
D787V6, binary
                 cls
clus                0   1
  LCE1A MUTATED     4   0
  LCE1A WILD-TYPE 342  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE1A MUTATED      4    0
  LCE1A WILD-TYPE  342   29
   clus
vv  LCE1A MUTATED LCE1A WILD-TYPE
  0             4             342
  1             0              29
[1] 2 2
[1] FALSE
D787V7, binary
                 cls
clus                0   1
  LCE1A MUTATED     1   3
  LCE1A WILD-TYPE 144 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE1A MUTATED      1    3
  LCE1A WILD-TYPE  144  245
        clus
vv       LCE1A MUTATED LCE1A WILD-TYPE
  FEMALE             1             144
  MALE               3             245
[1] 2 2
[1] FALSE
D787V8, binary
                 cls
clus                0   1
  LCE1A MUTATED     4   0
  LCE1A WILD-TYPE 288  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE1A MUTATED      4    0
  LCE1A WILD-TYPE  288   59
     clus
vv    LCE1A MUTATED LCE1A WILD-TYPE
  NO              4             288
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LCE1A MUTATED                                          0
  LCE1A WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LCE1A MUTATED                                       1
  LCE1A WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LCE1A MUTATED                                                        1
  LCE1A WILD-TYPE                                                    157
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LCE1A MUTATED                                                   0
  LCE1A WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LCE1A MUTATED                                                                   1
  LCE1A WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LCE1A MUTATED                                                    0
  LCE1A WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LCE1A MUTATED                                                  1
  LCE1A WILD-TYPE                                               60
D787V9, multiclass
                                                                   clus
vv                                                                  LCE1A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  LCE1A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LCE1A MUTATED     4   0   0   0
  LCE1A WILD-TYPE 307  14  15  24
D787V10, multiclass
    clus
vv   LCE1A MUTATED LCE1A WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D787V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LCE1A MUTATED       1                         0
  LCE1A WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LCE1A MUTATED                                           0     3
  LCE1A WILD-TYPE                                         1   240
D787V12, multiclass
                                           clus
vv                                          LCE1A MUTATED LCE1A WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D787V13, binary
                 cls
clus                0   1
  LCE1A MUTATED     0   4
  LCE1A WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE1A MUTATED      0    4
  LCE1A WILD-TYPE    4  306
                        clus
vv                       LCE1A MUTATED LCE1A WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(788) Variable = PPARGC1B MUTATION ANALYSIS
D788V1, survival
                    sevent
clus2                  0   1
  PPARGC1B MUTATED     6   2
  PPARGC1B WILD-TYPE 224 137
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 8                361 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 2                137 
$`PPARGC1B MUTATED`
TCGA-CG-4460 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8591 TCGA-D7-A6EZ TCGA-HF-A5NB 
       21.99        31.10         1.12        28.14        20.32        30.51 
TCGA-HU-8602 TCGA-HU-A4GN 
       22.32        29.98 

$`PPARGC1B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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 

  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
              1.12               0.00 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
              31.1              122.3 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
             25.23              14.07 
[1] "1.1 - 31.1 (25.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.1"
D788V2, 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       2       15       40       30        35        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPARGC1B MUTATED           0          1          0          3        1
  PPARGC1B WILD-TYPE         3         69         53         29       37
D788V3, multiclass
            clus
vv           PPARGC1B MUTATED PPARGC1B WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 2                 35
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                0                 53
  STAGE IIIC                3                 29
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PPARGC1B MUTATED     0   1   2   6
  PPARGC1B WILD-TYPE  22  91 171  91
D788V4, multiclass
    clus
vv   PPARGC1B MUTATED PPARGC1B WILD-TYPE
  T1                0                 22
  T2                1                 91
  T3                2                171
  T4                6                 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
  PPARGC1B MUTATED     3   2   2   2
  PPARGC1B WILD-TYPE 115 102  75  75
D788V5, multiclass
    clus
vv   PPARGC1B MUTATED PPARGC1B WILD-TYPE
  N0                3                115
  N1                2                102
  N2                2                 75
  N3                2                 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"
D788V6, binary
                    cls
clus                   0   1
  PPARGC1B MUTATED     9   1
  PPARGC1B WILD-TYPE 337  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      9    1
  PPARGC1B WILD-TYPE  337   28
   clus
vv  PPARGC1B MUTATED PPARGC1B WILD-TYPE
  0                9                337
  1                1                 28
[1] 2 2
[1] FALSE
D788V7, binary
                    cls
clus                   0   1
  PPARGC1B MUTATED     6   4
  PPARGC1B WILD-TYPE 139 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      6    4
  PPARGC1B WILD-TYPE  139  244
        clus
vv       PPARGC1B MUTATED PPARGC1B WILD-TYPE
  FEMALE                6                139
  MALE                  4                244
[1] 2 2
[1] FALSE
D788V8, binary
                    cls
clus                   0   1
  PPARGC1B MUTATED     8   1
  PPARGC1B WILD-TYPE 284  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      8    1
  PPARGC1B WILD-TYPE  284   58
     clus
vv    PPARGC1B MUTATED PPARGC1B WILD-TYPE
  NO                 8                284
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PPARGC1B MUTATED                                          0
  PPARGC1B WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PPARGC1B MUTATED                                       1
  PPARGC1B WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPARGC1B MUTATED                                                        4
  PPARGC1B WILD-TYPE                                                    154
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PPARGC1B MUTATED                                                   1
  PPARGC1B WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPARGC1B MUTATED                                                                   3
  PPARGC1B WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PPARGC1B MUTATED                                                    0
  PPARGC1B WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PPARGC1B MUTATED                                                  1
  PPARGC1B WILD-TYPE                                               60
D788V9, multiclass
                                                                   clus
vv                                                                  PPARGC1B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  PPARGC1B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  PPARGC1B MUTATED     7   1   1   1
  PPARGC1B WILD-TYPE 304  13  14  23
D788V10, multiclass
    clus
vv   PPARGC1B MUTATED PPARGC1B WILD-TYPE
  R0                7                304
  R1                1                 13
  R2                1                 14
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D788V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PPARGC1B MUTATED       2                         0
  PPARGC1B WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPARGC1B MUTATED                                           0     6
  PPARGC1B WILD-TYPE                                         1   237
D788V12, multiclass
                                           clus
vv                                          PPARGC1B MUTATED PPARGC1B WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D788V13, binary
                    cls
clus                   0   1
  PPARGC1B MUTATED     0   8
  PPARGC1B WILD-TYPE   4 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      0    8
  PPARGC1B WILD-TYPE    4  302
                        clus
vv                       PPARGC1B MUTATED PPARGC1B WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                8                302
[1] 2 2
[1] FALSE

Clustering(789) Variable = MRPL24 MUTATION ANALYSIS
D789V1, survival
                  sevent
clus2                0   1
  MRPL24 MUTATED     5   1
  MRPL24 WILD-TYPE 225 138
  MRPL24 MUTATED MRPL24 WILD-TYPE 
               6              363 
  MRPL24 MUTATED MRPL24 WILD-TYPE 
               1              138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  MRPL24 MUTATED MRPL24 WILD-TYPE 
           15.95             0.00 
  MRPL24 MUTATED MRPL24 WILD-TYPE 
           44.94           122.30 
  MRPL24 MUTATED MRPL24 WILD-TYPE 
           31.82            14.07 
[1] "15.9 - 44.9 (31.8)" "0.0 - 122.3 (14.1)"
[1] "hr=" "3.7"
D789V2, 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       2       14       40       29        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPL24 MUTATED           0          2          0          0        0
  MRPL24 WILD-TYPE         3         68         53         32       38
D789V3, multiclass
            clus
vv           MRPL24 MUTATED MRPL24 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MRPL24 MUTATED     1   1   3   1
  MRPL24 WILD-TYPE  21  91 170  96
D789V4, multiclass
    clus
vv   MRPL24 MUTATED MRPL24 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              3              170
  T4              1               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
  MRPL24 MUTATED     3   2   1   0
  MRPL24 WILD-TYPE 115 102  76  77
D789V5, multiclass
    clus
vv   MRPL24 MUTATED MRPL24 WILD-TYPE
  N0              3              115
  N1              2              102
  N2              1               76
  N3              0               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"
D789V6, binary
                  cls
clus                 0   1
  MRPL24 MUTATED     6   0
  MRPL24 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL24 MUTATED      6    0
  MRPL24 WILD-TYPE  340   29
   clus
vv  MRPL24 MUTATED MRPL24 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D789V7, binary
                  cls
clus                 0   1
  MRPL24 MUTATED     3   3
  MRPL24 WILD-TYPE 142 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL24 MUTATED      3    3
  MRPL24 WILD-TYPE  142  245
        clus
vv       MRPL24 MUTATED MRPL24 WILD-TYPE
  FEMALE              3              142
  MALE                3              245
[1] 2 2
[1] FALSE
D789V8, binary
                  cls
clus                 0   1
  MRPL24 MUTATED     4   1
  MRPL24 WILD-TYPE 288  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL24 MUTATED      4    1
  MRPL24 WILD-TYPE  288   58
     clus
vv    MRPL24 MUTATED MRPL24 WILD-TYPE
  NO               4              288
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MRPL24 MUTATED                                          0
  MRPL24 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MRPL24 MUTATED                                       0
  MRPL24 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MRPL24 MUTATED                                                        3
  MRPL24 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MRPL24 MUTATED                                                   1
  MRPL24 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MRPL24 MUTATED                                                                   1
  MRPL24 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MRPL24 MUTATED                                                    0
  MRPL24 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MRPL24 MUTATED                                                  1
  MRPL24 WILD-TYPE                                               60
D789V9, multiclass
                                                                   clus
vv                                                                  MRPL24 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  MRPL24 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MRPL24 MUTATED     6   0   0   0
  MRPL24 WILD-TYPE 305  14  15  24
D789V10, multiclass
    clus
vv   MRPL24 MUTATED MRPL24 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D789V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MRPL24 MUTATED       0                         0
  MRPL24 WILD-TYPE    87                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MRPL24 MUTATED                                           0     4
  MRPL24 WILD-TYPE                                         1   239
D789V12, multiclass
                                           clus
vv                                          MRPL24 MUTATED MRPL24 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D789V13, binary
                  cls
clus                 0   1
  MRPL24 MUTATED     0   3
  MRPL24 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL24 MUTATED      0    3
  MRPL24 WILD-TYPE    4  307
                        clus
vv                       MRPL24 MUTATED MRPL24 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(790) Variable = F8 MUTATION ANALYSIS
D790V1, survival
              sevent
clus2            0   1
  F8 MUTATED    15  11
  F8 WILD-TYPE 215 128
  F8 MUTATED F8 WILD-TYPE 
          26          343 
  F8 MUTATED F8 WILD-TYPE 
          11          128 
$`F8 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8289 
       21.99         6.97         6.61        34.68        29.59         2.66 
TCGA-BR-8366 TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-8690 TCGA-CD-A4MG TCGA-CG-4465 
        0.95        25.05        31.96        10.68         6.58         9.01 
TCGA-CG-5721 TCGA-D7-5577 TCGA-D7-6521 TCGA-D7-8576 TCGA-D7-A6F2 TCGA-HF-7132 
        6.02        25.71        18.54        14.66        15.65        77.29 
TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4H8 TCGA-R5-A7ZE 
       30.51        22.68        11.77         6.51        14.07        18.21 
TCGA-RD-A7C1 TCGA-VQ-A8P2 
       16.67        38.14 

$`F8 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-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-D7-5578 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-D7-6522 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-D7-8578 
       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-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-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-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       24.26        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-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-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 

  F8 MUTATED F8 WILD-TYPE 
        0.95         0.00 
  F8 MUTATED F8 WILD-TYPE 
       77.29       122.30 
  F8 MUTATED F8 WILD-TYPE 
       16.16        14.07 
[1] "0.9 - 77.3 (16.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D790V2, continuous
              vv
clus           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  F8 MUTATED         0        1        4        1         5         2         1
  F8 WILD-TYPE       2       14       36       29        32        50         2
              vv
clus           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  F8 MUTATED            4          2          2        5
  F8 WILD-TYPE         66         51         30       33
D790V3, multiclass
            clus
vv           F8 MUTATED F8 WILD-TYPE
  STAGE I             0            2
  STAGE IA            1           14
  STAGE IB            4           36
  STAGE II            1           29
  STAGE IIA           5           32
  STAGE IIB           2           50
  STAGE III           1            2
  STAGE IIIA          4           66
  STAGE IIIB          2           51
  STAGE IIIC          2           30
  STAGE IV            5           33
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            T1  T2  T3  T4
  F8 MUTATED     3   7  10   9
  F8 WILD-TYPE  19  85 163  88
D790V4, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  T1          3           19
  T2          7           85
  T3         10          163
  T4          9           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
  F8 MUTATED    10   9   3   7
  F8 WILD-TYPE 108  95  74  70
D790V5, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  N0         10          108
  N1          9           95
  N2          3           74
  N3          7           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"
D790V6, binary
              cls
clus             0   1
  F8 MUTATED    25   4
  F8 WILD-TYPE 321  25
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     25    4
  F8 WILD-TYPE  321   25
   clus
vv  F8 MUTATED F8 WILD-TYPE
  0         25          321
  1          4           25
[1] 2 2
[1] FALSE
D790V7, binary
              cls
clus             0   1
  F8 MUTATED    16  14
  F8 WILD-TYPE 129 234
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     16   14
  F8 WILD-TYPE  129  234
        clus
vv       F8 MUTATED F8 WILD-TYPE
  FEMALE         16          129
  MALE           14          234
[1] 2 2
[1] FALSE
D790V8, binary
              cls
clus             0   1
  F8 MUTATED    22   3
  F8 WILD-TYPE 270  56
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     22    3
  F8 WILD-TYPE  270   56
     clus
vv    F8 MUTATED F8 WILD-TYPE
  NO          22          270
  YES          3           56
[1] 2 2
[1] FALSE
              vv
clus           STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  F8 MUTATED                                          0
  F8 WILD-TYPE                                        8
              vv
clus           STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  F8 MUTATED                                       5
  F8 WILD-TYPE                                    65
              vv
clus           STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  F8 MUTATED                                                       10
  F8 WILD-TYPE                                                    148
              vv
clus           STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  F8 MUTATED                                                   3
  F8 WILD-TYPE                                                18
              vv
clus           STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  F8 MUTATED                                                                   4
  F8 WILD-TYPE                                                                64
              vv
clus           STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  F8 MUTATED                                                    0
  F8 WILD-TYPE                                                  5
              vv
clus           STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  F8 MUTATED                                                  8
  F8 WILD-TYPE                                               53
D790V9, multiclass
                                                                   clus
vv                                                                  F8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                   0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                      5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                    10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)          4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                         0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                           8
                                                                   clus
vv                                                                  F8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                     148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            53
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            R0  R1  R2  RX
  F8 MUTATED    20   1   2   4
  F8 WILD-TYPE 291  13  13  20
D790V10, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  R0         20          291
  R1          1           13
  R2          2           13
  RX          4           20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D790V11, continuous
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN
  F8 MUTATED       6                         0
  F8 WILD-TYPE    81                         9
              vv
clus           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  F8 MUTATED                                           0    18
  F8 WILD-TYPE                                         1   225
D790V12, multiclass
                                           clus
vv                                          F8 MUTATED F8 WILD-TYPE
  ASIAN                                              6           81
  BLACK OR AFRICAN AMERICAN                          0            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER          0            1
  WHITE                                             18          225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D790V13, binary
              cls
clus             0   1
  F8 MUTATED     0  23
  F8 WILD-TYPE   4 287
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED      0   23
  F8 WILD-TYPE    4  287
                        clus
vv                       F8 MUTATED F8 WILD-TYPE
  HISPANIC OR LATINO              0            4
  NOT HISPANIC OR LATINO         23          287
[1] 2 2
[1] FALSE

Clustering(791) Variable = GOLT1B MUTATION ANALYSIS
D791V1, survival
                  sevent
clus2                0   1
  GOLT1B MUTATED     4   1
  GOLT1B WILD-TYPE 226 138
  GOLT1B MUTATED GOLT1B WILD-TYPE 
               5              364 
  GOLT1B MUTATED GOLT1B WILD-TYPE 
               1              138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  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            14.07 
[1] "22.0 - 35.8 (29.6)" "0.0 - 122.3 (14.1)"
[1] "hr=" "3.2"
D791V2, 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       2       15       39       30        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GOLT1B MUTATED           0          1          0          1        1
  GOLT1B WILD-TYPE         3         69         53         31       37
D791V3, multiclass
            clus
vv           GOLT1B MUTATED GOLT1B WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GOLT1B MUTATED     0   1   1   3
  GOLT1B WILD-TYPE  22  91 172  94
D791V4, multiclass
    clus
vv   GOLT1B MUTATED GOLT1B WILD-TYPE
  T1              0               22
  T2              1               91
  T3              1              172
  T4              3               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
  GOLT1B MUTATED     2   1   1   1
  GOLT1B WILD-TYPE 116 103  76  76
D791V5, multiclass
    clus
vv   GOLT1B MUTATED GOLT1B WILD-TYPE
  N0              2              116
  N1              1              103
  N2              1               76
  N3              1               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"
D791V6, binary
                  cls
clus                 0   1
  GOLT1B MUTATED     4   1
  GOLT1B WILD-TYPE 342  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLT1B MUTATED      4    1
  GOLT1B WILD-TYPE  342   28
   clus
vv  GOLT1B MUTATED GOLT1B WILD-TYPE
  0              4              342
  1              1               28
[1] 2 2
[1] FALSE
D791V7, binary
                  cls
clus                 0   1
  GOLT1B MUTATED     3   2
  GOLT1B WILD-TYPE 142 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLT1B MUTATED      3    2
  GOLT1B WILD-TYPE  142  246
        clus
vv       GOLT1B MUTATED GOLT1B WILD-TYPE
  FEMALE              3              142
  MALE                2              246
[1] 2 2
[1] FALSE
D791V8, binary
                  cls
clus                 0   1
  GOLT1B MUTATED     5   0
  GOLT1B WILD-TYPE 287  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLT1B MUTATED      5    0
  GOLT1B WILD-TYPE  287   59
     clus
vv    GOLT1B MUTATED GOLT1B WILD-TYPE
  NO               5              287
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GOLT1B MUTATED                                          0
  GOLT1B WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GOLT1B MUTATED                                       0
  GOLT1B WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GOLT1B MUTATED                                                        4
  GOLT1B WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GOLT1B MUTATED                                                   0
  GOLT1B WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GOLT1B MUTATED                                                                   1
  GOLT1B WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GOLT1B MUTATED                                                    0
  GOLT1B WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GOLT1B MUTATED                                                  0
  GOLT1B WILD-TYPE                                               61
D791V9, multiclass
                                                                   clus
vv                                                                  GOLT1B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  GOLT1B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GOLT1B MUTATED     4   0   1   0
  GOLT1B WILD-TYPE 307  14  14  24
D791V10, multiclass
    clus
vv   GOLT1B MUTATED GOLT1B WILD-TYPE
  R0              4              307
  R1              0               14
  R2              1               14
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D791V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GOLT1B MUTATED       0                         0
  GOLT1B WILD-TYPE    87                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GOLT1B MUTATED                                           0     4
  GOLT1B WILD-TYPE                                         1   239
D791V12, multiclass
                                           clus
vv                                          GOLT1B MUTATED GOLT1B WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D791V13, binary
                  cls
clus                 0   1
  GOLT1B MUTATED     0   4
  GOLT1B WILD-TYPE   4 306
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLT1B MUTATED      0    4
  GOLT1B WILD-TYPE    4  306
                        clus
vv                       GOLT1B MUTATED GOLT1B WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              306
[1] 2 2
[1] FALSE

Clustering(792) Variable = HOOK1 MUTATION ANALYSIS
D792V1, survival
                 sevent
clus2               0   1
  HOOK1 MUTATED     4   2
  HOOK1 WILD-TYPE 226 137
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              6             363 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
              2             137 
$`HOOK1 MUTATED`
TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-5717 TCGA-VQ-A8P2 
       34.68        32.25         1.12        16.14         6.97        38.14 

$`HOOK1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07        30.97        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-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 

  HOOK1 MUTATED HOOK1 WILD-TYPE 
           1.12            0.00 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
          38.14          122.30 
  HOOK1 MUTATED HOOK1 WILD-TYPE 
         24.195          14.170 
[1] "1.1 - 38.1 (24.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D792V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HOOK1 MUTATED         0        0        0        1         2         1
  HOOK1 WILD-TYPE       2       15       40       29        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HOOK1 MUTATED           0          2          1          0        0
  HOOK1 WILD-TYPE         3         68         52         32       38
D792V3, multiclass
            clus
vv           HOOK1 MUTATED HOOK1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HOOK1 MUTATED     0   1   3   3
  HOOK1 WILD-TYPE  22  91 170  94
D792V4, multiclass
    clus
vv   HOOK1 MUTATED HOOK1 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             3             170
  T4             3              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
  HOOK1 MUTATED     4   2   0   1
  HOOK1 WILD-TYPE 114 102  77  76
D792V5, multiclass
    clus
vv   HOOK1 MUTATED HOOK1 WILD-TYPE
  N0             4             114
  N1             2             102
  N2             0              77
  N3             1              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"
D792V6, binary
                 cls
clus                0   1
  HOOK1 MUTATED     7   0
  HOOK1 WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK1 MUTATED      7    0
  HOOK1 WILD-TYPE  339   29
   clus
vv  HOOK1 MUTATED HOOK1 WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D792V7, binary
                 cls
clus                0   1
  HOOK1 MUTATED     5   2
  HOOK1 WILD-TYPE 140 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK1 MUTATED      5    2
  HOOK1 WILD-TYPE  140  246
        clus
vv       HOOK1 MUTATED HOOK1 WILD-TYPE
  FEMALE             5             140
  MALE               2             246
[1] 2 2
[1] FALSE
D792V8, binary
                 cls
clus                0   1
  HOOK1 MUTATED     5   1
  HOOK1 WILD-TYPE 287  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK1 MUTATED      5    1
  HOOK1 WILD-TYPE  287   58
     clus
vv    HOOK1 MUTATED HOOK1 WILD-TYPE
  NO              5             287
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HOOK1 MUTATED                                          0
  HOOK1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HOOK1 MUTATED                                       0
  HOOK1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HOOK1 MUTATED                                                        6
  HOOK1 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HOOK1 MUTATED                                                   1
  HOOK1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HOOK1 MUTATED                                                                   0
  HOOK1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HOOK1 MUTATED                                                    0
  HOOK1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HOOK1 MUTATED                                                  0
  HOOK1 WILD-TYPE                                               61
D792V9, multiclass
                                                                   clus
vv                                                                  HOOK1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  HOOK1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HOOK1 MUTATED     6   0   0   1
  HOOK1 WILD-TYPE 305  14  15  23
D792V10, multiclass
    clus
vv   HOOK1 MUTATED HOOK1 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D792V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HOOK1 MUTATED       0                         0
  HOOK1 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HOOK1 MUTATED                                           0     6
  HOOK1 WILD-TYPE                                         1   237
D792V12, multiclass
                                           clus
vv                                          HOOK1 MUTATED HOOK1 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D792V13, binary
                 cls
clus                0   1
  HOOK1 MUTATED     0   5
  HOOK1 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK1 MUTATED      0    5
  HOOK1 WILD-TYPE    4  305
                        clus
vv                       HOOK1 MUTATED HOOK1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(793) Variable = ARHGEF5 MUTATION ANALYSIS
D793V1, survival
                   sevent
clus2                 0   1
  ARHGEF5 MUTATED     6   1
  ARHGEF5 WILD-TYPE 224 138
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                7               362 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                1               138 
$`ARHGEF5 MUTATED`
TCGA-B7-5816 TCGA-BR-8078 TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-5721 TCGA-FP-A4BE 
       26.70        29.59        16.14        12.62         6.02        11.08 
TCGA-HF-7132 
       77.29 

$`ARHGEF5 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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 

  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
             6.02              0.00 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
            77.29            122.30 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
            16.14             14.22 
[1] "6.0 - 77.3 (16.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3.4"
D793V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARHGEF5 MUTATED         0        0        1        1         1         2
  ARHGEF5 WILD-TYPE       2       15       39       29        36        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF5 MUTATED           0          0          1          0        1
  ARHGEF5 WILD-TYPE         3         70         52         32       37
D793V3, multiclass
            clus
vv           ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ARHGEF5 MUTATED     0   2   2   3
  ARHGEF5 WILD-TYPE  22  90 171  94
D793V4, multiclass
    clus
vv   ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  T1               0                22
  T2               2                90
  T3               2               171
  T4               3                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
  ARHGEF5 MUTATED     4   2   0   1
  ARHGEF5 WILD-TYPE 114 102  77  76
D793V5, multiclass
    clus
vv   ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  N0               4               114
  N1               2               102
  N2               0                77
  N3               1                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"
D793V6, binary
                   cls
clus                  0   1
  ARHGEF5 MUTATED     7   0
  ARHGEF5 WILD-TYPE 339  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      7    0
  ARHGEF5 WILD-TYPE  339   29
   clus
vv  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  0               7               339
  1               0                29
[1] 2 2
[1] FALSE
D793V7, binary
                   cls
clus                  0   1
  ARHGEF5 MUTATED     3   4
  ARHGEF5 WILD-TYPE 142 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      3    4
  ARHGEF5 WILD-TYPE  142  244
        clus
vv       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  FEMALE               3               142
  MALE                 4               244
[1] 2 2
[1] FALSE
D793V8, binary
                   cls
clus                  0   1
  ARHGEF5 MUTATED     5   2
  ARHGEF5 WILD-TYPE 287  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      5    2
  ARHGEF5 WILD-TYPE  287   57
     clus
vv    ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  NO                5               287
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARHGEF5 MUTATED                                          0
  ARHGEF5 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARHGEF5 MUTATED                                       1
  ARHGEF5 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARHGEF5 MUTATED                                                        4
  ARHGEF5 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARHGEF5 MUTATED                                                   1
  ARHGEF5 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARHGEF5 MUTATED                                                                   1
  ARHGEF5 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARHGEF5 MUTATED                                                    0
  ARHGEF5 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARHGEF5 MUTATED                                                  0
  ARHGEF5 WILD-TYPE                                               61
D793V9, multiclass
                                                                   clus
vv                                                                  ARHGEF5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  ARHGEF5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ARHGEF5 MUTATED     6   0   0   0
  ARHGEF5 WILD-TYPE 305  14  15  24
D793V10, multiclass
    clus
vv   ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  R0               6               305
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D793V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ARHGEF5 MUTATED       1                         1
  ARHGEF5 WILD-TYPE    86                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARHGEF5 MUTATED                                           0     3
  ARHGEF5 WILD-TYPE                                         1   240
D793V12, multiclass
                                           clus
vv                                          ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D793V13, binary
                   cls
clus                  0   1
  ARHGEF5 MUTATED     0   5
  ARHGEF5 WILD-TYPE   4 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      0    5
  ARHGEF5 WILD-TYPE    4  305
                        clus
vv                       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(794) Variable = CIB3 MUTATION ANALYSIS
D794V1, survival
                sevent
clus2              0   1
  CIB3 MUTATED     2   2
  CIB3 WILD-TYPE 228 137
  CIB3 MUTATED CIB3 WILD-TYPE 
             4            365 
  CIB3 MUTATED CIB3 WILD-TYPE 
             2            137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-5578 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 

  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          14.17 
[1] "11.1 - 30.9 (23.1)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1"  
D794V2, 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       2       15       39       30        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CIB3 MUTATED           0          2          0          1        0
  CIB3 WILD-TYPE         3         68         53         31       38
D794V3, multiclass
            clus
vv           CIB3 MUTATED CIB3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CIB3 MUTATED     0   2   2   1
  CIB3 WILD-TYPE  22  90 171  96
D794V4, multiclass
    clus
vv   CIB3 MUTATED CIB3 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            2            171
  T4            1             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
  CIB3 MUTATED     2   0   2   1
  CIB3 WILD-TYPE 116 104  75  76
D794V5, multiclass
    clus
vv   CIB3 MUTATED CIB3 WILD-TYPE
  N0            2            116
  N1            0            104
  N2            2             75
  N3            1             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"
D794V6, binary
                cls
clus               0   1
  CIB3 MUTATED     5   0
  CIB3 WILD-TYPE 341  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIB3 MUTATED      5    0
  CIB3 WILD-TYPE  341   29
   clus
vv  CIB3 MUTATED CIB3 WILD-TYPE
  0            5            341
  1            0             29
[1] 2 2
[1] FALSE
D794V7, binary
                cls
clus               0   1
  CIB3 MUTATED     2   3
  CIB3 WILD-TYPE 143 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIB3 MUTATED      2    3
  CIB3 WILD-TYPE  143  245
        clus
vv       CIB3 MUTATED CIB3 WILD-TYPE
  FEMALE            2            143
  MALE              3            245
[1] 2 2
[1] FALSE
D794V8, binary
                cls
clus               0   1
  CIB3 MUTATED     3   1
  CIB3 WILD-TYPE 289  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIB3 MUTATED      3    1
  CIB3 WILD-TYPE  289   58
     clus
vv    CIB3 MUTATED CIB3 WILD-TYPE
  NO             3            289
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CIB3 MUTATED                                          0
  CIB3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CIB3 MUTATED                                       0
  CIB3 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CIB3 MUTATED                                                        3
  CIB3 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CIB3 MUTATED                                                   0
  CIB3 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CIB3 MUTATED                                                                   2
  CIB3 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CIB3 MUTATED                                                    0
  CIB3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CIB3 MUTATED                                                  0
  CIB3 WILD-TYPE                                               61
D794V9, multiclass
                                                                   clus
vv                                                                  CIB3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  CIB3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CIB3 MUTATED     5   0   0   0
  CIB3 WILD-TYPE 306  14  15  24
D794V10, multiclass
    clus
vv   CIB3 MUTATED CIB3 WILD-TYPE
  R0            5            306
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D794V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CIB3 MUTATED       0                         1
  CIB3 WILD-TYPE    87                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CIB3 MUTATED                                           0     2
  CIB3 WILD-TYPE                                         1   241
D794V12, multiclass
                                           clus
vv                                          CIB3 MUTATED CIB3 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D794V13, binary
                cls
clus               0   1
  CIB3 MUTATED     0   3
  CIB3 WILD-TYPE   4 307
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIB3 MUTATED      0    3
  CIB3 WILD-TYPE    4  307
                        clus
vv                       CIB3 MUTATED CIB3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            3            307
[1] 2 2
[1] FALSE

Clustering(795) Variable = TBL1XR1 MUTATION ANALYSIS
D795V1, survival
                   sevent
clus2                 0   1
  TBL1XR1 MUTATED     4   2
  TBL1XR1 WILD-TYPE 226 137
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                6               363 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                2               137 
$`TBL1XR1 MUTATED`
TCGA-BR-4256 TCGA-BR-8078 TCGA-BR-8680 TCGA-CG-5726 TCGA-FP-A4BE TCGA-VQ-A8P2 
        9.34        29.59        31.96        28.96        11.08        38.14 

$`TBL1XR1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
             9.34              0.00 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
            38.14            122.30 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
           29.275            14.170 
[1] "9.3 - 38.1 (29.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D795V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TBL1XR1 MUTATED         0        1        0        0         1         1
  TBL1XR1 WILD-TYPE       2       14       40       30        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBL1XR1 MUTATED           0          2          0          0        2
  TBL1XR1 WILD-TYPE         3         68         53         32       36
D795V3, multiclass
            clus
vv           TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TBL1XR1 MUTATED     1   0   1   5
  TBL1XR1 WILD-TYPE  21  92 172  92
D795V4, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  T1               1                21
  T2               0                92
  T3               1               172
  T4               5                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
  TBL1XR1 MUTATED     4   2   2   0
  TBL1XR1 WILD-TYPE 114 102  75  77
D795V5, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  N0               4               114
  N1               2               102
  N2               2                75
  N3               0                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"
D795V6, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     7   1
  TBL1XR1 WILD-TYPE 339  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      7    1
  TBL1XR1 WILD-TYPE  339   28
   clus
vv  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  0               7               339
  1               1                28
[1] 2 2
[1] FALSE
D795V7, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     3   5
  TBL1XR1 WILD-TYPE 142 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      3    5
  TBL1XR1 WILD-TYPE  142  243
        clus
vv       TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  FEMALE               3               142
  MALE                 5               243
[1] 2 2
[1] FALSE
D795V8, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     3   2
  TBL1XR1 WILD-TYPE 289  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      3    2
  TBL1XR1 WILD-TYPE  289   57
     clus
vv    TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  NO                3               289
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TBL1XR1 MUTATED                                          0
  TBL1XR1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TBL1XR1 MUTATED                                       0
  TBL1XR1 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TBL1XR1 MUTATED                                                        5
  TBL1XR1 WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TBL1XR1 MUTATED                                                   1
  TBL1XR1 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TBL1XR1 MUTATED                                                                   1
  TBL1XR1 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TBL1XR1 MUTATED                                                    0
  TBL1XR1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TBL1XR1 MUTATED                                                  1
  TBL1XR1 WILD-TYPE                                               60
D795V9, multiclass
                                                                   clus
vv                                                                  TBL1XR1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  TBL1XR1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TBL1XR1 MUTATED     5   0   0   3
  TBL1XR1 WILD-TYPE 306  14  15  21
D795V10, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  R0               5               306
  R1               0                14
  R2               0                15
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D795V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TBL1XR1 MUTATED       1                         1
  TBL1XR1 WILD-TYPE    86                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TBL1XR1 MUTATED                                           0     5
  TBL1XR1 WILD-TYPE                                         1   238
D795V12, multiclass
                                           clus
vv                                          TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D795V13, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     0   6
  TBL1XR1 WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      0    6
  TBL1XR1 WILD-TYPE    4  304
                        clus
vv                       TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(796) Variable = WHSC1L1 MUTATION ANALYSIS
D796V1, survival
                   sevent
clus2                 0   1
  WHSC1L1 MUTATED    13   1
  WHSC1L1 WILD-TYPE 217 138
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
               14               355 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                1               138 
$`WHSC1L1 MUTATED`
TCGA-KB-A93G TCGA-B7-5816 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8368 TCGA-CD-8536 
       20.15        26.70         9.34        34.68         4.31        12.43 
TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-D7-6822 TCGA-HU-A4GN TCGA-HU-A4GU 
       12.62        27.02        15.95        12.33        29.98         6.58 
TCGA-RD-A8N1 TCGA-VQ-A8P2 
      115.69        38.14 

$`WHSC1L1 WILD-TYPE`
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-MX-A663 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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 
            18.05             14.17 
[1] "4.3 - 115.7 (18.0)" "0.0 - 122.3 (14.2)"
[1] "hr=" "6.7"
D796V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WHSC1L1 MUTATED         0        0        6        2         2         2
  WHSC1L1 WILD-TYPE       2       15       34       28        35        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WHSC1L1 MUTATED           0          2          1          0        0
  WHSC1L1 WILD-TYPE         3         68         52         32       38
D796V3, multiclass
            clus
vv           WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 6                34
  STAGE II                 2                28
  STAGE IIA                2                35
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  WHSC1L1 MUTATED     0   8   4   3
  WHSC1L1 WILD-TYPE  22  84 169  94
D796V4, multiclass
    clus
vv   WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  T1               0                22
  T2               8                84
  T3               4               169
  T4               3                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
  WHSC1L1 MUTATED    10   6   1   0
  WHSC1L1 WILD-TYPE 108  98  76  77
D796V5, multiclass
    clus
vv   WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  N0              10               108
  N1               6                98
  N2               1                76
  N3               0                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"
D796V6, binary
                   cls
clus                  0   1
  WHSC1L1 MUTATED    18   0
  WHSC1L1 WILD-TYPE 328  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED     18    0
  WHSC1L1 WILD-TYPE  328   29
   clus
vv  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  0              18               328
  1               0                29
[1] 2 2
[1] FALSE
D796V7, binary
                   cls
clus                  0   1
  WHSC1L1 MUTATED     6  12
  WHSC1L1 WILD-TYPE 139 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED      6   12
  WHSC1L1 WILD-TYPE  139  236
        clus
vv       WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  FEMALE               6               139
  MALE                12               236
[1] 2 2
[1] FALSE
D796V8, binary
                   cls
clus                  0   1
  WHSC1L1 MUTATED    11   2
  WHSC1L1 WILD-TYPE 281  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED     11    2
  WHSC1L1 WILD-TYPE  281   57
     clus
vv    WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  NO               11               281
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  WHSC1L1 MUTATED                                          1
  WHSC1L1 WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  WHSC1L1 MUTATED                                       3
  WHSC1L1 WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WHSC1L1 MUTATED                                                       10
  WHSC1L1 WILD-TYPE                                                    148
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  WHSC1L1 MUTATED                                                   1
  WHSC1L1 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WHSC1L1 MUTATED                                                                   1
  WHSC1L1 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  WHSC1L1 MUTATED                                                    0
  WHSC1L1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  WHSC1L1 MUTATED                                                  2
  WHSC1L1 WILD-TYPE                                               59
D796V9, multiclass
                                                                   clus
vv                                                                  WHSC1L1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  WHSC1L1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  WHSC1L1 MUTATED    12   1   0   4
  WHSC1L1 WILD-TYPE 299  13  15  20
D796V10, multiclass
    clus
vv   WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  R0              12               299
  R1               1                13
  R2               0                15
  RX               4                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D796V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  WHSC1L1 MUTATED       4                         0
  WHSC1L1 WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WHSC1L1 MUTATED                                           0    11
  WHSC1L1 WILD-TYPE                                         1   232
D796V12, multiclass
                                           clus
vv                                          WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D796V13, binary
                   cls
clus                  0   1
  WHSC1L1 MUTATED     0  13
  WHSC1L1 WILD-TYPE   4 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED      0   13
  WHSC1L1 WILD-TYPE    4  297
                        clus
vv                       WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              13               297
[1] 2 2
[1] FALSE

Clustering(797) Variable = C1ORF14 MUTATION ANALYSIS
D797V1, survival
                   sevent
clus2                 0   1
  C1ORF14 MUTATED     7   5
  C1ORF14 WILD-TYPE 223 134
  C1ORF14 MUTATED C1ORF14 WILD-TYPE 
               12               357 
  C1ORF14 MUTATED C1ORF14 WILD-TYPE 
                5               134 
$`C1ORF14 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8591 TCGA-BR-8680 
        6.97         6.61        35.84        32.25        28.14        31.96 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-F1-6874 TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H8 
       21.44        16.14        14.47         0.10        20.25        14.07 

$`C1ORF14 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.65        20.42         1.15         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-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-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-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 

  C1ORF14 MUTATED C1ORF14 WILD-TYPE 
              0.1               0.0 
  C1ORF14 MUTATED C1ORF14 WILD-TYPE 
            35.84            122.30 
  C1ORF14 MUTATED C1ORF14 WILD-TYPE 
           18.195            14.070 
[1] "0.1 - 35.8 (18.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D797V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C1ORF14 MUTATED         0        0        4        0         1         2
  C1ORF14 WILD-TYPE       2       15       36       30        36        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF14 MUTATED           1          1          1          3        1
  C1ORF14 WILD-TYPE         2         69         52         29       37
D797V3, multiclass
            clus
vv           C1ORF14 MUTATED C1ORF14 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 4                36
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                2                50
  STAGE III                1                 2
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               3                29
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C1ORF14 MUTATED     1   4   3   6
  C1ORF14 WILD-TYPE  21  88 170  91
D797V4, multiclass
    clus
vv   C1ORF14 MUTATED C1ORF14 WILD-TYPE
  T1               1                21
  T2               4                88
  T3               3               170
  T4               6                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
  C1ORF14 MUTATED     6   3   3   2
  C1ORF14 WILD-TYPE 112 101  74  75
D797V5, multiclass
    clus
vv   C1ORF14 MUTATED C1ORF14 WILD-TYPE
  N0               6               112
  N1               3               101
  N2               3                74
  N3               2                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"
D797V6, binary
                   cls
clus                  0   1
  C1ORF14 MUTATED    12   1
  C1ORF14 WILD-TYPE 334  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF14 MUTATED     12    1
  C1ORF14 WILD-TYPE  334   28
   clus
vv  C1ORF14 MUTATED C1ORF14 WILD-TYPE
  0              12               334
  1               1                28
[1] 2 2
[1] FALSE
D797V7, binary
                   cls
clus                  0   1
  C1ORF14 MUTATED     6   8
  C1ORF14 WILD-TYPE 139 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF14 MUTATED      6    8
  C1ORF14 WILD-TYPE  139  240
        clus
vv       C1ORF14 MUTATED C1ORF14 WILD-TYPE
  FEMALE               6               139
  MALE                 8               240
[1] 2 2
[1] FALSE
D797V8, binary
                   cls
clus                  0   1
  C1ORF14 MUTATED    13   0
  C1ORF14 WILD-TYPE 279  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF14 MUTATED     13    0
  C1ORF14 WILD-TYPE  279   59
     clus
vv    C1ORF14 MUTATED C1ORF14 WILD-TYPE
  NO               13               279
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C1ORF14 MUTATED                                          0
  C1ORF14 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C1ORF14 MUTATED                                       1
  C1ORF14 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C1ORF14 MUTATED                                                        7
  C1ORF14 WILD-TYPE                                                    151
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C1ORF14 MUTATED                                                   0
  C1ORF14 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C1ORF14 MUTATED                                                                   3
  C1ORF14 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C1ORF14 MUTATED                                                    0
  C1ORF14 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C1ORF14 MUTATED                                                  3
  C1ORF14 WILD-TYPE                                               58
D797V9, multiclass
                                                                   clus
vv                                                                  C1ORF14 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  C1ORF14 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C1ORF14 MUTATED    12   0   0   2
  C1ORF14 WILD-TYPE 299  14  15  22
D797V10, multiclass
    clus
vv   C1ORF14 MUTATED C1ORF14 WILD-TYPE
  R0              12               299
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D797V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C1ORF14 MUTATED       4                         0
  C1ORF14 WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C1ORF14 MUTATED                                           0     9
  C1ORF14 WILD-TYPE                                         1   234
D797V12, multiclass
                                           clus
vv                                          C1ORF14 MUTATED C1ORF14 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D797V13, binary
                   cls
clus                  0   1
  C1ORF14 MUTATED     0  13
  C1ORF14 WILD-TYPE   4 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF14 MUTATED      0   13
  C1ORF14 WILD-TYPE    4  297
                        clus
vv                       C1ORF14 MUTATED C1ORF14 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              13               297
[1] 2 2
[1] FALSE

Clustering(798) Variable = CUL1 MUTATION ANALYSIS
D798V1, survival
                sevent
clus2              0   1
  CUL1 MUTATED    14   4
  CUL1 WILD-TYPE 216 135
  CUL1 MUTATED CUL1 WILD-TYPE 
            18            351 
  CUL1 MUTATED CUL1 WILD-TYPE 
             4            135 
$`CUL1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8368 
       26.70         6.97         9.67        34.68        35.84         4.31 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-A4PD TCGA-CD-5804 TCGA-CG-5733 TCGA-F1-6874 
       25.05         1.12        20.65        12.10        21.07        14.47 
TCGA-FP-8211 TCGA-HF-7132 TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GX TCGA-MX-A5UJ 
       13.58        77.29        11.77        29.98        20.25        19.73 

$`CUL1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18        13.35        11.21        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-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-F1-6875 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-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-A4GJ 
       22.68        24.20         3.25        22.75        25.81        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-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 

  CUL1 MUTATED CUL1 WILD-TYPE 
          1.12           0.00 
  CUL1 MUTATED CUL1 WILD-TYPE 
         77.29         122.30 
  CUL1 MUTATED CUL1 WILD-TYPE 
         19.99          14.07 
[1] "1.1 - 77.3 (20.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2"  
D798V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CUL1 MUTATED         0        1        4        1         3         4
  CUL1 WILD-TYPE       2       14       36       29        34        48
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CUL1 MUTATED           0          3          0          2        0
  CUL1 WILD-TYPE         3         67         53         30       38
D798V3, multiclass
            clus
vv           CUL1 MUTATED CUL1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              4             36
  STAGE II              1             29
  STAGE IIA             3             34
  STAGE IIB             4             48
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CUL1 MUTATED     1   7   6   5
  CUL1 WILD-TYPE  21  85 167  92
D798V4, multiclass
    clus
vv   CUL1 MUTATED CUL1 WILD-TYPE
  T1            1             21
  T2            7             85
  T3            6            167
  T4            5             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
  CUL1 MUTATED    10   5   3   1
  CUL1 WILD-TYPE 108  99  74  76
D798V5, multiclass
    clus
vv   CUL1 MUTATED CUL1 WILD-TYPE
  N0           10            108
  N1            5             99
  N2            3             74
  N3            1             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"
D798V6, binary
                cls
clus               0   1
  CUL1 MUTATED    18   0
  CUL1 WILD-TYPE 328  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED     18    0
  CUL1 WILD-TYPE  328   29
   clus
vv  CUL1 MUTATED CUL1 WILD-TYPE
  0           18            328
  1            0             29
[1] 2 2
[1] FALSE
D798V7, binary
                cls
clus               0   1
  CUL1 MUTATED    11   9
  CUL1 WILD-TYPE 134 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED     11    9
  CUL1 WILD-TYPE  134  239
        clus
vv       CUL1 MUTATED CUL1 WILD-TYPE
  FEMALE           11            134
  MALE              9            239
[1] 2 2
[1] FALSE
D798V8, binary
                cls
clus               0   1
  CUL1 MUTATED    17   2
  CUL1 WILD-TYPE 275  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED     17    2
  CUL1 WILD-TYPE  275   57
     clus
vv    CUL1 MUTATED CUL1 WILD-TYPE
  NO            17            275
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CUL1 MUTATED                                          0
  CUL1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CUL1 MUTATED                                       2
  CUL1 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CUL1 MUTATED                                                       10
  CUL1 WILD-TYPE                                                    148
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CUL1 MUTATED                                                   1
  CUL1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CUL1 MUTATED                                                                   4
  CUL1 WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CUL1 MUTATED                                                    0
  CUL1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CUL1 MUTATED                                                  3
  CUL1 WILD-TYPE                                               58
D798V9, multiclass
                                                                   clus
vv                                                                  CUL1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  CUL1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CUL1 MUTATED    17   1   0   2
  CUL1 WILD-TYPE 294  13  15  22
D798V10, multiclass
    clus
vv   CUL1 MUTATED CUL1 WILD-TYPE
  R0           17            294
  R1            1             13
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D798V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CUL1 MUTATED       4                         0
  CUL1 WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CUL1 MUTATED                                           0    13
  CUL1 WILD-TYPE                                         1   230
D798V12, multiclass
                                           clus
vv                                          CUL1 MUTATED CUL1 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D798V13, binary
                cls
clus               0   1
  CUL1 MUTATED     0  17
  CUL1 WILD-TYPE   4 293
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL1 MUTATED      0   17
  CUL1 WILD-TYPE    4  293
                        clus
vv                       CUL1 MUTATED CUL1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           17            293
[1] 2 2
[1] FALSE

Clustering(799) Variable = C9ORF46 MUTATION ANALYSIS
D799V1, survival
                   sevent
clus2                 0   1
  C9ORF46 MUTATED     2   1
  C9ORF46 WILD-TYPE 228 138
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
                3               366 
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
                1               138 
$`C9ORF46 MUTATED`
TCGA-BR-A4QL TCGA-CG-4437 TCGA-HF-7132 
       16.14         8.05        77.29 

$`C9ORF46 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
             8.05              0.00 
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
            77.29            122.30 
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
            16.14             14.22 
[1] "8.1 - 77.3 (16.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D799V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C9ORF46 MUTATED         0        0        1        2         0         0
  C9ORF46 WILD-TYPE       2       15       39       28        37        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF46 MUTATED           0          0          1          0        0
  C9ORF46 WILD-TYPE         3         70         52         32       38
D799V3, multiclass
            clus
vv           C9ORF46 MUTATED C9ORF46 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 2                28
  STAGE IIA                0                37
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C9ORF46 MUTATED     0   3   1   0
  C9ORF46 WILD-TYPE  22  89 172  97
D799V4, multiclass
    clus
vv   C9ORF46 MUTATED C9ORF46 WILD-TYPE
  T1               0                22
  T2               3                89
  T3               1               172
  T4               0                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
  C9ORF46 MUTATED     1   2   0   1
  C9ORF46 WILD-TYPE 117 102  77  76
D799V5, multiclass
    clus
vv   C9ORF46 MUTATED C9ORF46 WILD-TYPE
  N0               1               117
  N1               2               102
  N2               0                77
  N3               1                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"
D799V6, binary
                   cls
clus                  0   1
  C9ORF46 MUTATED     4   0
  C9ORF46 WILD-TYPE 342  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF46 MUTATED      4    0
  C9ORF46 WILD-TYPE  342   29
   clus
vv  C9ORF46 MUTATED C9ORF46 WILD-TYPE
  0               4               342
  1               0                29
[1] 2 2
[1] FALSE
D799V7, binary
                   cls
clus                  0   1
  C9ORF46 MUTATED     1   3
  C9ORF46 WILD-TYPE 144 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF46 MUTATED      1    3
  C9ORF46 WILD-TYPE  144  245
        clus
vv       C9ORF46 MUTATED C9ORF46 WILD-TYPE
  FEMALE               1               144
  MALE                 3               245
[1] 2 2
[1] FALSE
D799V8, binary
                   cls
clus                  0   1
  C9ORF46 MUTATED     2   1
  C9ORF46 WILD-TYPE 290  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF46 MUTATED      2    1
  C9ORF46 WILD-TYPE  290   58
     clus
vv    C9ORF46 MUTATED C9ORF46 WILD-TYPE
  NO                2               290
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C9ORF46 MUTATED                                          0
  C9ORF46 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C9ORF46 MUTATED                                       0
  C9ORF46 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C9ORF46 MUTATED                                                        1
  C9ORF46 WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C9ORF46 MUTATED                                                   1
  C9ORF46 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C9ORF46 MUTATED                                                                   2
  C9ORF46 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C9ORF46 MUTATED                                                    0
  C9ORF46 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C9ORF46 MUTATED                                                  0
  C9ORF46 WILD-TYPE                                               61
D799V9, multiclass
                                                                   clus
vv                                                                  C9ORF46 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  C9ORF46 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C9ORF46 MUTATED     4   0   0   0
  C9ORF46 WILD-TYPE 307  14  15  24
D799V10, multiclass
    clus
vv   C9ORF46 MUTATED C9ORF46 WILD-TYPE
  R0               4               307
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D799V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C9ORF46 MUTATED       0                         0
  C9ORF46 WILD-TYPE    87                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C9ORF46 MUTATED                                           0     1
  C9ORF46 WILD-TYPE                                         1   242
D799V12, multiclass
[1] "Remove cluster labels:" "C9ORF46 MUTATED"       
clus
  C9ORF46 MUTATED C9ORF46 WILD-TYPE 
                1               339 
       TCGA-EQ-A4SO        TCGA-F1-6177        TCGA-FP-A8CX        TCGA-KB-A93G 
"C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" "C9ORF46 WILD-TYPE" 
       TCGA-MX-A663        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" 
D799V13, binary
                   cls
clus                  0   1
  C9ORF46 MUTATED     0   1
  C9ORF46 WILD-TYPE   4 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF46 MUTATED      0    1
  C9ORF46 WILD-TYPE    4  309
                        clus
vv                       C9ORF46 MUTATED C9ORF46 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               1               309
[1] 2 2
[1] FALSE

Clustering(800) Variable = VPRBP MUTATION ANALYSIS
D800V1, survival
                 sevent
clus2               0   1
  VPRBP MUTATED     5   1
  VPRBP WILD-TYPE 225 138
  VPRBP MUTATED VPRBP WILD-TYPE 
              6             363 
  VPRBP MUTATED VPRBP WILD-TYPE 
              1             138 
$`VPRBP MUTATED`
TCGA-B7-5816 TCGA-BR-6457 TCGA-BR-8680 TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-4306 
       26.70        13.68        31.96        12.43        15.95         1.02 

$`VPRBP WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  VPRBP MUTATED VPRBP WILD-TYPE 
           1.02            0.00 
  VPRBP MUTATED VPRBP WILD-TYPE 
          31.96          122.30 
  VPRBP MUTATED VPRBP WILD-TYPE 
         14.815          14.270 
[1] "1.0 - 32.0 (14.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.3"
D800V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VPRBP MUTATED         0        0        1        2         1         1
  VPRBP WILD-TYPE       2       15       39       28        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPRBP MUTATED           0          0          0          0        2
  VPRBP WILD-TYPE         3         70         53         32       36
D800V3, multiclass
            clus
vv           VPRBP MUTATED VPRBP WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VPRBP MUTATED     0   2   3   2
  VPRBP WILD-TYPE  22  90 170  95
D800V4, multiclass
    clus
vv   VPRBP MUTATED VPRBP WILD-TYPE
  T1             0              22
  T2             2              90
  T3             3             170
  T4             2              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
  VPRBP MUTATED     4   2   2   0
  VPRBP WILD-TYPE 114 102  75  77
D800V5, multiclass
    clus
vv   VPRBP MUTATED VPRBP WILD-TYPE
  N0             4             114
  N1             2             102
  N2             2              75
  N3             0              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"
D800V6, binary
                 cls
clus                0   1
  VPRBP MUTATED     6   2
  VPRBP WILD-TYPE 340  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED      6    2
  VPRBP WILD-TYPE  340   27
   clus
vv  VPRBP MUTATED VPRBP WILD-TYPE
  0             6             340
  1             2              27
[1] 2 2
[1] FALSE
D800V7, binary
                 cls
clus                0   1
  VPRBP MUTATED     2   6
  VPRBP WILD-TYPE 143 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED      2    6
  VPRBP WILD-TYPE  143  242
        clus
vv       VPRBP MUTATED VPRBP WILD-TYPE
  FEMALE             2             143
  MALE               6             242
[1] 2 2
[1] FALSE
D800V8, binary
                 cls
clus                0   1
  VPRBP MUTATED     5   0
  VPRBP WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED      5    0
  VPRBP WILD-TYPE  287   59
     clus
vv    VPRBP MUTATED VPRBP WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  VPRBP MUTATED                                          0
  VPRBP WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  VPRBP MUTATED                                       1
  VPRBP WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  VPRBP MUTATED                                                        5
  VPRBP WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  VPRBP MUTATED                                                   0
  VPRBP WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  VPRBP MUTATED                                                                   1
  VPRBP WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  VPRBP MUTATED                                                    0
  VPRBP WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  VPRBP MUTATED                                                  1
  VPRBP WILD-TYPE                                               60
D800V9, multiclass
                                                                   clus
vv                                                                  VPRBP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  VPRBP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  VPRBP MUTATED     6   0   1   1
  VPRBP WILD-TYPE 305  14  14  23
D800V10, multiclass
    clus
vv   VPRBP MUTATED VPRBP WILD-TYPE
  R0             6             305
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D800V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  VPRBP MUTATED       2                         0
  VPRBP WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  VPRBP MUTATED                                           0     3
  VPRBP WILD-TYPE                                         1   240
D800V12, multiclass
                                           clus
vv                                          VPRBP MUTATED VPRBP WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D800V13, binary
                 cls
clus                0   1
  VPRBP MUTATED     0   5
  VPRBP WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPRBP MUTATED      0    5
  VPRBP WILD-TYPE    4  305
                        clus
vv                       VPRBP MUTATED VPRBP WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(801) Variable = INO80D MUTATION ANALYSIS
D801V1, survival
                  sevent
clus2                0   1
  INO80D MUTATED     8   5
  INO80D WILD-TYPE 222 134
  INO80D MUTATED INO80D WILD-TYPE 
              13              356 
  INO80D MUTATED INO80D WILD-TYPE 
               5              134 
$`INO80D MUTATED`
TCGA-BR-4201 TCGA-BR-6852 TCGA-BR-7901 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8535 
       30.90        44.94         3.45        31.96        16.14        12.82 
TCGA-CD-8536 TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5723 TCGA-HF-7132 TCGA-HU-A4H0 
       12.43         1.02         9.01       105.07        77.29         2.10 
TCGA-VQ-A8P2 
       38.14 

$`INO80D WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-A4H2 
        0.10         6.51         6.58        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-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 

  INO80D MUTATED INO80D WILD-TYPE 
            1.02             0.00 
  INO80D MUTATED INO80D WILD-TYPE 
          105.07           122.30 
  INO80D MUTATED INO80D WILD-TYPE 
           16.14            14.22 
[1] "1.0 - 105.1 (16.1)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D801V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INO80D MUTATED         0        0        0        3         1         1
  INO80D WILD-TYPE       2       15       40       27        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INO80D MUTATED           0          3          1          1        3
  INO80D WILD-TYPE         3         67         52         31       35
D801V3, multiclass
            clus
vv           INO80D MUTATED INO80D WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                3               27
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  INO80D MUTATED     1   3   6   5
  INO80D WILD-TYPE  21  89 167  92
D801V4, multiclass
    clus
vv   INO80D MUTATED INO80D WILD-TYPE
  T1              1               21
  T2              3               89
  T3              6              167
  T4              5               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
  INO80D MUTATED     3   6   2   3
  INO80D WILD-TYPE 115  98  75  74
D801V5, multiclass
    clus
vv   INO80D MUTATED INO80D WILD-TYPE
  N0              3              115
  N1              6               98
  N2              2               75
  N3              3               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"
D801V6, binary
                  cls
clus                 0   1
  INO80D MUTATED    13   3
  INO80D WILD-TYPE 333  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INO80D MUTATED     13    3
  INO80D WILD-TYPE  333   26
   clus
vv  INO80D MUTATED INO80D WILD-TYPE
  0             13              333
  1              3               26
[1] 2 2
[1] FALSE
D801V7, binary
                  cls
clus                 0   1
  INO80D MUTATED     7   9
  INO80D WILD-TYPE 138 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INO80D MUTATED      7    9
  INO80D WILD-TYPE  138  239
        clus
vv       INO80D MUTATED INO80D WILD-TYPE
  FEMALE              7              138
  MALE                9              239
[1] 2 2
[1] FALSE
D801V8, binary
                  cls
clus                 0   1
  INO80D MUTATED     9   2
  INO80D WILD-TYPE 283  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INO80D MUTATED      9    2
  INO80D WILD-TYPE  283   57
     clus
vv    INO80D MUTATED INO80D WILD-TYPE
  NO               9              283
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  INO80D MUTATED                                          0
  INO80D WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  INO80D MUTATED                                       2
  INO80D WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  INO80D MUTATED                                                       11
  INO80D WILD-TYPE                                                    147
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  INO80D MUTATED                                                   2
  INO80D WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  INO80D MUTATED                                                                   0
  INO80D WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  INO80D MUTATED                                                    0
  INO80D WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  INO80D MUTATED                                                  1
  INO80D WILD-TYPE                                               60
D801V9, multiclass
                                                                   clus
vv                                                                  INO80D MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  INO80D WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  INO80D MUTATED    10   0   2   4
  INO80D WILD-TYPE 301  14  13  20
D801V10, multiclass
    clus
vv   INO80D MUTATED INO80D WILD-TYPE
  R0             10              301
  R1              0               14
  R2              2               13
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D801V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  INO80D MUTATED       4                         0
  INO80D WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INO80D MUTATED                                           0     8
  INO80D WILD-TYPE                                         1   235
D801V12, multiclass
                                           clus
vv                                          INO80D MUTATED INO80D WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D801V13, binary
                  cls
clus                 0   1
  INO80D MUTATED     0  11
  INO80D WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INO80D MUTATED      0   11
  INO80D WILD-TYPE    4  299
                        clus
vv                       INO80D MUTATED INO80D WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(802) Variable = B4GALNT4 MUTATION ANALYSIS
D802V1, survival
                    sevent
clus2                  0   1
  B4GALNT4 MUTATED     8   6
  B4GALNT4 WILD-TYPE 222 133
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                14                355 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                 6                133 
$`B4GALNT4 MUTATED`
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8591 TCGA-BR-8680 
        9.67         6.18        29.59         4.31        28.14        31.96 
TCGA-BR-A4QL TCGA-CG-5721 TCGA-D7-A6EY TCGA-HU-A4G8 TCGA-MX-A5UJ TCGA-R5-A7ZR 
       16.14         6.02        11.44        22.68        19.73         6.08 
TCGA-RD-A8N5 TCGA-VQ-A8P2 
       57.44        38.14 

$`B4GALNT4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-4279 
       18.35        30.90         4.08         4.08         9.34         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-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-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-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-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-A8N6 
       37.91        40.64       115.69       116.38        71.38         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 

  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
              4.31               0.00 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
             57.44             122.30 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
            17.935             14.170 
[1] "4.3 - 57.4 (17.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D802V2, 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       2       15       38       30        37        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B4GALNT4 MUTATED           1          4          2          1        3
  B4GALNT4 WILD-TYPE         2         66         51         31       35
D802V3, multiclass
            clus
vv           B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  2                 38
  STAGE II                  0                 30
  STAGE IIA                 0                 37
  STAGE IIB                 3                 49
  STAGE III                 1                  2
  STAGE IIIA                4                 66
  STAGE IIIB                2                 51
  STAGE IIIC                1                 31
  STAGE IV                  3                 35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  B4GALNT4 MUTATED     1   2   6   8
  B4GALNT4 WILD-TYPE  21  90 167  89
D802V4, multiclass
    clus
vv   B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  T1                1                 21
  T2                2                 90
  T3                6                167
  T4                8                 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
  B4GALNT4 MUTATED     5   4   3   3
  B4GALNT4 WILD-TYPE 113 100  74  74
D802V5, multiclass
    clus
vv   B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  N0                5                113
  N1                4                100
  N2                3                 74
  N3                3                 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"
D802V6, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED    17   1
  B4GALNT4 WILD-TYPE 329  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED     17    1
  B4GALNT4 WILD-TYPE  329   28
   clus
vv  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  0               17                329
  1                1                 28
[1] 2 2
[1] FALSE
D802V7, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED    11   7
  B4GALNT4 WILD-TYPE 134 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED     11    7
  B4GALNT4 WILD-TYPE  134  241
        clus
vv       B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  FEMALE               11                134
  MALE                  7                241
[1] 2 2
[1] FALSE
D802V8, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED    13   2
  B4GALNT4 WILD-TYPE 279  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED     13    2
  B4GALNT4 WILD-TYPE  279   57
     clus
vv    B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  NO                13                279
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  B4GALNT4 MUTATED                                          0
  B4GALNT4 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  B4GALNT4 MUTATED                                       1
  B4GALNT4 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  B4GALNT4 MUTATED                                                        9
  B4GALNT4 WILD-TYPE                                                    149
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  B4GALNT4 MUTATED                                                   2
  B4GALNT4 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  B4GALNT4 MUTATED                                                                   2
  B4GALNT4 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  B4GALNT4 MUTATED                                                    0
  B4GALNT4 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  B4GALNT4 MUTATED                                                  4
  B4GALNT4 WILD-TYPE                                               57
D802V9, multiclass
                                                                   clus
vv                                                                  B4GALNT4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 4
                                                                   clus
vv                                                                  B4GALNT4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  B4GALNT4 MUTATED    11   0   0   5
  B4GALNT4 WILD-TYPE 300  14  15  19
D802V10, multiclass
    clus
vv   B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  R0               11                300
  R1                0                 14
  R2                0                 15
  RX                5                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D802V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  B4GALNT4 MUTATED       2                         1
  B4GALNT4 WILD-TYPE    85                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  B4GALNT4 MUTATED                                           0    14
  B4GALNT4 WILD-TYPE                                         1   229
D802V12, multiclass
                                           clus
vv                                          B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D802V13, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED     0  16
  B4GALNT4 WILD-TYPE   4 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED      0   16
  B4GALNT4 WILD-TYPE    4  294
                        clus
vv                       B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               16                294
[1] 2 2
[1] FALSE

Clustering(803) Variable = PTX4 MUTATION ANALYSIS
D803V1, survival
                sevent
clus2              0   1
  PTX4 MUTATED     5   5
  PTX4 WILD-TYPE 225 134
  PTX4 MUTATED PTX4 WILD-TYPE 
            10            359 
  PTX4 MUTATED PTX4 WILD-TYPE 
             5            134 
$`PTX4 MUTATED`
TCGA-BR-8372 TCGA-BR-8591 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-D7-A4YV TCGA-D7-A6EZ 
       31.27        28.14         6.58        11.77         5.92        20.32 
TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4GN 
       11.08        30.51        26.47        29.98 

$`PTX4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  PTX4 MUTATED PTX4 WILD-TYPE 
          5.92           0.00 
  PTX4 MUTATED PTX4 WILD-TYPE 
         31.27         122.30 
  PTX4 MUTATED PTX4 WILD-TYPE 
        23.395         14.170 
[1] "5.9 - 31.3 (23.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D803V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTX4 MUTATED         0        0        1        0         3         2
  PTX4 WILD-TYPE       2       15       39       30        34        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTX4 MUTATED           0          2          0          3        0
  PTX4 WILD-TYPE         3         68         53         29       38
D803V3, multiclass
            clus
vv           PTX4 MUTATED PTX4 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             3             34
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            3             29
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PTX4 MUTATED     0   2   6   4
  PTX4 WILD-TYPE  22  90 167  93
D803V4, multiclass
    clus
vv   PTX4 MUTATED PTX4 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            6            167
  T4            4             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
  PTX4 MUTATED     4   3   1   3
  PTX4 WILD-TYPE 114 101  76  74
D803V5, multiclass
    clus
vv   PTX4 MUTATED PTX4 WILD-TYPE
  N0            4            114
  N1            3            101
  N2            1             76
  N3            3             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"
D803V6, binary
                cls
clus               0   1
  PTX4 MUTATED    10   0
  PTX4 WILD-TYPE 336  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTX4 MUTATED     10    0
  PTX4 WILD-TYPE  336   29
   clus
vv  PTX4 MUTATED PTX4 WILD-TYPE
  0           10            336
  1            0             29
[1] 2 2
[1] FALSE
D803V7, binary
                cls
clus               0   1
  PTX4 MUTATED     4   8
  PTX4 WILD-TYPE 141 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTX4 MUTATED      4    8
  PTX4 WILD-TYPE  141  240
        clus
vv       PTX4 MUTATED PTX4 WILD-TYPE
  FEMALE            4            141
  MALE              8            240
[1] 2 2
[1] FALSE
D803V8, binary
                cls
clus               0   1
  PTX4 MUTATED     9   2
  PTX4 WILD-TYPE 283  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTX4 MUTATED      9    2
  PTX4 WILD-TYPE  283   57
     clus
vv    PTX4 MUTATED PTX4 WILD-TYPE
  NO             9            283
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PTX4 MUTATED                                          1
  PTX4 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PTX4 MUTATED                                       1
  PTX4 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTX4 MUTATED                                                        5
  PTX4 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PTX4 MUTATED                                                   1
  PTX4 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTX4 MUTATED                                                                   2
  PTX4 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PTX4 MUTATED                                                    0
  PTX4 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PTX4 MUTATED                                                  2
  PTX4 WILD-TYPE                                               59
D803V9, multiclass
                                                                   clus
vv                                                                  PTX4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  PTX4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PTX4 MUTATED     8   1   0   1
  PTX4 WILD-TYPE 303  13  15  23
D803V10, multiclass
    clus
vv   PTX4 MUTATED PTX4 WILD-TYPE
  R0            8            303
  R1            1             13
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D803V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PTX4 MUTATED       3                         1
  PTX4 WILD-TYPE    84                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTX4 MUTATED                                           0     7
  PTX4 WILD-TYPE                                         1   236
D803V12, multiclass
                                           clus
vv                                          PTX4 MUTATED PTX4 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D803V13, binary
                cls
clus               0   1
  PTX4 MUTATED     0  11
  PTX4 WILD-TYPE   4 299
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTX4 MUTATED      0   11
  PTX4 WILD-TYPE    4  299
                        clus
vv                       PTX4 MUTATED PTX4 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           11            299
[1] 2 2
[1] FALSE

Clustering(804) Variable = ARHGEF17 MUTATION ANALYSIS
D804V1, survival
                    sevent
clus2                  0   1
  ARHGEF17 MUTATED    15   5
  ARHGEF17 WILD-TYPE 215 134
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
                20                349 
  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE 
                 5                134 
$`ARHGEF17 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-8078 TCGA-BR-8360 
       21.99         6.97        35.84        39.78        29.59         6.18 
TCGA-BR-8368 TCGA-BR-8381 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-A4IY TCGA-CD-A4MI 
        4.31         7.36         1.12        28.14        12.89        11.77 
TCGA-CG-5721 TCGA-D7-8579 TCGA-D7-A6EY TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-A4GH 
        6.02        20.91        11.44        11.08        77.29        11.77 
TCGA-RD-A7BT TCGA-VQ-A8P2 
        8.61        38.14 

$`ARHGEF17 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.27        14.79        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-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-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-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-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-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-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 

  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              14.47 
[1] "1.1 - 77.3 (11.8)"  "0.0 - 122.3 (14.5)"
[1] "hr=" "1.5"
D804V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARHGEF17 MUTATED         0        1        3        1         3         5
  ARHGEF17 WILD-TYPE       2       14       37       29        34        47
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF17 MUTATED           0          3          1          1        4
  ARHGEF17 WILD-TYPE         3         67         52         31       34
D804V3, multiclass
            clus
vv           ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  3                 37
  STAGE II                  1                 29
  STAGE IIA                 3                 34
  STAGE IIB                 5                 47
  STAGE III                 0                  3
  STAGE IIIA                3                 67
  STAGE IIIB                1                 52
  STAGE IIIC                1                 31
  STAGE IV                  4                 34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGEF17 MUTATED     1   5   9   7
  ARHGEF17 WILD-TYPE  21  87 164  90
D804V4, multiclass
    clus
vv   ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  T1                1                 21
  T2                5                 87
  T3                9                164
  T4                7                 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
  ARHGEF17 MUTATED     9   8   2   3
  ARHGEF17 WILD-TYPE 109  96  75  74
D804V5, multiclass
    clus
vv   ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  N0                9                109
  N1                8                 96
  N2                2                 75
  N3                3                 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"
D804V6, binary
                    cls
clus                   0   1
  ARHGEF17 MUTATED    20   1
  ARHGEF17 WILD-TYPE 326  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF17 MUTATED     20    1
  ARHGEF17 WILD-TYPE  326   28
   clus
vv  ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  0               20                326
  1                1                 28
[1] 2 2
[1] FALSE
D804V7, binary
                    cls
clus                   0   1
  ARHGEF17 MUTATED     9  13
  ARHGEF17 WILD-TYPE 136 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF17 MUTATED      9   13
  ARHGEF17 WILD-TYPE  136  235
        clus
vv       ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  FEMALE                9                136
  MALE                 13                235
[1] 2 2
[1] FALSE
D804V8, binary
                    cls
clus                   0   1
  ARHGEF17 MUTATED    16   4
  ARHGEF17 WILD-TYPE 276  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF17 MUTATED     16    4
  ARHGEF17 WILD-TYPE  276   55
     clus
vv    ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  NO                16                276
  YES                4                 55
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARHGEF17 MUTATED                                          0
  ARHGEF17 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARHGEF17 MUTATED                                       0
  ARHGEF17 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARHGEF17 MUTATED                                                       12
  ARHGEF17 WILD-TYPE                                                    146
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARHGEF17 MUTATED                                                   2
  ARHGEF17 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARHGEF17 MUTATED                                                                   6
  ARHGEF17 WILD-TYPE                                                                62
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARHGEF17 MUTATED                                                    0
  ARHGEF17 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARHGEF17 MUTATED                                                  2
  ARHGEF17 WILD-TYPE                                               59
D804V9, multiclass
                                                                   clus
vv                                                                  ARHGEF17 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  ARHGEF17 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ARHGEF17 MUTATED    17   0   2   2
  ARHGEF17 WILD-TYPE 294  14  13  22
D804V10, multiclass
    clus
vv   ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  R0               17                294
  R1                0                 14
  R2                2                 13
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D804V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ARHGEF17 MUTATED       3                         1
  ARHGEF17 WILD-TYPE    84                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARHGEF17 MUTATED                                           1    13
  ARHGEF17 WILD-TYPE                                         0   230
D804V12, multiclass
                                           clus
vv                                          ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   13                230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D804V13, binary
                    cls
clus                   0   1
  ARHGEF17 MUTATED     0  17
  ARHGEF17 WILD-TYPE   4 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF17 MUTATED      0   17
  ARHGEF17 WILD-TYPE    4  293
                        clus
vv                       ARHGEF17 MUTATED ARHGEF17 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               17                293
[1] 2 2
[1] FALSE

Clustering(805) Variable = GPR137B MUTATION ANALYSIS
D805V1, survival
                   sevent
clus2                 0   1
  GPR137B MUTATED     4   1
  GPR137B WILD-TYPE 226 138
  GPR137B MUTATED GPR137B WILD-TYPE 
                5               364 
  GPR137B MUTATED GPR137B WILD-TYPE 
                1               138 
$`GPR137B MUTATED`
TCGA-BR-8487 TCGA-BR-8683 TCGA-HU-8602 TCGA-MX-A5UJ TCGA-R5-A7O7 
        1.12         9.86        22.32        19.73        45.67 

$`GPR137B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58        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-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-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 

  GPR137B MUTATED GPR137B WILD-TYPE 
             1.12              0.00 
  GPR137B MUTATED GPR137B WILD-TYPE 
            45.67            122.30 
  GPR137B MUTATED GPR137B WILD-TYPE 
            19.73             14.22 
[1] "1.1 - 45.7 (19.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2"  
D805V2, 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       2       15       40       30        36        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR137B MUTATED           0          1          1          0        1
  GPR137B WILD-TYPE         3         69         52         32       37
D805V3, multiclass
            clus
vv           GPR137B MUTATED GPR137B WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GPR137B MUTATED     0   0   3   3
  GPR137B WILD-TYPE  22  92 170  94
D805V4, multiclass
    clus
vv   GPR137B MUTATED GPR137B WILD-TYPE
  T1               0                22
  T2               0                92
  T3               3               170
  T4               3                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
  GPR137B MUTATED     3   1   2   0
  GPR137B WILD-TYPE 115 103  75  77
D805V5, multiclass
    clus
vv   GPR137B MUTATED GPR137B WILD-TYPE
  N0               3               115
  N1               1               103
  N2               2                75
  N3               0                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"
D805V6, binary
                   cls
clus                  0   1
  GPR137B MUTATED     5   1
  GPR137B WILD-TYPE 341  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR137B MUTATED      5    1
  GPR137B WILD-TYPE  341   28
   clus
vv  GPR137B MUTATED GPR137B WILD-TYPE
  0               5               341
  1               1                28
[1] 2 2
[1] FALSE
D805V7, binary
                   cls
clus                  0   1
  GPR137B MUTATED     3   3
  GPR137B WILD-TYPE 142 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR137B MUTATED      3    3
  GPR137B WILD-TYPE  142  245
        clus
vv       GPR137B MUTATED GPR137B WILD-TYPE
  FEMALE               3               142
  MALE                 3               245
[1] 2 2
[1] FALSE
D805V8, binary
                   cls
clus                  0   1
  GPR137B MUTATED     6   0
  GPR137B WILD-TYPE 286  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR137B MUTATED      6    0
  GPR137B WILD-TYPE  286   59
     clus
vv    GPR137B MUTATED GPR137B WILD-TYPE
  NO                6               286
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GPR137B MUTATED                                          0
  GPR137B WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GPR137B MUTATED                                       1
  GPR137B WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR137B MUTATED                                                        1
  GPR137B WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GPR137B MUTATED                                                   0
  GPR137B WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR137B MUTATED                                                                   1
  GPR137B WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GPR137B MUTATED                                                    0
  GPR137B WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GPR137B MUTATED                                                  3
  GPR137B WILD-TYPE                                               58
D805V9, multiclass
                                                                   clus
vv                                                                  GPR137B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  GPR137B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GPR137B MUTATED     5   0   0   0
  GPR137B WILD-TYPE 306  14  15  24
D805V10, multiclass
    clus
vv   GPR137B MUTATED GPR137B WILD-TYPE
  R0               5               306
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D805V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  GPR137B MUTATED       2                         0
  GPR137B WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR137B MUTATED                                           0     4
  GPR137B WILD-TYPE                                         1   239
D805V12, multiclass
                                           clus
vv                                          GPR137B MUTATED GPR137B WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D805V13, binary
                   cls
clus                  0   1
  GPR137B MUTATED     1   5
  GPR137B WILD-TYPE   3 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR137B MUTATED      1    5
  GPR137B WILD-TYPE    3  305
                        clus
vv                       GPR137B MUTATED GPR137B WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(806) Variable = FAM109B MUTATION ANALYSIS
D806V1, survival
                   sevent
clus2                 0   1
  FAM109B MUTATED     5   1
  FAM109B WILD-TYPE 225 138
  FAM109B MUTATED FAM109B WILD-TYPE 
                6               363 
  FAM109B MUTATED FAM109B WILD-TYPE 
                1               138 
$`FAM109B MUTATED`
TCGA-BR-8363 TCGA-BR-8487 TCGA-CG-4437 TCGA-HU-A4GH TCGA-HU-A4H8 TCGA-VQ-A8P2 
        0.26         1.12         8.05        11.77        14.07        38.14 

$`FAM109B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  FAM109B MUTATED FAM109B WILD-TYPE 
             0.26              0.00 
  FAM109B MUTATED FAM109B WILD-TYPE 
            38.14            122.30 
  FAM109B MUTATED FAM109B WILD-TYPE 
             9.91             14.47 
[1] "0.3 - 38.1 (9.9)"   "0.0 - 122.3 (14.5)"
[1] "hr=" "1.5"
D806V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM109B MUTATED         0        1        2        1         1         0
  FAM109B WILD-TYPE       2       14       38       29        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM109B MUTATED           0          1          0          0        1
  FAM109B WILD-TYPE         3         69         53         32       37
D806V3, multiclass
            clus
vv           FAM109B MUTATED FAM109B WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 2                38
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM109B MUTATED     2   2   1   2
  FAM109B WILD-TYPE  20  90 172  95
D806V4, multiclass
    clus
vv   FAM109B MUTATED FAM109B WILD-TYPE
  T1               2                20
  T2               2                90
  T3               1               172
  T4               2                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
  FAM109B MUTATED     3   3   1   0
  FAM109B WILD-TYPE 115 101  76  77
D806V5, multiclass
    clus
vv   FAM109B MUTATED FAM109B WILD-TYPE
  N0               3               115
  N1               3               101
  N2               1                76
  N3               0                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"
D806V6, binary
                   cls
clus                  0   1
  FAM109B MUTATED     7   0
  FAM109B WILD-TYPE 339  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM109B MUTATED      7    0
  FAM109B WILD-TYPE  339   29
   clus
vv  FAM109B MUTATED FAM109B WILD-TYPE
  0               7               339
  1               0                29
[1] 2 2
[1] FALSE
D806V7, binary
                   cls
clus                  0   1
  FAM109B MUTATED     3   4
  FAM109B WILD-TYPE 142 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM109B MUTATED      3    4
  FAM109B WILD-TYPE  142  244
        clus
vv       FAM109B MUTATED FAM109B WILD-TYPE
  FEMALE               3               142
  MALE                 4               244
[1] 2 2
[1] FALSE
D806V8, binary
                   cls
clus                  0   1
  FAM109B MUTATED     5   1
  FAM109B WILD-TYPE 287  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM109B MUTATED      5    1
  FAM109B WILD-TYPE  287   58
     clus
vv    FAM109B MUTATED FAM109B WILD-TYPE
  NO                5               287
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM109B MUTATED                                          0
  FAM109B WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM109B MUTATED                                       0
  FAM109B WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM109B MUTATED                                                        3
  FAM109B WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM109B MUTATED                                                   1
  FAM109B WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM109B MUTATED                                                                   1
  FAM109B WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM109B MUTATED                                                    0
  FAM109B WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM109B MUTATED                                                  2
  FAM109B WILD-TYPE                                               59
D806V9, multiclass
                                                                   clus
vv                                                                  FAM109B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  FAM109B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM109B MUTATED     6   0   0   1
  FAM109B WILD-TYPE 305  14  15  23
D806V10, multiclass
    clus
vv   FAM109B MUTATED FAM109B WILD-TYPE
  R0               6               305
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D806V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM109B MUTATED       2                         0
  FAM109B WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM109B MUTATED                                           0     4
  FAM109B WILD-TYPE                                         1   239
D806V12, multiclass
                                           clus
vv                                          FAM109B MUTATED FAM109B WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D806V13, binary
                   cls
clus                  0   1
  FAM109B MUTATED     0   5
  FAM109B WILD-TYPE   4 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM109B MUTATED      0    5
  FAM109B WILD-TYPE    4  305
                        clus
vv                       FAM109B MUTATED FAM109B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(807) Variable = HGF MUTATION ANALYSIS
D807V1, survival
               sevent
clus2             0   1
  HGF MUTATED    10   4
  HGF WILD-TYPE 220 135
  HGF MUTATED HGF WILD-TYPE 
           14           355 
  HGF MUTATED HGF WILD-TYPE 
            4           135 
$`HGF MUTATED`
TCGA-BR-6452 TCGA-BR-8297 TCGA-BR-8485 TCGA-CD-5800 TCGA-CG-5721 TCGA-CG-5723 
       34.68         7.40         9.21        13.15         6.02       105.07 
TCGA-CG-5726 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A747 TCGA-HU-A4GX TCGA-SW-A7EA 
       28.96        12.33        18.21         8.38        20.25        19.04 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

$`HGF WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-5801 
       21.44        16.14         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-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-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       11.31        24.72        16.80        19.50        17.19        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-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-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 
       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        14.270 
[1] "6.0 - 105.1 (15.2)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D807V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HGF MUTATED         0        2        4        2         1         1
  HGF WILD-TYPE       2       13       36       28        36        51
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HGF MUTATED           0          1          0          4        2
  HGF WILD-TYPE         3         69         53         28       36
D807V3, multiclass
            clus
vv           HGF MUTATED HGF WILD-TYPE
  STAGE I              0             2
  STAGE IA             2            13
  STAGE IB             4            36
  STAGE II             2            28
  STAGE IIA            1            36
  STAGE IIB            1            51
  STAGE III            0             3
  STAGE IIIA           1            69
  STAGE IIIB           0            53
  STAGE IIIC           4            28
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  HGF MUTATED     2   5   4   6
  HGF WILD-TYPE  20  87 169  91
D807V4, multiclass
    clus
vv   HGF MUTATED HGF WILD-TYPE
  T1           2            20
  T2           5            87
  T3           4           169
  T4           6            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
  HGF MUTATED     8   4   3   3
  HGF WILD-TYPE 110 100  74  74
D807V5, multiclass
    clus
vv   HGF MUTATED HGF WILD-TYPE
  N0           8           110
  N1           4           100
  N2           3            74
  N3           3            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"
D807V6, binary
               cls
clus              0   1
  HGF MUTATED    16   1
  HGF WILD-TYPE 330  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGF MUTATED     16    1
  HGF WILD-TYPE  330   28
   clus
vv  HGF MUTATED HGF WILD-TYPE
  0          16           330
  1           1            28
[1] 2 2
[1] FALSE
D807V7, binary
               cls
clus              0   1
  HGF MUTATED     8  10
  HGF WILD-TYPE 137 238
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGF MUTATED      8   10
  HGF WILD-TYPE  137  238
        clus
vv       HGF MUTATED HGF WILD-TYPE
  FEMALE           8           137
  MALE            10           238
[1] 2 2
[1] FALSE
D807V8, binary
               cls
clus              0   1
  HGF MUTATED    13   2
  HGF WILD-TYPE 279  57
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGF MUTATED     13    2
  HGF WILD-TYPE  279   57
     clus
vv    HGF MUTATED HGF WILD-TYPE
  NO           13           279
  YES           2            57
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HGF MUTATED                                          1
  HGF WILD-TYPE                                        7
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HGF MUTATED                                       5
  HGF WILD-TYPE                                    65
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HGF MUTATED                                                        6
  HGF WILD-TYPE                                                    152
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HGF MUTATED                                                   0
  HGF WILD-TYPE                                                21
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HGF MUTATED                                                                   3
  HGF WILD-TYPE                                                                65
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HGF MUTATED                                                    1
  HGF WILD-TYPE                                                  4
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HGF MUTATED                                                  2
  HGF WILD-TYPE                                               59
D807V9, multiclass
                                                                   clus
vv                                                                  HGF MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            2
                                                                   clus
vv                                                                  HGF WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  HGF MUTATED    15   1   1   1
  HGF WILD-TYPE 296  13  14  23
D807V10, multiclass
    clus
vv   HGF MUTATED HGF WILD-TYPE
  R0          15           296
  R1           1            13
  R2           1            14
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D807V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  HGF MUTATED       3                         0
  HGF WILD-TYPE    84                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HGF MUTATED                                           0    11
  HGF WILD-TYPE                                         1   232
D807V12, multiclass
                                           clus
vv                                          HGF MUTATED HGF WILD-TYPE
  ASIAN                                               3            84
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              11           232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D807V13, binary
               cls
clus              0   1
  HGF MUTATED     0  13
  HGF WILD-TYPE   4 297
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGF MUTATED      0   13
  HGF WILD-TYPE    4  297
                        clus
vv                       HGF MUTATED HGF WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          13           297
[1] 2 2
[1] FALSE

Clustering(808) Variable = GPR114 MUTATION ANALYSIS
D808V1, survival
                  sevent
clus2                0   1
  GPR114 MUTATED     7   2
  GPR114 WILD-TYPE 223 137
  GPR114 MUTATED GPR114 WILD-TYPE 
               9              360 
  GPR114 MUTATED GPR114 WILD-TYPE 
               2              137 
$`GPR114 MUTATED`
TCGA-BR-6706 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8680 TCGA-CD-8536 TCGA-D7-8578 
       18.05         4.31        25.05        31.96        12.43        21.14 
TCGA-F1-6874 TCGA-HU-A4G8 TCGA-HU-A4GU 
       14.47        22.68         6.58 

$`GPR114 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-D7-8579 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-F1-6875 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-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 

  GPR114 MUTATED GPR114 WILD-TYPE 
            4.31             0.00 
  GPR114 MUTATED GPR114 WILD-TYPE 
           31.96           122.30 
  GPR114 MUTATED GPR114 WILD-TYPE 
           18.05            14.12 
[1] "4.3 - 32.0 (18.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D808V2, 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       2       15       37       29        37        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR114 MUTATED           0          1          0          1        1
  GPR114 WILD-TYPE         3         69         53         31       37
D808V3, multiclass
            clus
vv           GPR114 MUTATED GPR114 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                1               29
  STAGE IIA               0               37
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR114 MUTATED     0   3   4   2
  GPR114 WILD-TYPE  22  89 169  95
D808V4, multiclass
    clus
vv   GPR114 MUTATED GPR114 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              4              169
  T4              2               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
  GPR114 MUTATED     4   3   1   1
  GPR114 WILD-TYPE 114 101  76  76
D808V5, multiclass
    clus
vv   GPR114 MUTATED GPR114 WILD-TYPE
  N0              4              114
  N1              3              101
  N2              1               76
  N3              1               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"
D808V6, binary
                  cls
clus                 0   1
  GPR114 MUTATED     8   1
  GPR114 WILD-TYPE 338  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR114 MUTATED      8    1
  GPR114 WILD-TYPE  338   28
   clus
vv  GPR114 MUTATED GPR114 WILD-TYPE
  0              8              338
  1              1               28
[1] 2 2
[1] FALSE
D808V7, binary
                  cls
clus                 0   1
  GPR114 MUTATED     3   6
  GPR114 WILD-TYPE 142 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR114 MUTATED      3    6
  GPR114 WILD-TYPE  142  242
        clus
vv       GPR114 MUTATED GPR114 WILD-TYPE
  FEMALE              3              142
  MALE                6              242
[1] 2 2
[1] FALSE
D808V8, binary
                  cls
clus                 0   1
  GPR114 MUTATED     9   0
  GPR114 WILD-TYPE 283  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR114 MUTATED      9    0
  GPR114 WILD-TYPE  283   59
     clus
vv    GPR114 MUTATED GPR114 WILD-TYPE
  NO               9              283
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GPR114 MUTATED                                          0
  GPR114 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GPR114 MUTATED                                       2
  GPR114 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR114 MUTATED                                                        5
  GPR114 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GPR114 MUTATED                                                   0
  GPR114 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR114 MUTATED                                                                   1
  GPR114 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GPR114 MUTATED                                                    0
  GPR114 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GPR114 MUTATED                                                  1
  GPR114 WILD-TYPE                                               60
D808V9, multiclass
                                                                   clus
vv                                                                  GPR114 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  GPR114 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR114 MUTATED     8   0   0   0
  GPR114 WILD-TYPE 303  14  15  24
D808V10, multiclass
    clus
vv   GPR114 MUTATED GPR114 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D808V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GPR114 MUTATED       4                         0
  GPR114 WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR114 MUTATED                                           0     5
  GPR114 WILD-TYPE                                         1   238
D808V12, multiclass
                                           clus
vv                                          GPR114 MUTATED GPR114 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D808V13, binary
                  cls
clus                 0   1
  GPR114 MUTATED     0   9
  GPR114 WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR114 MUTATED      0    9
  GPR114 WILD-TYPE    4  301
                        clus
vv                       GPR114 MUTATED GPR114 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(809) Variable = DHRS9 MUTATION ANALYSIS
D809V1, survival
                 sevent
clus2               0   1
  DHRS9 MUTATED     5   3
  DHRS9 WILD-TYPE 225 136
  DHRS9 MUTATED DHRS9 WILD-TYPE 
              8             361 
  DHRS9 MUTATED DHRS9 WILD-TYPE 
              3             136 
$`DHRS9 MUTATED`
TCGA-CG-4444 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8291 TCGA-D7-6528 
       47.05        30.90         9.67        34.68        19.96        15.22 
TCGA-HU-A4H0 TCGA-VQ-A8P2 
        2.10        38.14 

$`DHRS9 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        2.66         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-D7-6815 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-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-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 

  DHRS9 MUTATED DHRS9 WILD-TYPE 
            2.1             0.0 
  DHRS9 MUTATED DHRS9 WILD-TYPE 
          47.05          122.30 
  DHRS9 MUTATED DHRS9 WILD-TYPE 
          25.43           14.07 
[1] "2.1 - 47.0 (25.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D809V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DHRS9 MUTATED         0        0        1        0         1         1
  DHRS9 WILD-TYPE       2       15       39       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DHRS9 MUTATED           0          3          0          1        0
  DHRS9 WILD-TYPE         3         67         53         31       38
D809V3, multiclass
            clus
vv           DHRS9 MUTATED DHRS9 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DHRS9 MUTATED     0   3   2   3
  DHRS9 WILD-TYPE  22  89 171  94
D809V4, multiclass
    clus
vv   DHRS9 MUTATED DHRS9 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             2             171
  T4             3              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
  DHRS9 MUTATED     3   2   1   1
  DHRS9 WILD-TYPE 115 102  76  76
D809V5, multiclass
    clus
vv   DHRS9 MUTATED DHRS9 WILD-TYPE
  N0             3             115
  N1             2             102
  N2             1              76
  N3             1              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"
D809V6, binary
                 cls
clus                0   1
  DHRS9 MUTATED     9   0
  DHRS9 WILD-TYPE 337  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS9 MUTATED      9    0
  DHRS9 WILD-TYPE  337   29
   clus
vv  DHRS9 MUTATED DHRS9 WILD-TYPE
  0             9             337
  1             0              29
[1] 2 2
[1] FALSE
D809V7, binary
                 cls
clus                0   1
  DHRS9 MUTATED     5   4
  DHRS9 WILD-TYPE 140 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS9 MUTATED      5    4
  DHRS9 WILD-TYPE  140  244
        clus
vv       DHRS9 MUTATED DHRS9 WILD-TYPE
  FEMALE             5             140
  MALE               4             244
[1] 2 2
[1] FALSE
D809V8, binary
                 cls
clus                0   1
  DHRS9 MUTATED     6   2
  DHRS9 WILD-TYPE 286  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS9 MUTATED      6    2
  DHRS9 WILD-TYPE  286   57
     clus
vv    DHRS9 MUTATED DHRS9 WILD-TYPE
  NO              6             286
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DHRS9 MUTATED                                          0
  DHRS9 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DHRS9 MUTATED                                       3
  DHRS9 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DHRS9 MUTATED                                                        4
  DHRS9 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DHRS9 MUTATED                                                   1
  DHRS9 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DHRS9 MUTATED                                                                   0
  DHRS9 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DHRS9 MUTATED                                                    0
  DHRS9 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DHRS9 MUTATED                                                  1
  DHRS9 WILD-TYPE                                               60
D809V9, multiclass
                                                                   clus
vv                                                                  DHRS9 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  DHRS9 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DHRS9 MUTATED     6   0   0   3
  DHRS9 WILD-TYPE 305  14  15  21
D809V10, multiclass
    clus
vv   DHRS9 MUTATED DHRS9 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D809V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DHRS9 MUTATED       1                         0
  DHRS9 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DHRS9 MUTATED                                           0     7
  DHRS9 WILD-TYPE                                         1   236
D809V12, multiclass
                                           clus
vv                                          DHRS9 MUTATED DHRS9 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D809V13, binary
                 cls
clus                0   1
  DHRS9 MUTATED     0   7
  DHRS9 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS9 MUTATED      0    7
  DHRS9 WILD-TYPE    4  303
                        clus
vv                       DHRS9 MUTATED DHRS9 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(810) Variable = RGS12 MUTATION ANALYSIS
D810V1, survival
                 sevent
clus2               0   1
  RGS12 MUTATED    18   9
  RGS12 WILD-TYPE 212 130
  RGS12 MUTATED RGS12 WILD-TYPE 
             27             342 
  RGS12 MUTATED RGS12 WILD-TYPE 
              9             130 
$`RGS12 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7197 TCGA-BR-8361 
       21.99         6.97         9.67        34.68         9.21        31.10 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-8686 TCGA-CD-8536 
       31.27        14.79         1.12        31.96        20.88        12.43 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4441 TCGA-CG-5721 TCGA-CG-5723 
        6.58        11.77        12.62        14.01         6.02       105.07 
TCGA-CG-5726 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-IP-7968 
       28.96        22.32         0.10        20.25        14.07         2.53 
TCGA-MX-A5UJ TCGA-SW-A7EB TCGA-VQ-A8P2 
       19.73         5.79        38.14 

$`RGS12 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       11.80         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-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-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
       12.43        11.61        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-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-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-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-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-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 

  RGS12 MUTATED RGS12 WILD-TYPE 
            0.1             0.0 
  RGS12 MUTATED RGS12 WILD-TYPE 
         105.07          122.30 
  RGS12 MUTATED RGS12 WILD-TYPE 
          14.07           14.35 
[1] "0.1 - 105.1 (14.1)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D810V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RGS12 MUTATED         0        1        3        3         3         1
  RGS12 WILD-TYPE       2       14       37       27        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RGS12 MUTATED           0          8          2          4        3
  RGS12 WILD-TYPE         3         62         51         28       35
D810V3, multiclass
            clus
vv           RGS12 MUTATED RGS12 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               3              27
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             8              62
  STAGE IIIB             2              51
  STAGE IIIC             4              28
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RGS12 MUTATED     2   4  10  12
  RGS12 WILD-TYPE  20  88 163  85
D810V4, multiclass
    clus
vv   RGS12 MUTATED RGS12 WILD-TYPE
  T1             2              20
  T2             4              88
  T3            10             163
  T4            12              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
  RGS12 MUTATED    10   9   8   1
  RGS12 WILD-TYPE 108  95  69  76
D810V5, multiclass
    clus
vv   RGS12 MUTATED RGS12 WILD-TYPE
  N0            10             108
  N1             9              95
  N2             8              69
  N3             1              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"
D810V6, binary
                 cls
clus                0   1
  RGS12 MUTATED    26   2
  RGS12 WILD-TYPE 320  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS12 MUTATED     26    2
  RGS12 WILD-TYPE  320   27
   clus
vv  RGS12 MUTATED RGS12 WILD-TYPE
  0            26             320
  1             2              27
[1] 2 2
[1] FALSE
D810V7, binary
                 cls
clus                0   1
  RGS12 MUTATED    11  19
  RGS12 WILD-TYPE 134 229
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS12 MUTATED     11   19
  RGS12 WILD-TYPE  134  229
        clus
vv       RGS12 MUTATED RGS12 WILD-TYPE
  FEMALE            11             134
  MALE              19             229
[1] 2 2
[1] FALSE
D810V8, binary
                 cls
clus                0   1
  RGS12 MUTATED    23   1
  RGS12 WILD-TYPE 269  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS12 MUTATED     23    1
  RGS12 WILD-TYPE  269   58
     clus
vv    RGS12 MUTATED RGS12 WILD-TYPE
  NO             23             269
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RGS12 MUTATED                                          0
  RGS12 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RGS12 MUTATED                                       3
  RGS12 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RGS12 MUTATED                                                       14
  RGS12 WILD-TYPE                                                    144
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RGS12 MUTATED                                                   2
  RGS12 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RGS12 MUTATED                                                                   6
  RGS12 WILD-TYPE                                                                62
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RGS12 MUTATED                                                    0
  RGS12 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RGS12 MUTATED                                                  5
  RGS12 WILD-TYPE                                               56
D810V9, multiclass
                                                                   clus
vv                                                                  RGS12 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              5
                                                                   clus
vv                                                                  RGS12 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RGS12 MUTATED    22   0   1   4
  RGS12 WILD-TYPE 289  14  14  20
D810V10, multiclass
    clus
vv   RGS12 MUTATED RGS12 WILD-TYPE
  R0            22             289
  R1             0              14
  R2             1              14
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D810V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RGS12 MUTATED      10                         0
  RGS12 WILD-TYPE    77                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RGS12 MUTATED                                           0    14
  RGS12 WILD-TYPE                                         1   229
D810V12, multiclass
                                           clus
vv                                          RGS12 MUTATED RGS12 WILD-TYPE
  ASIAN                                                10              77
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D810V13, binary
                 cls
clus                0   1
  RGS12 MUTATED     0  23
  RGS12 WILD-TYPE   4 287
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS12 MUTATED      0   23
  RGS12 WILD-TYPE    4  287
                        clus
vv                       RGS12 MUTATED RGS12 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            23             287
[1] 2 2
[1] FALSE

Clustering(811) Variable = TRIP10 MUTATION ANALYSIS
D811V1, survival
                  sevent
clus2                0   1
  TRIP10 MUTATED     9   0
  TRIP10 WILD-TYPE 221 139
  TRIP10 MUTATED TRIP10 WILD-TYPE 
               9              360 
  TRIP10 MUTATED TRIP10 WILD-TYPE 
               0              139 
$`TRIP10 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 
        0.10        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 

  TRIP10 MUTATED TRIP10 WILD-TYPE 
            6.02             0.00 
  TRIP10 MUTATED TRIP10 WILD-TYPE 
          105.07           122.30 
  TRIP10 MUTATED TRIP10 WILD-TYPE 
           19.73            14.22 
[1] "6.0 - 105.1 (19.7)" "0.0 - 122.3 (14.2)"
[1] "hr="     "2.6e+07"
D811V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIP10 MUTATED         0        0        0        1         3         1
  TRIP10 WILD-TYPE       2       15       40       29        34        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIP10 MUTATED           0          1          0          2        1
  TRIP10 WILD-TYPE         3         69         53         30       37
D811V3, multiclass
            clus
vv           TRIP10 MUTATED TRIP10 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIP10 MUTATED     0   1   5   3
  TRIP10 WILD-TYPE  22  91 168  94
D811V4, multiclass
    clus
vv   TRIP10 MUTATED TRIP10 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              5              168
  T4              3               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
  TRIP10 MUTATED     3   3   1   2
  TRIP10 WILD-TYPE 115 101  76  75
D811V5, multiclass
    clus
vv   TRIP10 MUTATED TRIP10 WILD-TYPE
  N0              3              115
  N1              3              101
  N2              1               76
  N3              2               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"
D811V6, binary
                  cls
clus                 0   1
  TRIP10 MUTATED     9   0
  TRIP10 WILD-TYPE 337  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP10 MUTATED      9    0
  TRIP10 WILD-TYPE  337   29
   clus
vv  TRIP10 MUTATED TRIP10 WILD-TYPE
  0              9              337
  1              0               29
[1] 2 2
[1] FALSE
D811V7, binary
                  cls
clus                 0   1
  TRIP10 MUTATED     5   4
  TRIP10 WILD-TYPE 140 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP10 MUTATED      5    4
  TRIP10 WILD-TYPE  140  244
        clus
vv       TRIP10 MUTATED TRIP10 WILD-TYPE
  FEMALE              5              140
  MALE                4              244
[1] 2 2
[1] FALSE
D811V8, binary
                  cls
clus                 0   1
  TRIP10 MUTATED     6   2
  TRIP10 WILD-TYPE 286  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP10 MUTATED      6    2
  TRIP10 WILD-TYPE  286   57
     clus
vv    TRIP10 MUTATED TRIP10 WILD-TYPE
  NO               6              286
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TRIP10 MUTATED                                          0
  TRIP10 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TRIP10 MUTATED                                       2
  TRIP10 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRIP10 MUTATED                                                        3
  TRIP10 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TRIP10 MUTATED                                                   1
  TRIP10 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRIP10 MUTATED                                                                   1
  TRIP10 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TRIP10 MUTATED                                                    0
  TRIP10 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TRIP10 MUTATED                                                  2
  TRIP10 WILD-TYPE                                               59
D811V9, multiclass
                                                                   clus
vv                                                                  TRIP10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  TRIP10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIP10 MUTATED     8   1   0   0
  TRIP10 WILD-TYPE 303  13  15  24
D811V10, multiclass
    clus
vv   TRIP10 MUTATED TRIP10 WILD-TYPE
  R0              8              303
  R1              1               13
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D811V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TRIP10 MUTATED       3                         1
  TRIP10 WILD-TYPE    84                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRIP10 MUTATED                                           0     2
  TRIP10 WILD-TYPE                                         1   241
D811V12, multiclass
                                           clus
vv                                          TRIP10 MUTATED TRIP10 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D811V13, binary
                  cls
clus                 0   1
  TRIP10 MUTATED     0   6
  TRIP10 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP10 MUTATED      0    6
  TRIP10 WILD-TYPE    4  304
                        clus
vv                       TRIP10 MUTATED TRIP10 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(812) Variable = BTBD12 MUTATION ANALYSIS
D812V1, survival
                  sevent
clus2                0   1
  BTBD12 MUTATED    15   7
  BTBD12 WILD-TYPE 215 132
  BTBD12 MUTATED BTBD12 WILD-TYPE 
              22              347 
  BTBD12 MUTATED BTBD12 WILD-TYPE 
               7              132 
$`BTBD12 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8367 
       26.70        30.90         6.61        34.68        35.84        26.33 
TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4PD TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4465 
        1.12        31.96        20.65         6.58        12.62         9.01 
TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5734 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-A4G9 
        6.02        65.10         7.99        11.08        77.29        24.20 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-VQ-A8P2 
        0.10         6.51         6.58        38.14 

$`BTBD12 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-5730 TCGA-CG-5732 TCGA-CG-5733 
       12.03        15.02        28.96         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-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-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-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-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 

  BTBD12 MUTATED BTBD12 WILD-TYPE 
             0.1              0.0 
  BTBD12 MUTATED BTBD12 WILD-TYPE 
           77.29           122.30 
  BTBD12 MUTATED BTBD12 WILD-TYPE 
          16.635           14.270 
[1] "0.1 - 77.3 (16.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D812V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BTBD12 MUTATED         0        1        3        1         5         3
  BTBD12 WILD-TYPE       2       14       37       29        32        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTBD12 MUTATED           1          2          1          2        4
  BTBD12 WILD-TYPE         2         68         52         30       34
D812V3, multiclass
            clus
vv           BTBD12 MUTATED BTBD12 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                3               37
  STAGE II                1               29
  STAGE IIA               5               32
  STAGE IIB               3               49
  STAGE III               1                2
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              2               30
  STAGE IV                4               34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BTBD12 MUTATED     1   6   8   9
  BTBD12 WILD-TYPE  21  86 165  88
D812V4, multiclass
    clus
vv   BTBD12 MUTATED BTBD12 WILD-TYPE
  T1              1               21
  T2              6               86
  T3              8              165
  T4              9               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
  BTBD12 MUTATED    11   7   3   3
  BTBD12 WILD-TYPE 107  97  74  74
D812V5, multiclass
    clus
vv   BTBD12 MUTATED BTBD12 WILD-TYPE
  N0             11              107
  N1              7               97
  N2              3               74
  N3              3               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"
D812V6, binary
                  cls
clus                 0   1
  BTBD12 MUTATED    23   2
  BTBD12 WILD-TYPE 323  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD12 MUTATED     23    2
  BTBD12 WILD-TYPE  323   27
   clus
vv  BTBD12 MUTATED BTBD12 WILD-TYPE
  0             23              323
  1              2               27
[1] 2 2
[1] FALSE
D812V7, binary
                  cls
clus                 0   1
  BTBD12 MUTATED    13  12
  BTBD12 WILD-TYPE 132 236
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD12 MUTATED     13   12
  BTBD12 WILD-TYPE  132  236
        clus
vv       BTBD12 MUTATED BTBD12 WILD-TYPE
  FEMALE             13              132
  MALE               12              236
[1] 2 2
[1] FALSE
D812V8, binary
                  cls
clus                 0   1
  BTBD12 MUTATED    16   3
  BTBD12 WILD-TYPE 276  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD12 MUTATED     16    3
  BTBD12 WILD-TYPE  276   56
     clus
vv    BTBD12 MUTATED BTBD12 WILD-TYPE
  NO              16              276
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BTBD12 MUTATED                                          0
  BTBD12 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BTBD12 MUTATED                                       5
  BTBD12 WILD-TYPE                                    65
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BTBD12 MUTATED                                                       11
  BTBD12 WILD-TYPE                                                    147
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BTBD12 MUTATED                                                   2
  BTBD12 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BTBD12 MUTATED                                                                   3
  BTBD12 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BTBD12 MUTATED                                                    0
  BTBD12 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BTBD12 MUTATED                                                  4
  BTBD12 WILD-TYPE                                               57
D812V9, multiclass
                                                                   clus
vv                                                                  BTBD12 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  BTBD12 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BTBD12 MUTATED    18   0   1   4
  BTBD12 WILD-TYPE 293  14  14  20
D812V10, multiclass
    clus
vv   BTBD12 MUTATED BTBD12 WILD-TYPE
  R0             18              293
  R1              0               14
  R2              1               14
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D812V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  BTBD12 MUTATED       7                         1
  BTBD12 WILD-TYPE    80                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BTBD12 MUTATED                                           0    11
  BTBD12 WILD-TYPE                                         1   232
D812V12, multiclass
                                           clus
vv                                          BTBD12 MUTATED BTBD12 WILD-TYPE
  ASIAN                                                  7               80
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D812V13, binary
                  cls
clus                 0   1
  BTBD12 MUTATED     0  18
  BTBD12 WILD-TYPE   4 292
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD12 MUTATED      0   18
  BTBD12 WILD-TYPE    4  292
                        clus
vv                       BTBD12 MUTATED BTBD12 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             18              292
[1] 2 2
[1] FALSE

Clustering(813) Variable = WAPAL MUTATION ANALYSIS
D813V1, survival
                 sevent
clus2               0   1
  WAPAL MUTATED    11   4
  WAPAL WILD-TYPE 219 135
  WAPAL MUTATED WAPAL WILD-TYPE 
             15             354 
  WAPAL MUTATED WAPAL WILD-TYPE 
              4             135 
$`WAPAL MUTATED`
TCGA-B7-5818 TCGA-BR-6457 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8361 TCGA-BR-8487 
       11.70        13.68        30.90        44.94        31.10         1.12 
TCGA-BR-A453 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-5721 
        6.08         6.58        11.77        12.62        15.95         6.02 
TCGA-CG-5726 TCGA-R5-A7ZI TCGA-VQ-A8P2 
       28.96        74.53        38.14 

$`WAPAL WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-A4CQ TCGA-BR-A4CS 
       10.68        34.13        13.87         7.53        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-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-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 

  WAPAL MUTATED WAPAL WILD-TYPE 
           1.12            0.00 
  WAPAL MUTATED WAPAL WILD-TYPE 
          74.53          122.30 
  WAPAL MUTATED WAPAL WILD-TYPE 
          13.68           14.35 
[1] "1.1 - 74.5 (13.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.6"
D813V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WAPAL MUTATED         0        1        2        1         4         0
  WAPAL WILD-TYPE       2       14       38       29        33        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WAPAL MUTATED           0          3          0          1        3
  WAPAL WILD-TYPE         3         67         53         31       35
D813V3, multiclass
            clus
vv           WAPAL MUTATED WAPAL WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              4              33
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WAPAL MUTATED     1   3   7   5
  WAPAL WILD-TYPE  21  89 166  92
D813V4, multiclass
    clus
vv   WAPAL MUTATED WAPAL WILD-TYPE
  T1             1              21
  T2             3              89
  T3             7             166
  T4             5              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
  WAPAL MUTATED     7   5   2   1
  WAPAL WILD-TYPE 111  99  75  76
D813V5, multiclass
    clus
vv   WAPAL MUTATED WAPAL WILD-TYPE
  N0             7             111
  N1             5              99
  N2             2              75
  N3             1              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"
D813V6, binary
                 cls
clus                0   1
  WAPAL MUTATED    13   2
  WAPAL WILD-TYPE 333  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WAPAL MUTATED     13    2
  WAPAL WILD-TYPE  333   27
   clus
vv  WAPAL MUTATED WAPAL WILD-TYPE
  0            13             333
  1             2              27
[1] 2 2
[1] FALSE
D813V7, binary
                 cls
clus                0   1
  WAPAL MUTATED     5  11
  WAPAL WILD-TYPE 140 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WAPAL MUTATED      5   11
  WAPAL WILD-TYPE  140  237
        clus
vv       WAPAL MUTATED WAPAL WILD-TYPE
  FEMALE             5             140
  MALE              11             237
[1] 2 2
[1] FALSE
D813V8, binary
                 cls
clus                0   1
  WAPAL MUTATED    13   1
  WAPAL WILD-TYPE 279  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WAPAL MUTATED     13    1
  WAPAL WILD-TYPE  279   58
     clus
vv    WAPAL MUTATED WAPAL WILD-TYPE
  NO             13             279
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  WAPAL MUTATED                                          1
  WAPAL WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  WAPAL MUTATED                                       3
  WAPAL WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WAPAL MUTATED                                                        9
  WAPAL WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  WAPAL MUTATED                                                   1
  WAPAL WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WAPAL MUTATED                                                                   2
  WAPAL WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  WAPAL MUTATED                                                    0
  WAPAL WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  WAPAL MUTATED                                                  0
  WAPAL WILD-TYPE                                               61
D813V9, multiclass
                                                                   clus
vv                                                                  WAPAL MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  WAPAL WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WAPAL MUTATED    12   0   0   1
  WAPAL WILD-TYPE 299  14  15  23
D813V10, multiclass
    clus
vv   WAPAL MUTATED WAPAL WILD-TYPE
  R0            12             299
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D813V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  WAPAL MUTATED       4                         0
  WAPAL WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WAPAL MUTATED                                           0     9
  WAPAL WILD-TYPE                                         1   234
D813V12, multiclass
                                           clus
vv                                          WAPAL MUTATED WAPAL WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D813V13, binary
                 cls
clus                0   1
  WAPAL MUTATED     1  11
  WAPAL WILD-TYPE   3 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WAPAL MUTATED      1   11
  WAPAL WILD-TYPE    3  299
                        clus
vv                       WAPAL MUTATED WAPAL WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(814) Variable = CAB39L MUTATION ANALYSIS
D814V1, survival
                  sevent
clus2                0   1
  CAB39L MUTATED     4   2
  CAB39L WILD-TYPE 226 137
  CAB39L MUTATED CAB39L WILD-TYPE 
               6              363 
  CAB39L MUTATED CAB39L WILD-TYPE 
               2              137 
$`CAB39L MUTATED`
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8680 TCGA-BR-A4QL TCGA-HU-8602 
        9.67        34.68         6.18        31.96        16.14        22.32 

$`CAB39L WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  CAB39L MUTATED CAB39L WILD-TYPE 
            6.18             0.00 
  CAB39L MUTATED CAB39L WILD-TYPE 
           34.68           122.30 
  CAB39L MUTATED CAB39L WILD-TYPE 
           19.23            14.17 
[1] "6.2 - 34.7 (19.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D814V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CAB39L MUTATED         0        0        0        0         2         1
  CAB39L WILD-TYPE       2       15       40       30        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAB39L MUTATED           0          0          1          1        1
  CAB39L WILD-TYPE         3         70         52         31       37
D814V3, multiclass
            clus
vv           CAB39L MUTATED CAB39L WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CAB39L MUTATED     0   0   3   3
  CAB39L WILD-TYPE  22  92 170  94
D814V4, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  T1              0               22
  T2              0               92
  T3              3              170
  T4              3               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
  CAB39L MUTATED     3   0   1   2
  CAB39L WILD-TYPE 115 104  76  75
D814V5, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  N0              3              115
  N1              0              104
  N2              1               76
  N3              2               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"
D814V6, binary
                  cls
clus                 0   1
  CAB39L MUTATED     6   1
  CAB39L WILD-TYPE 340  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      6    1
  CAB39L WILD-TYPE  340   28
   clus
vv  CAB39L MUTATED CAB39L WILD-TYPE
  0              6              340
  1              1               28
[1] 2 2
[1] FALSE
D814V7, binary
                  cls
clus                 0   1
  CAB39L MUTATED     4   3
  CAB39L WILD-TYPE 141 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      4    3
  CAB39L WILD-TYPE  141  245
        clus
vv       CAB39L MUTATED CAB39L WILD-TYPE
  FEMALE              4              141
  MALE                3              245
[1] 2 2
[1] FALSE
D814V8, binary
                  cls
clus                 0   1
  CAB39L MUTATED     6   0
  CAB39L WILD-TYPE 286  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      6    0
  CAB39L WILD-TYPE  286   59
     clus
vv    CAB39L MUTATED CAB39L WILD-TYPE
  NO               6              286
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CAB39L MUTATED                                          0
  CAB39L WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CAB39L MUTATED                                       2
  CAB39L WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CAB39L MUTATED                                                        3
  CAB39L WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CAB39L MUTATED                                                   0
  CAB39L WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CAB39L MUTATED                                                                   1
  CAB39L WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CAB39L MUTATED                                                    0
  CAB39L WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CAB39L MUTATED                                                  1
  CAB39L WILD-TYPE                                               60
D814V9, multiclass
                                                                   clus
vv                                                                  CAB39L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  CAB39L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CAB39L MUTATED     6   0   0   1
  CAB39L WILD-TYPE 305  14  15  23
D814V10, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D814V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CAB39L MUTATED       2                         0
  CAB39L WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CAB39L MUTATED                                           0     4
  CAB39L WILD-TYPE                                         1   239
D814V12, multiclass
                                           clus
vv                                          CAB39L MUTATED CAB39L WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D814V13, binary
                  cls
clus                 0   1
  CAB39L MUTATED     0   6
  CAB39L WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      0    6
  CAB39L WILD-TYPE    4  304
                        clus
vv                       CAB39L MUTATED CAB39L WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(815) Variable = ZCCHC2 MUTATION ANALYSIS
D815V1, survival
                  sevent
clus2                0   1
  ZCCHC2 MUTATED     3   3
  ZCCHC2 WILD-TYPE 227 136
  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
               6              363 
  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
               3              136 
$`ZCCHC2 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8285 TCGA-CD-8536 TCGA-VQ-A8PE 
        6.97        34.68        36.16         0.56        12.43        22.19 

$`ZCCHC2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8286 
        0.69        29.59         9.60        32.25         8.05        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-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-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 

  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
            0.56             0.00 
  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
           36.16           122.30 
  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE 
           17.31            14.27 
[1] "0.6 - 36.2 (17.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D815V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZCCHC2 MUTATED         0        1        0        1         1         0
  ZCCHC2 WILD-TYPE       2       14       40       29        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZCCHC2 MUTATED           0          1          1          1        0
  ZCCHC2 WILD-TYPE         3         69         52         31       38
D815V3, multiclass
            clus
vv           ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZCCHC2 MUTATED     1   0   4   1
  ZCCHC2 WILD-TYPE  21  92 169  96
D815V4, multiclass
    clus
vv   ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  T1              1               21
  T2              0               92
  T3              4              169
  T4              1               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
  ZCCHC2 MUTATED     3   1   0   2
  ZCCHC2 WILD-TYPE 115 103  77  75
D815V5, multiclass
    clus
vv   ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  N0              3              115
  N1              1              103
  N2              0               77
  N3              2               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"
D815V6, binary
                  cls
clus                 0   1
  ZCCHC2 MUTATED     5   0
  ZCCHC2 WILD-TYPE 341  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC2 MUTATED      5    0
  ZCCHC2 WILD-TYPE  341   29
   clus
vv  ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  0              5              341
  1              0               29
[1] 2 2
[1] FALSE
D815V7, binary
                  cls
clus                 0   1
  ZCCHC2 MUTATED     2   4
  ZCCHC2 WILD-TYPE 143 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC2 MUTATED      2    4
  ZCCHC2 WILD-TYPE  143  244
        clus
vv       ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  FEMALE              2              143
  MALE                4              244
[1] 2 2
[1] FALSE
D815V8, binary
                  cls
clus                 0   1
  ZCCHC2 MUTATED     6   0
  ZCCHC2 WILD-TYPE 286  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC2 MUTATED      6    0
  ZCCHC2 WILD-TYPE  286   59
     clus
vv    ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  NO               6              286
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZCCHC2 MUTATED                                          0
  ZCCHC2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZCCHC2 MUTATED                                       0
  ZCCHC2 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZCCHC2 MUTATED                                                        3
  ZCCHC2 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZCCHC2 MUTATED                                                   0
  ZCCHC2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZCCHC2 MUTATED                                                                   1
  ZCCHC2 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZCCHC2 MUTATED                                                    1
  ZCCHC2 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZCCHC2 MUTATED                                                  1
  ZCCHC2 WILD-TYPE                                               60
D815V9, multiclass
                                                                   clus
vv                                                                  ZCCHC2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ZCCHC2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZCCHC2 MUTATED     5   0   0   1
  ZCCHC2 WILD-TYPE 306  14  15  23
D815V10, multiclass
    clus
vv   ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D815V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZCCHC2 MUTATED       1                         0
  ZCCHC2 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZCCHC2 MUTATED                                           0     5
  ZCCHC2 WILD-TYPE                                         1   238
D815V12, multiclass
                                           clus
vv                                          ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D815V13, binary
                  cls
clus                 0   1
  ZCCHC2 MUTATED     0   5
  ZCCHC2 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC2 MUTATED      0    5
  ZCCHC2 WILD-TYPE    4  305
                        clus
vv                       ZCCHC2 MUTATED ZCCHC2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(816) Variable = WDR90 MUTATION ANALYSIS
D816V1, survival
                 sevent
clus2               0   1
  WDR90 MUTATED    13   5
  WDR90 WILD-TYPE 217 134
  WDR90 MUTATED WDR90 WILD-TYPE 
             18             351 
  WDR90 MUTATED WDR90 WILD-TYPE 
              5             134 
$`WDR90 MUTATED`
TCGA-CG-4444 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6566 TCGA-BR-8361 
       47.05         6.97        30.90         9.67        32.78        31.10 
TCGA-BR-8487 TCGA-BR-8683 TCGA-CD-A4MJ TCGA-D7-6518 TCGA-D7-A6EY TCGA-FP-8211 
        1.12         9.86        12.62        19.13        11.44        13.58 
TCGA-HF-7132 TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-VQ-A8P2 
       77.29        22.68        20.25        29.00        14.07        38.14 

$`WDR90 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58        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-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-D7-8572 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-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-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-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-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 

  WDR90 MUTATED WDR90 WILD-TYPE 
           1.12            0.00 
  WDR90 MUTATED WDR90 WILD-TYPE 
          77.29          122.30 
  WDR90 MUTATED WDR90 WILD-TYPE 
          19.69           14.17 
[1] "1.1 - 77.3 (19.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.7"
D816V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WDR90 MUTATED         0        0        3        1         2         2
  WDR90 WILD-TYPE       2       15       37       29        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WDR90 MUTATED           0          4          2          3        0
  WDR90 WILD-TYPE         3         66         51         29       38
D816V3, multiclass
            clus
vv           WDR90 MUTATED WDR90 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             2              51
  STAGE IIIC             3              29
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WDR90 MUTATED     1   6   6   5
  WDR90 WILD-TYPE  21  86 167  92
D816V4, multiclass
    clus
vv   WDR90 MUTATED WDR90 WILD-TYPE
  T1             1              21
  T2             6              86
  T3             6             167
  T4             5              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
  WDR90 MUTATED     4   6   4   3
  WDR90 WILD-TYPE 114  98  73  74
D816V5, multiclass
    clus
vv   WDR90 MUTATED WDR90 WILD-TYPE
  N0             4             114
  N1             6              98
  N2             4              73
  N3             3              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"
D816V6, binary
                 cls
clus                0   1
  WDR90 MUTATED    18   0
  WDR90 WILD-TYPE 328  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR90 MUTATED     18    0
  WDR90 WILD-TYPE  328   29
   clus
vv  WDR90 MUTATED WDR90 WILD-TYPE
  0            18             328
  1             0              29
[1] 2 2
[1] FALSE
D816V7, binary
                 cls
clus                0   1
  WDR90 MUTATED    10  10
  WDR90 WILD-TYPE 135 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR90 MUTATED     10   10
  WDR90 WILD-TYPE  135  238
        clus
vv       WDR90 MUTATED WDR90 WILD-TYPE
  FEMALE            10             135
  MALE              10             238
[1] 2 2
[1] FALSE
D816V8, binary
                 cls
clus                0   1
  WDR90 MUTATED    13   4
  WDR90 WILD-TYPE 279  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR90 MUTATED     13    4
  WDR90 WILD-TYPE  279   55
     clus
vv    WDR90 MUTATED WDR90 WILD-TYPE
  NO             13             279
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  WDR90 MUTATED                                          0
  WDR90 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  WDR90 MUTATED                                       5
  WDR90 WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WDR90 MUTATED                                                        9
  WDR90 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  WDR90 MUTATED                                                   2
  WDR90 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WDR90 MUTATED                                                                   1
  WDR90 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  WDR90 MUTATED                                                    0
  WDR90 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  WDR90 MUTATED                                                  3
  WDR90 WILD-TYPE                                               58
D816V9, multiclass
                                                                   clus
vv                                                                  WDR90 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  WDR90 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WDR90 MUTATED    12   2   0   4
  WDR90 WILD-TYPE 299  12  15  20
D816V10, multiclass
    clus
vv   WDR90 MUTATED WDR90 WILD-TYPE
  R0            12             299
  R1             2              12
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D816V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  WDR90 MUTATED       6                         0
  WDR90 WILD-TYPE    81                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WDR90 MUTATED                                           0    11
  WDR90 WILD-TYPE                                         1   232
D816V12, multiclass
                                           clus
vv                                          WDR90 MUTATED WDR90 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D816V13, binary
                 cls
clus                0   1
  WDR90 MUTATED     0  16
  WDR90 WILD-TYPE   4 294
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR90 MUTATED      0   16
  WDR90 WILD-TYPE    4  294
                        clus
vv                       WDR90 MUTATED WDR90 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            16             294
[1] 2 2
[1] FALSE

Clustering(817) Variable = UGT2A3 MUTATION ANALYSIS
D817V1, survival
                  sevent
clus2                0   1
  UGT2A3 MUTATED     4   2
  UGT2A3 WILD-TYPE 226 137
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
               6              363 
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
               2              137 
$`UGT2A3 MUTATED`
TCGA-BR-4184 TCGA-CG-4465 TCGA-CG-5721 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4H2 
        6.97         9.01         6.02        22.32        22.68        12.95 

$`UGT2A3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
            6.02             0.00 
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
           22.68           122.30 
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
           10.98            14.43 
[1] "6.0 - 22.7 (11.0)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D817V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UGT2A3 MUTATED         0        0        0        0         0         2
  UGT2A3 WILD-TYPE       2       15       40       30        37        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT2A3 MUTATED           0          1          1          0        3
  UGT2A3 WILD-TYPE         3         69         52         32       35
D817V3, multiclass
            clus
vv           UGT2A3 MUTATED UGT2A3 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UGT2A3 MUTATED     0   0   3   4
  UGT2A3 WILD-TYPE  22  92 170  93
D817V4, multiclass
    clus
vv   UGT2A3 MUTATED UGT2A3 WILD-TYPE
  T1              0               22
  T2              0               92
  T3              3              170
  T4              4               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
  UGT2A3 MUTATED     1   3   1   2
  UGT2A3 WILD-TYPE 117 101  76  75
D817V5, multiclass
    clus
vv   UGT2A3 MUTATED UGT2A3 WILD-TYPE
  N0              1              117
  N1              3              101
  N2              1               76
  N3              2               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"
D817V6, binary
                  cls
clus                 0   1
  UGT2A3 MUTATED     5   1
  UGT2A3 WILD-TYPE 341  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A3 MUTATED      5    1
  UGT2A3 WILD-TYPE  341   28
   clus
vv  UGT2A3 MUTATED UGT2A3 WILD-TYPE
  0              5              341
  1              1               28
[1] 2 2
[1] FALSE
D817V7, binary
                  cls
clus                 0   1
  UGT2A3 MUTATED     5   2
  UGT2A3 WILD-TYPE 140 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A3 MUTATED      5    2
  UGT2A3 WILD-TYPE  140  246
        clus
vv       UGT2A3 MUTATED UGT2A3 WILD-TYPE
  FEMALE              5              140
  MALE                2              246
[1] 2 2
[1] FALSE
D817V8, binary
                  cls
clus                 0   1
  UGT2A3 MUTATED     5   0
  UGT2A3 WILD-TYPE 287  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A3 MUTATED      5    0
  UGT2A3 WILD-TYPE  287   59
     clus
vv    UGT2A3 MUTATED UGT2A3 WILD-TYPE
  NO               5              287
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  UGT2A3 MUTATED                                          0
  UGT2A3 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  UGT2A3 MUTATED                                       3
  UGT2A3 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UGT2A3 MUTATED                                                        2
  UGT2A3 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  UGT2A3 MUTATED                                                   0
  UGT2A3 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UGT2A3 MUTATED                                                                   1
  UGT2A3 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  UGT2A3 MUTATED                                                    0
  UGT2A3 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  UGT2A3 MUTATED                                                  1
  UGT2A3 WILD-TYPE                                               60
D817V9, multiclass
                                                                   clus
vv                                                                  UGT2A3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  UGT2A3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  UGT2A3 MUTATED     3   0   1   2
  UGT2A3 WILD-TYPE 308  14  14  22
D817V10, multiclass
    clus
vv   UGT2A3 MUTATED UGT2A3 WILD-TYPE
  R0              3              308
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D817V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  UGT2A3 MUTATED       3                         0
  UGT2A3 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UGT2A3 MUTATED                                           0     2
  UGT2A3 WILD-TYPE                                         1   241
D817V12, multiclass
                                           clus
vv                                          UGT2A3 MUTATED UGT2A3 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D817V13, binary
                  cls
clus                 0   1
  UGT2A3 MUTATED     0   5
  UGT2A3 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A3 MUTATED      0    5
  UGT2A3 WILD-TYPE    4  305
                        clus
vv                       UGT2A3 MUTATED UGT2A3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(818) Variable = BRF1 MUTATION ANALYSIS
D818V1, survival
                sevent
clus2              0   1
  BRF1 MUTATED     5   5
  BRF1 WILD-TYPE 225 134
  BRF1 MUTATED BRF1 WILD-TYPE 
            10            359 
  BRF1 MUTATED BRF1 WILD-TYPE 
             5            134 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       14.76        26.43        11.24        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-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 

  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          14.43 
[1] "7.0 - 38.1 (12.6)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.3"
D818V2, 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       2       14       40       30        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BRF1 MUTATED           0          5          1          0        0
  BRF1 WILD-TYPE         3         65         52         32       38
D818V3, multiclass
            clus
vv           BRF1 MUTATED BRF1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            5             65
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BRF1 MUTATED     1   2   5   1
  BRF1 WILD-TYPE  21  90 168  96
D818V4, multiclass
    clus
vv   BRF1 MUTATED BRF1 WILD-TYPE
  T1            1             21
  T2            2             90
  T3            5            168
  T4            1             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
  BRF1 MUTATED     2   4   2   1
  BRF1 WILD-TYPE 116 100  75  76
D818V5, multiclass
    clus
vv   BRF1 MUTATED BRF1 WILD-TYPE
  N0            2            116
  N1            4            100
  N2            2             75
  N3            1             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"
D818V6, binary
                cls
clus               0   1
  BRF1 MUTATED    10   0
  BRF1 WILD-TYPE 336  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRF1 MUTATED     10    0
  BRF1 WILD-TYPE  336   29
   clus
vv  BRF1 MUTATED BRF1 WILD-TYPE
  0           10            336
  1            0             29
[1] 2 2
[1] FALSE
D818V7, binary
                cls
clus               0   1
  BRF1 MUTATED     6   5
  BRF1 WILD-TYPE 139 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRF1 MUTATED      6    5
  BRF1 WILD-TYPE  139  243
        clus
vv       BRF1 MUTATED BRF1 WILD-TYPE
  FEMALE            6            139
  MALE              5            243
[1] 2 2
[1] FALSE
D818V8, binary
                cls
clus               0   1
  BRF1 MUTATED     9   1
  BRF1 WILD-TYPE 283  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRF1 MUTATED      9    1
  BRF1 WILD-TYPE  283   58
     clus
vv    BRF1 MUTATED BRF1 WILD-TYPE
  NO             9            283
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BRF1 MUTATED                                          0
  BRF1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BRF1 MUTATED                                       0
  BRF1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BRF1 MUTATED                                                        6
  BRF1 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BRF1 MUTATED                                                   1
  BRF1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BRF1 MUTATED                                                                   0
  BRF1 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BRF1 MUTATED                                                    0
  BRF1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BRF1 MUTATED                                                  4
  BRF1 WILD-TYPE                                               57
D818V9, multiclass
                                                                   clus
vv                                                                  BRF1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  BRF1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BRF1 MUTATED     7   0   0   4
  BRF1 WILD-TYPE 304  14  15  20
D818V10, multiclass
    clus
vv   BRF1 MUTATED BRF1 WILD-TYPE
  R0            7            304
  R1            0             14
  R2            0             15
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D818V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BRF1 MUTATED       1                         0
  BRF1 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRF1 MUTATED                                           0    10
  BRF1 WILD-TYPE                                         1   233
D818V12, multiclass
                                           clus
vv                                          BRF1 MUTATED BRF1 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D818V13, binary
                cls
clus               0   1
  BRF1 MUTATED     0  10
  BRF1 WILD-TYPE   4 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRF1 MUTATED      0   10
  BRF1 WILD-TYPE    4  300
                        clus
vv                       BRF1 MUTATED BRF1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           10            300
[1] 2 2
[1] FALSE

Clustering(819) Variable = PLK1 MUTATION ANALYSIS
D819V1, survival
                sevent
clus2              0   1
  PLK1 MUTATED     9   6
  PLK1 WILD-TYPE 221 133
  PLK1 MUTATED PLK1 WILD-TYPE 
            15            354 
  PLK1 MUTATED PLK1 WILD-TYPE 
             6            133 
$`PLK1 MUTATED`
TCGA-BR-4280 TCGA-BR-8285 TCGA-BR-8682 TCGA-CD-A4MI TCGA-CG-5721 TCGA-FP-7998 
        6.61         0.56        32.58        11.77         6.02        22.29 
TCGA-HU-8238 TCGA-HU-8608 TCGA-HU-A4GQ TCGA-HU-A4H3 TCGA-MX-A5UJ TCGA-RD-A7BT 
        1.51        21.07         0.10        29.00        19.73         8.61 
TCGA-SW-A7EA TCGA-VQ-A8P2 TCGA-VQ-AA64 
       19.04        38.14        18.41 

$`PLK1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       22.32        22.82         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-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-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-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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        16.14        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 
         18.41          14.22 
[1] "0.1 - 38.1 (18.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D819V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLK1 MUTATED         0        0        2        0         0         1
  PLK1 WILD-TYPE       2       15       38       30        37        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLK1 MUTATED           1          3          2          4        2
  PLK1 WILD-TYPE         2         67         51         28       36
D819V3, multiclass
            clus
vv           PLK1 MUTATED PLK1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             1             51
  STAGE III             1              2
  STAGE IIIA            3             67
  STAGE IIIB            2             51
  STAGE IIIC            4             28
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PLK1 MUTATED     0   3   5   8
  PLK1 WILD-TYPE  22  89 168  89
D819V4, multiclass
    clus
vv   PLK1 MUTATED PLK1 WILD-TYPE
  T1            0             22
  T2            3             89
  T3            5            168
  T4            8             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
  PLK1 MUTATED     3   4   5   4
  PLK1 WILD-TYPE 115 100  72  73
D819V5, multiclass
    clus
vv   PLK1 MUTATED PLK1 WILD-TYPE
  N0            3            115
  N1            4            100
  N2            5             72
  N3            4             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"
D819V6, binary
                cls
clus               0   1
  PLK1 MUTATED    15   0
  PLK1 WILD-TYPE 331  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK1 MUTATED     15    0
  PLK1 WILD-TYPE  331   29
   clus
vv  PLK1 MUTATED PLK1 WILD-TYPE
  0           15            331
  1            0             29
[1] 2 2
[1] FALSE
D819V7, binary
                cls
clus               0   1
  PLK1 MUTATED     5  11
  PLK1 WILD-TYPE 140 237
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK1 MUTATED      5   11
  PLK1 WILD-TYPE  140  237
        clus
vv       PLK1 MUTATED PLK1 WILD-TYPE
  FEMALE            5            140
  MALE             11            237
[1] 2 2
[1] FALSE
D819V8, binary
                cls
clus               0   1
  PLK1 MUTATED    11   3
  PLK1 WILD-TYPE 281  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK1 MUTATED     11    3
  PLK1 WILD-TYPE  281   56
     clus
vv    PLK1 MUTATED PLK1 WILD-TYPE
  NO            11            281
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PLK1 MUTATED                                          0
  PLK1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PLK1 MUTATED                                       4
  PLK1 WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLK1 MUTATED                                                        2
  PLK1 WILD-TYPE                                                    156
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PLK1 MUTATED                                                   2
  PLK1 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLK1 MUTATED                                                                   5
  PLK1 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PLK1 MUTATED                                                    0
  PLK1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PLK1 MUTATED                                                  3
  PLK1 WILD-TYPE                                               58
D819V9, multiclass
                                                                   clus
vv                                                                  PLK1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  PLK1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PLK1 MUTATED    13   0   1   1
  PLK1 WILD-TYPE 298  14  14  23
D819V10, multiclass
    clus
vv   PLK1 MUTATED PLK1 WILD-TYPE
  R0           13            298
  R1            0             14
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D819V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PLK1 MUTATED       6                         0
  PLK1 WILD-TYPE    81                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLK1 MUTATED                                           1     7
  PLK1 WILD-TYPE                                         0   236
D819V12, multiclass
                                           clus
vv                                          PLK1 MUTATED PLK1 WILD-TYPE
  ASIAN                                                6             81
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D819V13, binary
                cls
clus               0   1
  PLK1 MUTATED     1  11
  PLK1 WILD-TYPE   3 299
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK1 MUTATED      1   11
  PLK1 WILD-TYPE    3  299
                        clus
vv                       PLK1 MUTATED PLK1 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           11            299
[1] 2 2
[1] FALSE

Clustering(820) Variable = DUSP9 MUTATION ANALYSIS
D820V1, survival
                 sevent
clus2               0   1
  DUSP9 MUTATED     5   2
  DUSP9 WILD-TYPE 225 137
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              7             362 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              2             137 
$`DUSP9 MUTATED`
TCGA-BR-4280 TCGA-BR-8081 TCGA-CD-8535 TCGA-HU-A4GH TCGA-IN-A6RP TCGA-RD-A8N6 
        6.61        32.25        12.82        11.77         6.44         8.94 
TCGA-VQ-A92D 
       66.81 

$`DUSP9 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  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           14.45 
[1] "6.4 - 66.8 (11.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D820V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DUSP9 MUTATED         0        1        1        0         0         1
  DUSP9 WILD-TYPE       2       14       39       30        37        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DUSP9 MUTATED           1          3          0          1        0
  DUSP9 WILD-TYPE         2         67         53         31       38
D820V3, multiclass
            clus
vv           DUSP9 MUTATED DUSP9 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DUSP9 MUTATED     2   3   1   2
  DUSP9 WILD-TYPE  20  89 172  95
D820V4, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  T1             2              20
  T2             3              89
  T3             1             172
  T4             2              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
  DUSP9 MUTATED     4   2   1   1
  DUSP9 WILD-TYPE 114 102  76  76
D820V5, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  N0             4             114
  N1             2             102
  N2             1              76
  N3             1              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"
D820V6, binary
                 cls
clus                0   1
  DUSP9 MUTATED     8   0
  DUSP9 WILD-TYPE 338  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      8    0
  DUSP9 WILD-TYPE  338   29
   clus
vv  DUSP9 MUTATED DUSP9 WILD-TYPE
  0             8             338
  1             0              29
[1] 2 2
[1] FALSE
D820V7, binary
                 cls
clus                0   1
  DUSP9 MUTATED     4   4
  DUSP9 WILD-TYPE 141 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      4    4
  DUSP9 WILD-TYPE  141  244
        clus
vv       DUSP9 MUTATED DUSP9 WILD-TYPE
  FEMALE             4             141
  MALE               4             244
[1] 2 2
[1] FALSE
D820V8, binary
                 cls
clus                0   1
  DUSP9 MUTATED     6   1
  DUSP9 WILD-TYPE 286  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      6    1
  DUSP9 WILD-TYPE  286   58
     clus
vv    DUSP9 MUTATED DUSP9 WILD-TYPE
  NO              6             286
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DUSP9 MUTATED                                          0
  DUSP9 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DUSP9 MUTATED                                       0
  DUSP9 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DUSP9 MUTATED                                                        5
  DUSP9 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DUSP9 MUTATED                                                   0
  DUSP9 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DUSP9 MUTATED                                                                   1
  DUSP9 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DUSP9 MUTATED                                                    0
  DUSP9 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DUSP9 MUTATED                                                  2
  DUSP9 WILD-TYPE                                               59
D820V9, multiclass
                                                                   clus
vv                                                                  DUSP9 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  DUSP9 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DUSP9 MUTATED     6   0   0   2
  DUSP9 WILD-TYPE 305  14  15  22
D820V10, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D820V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DUSP9 MUTATED       2                         0
  DUSP9 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DUSP9 MUTATED                                           0     6
  DUSP9 WILD-TYPE                                         1   237
D820V12, multiclass
                                           clus
vv                                          DUSP9 MUTATED DUSP9 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D820V13, binary
                 cls
clus                0   1
  DUSP9 MUTATED     0   7
  DUSP9 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      0    7
  DUSP9 WILD-TYPE    4  303
                        clus
vv                       DUSP9 MUTATED DUSP9 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(821) Variable = KIAA0427 MUTATION ANALYSIS
D821V1, survival
                    sevent
clus2                  0   1
  KIAA0427 MUTATED     7   5
  KIAA0427 WILD-TYPE 223 134
  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
                12                357 
  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
                 5                134 
$`KIAA0427 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8372 TCGA-CG-5726 
       26.70         6.97         6.61        34.68        31.27        28.96 
TCGA-CG-5733 TCGA-F1-6874 TCGA-HU-A4GX TCGA-MX-A5UJ TCGA-VQ-A8DU TCGA-VQ-A8P2 
       21.07        14.47        20.25        19.73         5.46        38.14 

$`KIAA0427 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-F1-6875 
        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-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-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 

  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
              5.46               0.00 
  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
             38.14             122.30 
  KIAA0427 MUTATED KIAA0427 WILD-TYPE 
             20.66              14.07 
[1] "5.5 - 38.1 (20.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D821V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0427 MUTATED         1        1        2        0         1         1
  KIAA0427 WILD-TYPE       1       14       38       30        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0427 MUTATED           1          6          0          2        0
  KIAA0427 WILD-TYPE         2         64         53         30       38
D821V3, multiclass
            clus
vv           KIAA0427 MUTATED KIAA0427 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  1                 14
  STAGE IB                  2                 38
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 1                 51
  STAGE III                 1                  2
  STAGE IIIA                6                 64
  STAGE IIIB                0                 53
  STAGE IIIC                2                 30
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0427 MUTATED     2   4   5   5
  KIAA0427 WILD-TYPE  20  88 168  92
D821V4, multiclass
    clus
vv   KIAA0427 MUTATED KIAA0427 WILD-TYPE
  T1                2                 20
  T2                4                 88
  T3                5                168
  T4                5                 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
  KIAA0427 MUTATED     6   4   4   1
  KIAA0427 WILD-TYPE 112 100  73  76
D821V5, multiclass
    clus
vv   KIAA0427 MUTATED KIAA0427 WILD-TYPE
  N0                6                112
  N1                4                100
  N2                4                 73
  N3                1                 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"
D821V6, binary
                    cls
clus                   0   1
  KIAA0427 MUTATED    13   0
  KIAA0427 WILD-TYPE 333  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0427 MUTATED     13    0
  KIAA0427 WILD-TYPE  333   29
   clus
vv  KIAA0427 MUTATED KIAA0427 WILD-TYPE
  0               13                333
  1                0                 29
[1] 2 2
[1] FALSE
D821V7, binary
                    cls
clus                   0   1
  KIAA0427 MUTATED     8   8
  KIAA0427 WILD-TYPE 137 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0427 MUTATED      8    8
  KIAA0427 WILD-TYPE  137  240
        clus
vv       KIAA0427 MUTATED KIAA0427 WILD-TYPE
  FEMALE                8                137
  MALE                  8                240
[1] 2 2
[1] FALSE
D821V8, binary
                    cls
clus                   0   1
  KIAA0427 MUTATED    11   1
  KIAA0427 WILD-TYPE 281  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0427 MUTATED     11    1
  KIAA0427 WILD-TYPE  281   58
     clus
vv    KIAA0427 MUTATED KIAA0427 WILD-TYPE
  NO                11                281
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA0427 MUTATED                                          0
  KIAA0427 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA0427 MUTATED                                       2
  KIAA0427 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0427 MUTATED                                                        7
  KIAA0427 WILD-TYPE                                                    151
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA0427 MUTATED                                                   1
  KIAA0427 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0427 MUTATED                                                                   4
  KIAA0427 WILD-TYPE                                                                64
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA0427 MUTATED                                                    0
  KIAA0427 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA0427 MUTATED                                                  2
  KIAA0427 WILD-TYPE                                               59
D821V9, multiclass
                                                                   clus
vv                                                                  KIAA0427 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  KIAA0427 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0427 MUTATED    12   0   0   4
  KIAA0427 WILD-TYPE 299  14  15  20
D821V10, multiclass
    clus
vv   KIAA0427 MUTATED KIAA0427 WILD-TYPE
  R0               12                299
  R1                0                 14
  R2                0                 15
  RX                4                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D821V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0427 MUTATED       1                         1
  KIAA0427 WILD-TYPE    86                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0427 MUTATED                                           0    11
  KIAA0427 WILD-TYPE                                         1   232
D821V12, multiclass
                                           clus
vv                                          KIAA0427 MUTATED KIAA0427 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   11                232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D821V13, binary
                    cls
clus                   0   1
  KIAA0427 MUTATED     0  11
  KIAA0427 WILD-TYPE   4 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0427 MUTATED      0   11
  KIAA0427 WILD-TYPE    4  299
                        clus
vv                       KIAA0427 MUTATED KIAA0427 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               11                299
[1] 2 2
[1] FALSE

Clustering(822) Variable = UBXN6 MUTATION ANALYSIS
D822V1, survival
                 sevent
clus2               0   1
  UBXN6 MUTATED     8   4
  UBXN6 WILD-TYPE 222 135
  UBXN6 MUTATED UBXN6 WILD-TYPE 
             12             357 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
              4             135 
$`UBXN6 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4437 
       26.70        30.90         1.12         6.58        12.62         8.05 
TCGA-CG-5733 TCGA-F1-A448 TCGA-HU-A4GN TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-VQ-AA64 
       21.07        21.27        29.98        29.00        14.07        18.41 

$`UBXN6 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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 

  UBXN6 MUTATED UBXN6 WILD-TYPE 
           1.12            0.00 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
           30.9           122.3 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
          19.74           14.17 
[1] "1.1 - 30.9 (19.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D822V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UBXN6 MUTATED         0        0        2        1         3         1
  UBXN6 WILD-TYPE       2       15       38       29        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UBXN6 MUTATED           0          1          2          1        0
  UBXN6 WILD-TYPE         3         69         51         31       38
D822V3, multiclass
            clus
vv           UBXN6 MUTATED UBXN6 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UBXN6 MUTATED     1   5   4   2
  UBXN6 WILD-TYPE  21  87 169  95
D822V4, multiclass
    clus
vv   UBXN6 MUTATED UBXN6 WILD-TYPE
  T1             1              21
  T2             5              87
  T3             4             169
  T4             2              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
  UBXN6 MUTATED     4   3   2   2
  UBXN6 WILD-TYPE 114 101  75  75
D822V5, multiclass
    clus
vv   UBXN6 MUTATED UBXN6 WILD-TYPE
  N0             4             114
  N1             3             101
  N2             2              75
  N3             2              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"
D822V6, binary
                 cls
clus                0   1
  UBXN6 MUTATED    12   0
  UBXN6 WILD-TYPE 334  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN6 MUTATED     12    0
  UBXN6 WILD-TYPE  334   29
   clus
vv  UBXN6 MUTATED UBXN6 WILD-TYPE
  0            12             334
  1             0              29
[1] 2 2
[1] FALSE
D822V7, binary
                 cls
clus                0   1
  UBXN6 MUTATED     5   7
  UBXN6 WILD-TYPE 140 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN6 MUTATED      5    7
  UBXN6 WILD-TYPE  140  241
        clus
vv       UBXN6 MUTATED UBXN6 WILD-TYPE
  FEMALE             5             140
  MALE               7             241
[1] 2 2
[1] FALSE
D822V8, binary
                 cls
clus                0   1
  UBXN6 MUTATED     9   2
  UBXN6 WILD-TYPE 283  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN6 MUTATED      9    2
  UBXN6 WILD-TYPE  283   57
     clus
vv    UBXN6 MUTATED UBXN6 WILD-TYPE
  NO              9             283
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  UBXN6 MUTATED                                          0
  UBXN6 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  UBXN6 MUTATED                                       3
  UBXN6 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UBXN6 MUTATED                                                        3
  UBXN6 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  UBXN6 MUTATED                                                   1
  UBXN6 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UBXN6 MUTATED                                                                   3
  UBXN6 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  UBXN6 MUTATED                                                    0
  UBXN6 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  UBXN6 MUTATED                                                  2
  UBXN6 WILD-TYPE                                               59
D822V9, multiclass
                                                                   clus
vv                                                                  UBXN6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  UBXN6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  UBXN6 MUTATED     9   0   0   1
  UBXN6 WILD-TYPE 302  14  15  23
D822V10, multiclass
    clus
vv   UBXN6 MUTATED UBXN6 WILD-TYPE
  R0             9             302
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D822V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  UBXN6 MUTATED       5                         0
  UBXN6 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UBXN6 MUTATED                                           0     5
  UBXN6 WILD-TYPE                                         1   238
D822V12, multiclass
                                           clus
vv                                          UBXN6 MUTATED UBXN6 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D822V13, binary
                 cls
clus                0   1
  UBXN6 MUTATED     1   8
  UBXN6 WILD-TYPE   3 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN6 MUTATED      1    8
  UBXN6 WILD-TYPE    3  302
                        clus
vv                       UBXN6 MUTATED UBXN6 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(823) Variable = EEF2K MUTATION ANALYSIS
D823V1, survival
                 sevent
clus2               0   1
  EEF2K MUTATED     5   2
  EEF2K WILD-TYPE 225 137
  EEF2K MUTATED EEF2K WILD-TYPE 
              7             362 
  EEF2K MUTATED EEF2K WILD-TYPE 
              2             137 
$`EEF2K MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-CG-4305 TCGA-CG-5721 TCGA-FP-7735 TCGA-FP-A4BE 
       19.56         6.97        15.95         6.02         3.48        11.08 
TCGA-HU-8602 
       22.32 

$`EEF2K WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  EEF2K MUTATED EEF2K WILD-TYPE 
           3.48            0.00 
  EEF2K MUTATED EEF2K WILD-TYPE 
          22.32          122.30 
  EEF2K MUTATED EEF2K WILD-TYPE 
          11.08           14.35 
[1] "3.5 - 22.3 (11.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D823V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EEF2K MUTATED         0        0        1        1         1         1
  EEF2K WILD-TYPE       2       15       39       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EEF2K MUTATED           0          3          0          1        2
  EEF2K WILD-TYPE         3         67         53         31       36
D823V3, multiclass
            clus
vv           EEF2K MUTATED EEF2K WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EEF2K MUTATED     0   2   3   5
  EEF2K WILD-TYPE  22  90 170  92
D823V4, multiclass
    clus
vv   EEF2K MUTATED EEF2K WILD-TYPE
  T1             0              22
  T2             2              90
  T3             3             170
  T4             5              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
  EEF2K MUTATED     4   4   1   1
  EEF2K WILD-TYPE 114 100  76  76
D823V5, multiclass
    clus
vv   EEF2K MUTATED EEF2K WILD-TYPE
  N0             4             114
  N1             4             100
  N2             1              76
  N3             1              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"
D823V6, binary
                 cls
clus                0   1
  EEF2K MUTATED     8   0
  EEF2K WILD-TYPE 338  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF2K MUTATED      8    0
  EEF2K WILD-TYPE  338   29
   clus
vv  EEF2K MUTATED EEF2K WILD-TYPE
  0             8             338
  1             0              29
[1] 2 2
[1] FALSE
D823V7, binary
                 cls
clus                0   1
  EEF2K MUTATED     3   7
  EEF2K WILD-TYPE 142 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF2K MUTATED      3    7
  EEF2K WILD-TYPE  142  241
        clus
vv       EEF2K MUTATED EEF2K WILD-TYPE
  FEMALE             3             142
  MALE               7             241
[1] 2 2
[1] FALSE
D823V8, binary
                 cls
clus                0   1
  EEF2K MUTATED     6   2
  EEF2K WILD-TYPE 286  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF2K MUTATED      6    2
  EEF2K WILD-TYPE  286   57
     clus
vv    EEF2K MUTATED EEF2K WILD-TYPE
  NO              6             286
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EEF2K MUTATED                                          0
  EEF2K WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EEF2K MUTATED                                       2
  EEF2K WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EEF2K MUTATED                                                        7
  EEF2K WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EEF2K MUTATED                                                   0
  EEF2K WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EEF2K MUTATED                                                                   1
  EEF2K WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EEF2K MUTATED                                                    0
  EEF2K WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EEF2K MUTATED                                                  0
  EEF2K WILD-TYPE                                               61
D823V9, multiclass
                                                                   clus
vv                                                                  EEF2K MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  EEF2K WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EEF2K MUTATED     5   1   0   3
  EEF2K WILD-TYPE 306  13  15  21
D823V10, multiclass
    clus
vv   EEF2K MUTATED EEF2K WILD-TYPE
  R0             5             306
  R1             1              13
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D823V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EEF2K MUTATED       1                         2
  EEF2K WILD-TYPE    86                         7
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EEF2K MUTATED                                           0     4
  EEF2K WILD-TYPE                                         1   239
D823V12, multiclass
                                           clus
vv                                          EEF2K MUTATED EEF2K WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             2               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D823V13, binary
                 cls
clus                0   1
  EEF2K MUTATED     0   7
  EEF2K WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF2K MUTATED      0    7
  EEF2K WILD-TYPE    4  303
                        clus
vv                       EEF2K MUTATED EEF2K WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(824) Variable = PYHIN1 MUTATION ANALYSIS
D824V1, survival
                  sevent
clus2                0   1
  PYHIN1 MUTATED     7   4
  PYHIN1 WILD-TYPE 223 135
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
              11              358 
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
               4              135 
$`PYHIN1 MUTATED`
TCGA-BR-8297 TCGA-BR-8372 TCGA-CD-8529 TCGA-CG-4306 TCGA-CG-5726 TCGA-D7-A4YV 
        7.40        31.27        12.30         1.02        28.96         5.92 
TCGA-D7-A6EX TCGA-HF-7132 TCGA-HU-A4GU TCGA-VQ-A91U TCGA-VQ-A91V 
       11.31        77.29         6.58         1.71        42.64 

$`PYHIN1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-A92D TCGA-VQ-A94T TCGA-VQ-AA64 
        1.87        15.65        20.81        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 

  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
            1.02             0.00 
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
           77.29           122.30 
  PYHIN1 MUTATED PYHIN1 WILD-TYPE 
           11.31            14.45 
[1] "1.0 - 77.3 (11.3)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1"  
D824V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PYHIN1 MUTATED         0        1        0        1         0         2
  PYHIN1 WILD-TYPE       2       14       40       29        37        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PYHIN1 MUTATED           0          3          0          2        2
  PYHIN1 WILD-TYPE         3         67         53         30       36
D824V3, multiclass
            clus
vv           PYHIN1 MUTATED PYHIN1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               0               37
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PYHIN1 MUTATED     1   1   6   3
  PYHIN1 WILD-TYPE  21  91 167  94
D824V4, multiclass
    clus
vv   PYHIN1 MUTATED PYHIN1 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              6              167
  T4              3               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
  PYHIN1 MUTATED     2   4   3   2
  PYHIN1 WILD-TYPE 116 100  74  75
D824V5, multiclass
    clus
vv   PYHIN1 MUTATED PYHIN1 WILD-TYPE
  N0              2              116
  N1              4              100
  N2              3               74
  N3              2               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"
D824V6, binary
                  cls
clus                 0   1
  PYHIN1 MUTATED     9   2
  PYHIN1 WILD-TYPE 337  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PYHIN1 MUTATED      9    2
  PYHIN1 WILD-TYPE  337   27
   clus
vv  PYHIN1 MUTATED PYHIN1 WILD-TYPE
  0              9              337
  1              2               27
[1] 2 2
[1] FALSE
D824V7, binary
                  cls
clus                 0   1
  PYHIN1 MUTATED     2   9
  PYHIN1 WILD-TYPE 143 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PYHIN1 MUTATED      2    9
  PYHIN1 WILD-TYPE  143  239
        clus
vv       PYHIN1 MUTATED PYHIN1 WILD-TYPE
  FEMALE              2              143
  MALE                9              239
[1] 2 2
[1] FALSE
D824V8, binary
                  cls
clus                 0   1
  PYHIN1 MUTATED     6   3
  PYHIN1 WILD-TYPE 286  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PYHIN1 MUTATED      6    3
  PYHIN1 WILD-TYPE  286   56
     clus
vv    PYHIN1 MUTATED PYHIN1 WILD-TYPE
  NO               6              286
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PYHIN1 MUTATED                                          0
  PYHIN1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PYHIN1 MUTATED                                       2
  PYHIN1 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PYHIN1 MUTATED                                                        2
  PYHIN1 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PYHIN1 MUTATED                                                   2
  PYHIN1 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PYHIN1 MUTATED                                                                   2
  PYHIN1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PYHIN1 MUTATED                                                    0
  PYHIN1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PYHIN1 MUTATED                                                  3
  PYHIN1 WILD-TYPE                                               58
D824V9, multiclass
                                                                   clus
vv                                                                  PYHIN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  PYHIN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PYHIN1 MUTATED    10   0   1   0
  PYHIN1 WILD-TYPE 301  14  14  24
D824V10, multiclass
    clus
vv   PYHIN1 MUTATED PYHIN1 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              1               14
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D824V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PYHIN1 MUTATED       3                         0
  PYHIN1 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PYHIN1 MUTATED                                           0     4
  PYHIN1 WILD-TYPE                                         1   239
D824V12, multiclass
                                           clus
vv                                          PYHIN1 MUTATED PYHIN1 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D824V13, binary
                  cls
clus                 0   1
  PYHIN1 MUTATED     0   6
  PYHIN1 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PYHIN1 MUTATED      0    6
  PYHIN1 WILD-TYPE    4  304
                        clus
vv                       PYHIN1 MUTATED PYHIN1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(825) Variable = C9ORF25 MUTATION ANALYSIS
D825V1, survival
                   sevent
clus2                 0   1
  C9ORF25 MUTATED     2   3
  C9ORF25 WILD-TYPE 228 136
  C9ORF25 MUTATED C9ORF25 WILD-TYPE 
                5               364 
  C9ORF25 MUTATED C9ORF25 WILD-TYPE 
                3               136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  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             14.35 
[1] "0.1 - 19.6 (6.6)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "3"  
D825V2, 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       2       15       40       30        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF25 MUTATED           0          0          1          2        1
  C9ORF25 WILD-TYPE         3         70         52         30       37
D825V3, multiclass
            clus
vv           C9ORF25 MUTATED C9ORF25 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               1                52
  STAGE IIIC               2                30
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C9ORF25 MUTATED     0   0   2   3
  C9ORF25 WILD-TYPE  22  92 171  94
D825V4, multiclass
    clus
vv   C9ORF25 MUTATED C9ORF25 WILD-TYPE
  T1               0                22
  T2               0                92
  T3               2               171
  T4               3                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
  C9ORF25 MUTATED     1   1   1   2
  C9ORF25 WILD-TYPE 117 103  76  75
D825V5, multiclass
    clus
vv   C9ORF25 MUTATED C9ORF25 WILD-TYPE
  N0               1               117
  N1               1               103
  N2               1                76
  N3               2                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"
D825V6, binary
                   cls
clus                  0   1
  C9ORF25 MUTATED     5   0
  C9ORF25 WILD-TYPE 341  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF25 MUTATED      5    0
  C9ORF25 WILD-TYPE  341   29
   clus
vv  C9ORF25 MUTATED C9ORF25 WILD-TYPE
  0               5               341
  1               0                29
[1] 2 2
[1] FALSE
D825V7, binary
                   cls
clus                  0   1
  C9ORF25 MUTATED     1   4
  C9ORF25 WILD-TYPE 144 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF25 MUTATED      1    4
  C9ORF25 WILD-TYPE  144  244
        clus
vv       C9ORF25 MUTATED C9ORF25 WILD-TYPE
  FEMALE               1               144
  MALE                 4               244
[1] 2 2
[1] FALSE
D825V8, binary
                   cls
clus                  0   1
  C9ORF25 MUTATED     5   0
  C9ORF25 WILD-TYPE 287  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF25 MUTATED      5    0
  C9ORF25 WILD-TYPE  287   59
     clus
vv    C9ORF25 MUTATED C9ORF25 WILD-TYPE
  NO                5               287
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C9ORF25 MUTATED                                          0
  C9ORF25 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C9ORF25 MUTATED                                       2
  C9ORF25 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C9ORF25 MUTATED                                                        1
  C9ORF25 WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C9ORF25 MUTATED                                                   0
  C9ORF25 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C9ORF25 MUTATED                                                                   1
  C9ORF25 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C9ORF25 MUTATED                                                    0
  C9ORF25 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C9ORF25 MUTATED                                                  1
  C9ORF25 WILD-TYPE                                               60
D825V9, multiclass
                                                                   clus
vv                                                                  C9ORF25 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  C9ORF25 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C9ORF25 MUTATED     3   0   0   0
  C9ORF25 WILD-TYPE 308  14  15  24
D825V10, multiclass
    clus
vv   C9ORF25 MUTATED C9ORF25 WILD-TYPE
  R0               3               308
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D825V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C9ORF25 MUTATED       2                         0
  C9ORF25 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C9ORF25 MUTATED                                           0     2
  C9ORF25 WILD-TYPE                                         1   241
D825V12, multiclass
                                           clus
vv                                          C9ORF25 MUTATED C9ORF25 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D825V13, binary
                   cls
clus                  0   1
  C9ORF25 MUTATED     0   4
  C9ORF25 WILD-TYPE   4 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF25 MUTATED      0    4
  C9ORF25 WILD-TYPE    4  306
                        clus
vv                       C9ORF25 MUTATED C9ORF25 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4               306
[1] 2 2
[1] FALSE

Clustering(826) Variable = CD58 MUTATION ANALYSIS
D826V1, survival
                sevent
clus2              0   1
  CD58 MUTATED     4   3
  CD58 WILD-TYPE 226 136
  CD58 MUTATED CD58 WILD-TYPE 
             7            362 
  CD58 MUTATED CD58 WILD-TYPE 
             3            136 
$`CD58 MUTATED`
TCGA-BR-4253 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8363 TCGA-CD-A4MG TCGA-CG-5721 
        4.08        34.68        29.59         0.26         6.58         6.02 
TCGA-HU-A4G8 
       22.68 

$`CD58 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  CD58 MUTATED CD58 WILD-TYPE 
          0.26           0.00 
  CD58 MUTATED CD58 WILD-TYPE 
         34.68         122.30 
  CD58 MUTATED CD58 WILD-TYPE 
          6.58          14.35 
[1] "0.3 - 34.7 (6.6)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D826V2, 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       2       15       39       30        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CD58 MUTATED           0          1          0          0        1
  CD58 WILD-TYPE         3         69         53         32       37
D826V3, multiclass
            clus
vv           CD58 MUTATED CD58 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD58 MUTATED     0   1   4   2
  CD58 WILD-TYPE  22  91 169  95
D826V4, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            4            169
  T4            2             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
  CD58 MUTATED     4   3   0   0
  CD58 WILD-TYPE 114 101  77  77
D826V5, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  N0            4            114
  N1            3            101
  N2            0             77
  N3            0             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"
D826V6, binary
                cls
clus               0   1
  CD58 MUTATED     7   0
  CD58 WILD-TYPE 339  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED      7    0
  CD58 WILD-TYPE  339   29
   clus
vv  CD58 MUTATED CD58 WILD-TYPE
  0            7            339
  1            0             29
[1] 2 2
[1] FALSE
D826V7, binary
                cls
clus               0   1
  CD58 MUTATED     5   2
  CD58 WILD-TYPE 140 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED      5    2
  CD58 WILD-TYPE  140  246
        clus
vv       CD58 MUTATED CD58 WILD-TYPE
  FEMALE            5            140
  MALE              2            246
[1] 2 2
[1] FALSE
D826V8, binary
                cls
clus               0   1
  CD58 MUTATED     7   0
  CD58 WILD-TYPE 285  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED      7    0
  CD58 WILD-TYPE  285   59
     clus
vv    CD58 MUTATED CD58 WILD-TYPE
  NO             7            285
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CD58 MUTATED                                          0
  CD58 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CD58 MUTATED                                       2
  CD58 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD58 MUTATED                                                        4
  CD58 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CD58 MUTATED                                                   0
  CD58 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD58 MUTATED                                                                   1
  CD58 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CD58 MUTATED                                                    0
  CD58 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CD58 MUTATED                                                  0
  CD58 WILD-TYPE                                               61
D826V9, multiclass
                                                                   clus
vv                                                                  CD58 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  CD58 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CD58 MUTATED     4   0   0   1
  CD58 WILD-TYPE 307  14  15  23
D826V10, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  R0            4            307
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D826V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CD58 MUTATED       2                         0
  CD58 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD58 MUTATED                                           0     4
  CD58 WILD-TYPE                                         1   239
D826V12, multiclass
                                           clus
vv                                          CD58 MUTATED CD58 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D826V13, binary
                cls
clus               0   1
  CD58 MUTATED     0   6
  CD58 WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED      0    6
  CD58 WILD-TYPE    4  304
                        clus
vv                       CD58 MUTATED CD58 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(827) Variable = C20ORF7 MUTATION ANALYSIS
D827V1, survival
                   sevent
clus2                 0   1
  C20ORF7 MUTATED     4   2
  C20ORF7 WILD-TYPE 226 137
  C20ORF7 MUTATED C20ORF7 WILD-TYPE 
                6               363 
  C20ORF7 MUTATED C20ORF7 WILD-TYPE 
                2               137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-5813 TCGA-CD-8524 TCGA-CD-8525 
       13.18        13.35        11.21        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-A5UJ 
       13.51         2.53         5.56        63.62        36.95        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 

  C20ORF7 MUTATED C20ORF7 WILD-TYPE 
             3.72              0.00 
  C20ORF7 MUTATED C20ORF7 WILD-TYPE 
            38.14            122.30 
  C20ORF7 MUTATED C20ORF7 WILD-TYPE 
            20.12             14.27 
[1] "3.7 - 38.1 (20.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D827V2, 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       2       15       40       30        37        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF7 MUTATED           1          2          0          1        0
  C20ORF7 WILD-TYPE         2         68         53         31       38
D827V3, multiclass
            clus
vv           C20ORF7 MUTATED C20ORF7 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                0                37
  STAGE IIB                1                51
  STAGE III                1                 2
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C20ORF7 MUTATED     0   1   2   3
  C20ORF7 WILD-TYPE  22  91 171  94
D827V4, multiclass
    clus
vv   C20ORF7 MUTATED C20ORF7 WILD-TYPE
  T1               0                22
  T2               1                91
  T3               2               171
  T4               3                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
  C20ORF7 MUTATED     1   4   0   1
  C20ORF7 WILD-TYPE 117 100  77  76
D827V5, multiclass
    clus
vv   C20ORF7 MUTATED C20ORF7 WILD-TYPE
  N0               1               117
  N1               4               100
  N2               0                77
  N3               1                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"
D827V6, binary
                   cls
clus                  0   1
  C20ORF7 MUTATED     6   0
  C20ORF7 WILD-TYPE 340  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C20ORF7 MUTATED      6    0
  C20ORF7 WILD-TYPE  340   29
   clus
vv  C20ORF7 MUTATED C20ORF7 WILD-TYPE
  0               6               340
  1               0                29
[1] 2 2
[1] FALSE
D827V7, binary
                   cls
clus                  0   1
  C20ORF7 MUTATED     2   4
  C20ORF7 WILD-TYPE 143 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C20ORF7 MUTATED      2    4
  C20ORF7 WILD-TYPE  143  244
        clus
vv       C20ORF7 MUTATED C20ORF7 WILD-TYPE
  FEMALE               2               143
  MALE                 4               244
[1] 2 2
[1] FALSE
D827V8, binary
                   cls
clus                  0   1
  C20ORF7 MUTATED     5   1
  C20ORF7 WILD-TYPE 287  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C20ORF7 MUTATED      5    1
  C20ORF7 WILD-TYPE  287   58
     clus
vv    C20ORF7 MUTATED C20ORF7 WILD-TYPE
  NO                5               287
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C20ORF7 MUTATED                                          0
  C20ORF7 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C20ORF7 MUTATED                                       1
  C20ORF7 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C20ORF7 MUTATED                                                        4
  C20ORF7 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C20ORF7 MUTATED                                                   1
  C20ORF7 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C20ORF7 MUTATED                                                                   0
  C20ORF7 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C20ORF7 MUTATED                                                    0
  C20ORF7 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C20ORF7 MUTATED                                                  0
  C20ORF7 WILD-TYPE                                               61
D827V9, multiclass
                                                                   clus
vv                                                                  C20ORF7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  C20ORF7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C20ORF7 MUTATED     5   0   0   1
  C20ORF7 WILD-TYPE 306  14  15  23
D827V10, multiclass
    clus
vv   C20ORF7 MUTATED C20ORF7 WILD-TYPE
  R0               5               306
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D827V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C20ORF7 MUTATED       2                         0
  C20ORF7 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C20ORF7 MUTATED                                           0     4
  C20ORF7 WILD-TYPE                                         1   239
D827V12, multiclass
                                           clus
vv                                          C20ORF7 MUTATED C20ORF7 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D827V13, binary
                   cls
clus                  0   1
  C20ORF7 MUTATED     0   5
  C20ORF7 WILD-TYPE   4 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C20ORF7 MUTATED      0    5
  C20ORF7 WILD-TYPE    4  305
                        clus
vv                       C20ORF7 MUTATED C20ORF7 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(828) Variable = POLE3 MUTATION ANALYSIS
D828V1, survival
                 sevent
clus2               0   1
  POLE3 MUTATED     1   1
  POLE3 WILD-TYPE 229 138
  POLE3 MUTATED POLE3 WILD-TYPE 
              2             367 
  POLE3 MUTATED POLE3 WILD-TYPE 
              1             138 
$`POLE3 MUTATED`
TCGA-BR-8078 TCGA-HU-A4GQ 
       29.59         0.10 

$`POLE3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  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          14.270 
[1] "0.1 - 29.6 (14.8)"  "0.0 - 122.3 (14.3)"
[1] "Remove cluster labels:" "POLE3 MUTATED"         
D828V2, 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       1       15       40       30        37        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POLE3 MUTATED           0          0          0          1        0
  POLE3 WILD-TYPE         3         70         53         31       38
D828V3, multiclass
            clus
vv           POLE3 MUTATED POLE3 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  POLE3 MUTATED     1   0   0   2
  POLE3 WILD-TYPE  21  92 173  95
D828V4, multiclass
    clus
vv   POLE3 MUTATED POLE3 WILD-TYPE
  T1             1              21
  T2             0              92
  T3             0             173
  T4             2              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
  POLE3 MUTATED     1   1   1   0
  POLE3 WILD-TYPE 117 103  76  77
D828V5, multiclass
    clus
vv   POLE3 MUTATED POLE3 WILD-TYPE
  N0             1             117
  N1             1             103
  N2             1              76
  N3             0              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"
D828V6, binary
                 cls
clus                0   1
  POLE3 MUTATED     2   0
  POLE3 WILD-TYPE 344  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLE3 MUTATED      2    0
  POLE3 WILD-TYPE  344   29
   clus
vv  POLE3 MUTATED POLE3 WILD-TYPE
  0             2             344
  1             0              29
[1] 2 2
[1] FALSE
D828V7, binary
                 cls
clus                0   1
  POLE3 MUTATED     1   2
  POLE3 WILD-TYPE 144 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLE3 MUTATED      1    2
  POLE3 WILD-TYPE  144  246
        clus
vv       POLE3 MUTATED POLE3 WILD-TYPE
  FEMALE             1             144
  MALE               2             246
[1] 2 2
[1] FALSE
D828V8, binary
                 cls
clus                0   1
  POLE3 MUTATED     3   0
  POLE3 WILD-TYPE 289  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLE3 MUTATED      3    0
  POLE3 WILD-TYPE  289   59
     clus
vv    POLE3 MUTATED POLE3 WILD-TYPE
  NO              3             289
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  POLE3 MUTATED                                          0
  POLE3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  POLE3 MUTATED                                       0
  POLE3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  POLE3 MUTATED                                                        2
  POLE3 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  POLE3 MUTATED                                                   0
  POLE3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  POLE3 MUTATED                                                                   0
  POLE3 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  POLE3 MUTATED                                                    0
  POLE3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  POLE3 MUTATED                                                  1
  POLE3 WILD-TYPE                                               60
D828V9, multiclass
                                                                   clus
vv                                                                  POLE3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  POLE3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  POLE3 MUTATED     3   0   0   0
  POLE3 WILD-TYPE 308  14  15  24
D828V10, multiclass
    clus
vv   POLE3 MUTATED POLE3 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D828V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  POLE3 MUTATED       1                         1
  POLE3 WILD-TYPE    86                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  POLE3 MUTATED                                           0     1
  POLE3 WILD-TYPE                                         1   242
D828V12, multiclass
                                           clus
vv                                          POLE3 MUTATED POLE3 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 1             242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D828V13, binary
                 cls
clus                0   1
  POLE3 MUTATED     0   3
  POLE3 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLE3 MUTATED      0    3
  POLE3 WILD-TYPE    4  307
                        clus
vv                       POLE3 MUTATED POLE3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(829) Variable = CHMP7 MUTATION ANALYSIS
D829V1, survival
                 sevent
clus2               0   1
  CHMP7 MUTATED     2   2
  CHMP7 WILD-TYPE 228 137
  CHMP7 MUTATED CHMP7 WILD-TYPE 
              4             365 
  CHMP7 MUTATED CHMP7 WILD-TYPE 
              2             137 
$`CHMP7 MUTATED`
TCGA-CG-4460 TCGA-BR-A4QL TCGA-CG-5728 TCGA-HU-A4GX 
       21.99        16.14        65.10        20.25 

$`CHMP7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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 

  CHMP7 MUTATED CHMP7 WILD-TYPE 
          16.14            0.00 
  CHMP7 MUTATED CHMP7 WILD-TYPE 
           65.1           122.3 
  CHMP7 MUTATED CHMP7 WILD-TYPE 
          21.12           14.07 
[1] "16.1 - 65.1 (21.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D829V2, 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       2       15       39       30        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHMP7 MUTATED           0          0          1          1        2
  CHMP7 WILD-TYPE         3         70         52         31       36
D829V3, multiclass
            clus
vv           CHMP7 MUTATED CHMP7 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CHMP7 MUTATED     0   1   1   3
  CHMP7 WILD-TYPE  22  91 172  94
D829V4, multiclass
    clus
vv   CHMP7 MUTATED CHMP7 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             1             172
  T4             3              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
  CHMP7 MUTATED     1   1   2   1
  CHMP7 WILD-TYPE 117 103  75  76
D829V5, multiclass
    clus
vv   CHMP7 MUTATED CHMP7 WILD-TYPE
  N0             1             117
  N1             1             103
  N2             2              75
  N3             1              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"
D829V6, binary
                 cls
clus                0   1
  CHMP7 MUTATED     4   1
  CHMP7 WILD-TYPE 342  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHMP7 MUTATED      4    1
  CHMP7 WILD-TYPE  342   28
   clus
vv  CHMP7 MUTATED CHMP7 WILD-TYPE
  0             4             342
  1             1              28
[1] 2 2
[1] FALSE
D829V7, binary
                 cls
clus                0   1
  CHMP7 MUTATED     5   0
  CHMP7 WILD-TYPE 140 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHMP7 MUTATED      5    0
  CHMP7 WILD-TYPE  140  248
        clus
vv       CHMP7 MUTATED CHMP7 WILD-TYPE
  FEMALE             5             140
  MALE               0             248
[1] 2 2
[1] FALSE
D829V8, binary
                 cls
clus                0   1
  CHMP7 MUTATED     3   0
  CHMP7 WILD-TYPE 289  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHMP7 MUTATED      3    0
  CHMP7 WILD-TYPE  289   59
     clus
vv    CHMP7 MUTATED CHMP7 WILD-TYPE
  NO              3             289
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CHMP7 MUTATED                                          0
  CHMP7 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CHMP7 MUTATED                                       1
  CHMP7 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CHMP7 MUTATED                                                        2
  CHMP7 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CHMP7 MUTATED                                                   0
  CHMP7 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CHMP7 MUTATED                                                                   2
  CHMP7 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CHMP7 MUTATED                                                    0
  CHMP7 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CHMP7 MUTATED                                                  0
  CHMP7 WILD-TYPE                                               61
D829V9, multiclass
                                                                   clus
vv                                                                  CHMP7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  CHMP7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CHMP7 MUTATED     3   0   1   1
  CHMP7 WILD-TYPE 308  14  14  23
D829V10, multiclass
    clus
vv   CHMP7 MUTATED CHMP7 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D829V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CHMP7 MUTATED       1                         0
  CHMP7 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CHMP7 MUTATED                                           0     2
  CHMP7 WILD-TYPE                                         1   241
D829V12, multiclass
                                           clus
vv                                          CHMP7 MUTATED CHMP7 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D829V13, binary
                 cls
clus                0   1
  CHMP7 MUTATED     0   3
  CHMP7 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHMP7 MUTATED      0    3
  CHMP7 WILD-TYPE    4  307
                        clus
vv                       CHMP7 MUTATED CHMP7 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(830) Variable = AMELX MUTATION ANALYSIS
D830V1, survival
                 sevent
clus2               0   1
  AMELX MUTATED     3   1
  AMELX WILD-TYPE 227 138
  AMELX MUTATED AMELX WILD-TYPE 
              4             365 
  AMELX MUTATED AMELX WILD-TYPE 
              1             138 
$`AMELX MUTATED`
TCGA-BR-6452 TCGA-D7-6528 TCGA-D7-A6EY TCGA-HF-A5NB 
       34.68        15.22        11.44        30.51 

$`AMELX WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  AMELX MUTATED AMELX WILD-TYPE 
          11.44            0.00 
  AMELX MUTATED AMELX WILD-TYPE 
          34.68          122.30 
  AMELX MUTATED AMELX WILD-TYPE 
         22.865          14.170 
[1] "11.4 - 34.7 (22.9)" "0.0 - 122.3 (14.2)"
[1] "hr=" "2"  
D830V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AMELX MUTATED         0        1        1        0         1         0
  AMELX WILD-TYPE       2       14       39       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMELX MUTATED           0          0          1          1        0
  AMELX WILD-TYPE         3         70         52         31       38
D830V3, multiclass
            clus
vv           AMELX MUTATED AMELX WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AMELX MUTATED     1   1   2   1
  AMELX WILD-TYPE  21  91 171  96
D830V4, multiclass
    clus
vv   AMELX MUTATED AMELX WILD-TYPE
  T1             1              21
  T2             1              91
  T3             2             171
  T4             1              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
  AMELX MUTATED     3   0   0   2
  AMELX WILD-TYPE 115 104  77  75
D830V5, multiclass
    clus
vv   AMELX MUTATED AMELX WILD-TYPE
  N0             3             115
  N1             0             104
  N2             0              77
  N3             2              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"
D830V6, binary
                 cls
clus                0   1
  AMELX MUTATED     5   0
  AMELX WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMELX MUTATED      5    0
  AMELX WILD-TYPE  341   29
   clus
vv  AMELX MUTATED AMELX WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D830V7, binary
                 cls
clus                0   1
  AMELX MUTATED     4   1
  AMELX WILD-TYPE 141 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMELX MUTATED      4    1
  AMELX WILD-TYPE  141  247
        clus
vv       AMELX MUTATED AMELX WILD-TYPE
  FEMALE             4             141
  MALE               1             247
[1] 2 2
[1] FALSE
D830V8, binary
                 cls
clus                0   1
  AMELX MUTATED     3   2
  AMELX WILD-TYPE 289  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMELX MUTATED      3    2
  AMELX WILD-TYPE  289   57
     clus
vv    AMELX MUTATED AMELX WILD-TYPE
  NO              3             289
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AMELX MUTATED                                          0
  AMELX WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AMELX MUTATED                                       0
  AMELX WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMELX MUTATED                                                        2
  AMELX WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AMELX MUTATED                                                   1
  AMELX WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AMELX MUTATED                                                                   0
  AMELX WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AMELX MUTATED                                                    0
  AMELX WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AMELX MUTATED                                                  2
  AMELX WILD-TYPE                                               59
D830V9, multiclass
                                                                   clus
vv                                                                  AMELX MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  AMELX WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AMELX MUTATED     4   1   0   0
  AMELX WILD-TYPE 307  13  15  24
D830V10, multiclass
    clus
vv   AMELX MUTATED AMELX WILD-TYPE
  R0             4             307
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D830V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AMELX MUTATED       1                         0
  AMELX WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMELX MUTATED                                           0     3
  AMELX WILD-TYPE                                         1   240
D830V12, multiclass
                                           clus
vv                                          AMELX MUTATED AMELX WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D830V13, binary
                 cls
clus                0   1
  AMELX MUTATED     0   4
  AMELX WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMELX MUTATED      0    4
  AMELX WILD-TYPE    4  306
                        clus
vv                       AMELX MUTATED AMELX WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(831) Variable = NEK8 MUTATION ANALYSIS
D831V1, survival
                sevent
clus2              0   1
  NEK8 MUTATED     7   4
  NEK8 WILD-TYPE 223 135
  NEK8 MUTATED NEK8 WILD-TYPE 
            11            358 
  NEK8 MUTATED NEK8 WILD-TYPE 
             4            135 
$`NEK8 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7715 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8690 
       30.90        34.68        33.63         4.31        25.05        10.68 
TCGA-CG-5721 TCGA-CG-5733 TCGA-HJ-7597 TCGA-HU-A4GX TCGA-HU-A4H3 
        6.02        21.07        26.47        20.25        29.00 

$`NEK8 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  NEK8 MUTATED NEK8 WILD-TYPE 
          4.31           0.00 
  NEK8 MUTATED NEK8 WILD-TYPE 
         34.68         122.30 
  NEK8 MUTATED NEK8 WILD-TYPE 
         25.05          14.07 
[1] "4.3 - 34.7 (25.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D831V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NEK8 MUTATED         0        0        2        0         2         0
  NEK8 WILD-TYPE       2       15       38       30        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NEK8 MUTATED           0          1          1          3        1
  NEK8 WILD-TYPE         3         69         52         29       37
D831V3, multiclass
            clus
vv           NEK8 MUTATED NEK8 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            3             29
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NEK8 MUTATED     0   4   3   4
  NEK8 WILD-TYPE  22  88 170  93
D831V4, multiclass
    clus
vv   NEK8 MUTATED NEK8 WILD-TYPE
  T1            0             22
  T2            4             88
  T3            3            170
  T4            4             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
  NEK8 MUTATED     4   1   2   3
  NEK8 WILD-TYPE 114 103  75  74
D831V5, multiclass
    clus
vv   NEK8 MUTATED NEK8 WILD-TYPE
  N0            4            114
  N1            1            103
  N2            2             75
  N3            3             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"
D831V6, binary
                cls
clus               0   1
  NEK8 MUTATED    10   0
  NEK8 WILD-TYPE 336  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK8 MUTATED     10    0
  NEK8 WILD-TYPE  336   29
   clus
vv  NEK8 MUTATED NEK8 WILD-TYPE
  0           10            336
  1            0             29
[1] 2 2
[1] FALSE
D831V7, binary
                cls
clus               0   1
  NEK8 MUTATED     9   2
  NEK8 WILD-TYPE 136 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK8 MUTATED      9    2
  NEK8 WILD-TYPE  136  246
        clus
vv       NEK8 MUTATED NEK8 WILD-TYPE
  FEMALE            9            136
  MALE              2            246
[1] 2 2
[1] FALSE
D831V8, binary
                cls
clus               0   1
  NEK8 MUTATED    10   0
  NEK8 WILD-TYPE 282  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK8 MUTATED     10    0
  NEK8 WILD-TYPE  282   59
     clus
vv    NEK8 MUTATED NEK8 WILD-TYPE
  NO            10            282
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NEK8 MUTATED                                          1
  NEK8 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NEK8 MUTATED                                       2
  NEK8 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NEK8 MUTATED                                                        6
  NEK8 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NEK8 MUTATED                                                   0
  NEK8 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NEK8 MUTATED                                                                   2
  NEK8 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NEK8 MUTATED                                                    0
  NEK8 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NEK8 MUTATED                                                  0
  NEK8 WILD-TYPE                                               61
D831V9, multiclass
                                                                   clus
vv                                                                  NEK8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  NEK8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NEK8 MUTATED    10   0   0   1
  NEK8 WILD-TYPE 301  14  15  23
D831V10, multiclass
    clus
vv   NEK8 MUTATED NEK8 WILD-TYPE
  R0           10            301
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D831V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NEK8 MUTATED       2                         0
  NEK8 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NEK8 MUTATED                                           0     7
  NEK8 WILD-TYPE                                         1   236
D831V12, multiclass
                                           clus
vv                                          NEK8 MUTATED NEK8 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D831V13, binary
                cls
clus               0   1
  NEK8 MUTATED     0   9
  NEK8 WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK8 MUTATED      0    9
  NEK8 WILD-TYPE    4  301
                        clus
vv                       NEK8 MUTATED NEK8 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(832) Variable = POMGNT1 MUTATION ANALYSIS
D832V1, survival
                   sevent
clus2                 0   1
  POMGNT1 MUTATED     4   6
  POMGNT1 WILD-TYPE 226 133
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
               10               359 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                6               133 
$`POMGNT1 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-A4PE TCGA-CD-A4MG TCGA-CG-4441 
       21.99        34.68        44.94        20.42         6.58        14.01 
TCGA-CG-4465 TCGA-D7-A6ET TCGA-FP-A4BF TCGA-VQ-AA6G 
        9.01        26.43         5.52        26.04 

$`POMGNT1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-4443 TCGA-CG-4449 
        7.99         8.05        54.08         4.01        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-A6EV TCGA-D7-A6EX 
        5.92        36.43        13.78        14.76        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-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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        16.14        27.55        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 
           21.205            14.170 
[1] "5.5 - 44.9 (21.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D832V2, 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       2       15       39       30        33        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POMGNT1 MUTATED           0          2          1          0        2
  POMGNT1 WILD-TYPE         3         68         52         32       36
D832V3, multiclass
            clus
vv           POMGNT1 MUTATED POMGNT1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                4                33
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  POMGNT1 MUTATED     0   2   6   2
  POMGNT1 WILD-TYPE  22  90 167  95
D832V4, multiclass
    clus
vv   POMGNT1 MUTATED POMGNT1 WILD-TYPE
  T1               0                22
  T2               2                90
  T3               6               167
  T4               2                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
  POMGNT1 MUTATED     5   1   2   2
  POMGNT1 WILD-TYPE 113 103  75  75
D832V5, multiclass
    clus
vv   POMGNT1 MUTATED POMGNT1 WILD-TYPE
  N0               5               113
  N1               1               103
  N2               2                75
  N3               2                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"
D832V6, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     8   2
  POMGNT1 WILD-TYPE 338  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      8    2
  POMGNT1 WILD-TYPE  338   27
   clus
vv  POMGNT1 MUTATED POMGNT1 WILD-TYPE
  0               8               338
  1               2                27
[1] 2 2
[1] FALSE
D832V7, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     5   5
  POMGNT1 WILD-TYPE 140 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      5    5
  POMGNT1 WILD-TYPE  140  243
        clus
vv       POMGNT1 MUTATED POMGNT1 WILD-TYPE
  FEMALE               5               140
  MALE                 5               243
[1] 2 2
[1] FALSE
D832V8, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     8   0
  POMGNT1 WILD-TYPE 284  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      8    0
  POMGNT1 WILD-TYPE  284   59
     clus
vv    POMGNT1 MUTATED POMGNT1 WILD-TYPE
  NO                8               284
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  POMGNT1 MUTATED                                          1
  POMGNT1 WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  POMGNT1 MUTATED                                       2
  POMGNT1 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  POMGNT1 MUTATED                                                        3
  POMGNT1 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  POMGNT1 MUTATED                                                   0
  POMGNT1 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  POMGNT1 MUTATED                                                                   3
  POMGNT1 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  POMGNT1 MUTATED                                                    0
  POMGNT1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  POMGNT1 MUTATED                                                  1
  POMGNT1 WILD-TYPE                                               60
D832V9, multiclass
                                                                   clus
vv                                                                  POMGNT1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  POMGNT1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  POMGNT1 MUTATED     6   1   2   0
  POMGNT1 WILD-TYPE 305  13  13  24
D832V10, multiclass
    clus
vv   POMGNT1 MUTATED POMGNT1 WILD-TYPE
  R0               6               305
  R1               1                13
  R2               2                13
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D832V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  POMGNT1 MUTATED       1                         0
  POMGNT1 WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  POMGNT1 MUTATED                                           0     6
  POMGNT1 WILD-TYPE                                         1   237
D832V12, multiclass
                                           clus
vv                                          POMGNT1 MUTATED POMGNT1 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D832V13, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     0   6
  POMGNT1 WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      0    6
  POMGNT1 WILD-TYPE    4  304
                        clus
vv                       POMGNT1 MUTATED POMGNT1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(833) Variable = ATP2B4 MUTATION ANALYSIS
D833V1, survival
                  sevent
clus2                0   1
  ATP2B4 MUTATED     9   5
  ATP2B4 WILD-TYPE 221 134
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
              14              355 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
               5              134 
$`ATP2B4 MUTATED`
TCGA-BR-6458 TCGA-BR-6852 TCGA-BR-8363 TCGA-BR-8372 TCGA-CD-8536 TCGA-CD-A4MG 
       19.33        44.94         0.26        31.27        12.43         6.58 
TCGA-CG-5723 TCGA-D7-A6EX TCGA-D7-A74B TCGA-F1-6874 TCGA-MX-A5UJ TCGA-RD-A7BT 
      105.07        11.31         7.13        14.47        19.73         8.61 
TCGA-SW-A7EA TCGA-VQ-A8P2 
       19.04        38.14 

$`ATP2B4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
       19.96         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-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-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-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 

  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
            0.26             0.00 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
          105.07           122.30 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
          16.755           14.170 
[1] "0.3 - 105.1 (16.8)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D833V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP2B4 MUTATED         0        0        3        2         2         1
  ATP2B4 WILD-TYPE       2       15       37       28        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP2B4 MUTATED           0          3          1          1        1
  ATP2B4 WILD-TYPE         3         67         52         31       37
D833V3, multiclass
            clus
vv           ATP2B4 MUTATED ATP2B4 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                2               28
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP2B4 MUTATED     0   4   9   2
  ATP2B4 WILD-TYPE  22  88 164  95
D833V4, multiclass
    clus
vv   ATP2B4 MUTATED ATP2B4 WILD-TYPE
  T1              0               22
  T2              4               88
  T3              9              164
  T4              2               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
  ATP2B4 MUTATED     6   3   2   3
  ATP2B4 WILD-TYPE 112 101  75  74
D833V5, multiclass
    clus
vv   ATP2B4 MUTATED ATP2B4 WILD-TYPE
  N0              6              112
  N1              3              101
  N2              2               75
  N3              3               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"
D833V6, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED    14   0
  ATP2B4 WILD-TYPE 332  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED     14    0
  ATP2B4 WILD-TYPE  332   29
   clus
vv  ATP2B4 MUTATED ATP2B4 WILD-TYPE
  0             14              332
  1              0               29
[1] 2 2
[1] FALSE
D833V7, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED     8   7
  ATP2B4 WILD-TYPE 137 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED      8    7
  ATP2B4 WILD-TYPE  137  241
        clus
vv       ATP2B4 MUTATED ATP2B4 WILD-TYPE
  FEMALE              8              137
  MALE                7              241
[1] 2 2
[1] FALSE
D833V8, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED    13   1
  ATP2B4 WILD-TYPE 279  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED     13    1
  ATP2B4 WILD-TYPE  279   58
     clus
vv    ATP2B4 MUTATED ATP2B4 WILD-TYPE
  NO              13              279
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ATP2B4 MUTATED                                          0
  ATP2B4 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ATP2B4 MUTATED                                       3
  ATP2B4 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATP2B4 MUTATED                                                        7
  ATP2B4 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ATP2B4 MUTATED                                                   1
  ATP2B4 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATP2B4 MUTATED                                                                   2
  ATP2B4 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ATP2B4 MUTATED                                                    0
  ATP2B4 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ATP2B4 MUTATED                                                  2
  ATP2B4 WILD-TYPE                                               59
D833V9, multiclass
                                                                   clus
vv                                                                  ATP2B4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  ATP2B4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATP2B4 MUTATED    12   0   1   1
  ATP2B4 WILD-TYPE 299  14  14  23
D833V10, multiclass
    clus
vv   ATP2B4 MUTATED ATP2B4 WILD-TYPE
  R0             12              299
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D833V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ATP2B4 MUTATED       2                         0
  ATP2B4 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATP2B4 MUTATED                                           1    11
  ATP2B4 WILD-TYPE                                         0   232
D833V12, multiclass
                                           clus
vv                                          ATP2B4 MUTATED ATP2B4 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              1                0
  WHITE                                                 11              232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D833V13, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED     0  13
  ATP2B4 WILD-TYPE   4 297
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED      0   13
  ATP2B4 WILD-TYPE    4  297
                        clus
vv                       ATP2B4 MUTATED ATP2B4 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             13              297
[1] 2 2
[1] FALSE

Clustering(834) Variable = KIAA1539 MUTATION ANALYSIS
D834V1, survival
                    sevent
clus2                  0   1
  KIAA1539 MUTATED     6   4
  KIAA1539 WILD-TYPE 224 135
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
                10                359 
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
                 4                135 
$`KIAA1539 MUTATED`
TCGA-B7-5818 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7957 TCGA-BR-8487 TCGA-BR-8591 
       11.70         9.67        34.68         9.07         1.12        28.14 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-HU-8602 TCGA-HU-A4GX 
       16.14         6.58        22.32        20.25 

$`KIAA1539 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
              1.12               0.00 
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
             34.68             122.30 
  KIAA1539 MUTATED KIAA1539 WILD-TYPE 
             13.92              14.27 
[1] "1.1 - 34.7 (13.9)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D834V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1539 MUTATED         0        0        1        0         3         1
  KIAA1539 WILD-TYPE       2       15       39       30        34        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1539 MUTATED           0          0          1          2        1
  KIAA1539 WILD-TYPE         3         70         52         30       37
D834V3, multiclass
            clus
vv           KIAA1539 MUTATED KIAA1539 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 3                 34
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                1                 52
  STAGE IIIC                2                 30
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1539 MUTATED     0   1   5   3
  KIAA1539 WILD-TYPE  22  91 168  94
D834V4, multiclass
    clus
vv   KIAA1539 MUTATED KIAA1539 WILD-TYPE
  T1                0                 22
  T2                1                 91
  T3                5                168
  T4                3                 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
  KIAA1539 MUTATED     5   0   1   3
  KIAA1539 WILD-TYPE 113 104  76  74
D834V5, multiclass
    clus
vv   KIAA1539 MUTATED KIAA1539 WILD-TYPE
  N0                5                113
  N1                0                104
  N2                1                 76
  N3                3                 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"
D834V6, binary
                    cls
clus                   0   1
  KIAA1539 MUTATED     9   1
  KIAA1539 WILD-TYPE 337  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1539 MUTATED      9    1
  KIAA1539 WILD-TYPE  337   28
   clus
vv  KIAA1539 MUTATED KIAA1539 WILD-TYPE
  0                9                337
  1                1                 28
[1] 2 2
[1] FALSE
D834V7, binary
                    cls
clus                   0   1
  KIAA1539 MUTATED     7   3
  KIAA1539 WILD-TYPE 138 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1539 MUTATED      7    3
  KIAA1539 WILD-TYPE  138  245
        clus
vv       KIAA1539 MUTATED KIAA1539 WILD-TYPE
  FEMALE                7                138
  MALE                  3                245
[1] 2 2
[1] FALSE
D834V8, binary
                    cls
clus                   0   1
  KIAA1539 MUTATED    10   0
  KIAA1539 WILD-TYPE 282  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1539 MUTATED     10    0
  KIAA1539 WILD-TYPE  282   59
     clus
vv    KIAA1539 MUTATED KIAA1539 WILD-TYPE
  NO                10                282
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA1539 MUTATED                                          0
  KIAA1539 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA1539 MUTATED                                       4
  KIAA1539 WILD-TYPE                                    66
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1539 MUTATED                                                        5
  KIAA1539 WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA1539 MUTATED                                                   0
  KIAA1539 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1539 MUTATED                                                                   1
  KIAA1539 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA1539 MUTATED                                                    0
  KIAA1539 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA1539 MUTATED                                                  0
  KIAA1539 WILD-TYPE                                               61
D834V9, multiclass
                                                                   clus
vv                                                                  KIAA1539 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 0
                                                                   clus
vv                                                                  KIAA1539 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1539 MUTATED     8   0   0   1
  KIAA1539 WILD-TYPE 303  14  15  23
D834V10, multiclass
    clus
vv   KIAA1539 MUTATED KIAA1539 WILD-TYPE
  R0                8                303
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D834V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1539 MUTATED       3                         0
  KIAA1539 WILD-TYPE    84                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1539 MUTATED                                           0     7
  KIAA1539 WILD-TYPE                                         1   236
D834V12, multiclass
                                           clus
vv                                          KIAA1539 MUTATED KIAA1539 WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D834V13, binary
                    cls
clus                   0   1
  KIAA1539 MUTATED     0  10
  KIAA1539 WILD-TYPE   4 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1539 MUTATED      0   10
  KIAA1539 WILD-TYPE    4  300
                        clus
vv                       KIAA1539 MUTATED KIAA1539 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               10                300
[1] 2 2
[1] FALSE

Clustering(835) Variable = SEZ6 MUTATION ANALYSIS
D835V1, survival
                sevent
clus2              0   1
  SEZ6 MUTATED     8   4
  SEZ6 WILD-TYPE 222 135
  SEZ6 MUTATED SEZ6 WILD-TYPE 
            12            357 
  SEZ6 MUTATED SEZ6 WILD-TYPE 
             4            135 
$`SEZ6 MUTATED`
TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8382 TCGA-BR-A4QL TCGA-CD-A4MI TCGA-D7-A4YU 
       32.25         6.18        25.05        16.14        11.77        16.44 
TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-IN-A6RL TCGA-KB-A93J TCGA-VQ-A8P2 
       30.51        22.68        20.25        13.35        36.95        38.14 

$`SEZ6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         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-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-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-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-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 

  SEZ6 MUTATED SEZ6 WILD-TYPE 
          6.18           0.00 
  SEZ6 MUTATED SEZ6 WILD-TYPE 
         38.14         122.30 
  SEZ6 MUTATED SEZ6 WILD-TYPE 
        21.465         14.070 
[1] "6.2 - 38.1 (21.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D835V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SEZ6 MUTATED         0        0        1        1         1         2
  SEZ6 WILD-TYPE       2       15       39       29        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SEZ6 MUTATED           0          3          2          3        0
  SEZ6 WILD-TYPE         3         67         51         29       38
D835V3, multiclass
            clus
vv           SEZ6 MUTATED SEZ6 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            2             51
  STAGE IIIC            3             29
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SEZ6 MUTATED     0   3   5   5
  SEZ6 WILD-TYPE  22  89 168  92
D835V4, multiclass
    clus
vv   SEZ6 MUTATED SEZ6 WILD-TYPE
  T1            0             22
  T2            3             89
  T3            5            168
  T4            5             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
  SEZ6 MUTATED     3   5   1   4
  SEZ6 WILD-TYPE 115  99  76  73
D835V5, multiclass
    clus
vv   SEZ6 MUTATED SEZ6 WILD-TYPE
  N0            3            115
  N1            5             99
  N2            1             76
  N3            4             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"
D835V6, binary
                cls
clus               0   1
  SEZ6 MUTATED    13   0
  SEZ6 WILD-TYPE 333  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  SEZ6 MUTATED     13    0
  SEZ6 WILD-TYPE  333   29
   clus
vv  SEZ6 MUTATED SEZ6 WILD-TYPE
  0           13            333
  1            0             29
[1] 2 2
[1] FALSE
D835V7, binary
                cls
clus               0   1
  SEZ6 MUTATED     6   7
  SEZ6 WILD-TYPE 139 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  SEZ6 MUTATED      6    7
  SEZ6 WILD-TYPE  139  241
        clus
vv       SEZ6 MUTATED SEZ6 WILD-TYPE
  FEMALE            6            139
  MALE              7            241
[1] 2 2
[1] FALSE
D835V8, binary
                cls
clus               0   1
  SEZ6 MUTATED     9   3
  SEZ6 WILD-TYPE 283  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  SEZ6 MUTATED      9    3
  SEZ6 WILD-TYPE  283   56
     clus
vv    SEZ6 MUTATED SEZ6 WILD-TYPE
  NO             9            283
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SEZ6 MUTATED                                          0
  SEZ6 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SEZ6 MUTATED                                       3
  SEZ6 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SEZ6 MUTATED                                                        5
  SEZ6 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SEZ6 MUTATED                                                   2
  SEZ6 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SEZ6 MUTATED                                                                   2
  SEZ6 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SEZ6 MUTATED                                                    0
  SEZ6 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SEZ6 MUTATED                                                  1
  SEZ6 WILD-TYPE                                               60
D835V9, multiclass
                                                                   clus
vv                                                                  SEZ6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  SEZ6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SEZ6 MUTATED    10   1   0   0
  SEZ6 WILD-TYPE 301  13  15  24
D835V10, multiclass
    clus
vv   SEZ6 MUTATED SEZ6 WILD-TYPE
  R0           10            301
  R1            1             13
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D835V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SEZ6 MUTATED       3                         0
  SEZ6 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SEZ6 MUTATED                                           0     8
  SEZ6 WILD-TYPE                                         1   235
D835V12, multiclass
                                           clus
vv                                          SEZ6 MUTATED SEZ6 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D835V13, binary
                cls
clus               0   1
  SEZ6 MUTATED     0   9
  SEZ6 WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  SEZ6 MUTATED      0    9
  SEZ6 WILD-TYPE    4  301
                        clus
vv                       SEZ6 MUTATED SEZ6 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(836) Variable = NARG2 MUTATION ANALYSIS
D836V1, survival
                 sevent
clus2               0   1
  NARG2 MUTATED     9   4
  NARG2 WILD-TYPE 221 135
  NARG2 MUTATED NARG2 WILD-TYPE 
             13             356 
  NARG2 MUTATED NARG2 WILD-TYPE 
              4             135 
$`NARG2 MUTATED`
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-8536 
        6.61        34.68        25.05        28.14        16.14        12.43 
TCGA-CD-A4MJ TCGA-CG-5721 TCGA-D7-A4YU TCGA-HJ-7597 TCGA-HU-A4GX TCGA-HU-A4H4 
       12.62         6.02        16.44        26.47        20.25        23.84 
TCGA-VQ-A8P2 
       38.14 

$`NARG2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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-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 

  NARG2 MUTATED NARG2 WILD-TYPE 
           6.02            0.00 
  NARG2 MUTATED NARG2 WILD-TYPE 
          38.14          122.30 
  NARG2 MUTATED NARG2 WILD-TYPE 
          20.25           14.07 
[1] "6.0 - 38.1 (20.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D836V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NARG2 MUTATED         0        0        2        1         1         1
  NARG2 WILD-TYPE       2       15       38       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NARG2 MUTATED           1          1          2          3        1
  NARG2 WILD-TYPE         2         69         51         29       37
D836V3, multiclass
            clus
vv           NARG2 MUTATED NARG2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             3              29
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NARG2 MUTATED     0   4   4   5
  NARG2 WILD-TYPE  22  88 169  92
D836V4, multiclass
    clus
vv   NARG2 MUTATED NARG2 WILD-TYPE
  T1             0              22
  T2             4              88
  T3             4             169
  T4             5              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
  NARG2 MUTATED     4   3   2   4
  NARG2 WILD-TYPE 114 101  75  73
D836V5, multiclass
    clus
vv   NARG2 MUTATED NARG2 WILD-TYPE
  N0             4             114
  N1             3             101
  N2             2              75
  N3             4              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"
D836V6, binary
                 cls
clus                0   1
  NARG2 MUTATED    12   0
  NARG2 WILD-TYPE 334  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NARG2 MUTATED     12    0
  NARG2 WILD-TYPE  334   29
   clus
vv  NARG2 MUTATED NARG2 WILD-TYPE
  0            12             334
  1             0              29
[1] 2 2
[1] FALSE
D836V7, binary
                 cls
clus                0   1
  NARG2 MUTATED     7   6
  NARG2 WILD-TYPE 138 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NARG2 MUTATED      7    6
  NARG2 WILD-TYPE  138  242
        clus
vv       NARG2 MUTATED NARG2 WILD-TYPE
  FEMALE             7             138
  MALE               6             242
[1] 2 2
[1] FALSE
D836V8, binary
                 cls
clus                0   1
  NARG2 MUTATED    12   1
  NARG2 WILD-TYPE 280  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NARG2 MUTATED     12    1
  NARG2 WILD-TYPE  280   58
     clus
vv    NARG2 MUTATED NARG2 WILD-TYPE
  NO             12             280
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NARG2 MUTATED                                          1
  NARG2 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NARG2 MUTATED                                       1
  NARG2 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NARG2 MUTATED                                                        7
  NARG2 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NARG2 MUTATED                                                   1
  NARG2 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NARG2 MUTATED                                                                   1
  NARG2 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NARG2 MUTATED                                                    0
  NARG2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NARG2 MUTATED                                                  2
  NARG2 WILD-TYPE                                               59
D836V9, multiclass
                                                                   clus
vv                                                                  NARG2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  NARG2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NARG2 MUTATED    11   0   0   1
  NARG2 WILD-TYPE 300  14  15  23
D836V10, multiclass
    clus
vv   NARG2 MUTATED NARG2 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D836V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NARG2 MUTATED       4                         0
  NARG2 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NARG2 MUTATED                                           0     8
  NARG2 WILD-TYPE                                         1   235
D836V12, multiclass
                                           clus
vv                                          NARG2 MUTATED NARG2 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D836V13, binary
                 cls
clus                0   1
  NARG2 MUTATED     0  11
  NARG2 WILD-TYPE   4 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NARG2 MUTATED      0   11
  NARG2 WILD-TYPE    4  299
                        clus
vv                       NARG2 MUTATED NARG2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(837) Variable = CHD3 MUTATION ANALYSIS
D837V1, survival
                sevent
clus2              0   1
  CHD3 MUTATED    17   8
  CHD3 WILD-TYPE 213 131
  CHD3 MUTATED CHD3 WILD-TYPE 
            25            344 
  CHD3 MUTATED CHD3 WILD-TYPE 
             8            131 
$`CHD3 MUTATED`
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8289 TCGA-BR-8382 TCGA-BR-8487 
        9.67        34.68        35.84         2.66        25.05         1.12 
TCGA-BR-8680 TCGA-CD-5804 TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-5718 TCGA-CG-5723 
       31.96        12.10        12.43        15.95        36.00       105.07 
TCGA-CG-5728 TCGA-D7-6817 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-A448 TCGA-HF-7132 
       65.10        12.79         7.13         0.62        21.27        77.29 
TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-RD-A7BT 
       30.51        22.68         0.10        20.25        14.07         8.61 
TCGA-VQ-A8P2 
       38.14 

$`CHD3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-5719 TCGA-CG-5720 TCGA-CG-5721 
        7.07        30.97         6.97         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-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.22        15.98        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-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 
       19.96         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-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-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-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-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-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-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 

  CHD3 MUTATED CHD3 WILD-TYPE 
           0.1            0.0 
  CHD3 MUTATED CHD3 WILD-TYPE 
        105.07         122.30 
  CHD3 MUTATED CHD3 WILD-TYPE 
         20.25          14.12 
[1] "0.1 - 105.1 (20.2)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D837V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CHD3 MUTATED         1        0        3        5         2         2
  CHD3 WILD-TYPE       1       15       37       25        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHD3 MUTATED           0          2          2          4        4
  CHD3 WILD-TYPE         3         68         51         28       34
D837V3, multiclass
            clus
vv           CHD3 MUTATED CHD3 WILD-TYPE
  STAGE I               1              1
  STAGE IA              0             15
  STAGE IB              3             37
  STAGE II              5             25
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            2             51
  STAGE IIIC            4             28
  STAGE IV              4             34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHD3 MUTATED     3   7   8   9
  CHD3 WILD-TYPE  19  85 165  88
D837V4, multiclass
    clus
vv   CHD3 MUTATED CHD3 WILD-TYPE
  T1            3             19
  T2            7             85
  T3            8            165
  T4            9             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
  CHD3 MUTATED     6   9   3   8
  CHD3 WILD-TYPE 112  95  74  69
D837V5, multiclass
    clus
vv   CHD3 MUTATED CHD3 WILD-TYPE
  N0            6            112
  N1            9             95
  N2            3             74
  N3            8             69
[1] 4 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
  CHD3 MUTATED    24   3
  CHD3 WILD-TYPE 322  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     24    3
  CHD3 WILD-TYPE  322   26
   clus
vv  CHD3 MUTATED CHD3 WILD-TYPE
  0           24            322
  1            3             26
[1] 2 2
[1] FALSE
D837V7, binary
                cls
clus               0   1
  CHD3 MUTATED    13  15
  CHD3 WILD-TYPE 132 233
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     13   15
  CHD3 WILD-TYPE  132  233
        clus
vv       CHD3 MUTATED CHD3 WILD-TYPE
  FEMALE           13            132
  MALE             15            233
[1] 2 2
[1] FALSE
D837V8, binary
                cls
clus               0   1
  CHD3 MUTATED    21   5
  CHD3 WILD-TYPE 271  54
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     21    5
  CHD3 WILD-TYPE  271   54
     clus
vv    CHD3 MUTATED CHD3 WILD-TYPE
  NO            21            271
  YES            5             54
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CHD3 MUTATED                                          0
  CHD3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CHD3 MUTATED                                       3
  CHD3 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CHD3 MUTATED                                                       12
  CHD3 WILD-TYPE                                                    146
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CHD3 MUTATED                                                   4
  CHD3 WILD-TYPE                                                17
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CHD3 MUTATED                                                                   5
  CHD3 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CHD3 MUTATED                                                    0
  CHD3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CHD3 MUTATED                                                  4
  CHD3 WILD-TYPE                                               57
D837V9, multiclass
                                                                   clus
vv                                                                  CHD3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  CHD3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             17
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CHD3 MUTATED    22   1   2   2
  CHD3 WILD-TYPE 289  13  13  22
D837V10, multiclass
    clus
vv   CHD3 MUTATED CHD3 WILD-TYPE
  R0           22            289
  R1            1             13
  R2            2             13
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D837V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CHD3 MUTATED       7                         1
  CHD3 WILD-TYPE    80                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CHD3 MUTATED                                           1    13
  CHD3 WILD-TYPE                                         0   230
D837V12, multiclass
                                           clus
vv                                          CHD3 MUTATED CHD3 WILD-TYPE
  ASIAN                                                7             80
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                               13            230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D837V13, binary
                cls
clus               0   1
  CHD3 MUTATED     1  20
  CHD3 WILD-TYPE   3 290
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED      1   20
  CHD3 WILD-TYPE    3  290
                        clus
vv                       CHD3 MUTATED CHD3 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           20            290
[1] 2 2
[1] FALSE

Clustering(838) Variable = THSD1 MUTATION ANALYSIS
D838V1, survival
                 sevent
clus2               0   1
  THSD1 MUTATED    18   2
  THSD1 WILD-TYPE 212 137
  THSD1 MUTATED THSD1 WILD-TYPE 
             20             349 
  THSD1 MUTATED THSD1 WILD-TYPE 
              2             137 
$`THSD1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8363 
       26.70         6.97        34.68        44.94        29.59         0.26 
TCGA-BR-8487 TCGA-CD-5800 TCGA-CD-8535 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 
        1.12        13.15        12.82        15.95         7.99         8.05 
TCGA-CG-5728 TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4H4 
       65.10        11.08        22.32        22.68        29.98        23.84 
TCGA-R5-A7ZI TCGA-RD-A8MV 
       74.53       122.30 

$`THSD1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-4306 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        1.02        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-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-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-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-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 

  THSD1 MUTATED THSD1 WILD-TYPE 
           0.26            0.00 
  THSD1 MUTATED THSD1 WILD-TYPE 
         122.30          116.38 
  THSD1 MUTATED THSD1 WILD-TYPE 
          22.50           14.07 
[1] "0.3 - 122.3 (22.5)" "0.0 - 116.4 (14.1)"
[1] "hr=" "5.2"
D838V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  THSD1 MUTATED         0        0        3        3         5         5
  THSD1 WILD-TYPE       2       15       37       27        32        47
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  THSD1 MUTATED           0          2          1          0        3
  THSD1 WILD-TYPE         3         68         52         32       35
D838V3, multiclass
            clus
vv           THSD1 MUTATED THSD1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               3              27
  STAGE IIA              5              32
  STAGE IIB              5              47
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  THSD1 MUTATED     0   7   9   6
  THSD1 WILD-TYPE  22  85 164  91
D838V4, multiclass
    clus
vv   THSD1 MUTATED THSD1 WILD-TYPE
  T1             0              22
  T2             7              85
  T3             9             164
  T4             6              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
  THSD1 MUTATED    11   7   4   0
  THSD1 WILD-TYPE 107  97  73  77
D838V5, multiclass
    clus
vv   THSD1 MUTATED THSD1 WILD-TYPE
  N0            11             107
  N1             7              97
  N2             4              73
  N3             0              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"
D838V6, binary
                 cls
clus                0   1
  THSD1 MUTATED    19   2
  THSD1 WILD-TYPE 327  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THSD1 MUTATED     19    2
  THSD1 WILD-TYPE  327   27
   clus
vv  THSD1 MUTATED THSD1 WILD-TYPE
  0            19             327
  1             2              27
[1] 2 2
[1] FALSE
D838V7, binary
                 cls
clus                0   1
  THSD1 MUTATED    14   8
  THSD1 WILD-TYPE 131 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THSD1 MUTATED     14    8
  THSD1 WILD-TYPE  131  240
        clus
vv       THSD1 MUTATED THSD1 WILD-TYPE
  FEMALE            14             131
  MALE               8             240
[1] 2 2
[1] FALSE
D838V8, binary
                 cls
clus                0   1
  THSD1 MUTATED    17   2
  THSD1 WILD-TYPE 275  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THSD1 MUTATED     17    2
  THSD1 WILD-TYPE  275   57
     clus
vv    THSD1 MUTATED THSD1 WILD-TYPE
  NO             17             275
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  THSD1 MUTATED                                          0
  THSD1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  THSD1 MUTATED                                       5
  THSD1 WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  THSD1 MUTATED                                                       10
  THSD1 WILD-TYPE                                                    148
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  THSD1 MUTATED                                                   0
  THSD1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  THSD1 MUTATED                                                                   4
  THSD1 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  THSD1 MUTATED                                                    1
  THSD1 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  THSD1 MUTATED                                                  2
  THSD1 WILD-TYPE                                               59
D838V9, multiclass
                                                                   clus
vv                                                                  THSD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  THSD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  THSD1 MUTATED    18   0   1   2
  THSD1 WILD-TYPE 293  14  14  22
D838V10, multiclass
    clus
vv   THSD1 MUTATED THSD1 WILD-TYPE
  R0            18             293
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D838V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  THSD1 MUTATED       6                         1
  THSD1 WILD-TYPE    81                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  THSD1 MUTATED                                           0    10
  THSD1 WILD-TYPE                                         1   233
D838V12, multiclass
                                           clus
vv                                          THSD1 MUTATED THSD1 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D838V13, binary
                 cls
clus                0   1
  THSD1 MUTATED     1  16
  THSD1 WILD-TYPE   3 294
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THSD1 MUTATED      1   16
  THSD1 WILD-TYPE    3  294
                        clus
vv                       THSD1 MUTATED THSD1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            16             294
[1] 2 2
[1] FALSE

Clustering(839) Variable = CTNNA1 MUTATION ANALYSIS
D839V1, survival
                  sevent
clus2                0   1
  CTNNA1 MUTATED     9   4
  CTNNA1 WILD-TYPE 221 135
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
              13              356 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
               4              135 
$`CTNNA1 MUTATED`
TCGA-BR-8361 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 
       31.10        31.96        16.14         6.97         0.99         6.02 
TCGA-CG-5723 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-HU-8602 TCGA-HU-A4H3 TCGA-MX-A5UJ 
      105.07        14.27         5.92        22.32        29.00        19.73 
TCGA-VQ-A8P2 
       38.14 

$`CTNNA1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-5722 
       18.97         7.07        30.97        36.00         1.02         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-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-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-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 

  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
            0.99             0.00 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
          105.07           122.30 
  CTNNA1 MUTATED CTNNA1 WILD-TYPE 
           19.73            14.07 
[1] "1.0 - 105.1 (19.7)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D839V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CTNNA1 MUTATED         0        0        1        2         0         2
  CTNNA1 WILD-TYPE       2       15       39       28        37        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNNA1 MUTATED           0          3          1          3        2
  CTNNA1 WILD-TYPE         3         67         52         29       36
D839V3, multiclass
            clus
vv           CTNNA1 MUTATED CTNNA1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               0               37
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              3               29
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CTNNA1 MUTATED     0   4   3   7
  CTNNA1 WILD-TYPE  22  88 170  90
D839V4, multiclass
    clus
vv   CTNNA1 MUTATED CTNNA1 WILD-TYPE
  T1              0               22
  T2              4               88
  T3              3              170
  T4              7               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
  CTNNA1 MUTATED     2   6   3   4
  CTNNA1 WILD-TYPE 116  98  74  73
D839V5, multiclass
    clus
vv   CTNNA1 MUTATED CTNNA1 WILD-TYPE
  N0              2              116
  N1              6               98
  N2              3               74
  N3              4               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"
D839V6, binary
                  cls
clus                 0   1
  CTNNA1 MUTATED    14   1
  CTNNA1 WILD-TYPE 332  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA1 MUTATED     14    1
  CTNNA1 WILD-TYPE  332   28
   clus
vv  CTNNA1 MUTATED CTNNA1 WILD-TYPE
  0             14              332
  1              1               28
[1] 2 2
[1] FALSE
D839V7, binary
                  cls
clus                 0   1
  CTNNA1 MUTATED     7   8
  CTNNA1 WILD-TYPE 138 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA1 MUTATED      7    8
  CTNNA1 WILD-TYPE  138  240
        clus
vv       CTNNA1 MUTATED CTNNA1 WILD-TYPE
  FEMALE              7              138
  MALE                8              240
[1] 2 2
[1] FALSE
D839V8, binary
                  cls
clus                 0   1
  CTNNA1 MUTATED    11   1
  CTNNA1 WILD-TYPE 281  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA1 MUTATED     11    1
  CTNNA1 WILD-TYPE  281   58
     clus
vv    CTNNA1 MUTATED CTNNA1 WILD-TYPE
  NO              11              281
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CTNNA1 MUTATED                                          0
  CTNNA1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CTNNA1 MUTATED                                       2
  CTNNA1 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTNNA1 MUTATED                                                        7
  CTNNA1 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CTNNA1 MUTATED                                                   1
  CTNNA1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CTNNA1 MUTATED                                                                   1
  CTNNA1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CTNNA1 MUTATED                                                    0
  CTNNA1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CTNNA1 MUTATED                                                  4
  CTNNA1 WILD-TYPE                                               57
D839V9, multiclass
                                                                   clus
vv                                                                  CTNNA1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  CTNNA1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CTNNA1 MUTATED    13   1   0   1
  CTNNA1 WILD-TYPE 298  13  15  23
D839V10, multiclass
    clus
vv   CTNNA1 MUTATED CTNNA1 WILD-TYPE
  R0             13              298
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D839V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CTNNA1 MUTATED       3                         0
  CTNNA1 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CTNNA1 MUTATED                                           0     8
  CTNNA1 WILD-TYPE                                         1   235
D839V12, multiclass
                                           clus
vv                                          CTNNA1 MUTATED CTNNA1 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D839V13, binary
                  cls
clus                 0   1
  CTNNA1 MUTATED     0  10
  CTNNA1 WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA1 MUTATED      0   10
  CTNNA1 WILD-TYPE    4  300
                        clus
vv                       CTNNA1 MUTATED CTNNA1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(840) Variable = BANK1 MUTATION ANALYSIS
D840V1, survival
                 sevent
clus2               0   1
  BANK1 MUTATED     6   3
  BANK1 WILD-TYPE 224 136
  BANK1 MUTATED BANK1 WILD-TYPE 
              9             360 
  BANK1 MUTATED BANK1 WILD-TYPE 
              3             136 
$`BANK1 MUTATED`
TCGA-BR-8363 TCGA-BR-A4QL TCGA-CG-4300 TCGA-CG-5728 TCGA-HF-7134 TCGA-HU-8238 
        0.26        16.14        20.02        65.10        52.21         1.51 
TCGA-HU-A4GU TCGA-MX-A5UJ TCGA-VQ-A8P2 
        6.58        19.73        38.14 

$`BANK1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-4301 TCGA-CG-4304 
        6.58        12.20        11.77        12.62         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-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
       77.29        63.06        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-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 

  BANK1 MUTATED BANK1 WILD-TYPE 
           0.26            0.00 
  BANK1 MUTATED BANK1 WILD-TYPE 
           65.1           122.3 
  BANK1 MUTATED BANK1 WILD-TYPE 
          19.73           14.12 
[1] "0.3 - 65.1 (19.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D840V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BANK1 MUTATED         0        1        3        0         0         1
  BANK1 WILD-TYPE       2       14       37       30        37        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BANK1 MUTATED           0          2          2          1        0
  BANK1 WILD-TYPE         3         68         51         31       38
D840V3, multiclass
            clus
vv           BANK1 MUTATED BANK1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BANK1 MUTATED     1   3   5   2
  BANK1 WILD-TYPE  21  89 168  95
D840V4, multiclass
    clus
vv   BANK1 MUTATED BANK1 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             5             168
  T4             2              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
  BANK1 MUTATED     4   2   3   2
  BANK1 WILD-TYPE 114 102  74  75
D840V5, multiclass
    clus
vv   BANK1 MUTATED BANK1 WILD-TYPE
  N0             4             114
  N1             2             102
  N2             3              74
  N3             2              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"
D840V6, binary
                 cls
clus                0   1
  BANK1 MUTATED    11   0
  BANK1 WILD-TYPE 335  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BANK1 MUTATED     11    0
  BANK1 WILD-TYPE  335   29
   clus
vv  BANK1 MUTATED BANK1 WILD-TYPE
  0            11             335
  1             0              29
[1] 2 2
[1] FALSE
D840V7, binary
                 cls
clus                0   1
  BANK1 MUTATED     4   7
  BANK1 WILD-TYPE 141 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BANK1 MUTATED      4    7
  BANK1 WILD-TYPE  141  241
        clus
vv       BANK1 MUTATED BANK1 WILD-TYPE
  FEMALE             4             141
  MALE               7             241
[1] 2 2
[1] FALSE
D840V8, binary
                 cls
clus                0   1
  BANK1 MUTATED     6   1
  BANK1 WILD-TYPE 286  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BANK1 MUTATED      6    1
  BANK1 WILD-TYPE  286   58
     clus
vv    BANK1 MUTATED BANK1 WILD-TYPE
  NO              6             286
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BANK1 MUTATED                                          0
  BANK1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BANK1 MUTATED                                       2
  BANK1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BANK1 MUTATED                                                        3
  BANK1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BANK1 MUTATED                                                   1
  BANK1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BANK1 MUTATED                                                                   3
  BANK1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BANK1 MUTATED                                                    0
  BANK1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BANK1 MUTATED                                                  2
  BANK1 WILD-TYPE                                               59
D840V9, multiclass
                                                                   clus
vv                                                                  BANK1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  BANK1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BANK1 MUTATED    11   0   0   0
  BANK1 WILD-TYPE 300  14  15  24
D840V10, multiclass
    clus
vv   BANK1 MUTATED BANK1 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D840V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BANK1 MUTATED       2                         0
  BANK1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BANK1 MUTATED                                           0     4
  BANK1 WILD-TYPE                                         1   239
D840V12, multiclass
                                           clus
vv                                          BANK1 MUTATED BANK1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D840V13, binary
                 cls
clus                0   1
  BANK1 MUTATED     0   5
  BANK1 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BANK1 MUTATED      0    5
  BANK1 WILD-TYPE    4  305
                        clus
vv                       BANK1 MUTATED BANK1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(841) Variable = ZNF441 MUTATION ANALYSIS
D841V1, survival
                  sevent
clus2                0   1
  ZNF441 MUTATED     7   1
  ZNF441 WILD-TYPE 223 138
  ZNF441 MUTATED ZNF441 WILD-TYPE 
               8              361 
  ZNF441 MUTATED ZNF441 WILD-TYPE 
               1              138 
$`ZNF441 MUTATED`
TCGA-BR-6452 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-8589 TCGA-BR-8680 
       34.68         0.95         4.31        25.05        27.12        31.96 
TCGA-VQ-A8P2 TCGA-VQ-AA6A 
       38.14        38.93 

$`ZNF441 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  ZNF441 MUTATED ZNF441 WILD-TYPE 
            0.95             0.00 
  ZNF441 MUTATED ZNF441 WILD-TYPE 
           38.93           122.30 
  ZNF441 MUTATED ZNF441 WILD-TYPE 
           29.54            14.07 
[1] "0.9 - 38.9 (29.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "4.2"
D841V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF441 MUTATED         0        0        1        0         2         0
  ZNF441 WILD-TYPE       2       15       39       30        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF441 MUTATED           0          2          1          2        1
  ZNF441 WILD-TYPE         3         68         52         30       37
D841V3, multiclass
            clus
vv           ZNF441 MUTATED ZNF441 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF441 MUTATED     0   1   2   6
  ZNF441 WILD-TYPE  22  91 171  91
D841V4, multiclass
    clus
vv   ZNF441 MUTATED ZNF441 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              2              171
  T4              6               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
  ZNF441 MUTATED     4   2   1   2
  ZNF441 WILD-TYPE 114 102  76  75
D841V5, multiclass
    clus
vv   ZNF441 MUTATED ZNF441 WILD-TYPE
  N0              4              114
  N1              2              102
  N2              1               76
  N3              2               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"
D841V6, binary
                  cls
clus                 0   1
  ZNF441 MUTATED     8   1
  ZNF441 WILD-TYPE 338  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF441 MUTATED      8    1
  ZNF441 WILD-TYPE  338   28
   clus
vv  ZNF441 MUTATED ZNF441 WILD-TYPE
  0              8              338
  1              1               28
[1] 2 2
[1] FALSE
D841V7, binary
                  cls
clus                 0   1
  ZNF441 MUTATED     5   4
  ZNF441 WILD-TYPE 140 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF441 MUTATED      5    4
  ZNF441 WILD-TYPE  140  244
        clus
vv       ZNF441 MUTATED ZNF441 WILD-TYPE
  FEMALE              5              140
  MALE                4              244
[1] 2 2
[1] FALSE
D841V8, binary
                  cls
clus                 0   1
  ZNF441 MUTATED     6   2
  ZNF441 WILD-TYPE 286  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF441 MUTATED      6    2
  ZNF441 WILD-TYPE  286   57
     clus
vv    ZNF441 MUTATED ZNF441 WILD-TYPE
  NO               6              286
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF441 MUTATED                                          0
  ZNF441 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF441 MUTATED                                       0
  ZNF441 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF441 MUTATED                                                        6
  ZNF441 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF441 MUTATED                                                   1
  ZNF441 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF441 MUTATED                                                                   1
  ZNF441 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF441 MUTATED                                                    0
  ZNF441 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF441 MUTATED                                                  1
  ZNF441 WILD-TYPE                                               60
D841V9, multiclass
                                                                   clus
vv                                                                  ZNF441 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ZNF441 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF441 MUTATED     8   0   0   1
  ZNF441 WILD-TYPE 303  14  15  23
D841V10, multiclass
    clus
vv   ZNF441 MUTATED ZNF441 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D841V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF441 MUTATED       1                         0
  ZNF441 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF441 MUTATED                                           0     8
  ZNF441 WILD-TYPE                                         1   235
D841V12, multiclass
                                           clus
vv                                          ZNF441 MUTATED ZNF441 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D841V13, binary
                  cls
clus                 0   1
  ZNF441 MUTATED     0   7
  ZNF441 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF441 MUTATED      0    7
  ZNF441 WILD-TYPE    4  303
                        clus
vv                       ZNF441 MUTATED ZNF441 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(842) Variable = TBC1D8B MUTATION ANALYSIS
D842V1, survival
                   sevent
clus2                 0   1
  TBC1D8B MUTATED     8   1
  TBC1D8B WILD-TYPE 222 138
  TBC1D8B MUTATED TBC1D8B WILD-TYPE 
                9               360 
  TBC1D8B MUTATED TBC1D8B WILD-TYPE 
                1               138 
$`TBC1D8B MUTATED`
TCGA-B7-5816 TCGA-BR-7958 TCGA-BR-8588 TCGA-CD-8533 TCGA-CG-4437 TCGA-CG-5723 
       26.70        29.56        12.79        15.39         8.05       105.07 
TCGA-D7-6818 TCGA-MX-A5UJ TCGA-SW-A7EA 
       12.36        19.73        19.04 

$`TBC1D8B WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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 

  TBC1D8B MUTATED TBC1D8B WILD-TYPE 
             8.05              0.00 
  TBC1D8B MUTATED TBC1D8B WILD-TYPE 
           105.07            122.30 
  TBC1D8B MUTATED TBC1D8B WILD-TYPE 
            19.04             14.12 
[1] "8.1 - 105.1 (19.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "4.5"
D842V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TBC1D8B MUTATED         0        0        1        3         0         2
  TBC1D8B WILD-TYPE       2       15       39       27        37        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBC1D8B MUTATED           0          2          1          0        0
  TBC1D8B WILD-TYPE         3         68         52         32       38
D842V3, multiclass
            clus
vv           TBC1D8B MUTATED TBC1D8B WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 3                27
  STAGE IIA                0                37
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TBC1D8B MUTATED     0   4   2   3
  TBC1D8B WILD-TYPE  22  88 171  94
D842V4, multiclass
    clus
vv   TBC1D8B MUTATED TBC1D8B WILD-TYPE
  T1               0                22
  T2               4                88
  T3               2               171
  T4               3                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
  TBC1D8B MUTATED     5   2   1   1
  TBC1D8B WILD-TYPE 113 102  76  76
D842V5, multiclass
    clus
vv   TBC1D8B MUTATED TBC1D8B WILD-TYPE
  N0               5               113
  N1               2               102
  N2               1                76
  N3               1                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"
D842V6, binary
                   cls
clus                  0   1
  TBC1D8B MUTATED     9   0
  TBC1D8B WILD-TYPE 337  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D8B MUTATED      9    0
  TBC1D8B WILD-TYPE  337   29
   clus
vv  TBC1D8B MUTATED TBC1D8B WILD-TYPE
  0               9               337
  1               0                29
[1] 2 2
[1] FALSE
D842V7, binary
                   cls
clus                  0   1
  TBC1D8B MUTATED     4   5
  TBC1D8B WILD-TYPE 141 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D8B MUTATED      4    5
  TBC1D8B WILD-TYPE  141  243
        clus
vv       TBC1D8B MUTATED TBC1D8B WILD-TYPE
  FEMALE               4               141
  MALE                 5               243
[1] 2 2
[1] FALSE
D842V8, binary
                   cls
clus                  0   1
  TBC1D8B MUTATED     8   1
  TBC1D8B WILD-TYPE 284  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D8B MUTATED      8    1
  TBC1D8B WILD-TYPE  284   58
     clus
vv    TBC1D8B MUTATED TBC1D8B WILD-TYPE
  NO                8               284
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TBC1D8B MUTATED                                          0
  TBC1D8B WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TBC1D8B MUTATED                                       3
  TBC1D8B WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TBC1D8B MUTATED                                                        4
  TBC1D8B WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TBC1D8B MUTATED                                                   0
  TBC1D8B WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TBC1D8B MUTATED                                                                   1
  TBC1D8B WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TBC1D8B MUTATED                                                    0
  TBC1D8B WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TBC1D8B MUTATED                                                  1
  TBC1D8B WILD-TYPE                                               60
D842V9, multiclass
                                                                   clus
vv                                                                  TBC1D8B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  TBC1D8B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TBC1D8B MUTATED     9   0   0   0
  TBC1D8B WILD-TYPE 302  14  15  24
D842V10, multiclass
    clus
vv   TBC1D8B MUTATED TBC1D8B WILD-TYPE
  R0               9               302
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D842V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TBC1D8B MUTATED       1                         0
  TBC1D8B WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TBC1D8B MUTATED                                           0     6
  TBC1D8B WILD-TYPE                                         1   237
D842V12, multiclass
                                           clus
vv                                          TBC1D8B MUTATED TBC1D8B WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D842V13, binary
                   cls
clus                  0   1
  TBC1D8B MUTATED     0   7
  TBC1D8B WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D8B MUTATED      0    7
  TBC1D8B WILD-TYPE    4  303
                        clus
vv                       TBC1D8B MUTATED TBC1D8B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(843) Variable = CD3EAP MUTATION ANALYSIS
D843V1, survival
                  sevent
clus2                0   1
  CD3EAP MUTATED     7   3
  CD3EAP WILD-TYPE 223 136
  CD3EAP MUTATED CD3EAP WILD-TYPE 
              10              359 
  CD3EAP MUTATED CD3EAP WILD-TYPE 
               3              136 
$`CD3EAP MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8060 TCGA-CG-4305 TCGA-CG-5721 
        6.97         9.34        34.68        11.44        15.95         6.02 
TCGA-D7-A74A TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4GT 
       19.96        77.29        22.32         6.51 

$`CD3EAP WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6874 
        8.38         4.34         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-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 

  CD3EAP MUTATED CD3EAP WILD-TYPE 
            6.02             0.00 
  CD3EAP MUTATED CD3EAP WILD-TYPE 
           77.29           122.30 
  CD3EAP MUTATED CD3EAP WILD-TYPE 
          13.695           14.270 
[1] "6.0 - 77.3 (13.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D843V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD3EAP MUTATED         0        0        0        2         2         2
  CD3EAP WILD-TYPE       2       15       40       28        35        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CD3EAP MUTATED           0          2          0          0        1
  CD3EAP WILD-TYPE         3         68         53         32       37
D843V3, multiclass
            clus
vv           CD3EAP MUTATED CD3EAP WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                2               28
  STAGE IIA               2               35
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CD3EAP MUTATED     0   3   4   2
  CD3EAP WILD-TYPE  22  89 169  95
D843V4, multiclass
    clus
vv   CD3EAP MUTATED CD3EAP WILD-TYPE
  T1              0               22
  T2              3               89
  T3              4              169
  T4              2               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
  CD3EAP MUTATED     3   5   2   0
  CD3EAP WILD-TYPE 115  99  75  77
D843V5, multiclass
    clus
vv   CD3EAP MUTATED CD3EAP WILD-TYPE
  N0              3              115
  N1              5               99
  N2              2               75
  N3              0               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"
D843V6, binary
                  cls
clus                 0   1
  CD3EAP MUTATED     9   0
  CD3EAP WILD-TYPE 337  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD3EAP MUTATED      9    0
  CD3EAP WILD-TYPE  337   29
   clus
vv  CD3EAP MUTATED CD3EAP WILD-TYPE
  0              9              337
  1              0               29
[1] 2 2
[1] FALSE
D843V7, binary
                  cls
clus                 0   1
  CD3EAP MUTATED     5   5
  CD3EAP WILD-TYPE 140 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD3EAP MUTATED      5    5
  CD3EAP WILD-TYPE  140  243
        clus
vv       CD3EAP MUTATED CD3EAP WILD-TYPE
  FEMALE              5              140
  MALE                5              243
[1] 2 2
[1] FALSE
D843V8, binary
                  cls
clus                 0   1
  CD3EAP MUTATED     9   1
  CD3EAP WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD3EAP MUTATED      9    1
  CD3EAP WILD-TYPE  283   58
     clus
vv    CD3EAP MUTATED CD3EAP WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CD3EAP MUTATED                                          0
  CD3EAP WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CD3EAP MUTATED                                       1
  CD3EAP WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD3EAP MUTATED                                                        5
  CD3EAP WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CD3EAP MUTATED                                                   1
  CD3EAP WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD3EAP MUTATED                                                                   1
  CD3EAP WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CD3EAP MUTATED                                                    0
  CD3EAP WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CD3EAP MUTATED                                                  2
  CD3EAP WILD-TYPE                                               59
D843V9, multiclass
                                                                   clus
vv                                                                  CD3EAP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  CD3EAP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CD3EAP MUTATED     8   0   0   2
  CD3EAP WILD-TYPE 303  14  15  22
D843V10, multiclass
    clus
vv   CD3EAP MUTATED CD3EAP WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D843V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CD3EAP MUTATED       2                         0
  CD3EAP WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD3EAP MUTATED                                           0     5
  CD3EAP WILD-TYPE                                         1   238
D843V12, multiclass
                                           clus
vv                                          CD3EAP MUTATED CD3EAP WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D843V13, binary
                  cls
clus                 0   1
  CD3EAP MUTATED     0   7
  CD3EAP WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD3EAP MUTATED      0    7
  CD3EAP WILD-TYPE    4  303
                        clus
vv                       CD3EAP MUTATED CD3EAP WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(844) Variable = EFNA4 MUTATION ANALYSIS
D844V1, survival
                 sevent
clus2               0   1
  EFNA4 MUTATED     4   1
  EFNA4 WILD-TYPE 226 138
  EFNA4 MUTATED EFNA4 WILD-TYPE 
              5             364 
  EFNA4 MUTATED EFNA4 WILD-TYPE 
              1             138 
$`EFNA4 MUTATED`
TCGA-BR-6452 TCGA-BR-A4QL TCGA-HU-8602 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       34.68        16.14        22.32        19.73        38.14 

$`EFNA4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  EFNA4 MUTATED EFNA4 WILD-TYPE 
          16.14            0.00 
  EFNA4 MUTATED EFNA4 WILD-TYPE 
          38.14          122.30 
  EFNA4 MUTATED EFNA4 WILD-TYPE 
          22.32           14.07 
[1] "16.1 - 38.1 (22.3)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.8"
D844V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EFNA4 MUTATED         0        0        0        0         1         1
  EFNA4 WILD-TYPE       2       15       40       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFNA4 MUTATED           0          2          1          0        0
  EFNA4 WILD-TYPE         3         68         52         32       38
D844V3, multiclass
            clus
vv           EFNA4 MUTATED EFNA4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EFNA4 MUTATED     0   0   3   2
  EFNA4 WILD-TYPE  22  92 170  95
D844V4, multiclass
    clus
vv   EFNA4 MUTATED EFNA4 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             3             170
  T4             2              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
  EFNA4 MUTATED     2   1   1   1
  EFNA4 WILD-TYPE 116 103  76  76
D844V5, multiclass
    clus
vv   EFNA4 MUTATED EFNA4 WILD-TYPE
  N0             2             116
  N1             1             103
  N2             1              76
  N3             1              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"
D844V6, binary
                 cls
clus                0   1
  EFNA4 MUTATED     5   0
  EFNA4 WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNA4 MUTATED      5    0
  EFNA4 WILD-TYPE  341   29
   clus
vv  EFNA4 MUTATED EFNA4 WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D844V7, binary
                 cls
clus                0   1
  EFNA4 MUTATED     4   1
  EFNA4 WILD-TYPE 141 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNA4 MUTATED      4    1
  EFNA4 WILD-TYPE  141  247
        clus
vv       EFNA4 MUTATED EFNA4 WILD-TYPE
  FEMALE             4             141
  MALE               1             247
[1] 2 2
[1] FALSE
D844V8, binary
                 cls
clus                0   1
  EFNA4 MUTATED     4   1
  EFNA4 WILD-TYPE 288  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNA4 MUTATED      4    1
  EFNA4 WILD-TYPE  288   58
     clus
vv    EFNA4 MUTATED EFNA4 WILD-TYPE
  NO              4             288
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EFNA4 MUTATED                                          0
  EFNA4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EFNA4 MUTATED                                       1
  EFNA4 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EFNA4 MUTATED                                                        2
  EFNA4 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EFNA4 MUTATED                                                   1
  EFNA4 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EFNA4 MUTATED                                                                   0
  EFNA4 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EFNA4 MUTATED                                                    0
  EFNA4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EFNA4 MUTATED                                                  1
  EFNA4 WILD-TYPE                                               60
D844V9, multiclass
                                                                   clus
vv                                                                  EFNA4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  EFNA4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EFNA4 MUTATED     5   0   0   0
  EFNA4 WILD-TYPE 306  14  15  24
D844V10, multiclass
    clus
vv   EFNA4 MUTATED EFNA4 WILD-TYPE
  R0             5             306
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D844V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EFNA4 MUTATED       1                         0
  EFNA4 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EFNA4 MUTATED                                           0     4
  EFNA4 WILD-TYPE                                         1   239
D844V12, multiclass
                                           clus
vv                                          EFNA4 MUTATED EFNA4 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D844V13, binary
                 cls
clus                0   1
  EFNA4 MUTATED     0   4
  EFNA4 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNA4 MUTATED      0    4
  EFNA4 WILD-TYPE    4  306
                        clus
vv                       EFNA4 MUTATED EFNA4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(845) Variable = COL20A1 MUTATION ANALYSIS
D845V1, survival
                   sevent
clus2                 0   1
  COL20A1 MUTATED    14   6
  COL20A1 WILD-TYPE 216 133
  COL20A1 MUTATED COL20A1 WILD-TYPE 
               20               349 
  COL20A1 MUTATED COL20A1 WILD-TYPE 
                6               133 
$`COL20A1 MUTATED`
TCGA-BR-6452 TCGA-BR-6563 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8487 
       34.68        39.12        35.84        29.59        31.10         1.12 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A4MG 
       31.96         9.86        16.14        12.43        12.30         6.58 
TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-6822 TCGA-HU-A4GY 
       11.77        15.95         6.02        21.07        12.33         0.26 
TCGA-R5-A7ZE TCGA-VQ-A8P2 
       18.21        38.14 

$`COL20A1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       24.79        32.58        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-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-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-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-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-A4H0 TCGA-HU-A4H2 
        0.10         6.51         6.58        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-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-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 

  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            14.170 
[1] "0.3 - 39.1 (16.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D845V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  COL20A1 MUTATED         0        0        2        2         3         3
  COL20A1 WILD-TYPE       2       15       38       28        34        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL20A1 MUTATED           0          5          2          1        2
  COL20A1 WILD-TYPE         3         65         51         31       36
D845V3, multiclass
            clus
vv           COL20A1 MUTATED COL20A1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 2                28
  STAGE IIA                3                34
  STAGE IIB                3                49
  STAGE III                0                 3
  STAGE IIIA               5                65
  STAGE IIIB               2                51
  STAGE IIIC               1                31
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  COL20A1 MUTATED     0   4   9   7
  COL20A1 WILD-TYPE  22  88 164  90
D845V4, multiclass
    clus
vv   COL20A1 MUTATED COL20A1 WILD-TYPE
  T1               0                22
  T2               4                88
  T3               9               164
  T4               7                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
  COL20A1 MUTATED     7   7   5   1
  COL20A1 WILD-TYPE 111  97  72  76
D845V5, multiclass
    clus
vv   COL20A1 MUTATED COL20A1 WILD-TYPE
  N0               7               111
  N1               7                97
  N2               5                72
  N3               1                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"
D845V6, binary
                   cls
clus                  0   1
  COL20A1 MUTATED    19   1
  COL20A1 WILD-TYPE 327  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL20A1 MUTATED     19    1
  COL20A1 WILD-TYPE  327   28
   clus
vv  COL20A1 MUTATED COL20A1 WILD-TYPE
  0              19               327
  1               1                28
[1] 2 2
[1] FALSE
D845V7, binary
                   cls
clus                  0   1
  COL20A1 MUTATED     9  11
  COL20A1 WILD-TYPE 136 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL20A1 MUTATED      9   11
  COL20A1 WILD-TYPE  136  237
        clus
vv       COL20A1 MUTATED COL20A1 WILD-TYPE
  FEMALE               9               136
  MALE                11               237
[1] 2 2
[1] FALSE
D845V8, binary
                   cls
clus                  0   1
  COL20A1 MUTATED    19   1
  COL20A1 WILD-TYPE 273  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL20A1 MUTATED     19    1
  COL20A1 WILD-TYPE  273   58
     clus
vv    COL20A1 MUTATED COL20A1 WILD-TYPE
  NO               19               273
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  COL20A1 MUTATED                                          0
  COL20A1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  COL20A1 MUTATED                                       3
  COL20A1 WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  COL20A1 MUTATED                                                       10
  COL20A1 WILD-TYPE                                                    148
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  COL20A1 MUTATED                                                   1
  COL20A1 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  COL20A1 MUTATED                                                                   2
  COL20A1 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  COL20A1 MUTATED                                                    0
  COL20A1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  COL20A1 MUTATED                                                  4
  COL20A1 WILD-TYPE                                               57
D845V9, multiclass
                                                                   clus
vv                                                                  COL20A1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                4
                                                                   clus
vv                                                                  COL20A1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  COL20A1 MUTATED    17   0   0   0
  COL20A1 WILD-TYPE 294  14  15  24
D845V10, multiclass
    clus
vv   COL20A1 MUTATED COL20A1 WILD-TYPE
  R0              17               294
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D845V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  COL20A1 MUTATED       7                         0
  COL20A1 WILD-TYPE    80                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  COL20A1 MUTATED                                           0    10
  COL20A1 WILD-TYPE                                         1   233
D845V12, multiclass
                                           clus
vv                                          COL20A1 MUTATED COL20A1 WILD-TYPE
  ASIAN                                                   7                80
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D845V13, binary
                   cls
clus                  0   1
  COL20A1 MUTATED     0  16
  COL20A1 WILD-TYPE   4 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL20A1 MUTATED      0   16
  COL20A1 WILD-TYPE    4  294
                        clus
vv                       COL20A1 MUTATED COL20A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              16               294
[1] 2 2
[1] FALSE

Clustering(846) Variable = SEC16B MUTATION ANALYSIS
D846V1, survival
                  sevent
clus2                0   1
  SEC16B MUTATED     4   3
  SEC16B WILD-TYPE 226 136
  SEC16B MUTATED SEC16B WILD-TYPE 
               7              362 
  SEC16B MUTATED SEC16B WILD-TYPE 
               3              136 
$`SEC16B MUTATED`
TCGA-BR-4256 TCGA-BR-6566 TCGA-BR-8368 TCGA-BR-8382 TCGA-CD-8528 TCGA-HF-A5NB 
        9.34        32.78         4.31        25.05        12.33        30.51 
TCGA-HU-A4GQ 
        0.10 

$`SEC16B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  SEC16B MUTATED SEC16B WILD-TYPE 
             0.1              0.0 
  SEC16B MUTATED SEC16B WILD-TYPE 
           32.78           122.30 
  SEC16B MUTATED SEC16B WILD-TYPE 
           12.33            14.35 
[1] "0.1 - 32.8 (12.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D846V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SEC16B MUTATED         0        0        1        0         1         0
  SEC16B WILD-TYPE       2       15       39       30        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SEC16B MUTATED           0          1          0          3        0
  SEC16B WILD-TYPE         3         69         53         29       38
D846V3, multiclass
            clus
vv           SEC16B MUTATED SEC16B WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              3               29
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SEC16B MUTATED     0   1   1   4
  SEC16B WILD-TYPE  22  91 172  93
D846V4, multiclass
    clus
vv   SEC16B MUTATED SEC16B WILD-TYPE
  T1              0               22
  T2              1               91
  T3              1              172
  T4              4               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
  SEC16B MUTATED     3   1   1   2
  SEC16B WILD-TYPE 115 103  76  75
D846V5, multiclass
    clus
vv   SEC16B MUTATED SEC16B WILD-TYPE
  N0              3              115
  N1              1              103
  N2              1               76
  N3              2               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"
D846V6, binary
                  cls
clus                 0   1
  SEC16B MUTATED     7   0
  SEC16B WILD-TYPE 339  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC16B MUTATED      7    0
  SEC16B WILD-TYPE  339   29
   clus
vv  SEC16B MUTATED SEC16B WILD-TYPE
  0              7              339
  1              0               29
[1] 2 2
[1] FALSE
D846V7, binary
                  cls
clus                 0   1
  SEC16B MUTATED     5   2
  SEC16B WILD-TYPE 140 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC16B MUTATED      5    2
  SEC16B WILD-TYPE  140  246
        clus
vv       SEC16B MUTATED SEC16B WILD-TYPE
  FEMALE              5              140
  MALE                2              246
[1] 2 2
[1] FALSE
D846V8, binary
                  cls
clus                 0   1
  SEC16B MUTATED     5   2
  SEC16B WILD-TYPE 287  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC16B MUTATED      5    2
  SEC16B WILD-TYPE  287   57
     clus
vv    SEC16B MUTATED SEC16B WILD-TYPE
  NO               5              287
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SEC16B MUTATED                                          0
  SEC16B WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SEC16B MUTATED                                       0
  SEC16B WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SEC16B MUTATED                                                        5
  SEC16B WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SEC16B MUTATED                                                   1
  SEC16B WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SEC16B MUTATED                                                                   0
  SEC16B WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SEC16B MUTATED                                                    0
  SEC16B WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SEC16B MUTATED                                                  1
  SEC16B WILD-TYPE                                               60
D846V9, multiclass
                                                                   clus
vv                                                                  SEC16B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  SEC16B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SEC16B MUTATED     5   1   0   1
  SEC16B WILD-TYPE 306  13  15  23
D846V10, multiclass
    clus
vv   SEC16B MUTATED SEC16B WILD-TYPE
  R0              5              306
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D846V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SEC16B MUTATED       2                         0
  SEC16B WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SEC16B MUTATED                                           0     4
  SEC16B WILD-TYPE                                         1   239
D846V12, multiclass
                                           clus
vv                                          SEC16B MUTATED SEC16B WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D846V13, binary
                  cls
clus                 0   1
  SEC16B MUTATED     0   6
  SEC16B WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC16B MUTATED      0    6
  SEC16B WILD-TYPE    4  304
                        clus
vv                       SEC16B MUTATED SEC16B WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(847) Variable = SIX3 MUTATION ANALYSIS
D847V1, survival
                sevent
clus2              0   1
  SIX3 MUTATED     4   4
  SIX3 WILD-TYPE 226 135
  SIX3 MUTATED SIX3 WILD-TYPE 
             8            361 
  SIX3 MUTATED SIX3 WILD-TYPE 
             4            135 
$`SIX3 MUTATED`
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CG-5718 
        9.34         9.67        31.27         1.12        16.14        36.00 
TCGA-HU-A4G8 TCGA-MX-A5UJ 
       22.68        19.73 

$`SIX3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         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-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 

  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         14.170 
[1] "1.1 - 36.0 (17.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D847V2, 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       1       15       40       29        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SIX3 MUTATED           0          2          1          1        0
  SIX3 WILD-TYPE         3         68         52         31       38
D847V3, multiclass
            clus
vv           SIX3 MUTATED SIX3 WILD-TYPE
  STAGE I               1              1
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SIX3 MUTATED     1   1   4   2
  SIX3 WILD-TYPE  21  91 169  95
D847V4, multiclass
    clus
vv   SIX3 MUTATED SIX3 WILD-TYPE
  T1            1             21
  T2            1             91
  T3            4            169
  T4            2             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
  SIX3 MUTATED     2   4   1   2
  SIX3 WILD-TYPE 116 100  76  75
D847V5, multiclass
    clus
vv   SIX3 MUTATED SIX3 WILD-TYPE
  N0            2            116
  N1            4            100
  N2            1             76
  N3            2             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"
D847V6, binary
                cls
clus               0   1
  SIX3 MUTATED     9   0
  SIX3 WILD-TYPE 337  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX3 MUTATED      9    0
  SIX3 WILD-TYPE  337   29
   clus
vv  SIX3 MUTATED SIX3 WILD-TYPE
  0            9            337
  1            0             29
[1] 2 2
[1] FALSE
D847V7, binary
                cls
clus               0   1
  SIX3 MUTATED     7   3
  SIX3 WILD-TYPE 138 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX3 MUTATED      7    3
  SIX3 WILD-TYPE  138  245
        clus
vv       SIX3 MUTATED SIX3 WILD-TYPE
  FEMALE            7            138
  MALE              3            245
[1] 2 2
[1] FALSE
D847V8, binary
                cls
clus               0   1
  SIX3 MUTATED     9   0
  SIX3 WILD-TYPE 283  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX3 MUTATED      9    0
  SIX3 WILD-TYPE  283   59
     clus
vv    SIX3 MUTATED SIX3 WILD-TYPE
  NO             9            283
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SIX3 MUTATED                                          0
  SIX3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SIX3 MUTATED                                       1
  SIX3 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SIX3 MUTATED                                                        7
  SIX3 WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SIX3 MUTATED                                                   0
  SIX3 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SIX3 MUTATED                                                                   1
  SIX3 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SIX3 MUTATED                                                    0
  SIX3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SIX3 MUTATED                                                  1
  SIX3 WILD-TYPE                                               60
D847V9, multiclass
                                                                   clus
vv                                                                  SIX3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  SIX3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SIX3 MUTATED     6   0   0   3
  SIX3 WILD-TYPE 305  14  15  21
D847V10, multiclass
    clus
vv   SIX3 MUTATED SIX3 WILD-TYPE
  R0            6            305
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D847V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SIX3 MUTATED       1                         1
  SIX3 WILD-TYPE    86                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SIX3 MUTATED                                           0     7
  SIX3 WILD-TYPE                                         1   236
D847V12, multiclass
                                           clus
vv                                          SIX3 MUTATED SIX3 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D847V13, binary
                cls
clus               0   1
  SIX3 MUTATED     0   9
  SIX3 WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX3 MUTATED      0    9
  SIX3 WILD-TYPE    4  301
                        clus
vv                       SIX3 MUTATED SIX3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(848) Variable = SLC7A13 MUTATION ANALYSIS
D848V1, survival
                   sevent
clus2                 0   1
  SLC7A13 MUTATED     8   1
  SLC7A13 WILD-TYPE 222 138
  SLC7A13 MUTATED SLC7A13 WILD-TYPE 
                9               360 
  SLC7A13 MUTATED SLC7A13 WILD-TYPE 
                1               138 
$`SLC7A13 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8368 TCGA-CD-A4MI TCGA-CD-A4MJ 
       26.70        34.68        29.59         4.31        11.77        12.62 
TCGA-CG-4305 TCGA-HU-A4G8 TCGA-HU-A4H8 
       15.95        22.68        14.07 

$`SLC7A13 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  SLC7A13 MUTATED SLC7A13 WILD-TYPE 
             4.31              0.00 
  SLC7A13 MUTATED SLC7A13 WILD-TYPE 
            34.68            122.30 
  SLC7A13 MUTATED SLC7A13 WILD-TYPE 
            15.95             14.22 
[1] "4.3 - 34.7 (15.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3.9"
D848V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC7A13 MUTATED         0        0        3        1         1         3
  SLC7A13 WILD-TYPE       2       15       37       29        36        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC7A13 MUTATED           0          1          0          0        0
  SLC7A13 WILD-TYPE         3         69         53         32       38
D848V3, multiclass
            clus
vv           SLC7A13 MUTATED SLC7A13 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 3                37
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                3                49
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC7A13 MUTATED     1   3   4   2
  SLC7A13 WILD-TYPE  21  89 169  95
D848V4, multiclass
    clus
vv   SLC7A13 MUTATED SLC7A13 WILD-TYPE
  T1               1                21
  T2               3                89
  T3               4               169
  T4               2                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
  SLC7A13 MUTATED     5   5   0   0
  SLC7A13 WILD-TYPE 113  99  77  77
D848V5, multiclass
    clus
vv   SLC7A13 MUTATED SLC7A13 WILD-TYPE
  N0               5               113
  N1               5                99
  N2               0                77
  N3               0                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"
D848V6, binary
                   cls
clus                  0   1
  SLC7A13 MUTATED    10   0
  SLC7A13 WILD-TYPE 336  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A13 MUTATED     10    0
  SLC7A13 WILD-TYPE  336   29
   clus
vv  SLC7A13 MUTATED SLC7A13 WILD-TYPE
  0              10               336
  1               0                29
[1] 2 2
[1] FALSE
D848V7, binary
                   cls
clus                  0   1
  SLC7A13 MUTATED     7   4
  SLC7A13 WILD-TYPE 138 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A13 MUTATED      7    4
  SLC7A13 WILD-TYPE  138  244
        clus
vv       SLC7A13 MUTATED SLC7A13 WILD-TYPE
  FEMALE               7               138
  MALE                 4               244
[1] 2 2
[1] FALSE
D848V8, binary
                   cls
clus                  0   1
  SLC7A13 MUTATED     9   0
  SLC7A13 WILD-TYPE 283  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A13 MUTATED      9    0
  SLC7A13 WILD-TYPE  283   59
     clus
vv    SLC7A13 MUTATED SLC7A13 WILD-TYPE
  NO                9               283
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC7A13 MUTATED                                          0
  SLC7A13 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC7A13 MUTATED                                       2
  SLC7A13 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC7A13 MUTATED                                                        8
  SLC7A13 WILD-TYPE                                                    150
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC7A13 MUTATED                                                   0
  SLC7A13 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC7A13 MUTATED                                                                   0
  SLC7A13 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC7A13 MUTATED                                                    0
  SLC7A13 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC7A13 MUTATED                                                  1
  SLC7A13 WILD-TYPE                                               60
D848V9, multiclass
                                                                   clus
vv                                                                  SLC7A13 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  SLC7A13 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC7A13 MUTATED     6   0   0   2
  SLC7A13 WILD-TYPE 305  14  15  22
D848V10, multiclass
    clus
vv   SLC7A13 MUTATED SLC7A13 WILD-TYPE
  R0               6               305
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D848V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC7A13 MUTATED       4                         0
  SLC7A13 WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC7A13 MUTATED                                           0     6
  SLC7A13 WILD-TYPE                                         1   237
D848V12, multiclass
                                           clus
vv                                          SLC7A13 MUTATED SLC7A13 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D848V13, binary
                   cls
clus                  0   1
  SLC7A13 MUTATED     0  10
  SLC7A13 WILD-TYPE   4 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A13 MUTATED      0   10
  SLC7A13 WILD-TYPE    4  300
                        clus
vv                       SLC7A13 MUTATED SLC7A13 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              10               300
[1] 2 2
[1] FALSE

Clustering(849) Variable = EMILIN3 MUTATION ANALYSIS
D849V1, survival
                   sevent
clus2                 0   1
  EMILIN3 MUTATED     8   5
  EMILIN3 WILD-TYPE 222 134
  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
               13               356 
  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
                5               134 
$`EMILIN3 MUTATED`
TCGA-BR-4184 TCGA-BR-7707 TCGA-BR-8680 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-A4MI 
        6.97        35.84        31.96        13.18        13.35        11.77 
TCGA-CG-5721 TCGA-CG-5730 TCGA-D7-A4YV TCGA-F1-A448 TCGA-HU-A4GQ TCGA-IN-A6RS 
        6.02         4.01         5.92        21.27         0.10        12.59 
TCGA-VQ-A8P2 
       38.14 

$`EMILIN3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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 

  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
              0.1               0.0 
  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
            38.14            122.30 
  EMILIN3 MUTATED EMILIN3 WILD-TYPE 
           12.590            14.565 
[1] "0.1 - 38.1 (12.6)"  "0.0 - 122.3 (14.6)"
[1] "hr=" "1.2"
D849V2, 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       2       14       39       29        37        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EMILIN3 MUTATED           0          5          1          1        3
  EMILIN3 WILD-TYPE         3         65         52         31       35
D849V3, multiclass
            clus
vv           EMILIN3 MUTATED EMILIN3 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                0                37
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               5                65
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 3                35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  EMILIN3 MUTATED     1   2   6   5
  EMILIN3 WILD-TYPE  21  90 167  92
D849V4, multiclass
    clus
vv   EMILIN3 MUTATED EMILIN3 WILD-TYPE
  T1               1                21
  T2               2                90
  T3               6               167
  T4               5                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
  EMILIN3 MUTATED     4   7   2   1
  EMILIN3 WILD-TYPE 114  97  75  76
D849V5, multiclass
    clus
vv   EMILIN3 MUTATED EMILIN3 WILD-TYPE
  N0               4               114
  N1               7                97
  N2               2                75
  N3               1                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"
D849V6, binary
                   cls
clus                  0   1
  EMILIN3 MUTATED    11   2
  EMILIN3 WILD-TYPE 335  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EMILIN3 MUTATED     11    2
  EMILIN3 WILD-TYPE  335   27
   clus
vv  EMILIN3 MUTATED EMILIN3 WILD-TYPE
  0              11               335
  1               2                27
[1] 2 2
[1] FALSE
D849V7, binary
                   cls
clus                  0   1
  EMILIN3 MUTATED     4  10
  EMILIN3 WILD-TYPE 141 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EMILIN3 MUTATED      4   10
  EMILIN3 WILD-TYPE  141  238
        clus
vv       EMILIN3 MUTATED EMILIN3 WILD-TYPE
  FEMALE               4               141
  MALE                10               238
[1] 2 2
[1] FALSE
D849V8, binary
                   cls
clus                  0   1
  EMILIN3 MUTATED     9   3
  EMILIN3 WILD-TYPE 283  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EMILIN3 MUTATED      9    3
  EMILIN3 WILD-TYPE  283   56
     clus
vv    EMILIN3 MUTATED EMILIN3 WILD-TYPE
  NO                9               283
  YES               3                56
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EMILIN3 MUTATED                                          0
  EMILIN3 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EMILIN3 MUTATED                                       0
  EMILIN3 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EMILIN3 MUTATED                                                        7
  EMILIN3 WILD-TYPE                                                    151
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EMILIN3 MUTATED                                                   2
  EMILIN3 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EMILIN3 MUTATED                                                                   2
  EMILIN3 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EMILIN3 MUTATED                                                    0
  EMILIN3 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EMILIN3 MUTATED                                                  3
  EMILIN3 WILD-TYPE                                               58
D849V9, multiclass
                                                                   clus
vv                                                                  EMILIN3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  EMILIN3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  EMILIN3 MUTATED     9   0   1   2
  EMILIN3 WILD-TYPE 302  14  14  22
D849V10, multiclass
    clus
vv   EMILIN3 MUTATED EMILIN3 WILD-TYPE
  R0               9               302
  R1               0                14
  R2               1                14
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D849V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  EMILIN3 MUTATED       5                         0
  EMILIN3 WILD-TYPE    82                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EMILIN3 MUTATED                                           0     7
  EMILIN3 WILD-TYPE                                         1   236
D849V12, multiclass
                                           clus
vv                                          EMILIN3 MUTATED EMILIN3 WILD-TYPE
  ASIAN                                                   5                82
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D849V13, binary
                   cls
clus                  0   1
  EMILIN3 MUTATED     1  10
  EMILIN3 WILD-TYPE   3 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EMILIN3 MUTATED      1   10
  EMILIN3 WILD-TYPE    3  300
                        clus
vv                       EMILIN3 MUTATED EMILIN3 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              10               300
[1] 2 2
[1] FALSE

Clustering(850) Variable = EPB41L5 MUTATION ANALYSIS
D850V1, survival
                   sevent
clus2                 0   1
  EPB41L5 MUTATED     7   3
  EPB41L5 WILD-TYPE 223 136
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
               10               359 
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
                3               136 
$`EPB41L5 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG 
       21.99         6.97        44.94        28.14        31.96         6.58 
TCGA-HU-A4G8 TCGA-HU-A4GX TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       22.68        20.25        38.14        37.22 

$`EPB41L5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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 

  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
             6.58              0.00 
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
            44.94            122.30 
  EPB41L5 MUTATED EPB41L5 WILD-TYPE 
            25.41             14.07 
[1] "6.6 - 44.9 (25.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D850V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPB41L5 MUTATED         0        0        0        0         2         1
  EPB41L5 WILD-TYPE       2       15       40       30        35        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPB41L5 MUTATED           0          3          0          2        2
  EPB41L5 WILD-TYPE         3         67         53         30       36
D850V3, multiclass
            clus
vv           EPB41L5 MUTATED EPB41L5 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               3                67
  STAGE IIIB               0                53
  STAGE IIIC               2                30
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  EPB41L5 MUTATED     0   0   4   6
  EPB41L5 WILD-TYPE  22  92 169  91
D850V4, multiclass
    clus
vv   EPB41L5 MUTATED EPB41L5 WILD-TYPE
  T1               0                22
  T2               0                92
  T3               4               169
  T4               6                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
  EPB41L5 MUTATED     2   5   2   1
  EPB41L5 WILD-TYPE 116  99  75  76
D850V5, multiclass
    clus
vv   EPB41L5 MUTATED EPB41L5 WILD-TYPE
  N0               2               116
  N1               5                99
  N2               2                75
  N3               1                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"
D850V6, binary
                   cls
clus                  0   1
  EPB41L5 MUTATED     7   2
  EPB41L5 WILD-TYPE 339  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EPB41L5 MUTATED      7    2
  EPB41L5 WILD-TYPE  339   27
   clus
vv  EPB41L5 MUTATED EPB41L5 WILD-TYPE
  0               7               339
  1               2                27
[1] 2 2
[1] FALSE
D850V7, binary
                   cls
clus                  0   1
  EPB41L5 MUTATED     4   6
  EPB41L5 WILD-TYPE 141 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EPB41L5 MUTATED      4    6
  EPB41L5 WILD-TYPE  141  242
        clus
vv       EPB41L5 MUTATED EPB41L5 WILD-TYPE
  FEMALE               4               141
  MALE                 6               242
[1] 2 2
[1] FALSE
D850V8, binary
                   cls
clus                  0   1
  EPB41L5 MUTATED     8   2
  EPB41L5 WILD-TYPE 284  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EPB41L5 MUTATED      8    2
  EPB41L5 WILD-TYPE  284   57
     clus
vv    EPB41L5 MUTATED EPB41L5 WILD-TYPE
  NO                8               284
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EPB41L5 MUTATED                                          0
  EPB41L5 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EPB41L5 MUTATED                                       3
  EPB41L5 WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPB41L5 MUTATED                                                        3
  EPB41L5 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EPB41L5 MUTATED                                                   1
  EPB41L5 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPB41L5 MUTATED                                                                   1
  EPB41L5 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EPB41L5 MUTATED                                                    0
  EPB41L5 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EPB41L5 MUTATED                                                  2
  EPB41L5 WILD-TYPE                                               59
D850V9, multiclass
                                                                   clus
vv                                                                  EPB41L5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  EPB41L5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  EPB41L5 MUTATED     6   0   1   1
  EPB41L5 WILD-TYPE 305  14  14  23
D850V10, multiclass
    clus
vv   EPB41L5 MUTATED EPB41L5 WILD-TYPE
  R0               6               305
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D850V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  EPB41L5 MUTATED       4                         0
  EPB41L5 WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPB41L5 MUTATED                                           0     5
  EPB41L5 WILD-TYPE                                         1   238
D850V12, multiclass
                                           clus
vv                                          EPB41L5 MUTATED EPB41L5 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D850V13, binary
                   cls
clus                  0   1
  EPB41L5 MUTATED     0   7
  EPB41L5 WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EPB41L5 MUTATED      0    7
  EPB41L5 WILD-TYPE    4  303
                        clus
vv                       EPB41L5 MUTATED EPB41L5 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(851) Variable = UTY MUTATION ANALYSIS
D851V1, survival
               sevent
clus2             0   1
  UTY MUTATED     1   1
  UTY WILD-TYPE 229 138
  UTY MUTATED UTY WILD-TYPE 
            2           367 
  UTY MUTATED UTY WILD-TYPE 
            1           138 
$`UTY MUTATED`
TCGA-BR-4184 TCGA-BR-8360 
        6.97         6.18 

$`UTY WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  UTY MUTATED UTY WILD-TYPE 
         6.18          0.00 
  UTY MUTATED UTY WILD-TYPE 
         6.97        122.30 
  UTY MUTATED UTY WILD-TYPE 
        6.575        14.430 
[1] "6.2 - 7.0 (6.6)"    "0.0 - 122.3 (14.4)"
[1] "Remove cluster labels:" "UTY MUTATED"           
D851V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UTY MUTATED         0        0        0        0         1         1
  UTY WILD-TYPE       2       15       40       30        36        51
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UTY MUTATED           0          1          0          0        0
  UTY WILD-TYPE         3         69         53         32       38
D851V3, multiclass
            clus
vv           UTY MUTATED UTY WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             0            40
  STAGE II             0            30
  STAGE IIA            1            36
  STAGE IIB            1            51
  STAGE III            0             3
  STAGE IIIA           1            69
  STAGE IIIB           0            53
  STAGE IIIC           0            32
  STAGE IV             0            38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  UTY MUTATED     0   0   2   1
  UTY WILD-TYPE  22  92 171  96
D851V4, multiclass
    clus
vv   UTY MUTATED UTY WILD-TYPE
  T1           0            22
  T2           0            92
  T3           2           171
  T4           1            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
  UTY MUTATED     2   1   0   0
  UTY WILD-TYPE 116 103  77  77
D851V5, multiclass
    clus
vv   UTY MUTATED UTY WILD-TYPE
  N0           2           116
  N1           1           103
  N2           0            77
  N3           0            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"
D851V6, binary
               cls
clus              0   1
  UTY MUTATED     2   0
  UTY WILD-TYPE 344  29
[1] "tbl2"
               cls
clus            [,1] [,2]
  UTY MUTATED      2    0
  UTY WILD-TYPE  344   29
   clus
vv  UTY MUTATED UTY WILD-TYPE
  0           2           344
  1           0            29
[1] 2 2
[1] FALSE
D851V7, binary
               cls
clus              0   1
  UTY MUTATED     0   3
  UTY WILD-TYPE 145 245
[1] "tbl2"
               cls
clus            [,1] [,2]
  UTY MUTATED      0    3
  UTY WILD-TYPE  145  245
        clus
vv       UTY MUTATED UTY WILD-TYPE
  FEMALE           0           145
  MALE             3           245
[1] 2 2
[1] FALSE
D851V8, binary
               cls
clus              0   1
  UTY MUTATED     3   0
  UTY WILD-TYPE 289  59
[1] "tbl2"
               cls
clus            [,1] [,2]
  UTY MUTATED      3    0
  UTY WILD-TYPE  289   59
     clus
vv    UTY MUTATED UTY WILD-TYPE
  NO            3           289
  YES           0            59
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  UTY MUTATED                                          0
  UTY WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  UTY MUTATED                                       0
  UTY WILD-TYPE                                    70
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UTY MUTATED                                                        1
  UTY WILD-TYPE                                                    157
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  UTY MUTATED                                                   0
  UTY WILD-TYPE                                                21
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UTY MUTATED                                                                   2
  UTY WILD-TYPE                                                                66
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  UTY MUTATED                                                    0
  UTY WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  UTY MUTATED                                                  0
  UTY WILD-TYPE                                               61
D851V9, multiclass
                                                                   clus
vv                                                                  UTY MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            0
                                                                   clus
vv                                                                  UTY WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  UTY MUTATED     2   0   0   1
  UTY WILD-TYPE 309  14  15  23
D851V10, multiclass
    clus
vv   UTY MUTATED UTY WILD-TYPE
  R0           2           309
  R1           0            14
  R2           0            15
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D851V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  UTY MUTATED       0                         0
  UTY WILD-TYPE    87                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UTY MUTATED                                           0     3
  UTY WILD-TYPE                                         1   240
D851V12, multiclass
                                           clus
vv                                          UTY MUTATED UTY WILD-TYPE
  ASIAN                                               0            87
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               3           240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D851V13, binary
               cls
clus              0   1
  UTY MUTATED     0   3
  UTY WILD-TYPE   4 307
[1] "tbl2"
               cls
clus            [,1] [,2]
  UTY MUTATED      0    3
  UTY WILD-TYPE    4  307
                        clus
vv                       UTY MUTATED UTY WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           3           307
[1] 2 2
[1] FALSE

Clustering(852) Variable = CCT6A MUTATION ANALYSIS
D852V1, survival
                 sevent
clus2               0   1
  CCT6A MUTATED     4   4
  CCT6A WILD-TYPE 226 135
  CCT6A MUTATED CCT6A WILD-TYPE 
              8             361 
  CCT6A MUTATED CCT6A WILD-TYPE 
              4             135 
$`CCT6A MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-5728 
        6.97        34.68        35.84         1.12         6.58        65.10 
TCGA-D7-A6EY TCGA-HU-A4GQ 
       11.44         0.10 

$`CCT6A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  CCT6A MUTATED CCT6A WILD-TYPE 
            0.1             0.0 
  CCT6A MUTATED CCT6A WILD-TYPE 
           65.1           122.3 
  CCT6A MUTATED CCT6A WILD-TYPE 
          9.205          14.430 
[1] "0.1 - 65.1 (9.2)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.5"
D852V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCT6A MUTATED         0        0        2        0         3         0
  CCT6A WILD-TYPE       2       15       38       30        34        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCT6A MUTATED           0          1          1          1        0
  CCT6A WILD-TYPE         3         69         52         31       38
D852V3, multiclass
            clus
vv           CCT6A MUTATED CCT6A WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CCT6A MUTATED     0   2   5   1
  CCT6A WILD-TYPE  22  90 168  96
D852V4, multiclass
    clus
vv   CCT6A MUTATED CCT6A WILD-TYPE
  T1             0              22
  T2             2              90
  T3             5             168
  T4             1              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
  CCT6A MUTATED     5   1   1   1
  CCT6A WILD-TYPE 113 103  76  76
D852V5, multiclass
    clus
vv   CCT6A MUTATED CCT6A WILD-TYPE
  N0             5             113
  N1             1             103
  N2             1              76
  N3             1              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"
D852V6, binary
                 cls
clus                0   1
  CCT6A MUTATED     7   0
  CCT6A WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCT6A MUTATED      7    0
  CCT6A WILD-TYPE  339   29
   clus
vv  CCT6A MUTATED CCT6A WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D852V7, binary
                 cls
clus                0   1
  CCT6A MUTATED     5   3
  CCT6A WILD-TYPE 140 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCT6A MUTATED      5    3
  CCT6A WILD-TYPE  140  245
        clus
vv       CCT6A MUTATED CCT6A WILD-TYPE
  FEMALE             5             140
  MALE               3             245
[1] 2 2
[1] FALSE
D852V8, binary
                 cls
clus                0   1
  CCT6A MUTATED     7   0
  CCT6A WILD-TYPE 285  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCT6A MUTATED      7    0
  CCT6A WILD-TYPE  285   59
     clus
vv    CCT6A MUTATED CCT6A WILD-TYPE
  NO              7             285
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CCT6A MUTATED                                          0
  CCT6A WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CCT6A MUTATED                                       1
  CCT6A WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCT6A MUTATED                                                        4
  CCT6A WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CCT6A MUTATED                                                   0
  CCT6A WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCT6A MUTATED                                                                   1
  CCT6A WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CCT6A MUTATED                                                    0
  CCT6A WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CCT6A MUTATED                                                  2
  CCT6A WILD-TYPE                                               59
D852V9, multiclass
                                                                   clus
vv                                                                  CCT6A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  CCT6A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CCT6A MUTATED     6   0   0   1
  CCT6A WILD-TYPE 305  14  15  23
D852V10, multiclass
    clus
vv   CCT6A MUTATED CCT6A WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D852V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CCT6A MUTATED       2                         0
  CCT6A WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCT6A MUTATED                                           0     5
  CCT6A WILD-TYPE                                         1   238
D852V12, multiclass
                                           clus
vv                                          CCT6A MUTATED CCT6A WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D852V13, binary
                 cls
clus                0   1
  CCT6A MUTATED     0   7
  CCT6A WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCT6A MUTATED      0    7
  CCT6A WILD-TYPE    4  303
                        clus
vv                       CCT6A MUTATED CCT6A WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(853) Variable = DGAT1 MUTATION ANALYSIS
D853V1, survival
                 sevent
clus2               0   1
  DGAT1 MUTATED     8   1
  DGAT1 WILD-TYPE 222 138
  DGAT1 MUTATED DGAT1 WILD-TYPE 
              9             360 
  DGAT1 MUTATED DGAT1 WILD-TYPE 
              1             138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  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           14.12 
[1] "4.3 - 74.5 (24.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "4.7"
D853V2, 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       2       14       38       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DGAT1 MUTATED           0          1          0          1        1
  DGAT1 WILD-TYPE         3         69         53         31       37
D853V3, multiclass
            clus
vv           DGAT1 MUTATED DGAT1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DGAT1 MUTATED     2   2   2   3
  DGAT1 WILD-TYPE  20  90 171  94
D853V4, multiclass
    clus
vv   DGAT1 MUTATED DGAT1 WILD-TYPE
  T1             2              20
  T2             2              90
  T3             2             171
  T4             3              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
  DGAT1 MUTATED     4   3   1   1
  DGAT1 WILD-TYPE 114 101  76  76
D853V5, multiclass
    clus
vv   DGAT1 MUTATED DGAT1 WILD-TYPE
  N0             4             114
  N1             3             101
  N2             1              76
  N3             1              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"
D853V6, binary
                 cls
clus                0   1
  DGAT1 MUTATED     8   1
  DGAT1 WILD-TYPE 338  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DGAT1 MUTATED      8    1
  DGAT1 WILD-TYPE  338   28
   clus
vv  DGAT1 MUTATED DGAT1 WILD-TYPE
  0             8             338
  1             1              28
[1] 2 2
[1] FALSE
D853V7, binary
                 cls
clus                0   1
  DGAT1 MUTATED     7   2
  DGAT1 WILD-TYPE 138 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DGAT1 MUTATED      7    2
  DGAT1 WILD-TYPE  138  246
        clus
vv       DGAT1 MUTATED DGAT1 WILD-TYPE
  FEMALE             7             138
  MALE               2             246
[1] 2 2
[1] FALSE
D853V8, binary
                 cls
clus                0   1
  DGAT1 MUTATED     9   0
  DGAT1 WILD-TYPE 283  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DGAT1 MUTATED      9    0
  DGAT1 WILD-TYPE  283   59
     clus
vv    DGAT1 MUTATED DGAT1 WILD-TYPE
  NO              9             283
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DGAT1 MUTATED                                          0
  DGAT1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DGAT1 MUTATED                                       1
  DGAT1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DGAT1 MUTATED                                                        3
  DGAT1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DGAT1 MUTATED                                                   0
  DGAT1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DGAT1 MUTATED                                                                   1
  DGAT1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DGAT1 MUTATED                                                    0
  DGAT1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DGAT1 MUTATED                                                  4
  DGAT1 WILD-TYPE                                               57
D853V9, multiclass
                                                                   clus
vv                                                                  DGAT1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  DGAT1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DGAT1 MUTATED     9   0   0   0
  DGAT1 WILD-TYPE 302  14  15  24
D853V10, multiclass
    clus
vv   DGAT1 MUTATED DGAT1 WILD-TYPE
  R0             9             302
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D853V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DGAT1 MUTATED       3                         0
  DGAT1 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DGAT1 MUTATED                                           0     5
  DGAT1 WILD-TYPE                                         1   238
D853V12, multiclass
                                           clus
vv                                          DGAT1 MUTATED DGAT1 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D853V13, binary
                 cls
clus                0   1
  DGAT1 MUTATED     1   7
  DGAT1 WILD-TYPE   3 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DGAT1 MUTATED      1    7
  DGAT1 WILD-TYPE    3  303
                        clus
vv                       DGAT1 MUTATED DGAT1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(854) Variable = VWA1 MUTATION ANALYSIS
D854V1, survival
                sevent
clus2              0   1
  VWA1 MUTATED     4   2
  VWA1 WILD-TYPE 226 137
  VWA1 MUTATED VWA1 WILD-TYPE 
             6            363 
  VWA1 MUTATED VWA1 WILD-TYPE 
             2            137 
$`VWA1 MUTATED`
TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8487 TCGA-CD-A4MG 
       34.68        13.87        29.59         4.31         1.12         6.58 

$`VWA1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  VWA1 MUTATED VWA1 WILD-TYPE 
          1.12           0.00 
  VWA1 MUTATED VWA1 WILD-TYPE 
         34.68         122.30 
  VWA1 MUTATED VWA1 WILD-TYPE 
        10.225         14.430 
[1] "1.1 - 34.7 (10.2)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D854V2, 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       2       15       38       30        34        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VWA1 MUTATED           0          0          0          0        0
  VWA1 WILD-TYPE         3         70         53         32       38
D854V3, multiclass
            clus
vv           VWA1 MUTATED VWA1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             3             34
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  VWA1 MUTATED     0   2   4   1
  VWA1 WILD-TYPE  22  90 169  96
D854V4, multiclass
    clus
vv   VWA1 MUTATED VWA1 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            4            169
  T4            1             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
  VWA1 MUTATED     6   1   0   0
  VWA1 WILD-TYPE 112 103  77  77
D854V5, multiclass
    clus
vv   VWA1 MUTATED VWA1 WILD-TYPE
  N0            6            112
  N1            1            103
  N2            0             77
  N3            0             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"
D854V6, binary
                cls
clus               0   1
  VWA1 MUTATED     7   0
  VWA1 WILD-TYPE 339  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  VWA1 MUTATED      7    0
  VWA1 WILD-TYPE  339   29
   clus
vv  VWA1 MUTATED VWA1 WILD-TYPE
  0            7            339
  1            0             29
[1] 2 2
[1] FALSE
D854V7, binary
                cls
clus               0   1
  VWA1 MUTATED     4   3
  VWA1 WILD-TYPE 141 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  VWA1 MUTATED      4    3
  VWA1 WILD-TYPE  141  245
        clus
vv       VWA1 MUTATED VWA1 WILD-TYPE
  FEMALE            4            141
  MALE              3            245
[1] 2 2
[1] FALSE
D854V8, binary
                cls
clus               0   1
  VWA1 MUTATED     6   0
  VWA1 WILD-TYPE 286  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  VWA1 MUTATED      6    0
  VWA1 WILD-TYPE  286   59
     clus
vv    VWA1 MUTATED VWA1 WILD-TYPE
  NO             6            286
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  VWA1 MUTATED                                          0
  VWA1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  VWA1 MUTATED                                       1
  VWA1 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  VWA1 MUTATED                                                        5
  VWA1 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  VWA1 MUTATED                                                   0
  VWA1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  VWA1 MUTATED                                                                   1
  VWA1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  VWA1 MUTATED                                                    0
  VWA1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  VWA1 MUTATED                                                  0
  VWA1 WILD-TYPE                                               61
D854V9, multiclass
                                                                   clus
vv                                                                  VWA1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  VWA1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  VWA1 MUTATED     6   0   0   0
  VWA1 WILD-TYPE 305  14  15  24
D854V10, multiclass
    clus
vv   VWA1 MUTATED VWA1 WILD-TYPE
  R0            6            305
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D854V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  VWA1 MUTATED       1                         0
  VWA1 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  VWA1 MUTATED                                           0     5
  VWA1 WILD-TYPE                                         1   238
D854V12, multiclass
                                           clus
vv                                          VWA1 MUTATED VWA1 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D854V13, binary
                cls
clus               0   1
  VWA1 MUTATED     0   6
  VWA1 WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  VWA1 MUTATED      0    6
  VWA1 WILD-TYPE    4  304
                        clus
vv                       VWA1 MUTATED VWA1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(855) Variable = ABCA5 MUTATION ANALYSIS
D855V1, survival
                 sevent
clus2               0   1
  ABCA5 MUTATED    15   3
  ABCA5 WILD-TYPE 215 136
  ABCA5 MUTATED ABCA5 WILD-TYPE 
             18             351 
  ABCA5 MUTATED ABCA5 WILD-TYPE 
              3             136 
$`ABCA5 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-7703 TCGA-BR-8368 TCGA-BR-8680 
        6.97        34.68        15.95        36.16         4.31        31.96 
TCGA-BR-A4PE TCGA-CD-A4MH TCGA-D7-5579 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4G8 
       20.42        12.20        20.91        30.51        26.47        22.68 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-AA6G 
        6.51         6.58        14.07        38.14        37.22        26.04 

$`ABCA5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
       11.61         6.58        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-D7-6518 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-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-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-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-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 

  ABCA5 MUTATED ABCA5 WILD-TYPE 
           4.31            0.00 
  ABCA5 MUTATED ABCA5 WILD-TYPE 
          38.14          122.30 
  ABCA5 MUTATED ABCA5 WILD-TYPE 
         21.795          14.040 
[1] "4.3 - 38.1 (21.8)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "2.9"
D855V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCA5 MUTATED         0        1        5        0         5         2
  ABCA5 WILD-TYPE       2       14       35       30        32        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABCA5 MUTATED           0          5          0          1        2
  ABCA5 WILD-TYPE         3         65         53         31       36
D855V3, multiclass
            clus
vv           ABCA5 MUTATED ABCA5 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               5              35
  STAGE II               0              30
  STAGE IIA              5              32
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             5              65
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCA5 MUTATED     2   5   8   6
  ABCA5 WILD-TYPE  20  87 165  91
D855V4, multiclass
    clus
vv   ABCA5 MUTATED ABCA5 WILD-TYPE
  T1             2              20
  T2             5              87
  T3             8             165
  T4             6              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
  ABCA5 MUTATED    10   7   3   1
  ABCA5 WILD-TYPE 108  97  74  76
D855V5, multiclass
    clus
vv   ABCA5 MUTATED ABCA5 WILD-TYPE
  N0            10             108
  N1             7              97
  N2             3              74
  N3             1              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"
D855V6, binary
                 cls
clus                0   1
  ABCA5 MUTATED    18   1
  ABCA5 WILD-TYPE 328  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA5 MUTATED     18    1
  ABCA5 WILD-TYPE  328   28
   clus
vv  ABCA5 MUTATED ABCA5 WILD-TYPE
  0            18             328
  1             1              28
[1] 2 2
[1] FALSE
D855V7, binary
                 cls
clus                0   1
  ABCA5 MUTATED    10  11
  ABCA5 WILD-TYPE 135 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA5 MUTATED     10   11
  ABCA5 WILD-TYPE  135  237
        clus
vv       ABCA5 MUTATED ABCA5 WILD-TYPE
  FEMALE            10             135
  MALE              11             237
[1] 2 2
[1] FALSE
D855V8, binary
                 cls
clus                0   1
  ABCA5 MUTATED    14   4
  ABCA5 WILD-TYPE 278  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA5 MUTATED     14    4
  ABCA5 WILD-TYPE  278   55
     clus
vv    ABCA5 MUTATED ABCA5 WILD-TYPE
  NO             14             278
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ABCA5 MUTATED                                          1
  ABCA5 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ABCA5 MUTATED                                       2
  ABCA5 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCA5 MUTATED                                                        8
  ABCA5 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ABCA5 MUTATED                                                   3
  ABCA5 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCA5 MUTATED                                                                   2
  ABCA5 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ABCA5 MUTATED                                                    1
  ABCA5 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ABCA5 MUTATED                                                  4
  ABCA5 WILD-TYPE                                               57
D855V9, multiclass
                                                                   clus
vv                                                                  ABCA5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  ABCA5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCA5 MUTATED    14   2   0   3
  ABCA5 WILD-TYPE 297  12  15  21
D855V10, multiclass
    clus
vv   ABCA5 MUTATED ABCA5 WILD-TYPE
  R0            14             297
  R1             2              12
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D855V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCA5 MUTATED       6                         0
  ABCA5 WILD-TYPE    81                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCA5 MUTATED                                           0    13
  ABCA5 WILD-TYPE                                         1   230
D855V12, multiclass
                                           clus
vv                                          ABCA5 MUTATED ABCA5 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D855V13, binary
                 cls
clus                0   1
  ABCA5 MUTATED     0  16
  ABCA5 WILD-TYPE   4 294
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA5 MUTATED      0   16
  ABCA5 WILD-TYPE    4  294
                        clus
vv                       ABCA5 MUTATED ABCA5 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            16             294
[1] 2 2
[1] FALSE

Clustering(856) Variable = LONRF1 MUTATION ANALYSIS
D856V1, survival
                  sevent
clus2                0   1
  LONRF1 MUTATED     4   2
  LONRF1 WILD-TYPE 226 137
  LONRF1 MUTATED LONRF1 WILD-TYPE 
               6              363 
  LONRF1 MUTATED LONRF1 WILD-TYPE 
               2              137 
$`LONRF1 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8368 TCGA-BR-8382 TCGA-BR-A4QL TCGA-FP-A4BE 
       34.68        44.94         4.31        25.05        16.14        11.08 

$`LONRF1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  LONRF1 MUTATED LONRF1 WILD-TYPE 
            4.31             0.00 
  LONRF1 MUTATED LONRF1 WILD-TYPE 
           44.94           122.30 
  LONRF1 MUTATED LONRF1 WILD-TYPE 
          20.595           14.170 
[1] "4.3 - 44.9 (20.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D856V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LONRF1 MUTATED         0        0        1        0         3         0
  LONRF1 WILD-TYPE       2       15       39       30        34        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LONRF1 MUTATED           0          0          1          1        0
  LONRF1 WILD-TYPE         3         70         52         31       38
D856V3, multiclass
            clus
vv           LONRF1 MUTATED LONRF1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LONRF1 MUTATED     0   1   4   1
  LONRF1 WILD-TYPE  22  91 169  96
D856V4, multiclass
    clus
vv   LONRF1 MUTATED LONRF1 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              4              169
  T4              1               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
  LONRF1 MUTATED     4   0   0   2
  LONRF1 WILD-TYPE 114 104  77  75
D856V5, multiclass
    clus
vv   LONRF1 MUTATED LONRF1 WILD-TYPE
  N0              4              114
  N1              0              104
  N2              0               77
  N3              2               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"
D856V6, binary
                  cls
clus                 0   1
  LONRF1 MUTATED     6   0
  LONRF1 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LONRF1 MUTATED      6    0
  LONRF1 WILD-TYPE  340   29
   clus
vv  LONRF1 MUTATED LONRF1 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D856V7, binary
                  cls
clus                 0   1
  LONRF1 MUTATED     5   1
  LONRF1 WILD-TYPE 140 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LONRF1 MUTATED      5    1
  LONRF1 WILD-TYPE  140  247
        clus
vv       LONRF1 MUTATED LONRF1 WILD-TYPE
  FEMALE              5              140
  MALE                1              247
[1] 2 2
[1] FALSE
D856V8, binary
                  cls
clus                 0   1
  LONRF1 MUTATED     5   1
  LONRF1 WILD-TYPE 287  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LONRF1 MUTATED      5    1
  LONRF1 WILD-TYPE  287   58
     clus
vv    LONRF1 MUTATED LONRF1 WILD-TYPE
  NO               5              287
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LONRF1 MUTATED                                          0
  LONRF1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LONRF1 MUTATED                                       0
  LONRF1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LONRF1 MUTATED                                                        6
  LONRF1 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LONRF1 MUTATED                                                   0
  LONRF1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LONRF1 MUTATED                                                                   0
  LONRF1 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LONRF1 MUTATED                                                    0
  LONRF1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LONRF1 MUTATED                                                  0
  LONRF1 WILD-TYPE                                               61
D856V9, multiclass
                                                                   clus
vv                                                                  LONRF1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  LONRF1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LONRF1 MUTATED     6   0   0   0
  LONRF1 WILD-TYPE 305  14  15  24
D856V10, multiclass
    clus
vv   LONRF1 MUTATED LONRF1 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D856V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  LONRF1 MUTATED       0                         1
  LONRF1 WILD-TYPE    87                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LONRF1 MUTATED                                           0     5
  LONRF1 WILD-TYPE                                         1   238
D856V12, multiclass
                                           clus
vv                                          LONRF1 MUTATED LONRF1 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D856V13, binary
                  cls
clus                 0   1
  LONRF1 MUTATED     0   6
  LONRF1 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LONRF1 MUTATED      0    6
  LONRF1 WILD-TYPE    4  304
                        clus
vv                       LONRF1 MUTATED LONRF1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(857) Variable = PHF10 MUTATION ANALYSIS
D857V1, survival
                 sevent
clus2               0   1
  PHF10 MUTATED     3   0
  PHF10 WILD-TYPE 227 139
  PHF10 MUTATED PHF10 WILD-TYPE 
              3             366 
  PHF10 MUTATED PHF10 WILD-TYPE 
              0             139 
$`PHF10 MUTATED`
TCGA-BR-8372 TCGA-BR-8589 TCGA-R5-A7ZI 
       31.27        27.12        74.53 

$`PHF10 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  PHF10 MUTATED PHF10 WILD-TYPE 
          27.12            0.00 
  PHF10 MUTATED PHF10 WILD-TYPE 
          74.53          122.30 
  PHF10 MUTATED PHF10 WILD-TYPE 
          31.27           14.12 
[1] "27.1 - 74.5 (31.3)" "0.0 - 122.3 (14.1)"
[1] "hr="     "9300000"
D857V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHF10 MUTATED         0        0        0        0         0         0
  PHF10 WILD-TYPE       2       15       40       30        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHF10 MUTATED           0          0          1          1        1
  PHF10 WILD-TYPE         3         70         52         31       37
D857V3, multiclass
            clus
vv           PHF10 MUTATED PHF10 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PHF10 MUTATED     1   0   0   3
  PHF10 WILD-TYPE  21  92 173  94
D857V4, multiclass
    clus
vv   PHF10 MUTATED PHF10 WILD-TYPE
  T1             1              21
  T2             0              92
  T3             0             173
  T4             3              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
  PHF10 MUTATED     0   2   0   1
  PHF10 WILD-TYPE 118 102  77  76
D857V5, multiclass
    clus
vv   PHF10 MUTATED PHF10 WILD-TYPE
  N0             0             118
  N1             2             102
  N2             0              77
  N3             1              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"
D857V6, binary
                 cls
clus                0   1
  PHF10 MUTATED     3   1
  PHF10 WILD-TYPE 343  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF10 MUTATED      3    1
  PHF10 WILD-TYPE  343   28
   clus
vv  PHF10 MUTATED PHF10 WILD-TYPE
  0             3             343
  1             1              28
[1] 2 2
[1] FALSE
D857V7, binary
                 cls
clus                0   1
  PHF10 MUTATED     2   2
  PHF10 WILD-TYPE 143 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF10 MUTATED      2    2
  PHF10 WILD-TYPE  143  246
        clus
vv       PHF10 MUTATED PHF10 WILD-TYPE
  FEMALE             2             143
  MALE               2             246
[1] 2 2
[1] FALSE
D857V8, binary
                 cls
clus                0   1
  PHF10 MUTATED     3   0
  PHF10 WILD-TYPE 289  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF10 MUTATED      3    0
  PHF10 WILD-TYPE  289   59
     clus
vv    PHF10 MUTATED PHF10 WILD-TYPE
  NO              3             289
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PHF10 MUTATED                                          0
  PHF10 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PHF10 MUTATED                                       1
  PHF10 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PHF10 MUTATED                                                        3
  PHF10 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PHF10 MUTATED                                                   0
  PHF10 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PHF10 MUTATED                                                                   0
  PHF10 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PHF10 MUTATED                                                    0
  PHF10 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PHF10 MUTATED                                                  0
  PHF10 WILD-TYPE                                               61
D857V9, multiclass
                                                                   clus
vv                                                                  PHF10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  PHF10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PHF10 MUTATED     3   0   0   1
  PHF10 WILD-TYPE 308  14  15  23
D857V10, multiclass
    clus
vv   PHF10 MUTATED PHF10 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D857V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PHF10 MUTATED       0                         0
  PHF10 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PHF10 MUTATED                                           0     4
  PHF10 WILD-TYPE                                         1   239
D857V12, multiclass
                                           clus
vv                                          PHF10 MUTATED PHF10 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D857V13, binary
                 cls
clus                0   1
  PHF10 MUTATED     1   3
  PHF10 WILD-TYPE   3 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF10 MUTATED      1    3
  PHF10 WILD-TYPE    3  307
                        clus
vv                       PHF10 MUTATED PHF10 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(858) Variable = CYP4B1 MUTATION ANALYSIS
D858V1, survival
                  sevent
clus2                0   1
  CYP4B1 MUTATED     6   3
  CYP4B1 WILD-TYPE 224 136
  CYP4B1 MUTATED CYP4B1 WILD-TYPE 
               9              360 
  CYP4B1 MUTATED CYP4B1 WILD-TYPE 
               3              136 
$`CYP4B1 MUTATED`
TCGA-BR-8059 TCGA-BR-8680 TCGA-BR-A4CS TCGA-D7-A4YV TCGA-HF-A5NB TCGA-HU-A4G9 
       14.43        31.96         1.48         5.92        30.51        24.20 
TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-VQ-AA6J 
        6.51        29.00        27.55 

$`CYP4B1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-AA6K TCGA-ZA-A8F6 
       32.94        54.12        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 
           24.20            14.12 
[1] "1.5 - 32.0 (24.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D858V2, 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       2       14       40       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP4B1 MUTATED           1          0          1          3        2
  CYP4B1 WILD-TYPE         2         70         52         29       36
D858V3, multiclass
            clus
vv           CYP4B1 MUTATED CYP4B1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               1                2
  STAGE IIIA              0               70
  STAGE IIIB              1               52
  STAGE IIIC              3               29
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CYP4B1 MUTATED     1   0   2   7
  CYP4B1 WILD-TYPE  21  92 171  90
D858V4, multiclass
    clus
vv   CYP4B1 MUTATED CYP4B1 WILD-TYPE
  T1              1               21
  T2              0               92
  T3              2              171
  T4              7               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
  CYP4B1 MUTATED     2   2   3   3
  CYP4B1 WILD-TYPE 116 102  74  74
D858V5, multiclass
    clus
vv   CYP4B1 MUTATED CYP4B1 WILD-TYPE
  N0              2              116
  N1              2              102
  N2              3               74
  N3              3               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"
D858V6, binary
                  cls
clus                 0   1
  CYP4B1 MUTATED     9   1
  CYP4B1 WILD-TYPE 337  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4B1 MUTATED      9    1
  CYP4B1 WILD-TYPE  337   28
   clus
vv  CYP4B1 MUTATED CYP4B1 WILD-TYPE
  0              9              337
  1              1               28
[1] 2 2
[1] FALSE
D858V7, binary
                  cls
clus                 0   1
  CYP4B1 MUTATED     6   4
  CYP4B1 WILD-TYPE 139 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4B1 MUTATED      6    4
  CYP4B1 WILD-TYPE  139  244
        clus
vv       CYP4B1 MUTATED CYP4B1 WILD-TYPE
  FEMALE              6              139
  MALE                4              244
[1] 2 2
[1] FALSE
D858V8, binary
                  cls
clus                 0   1
  CYP4B1 MUTATED     7   1
  CYP4B1 WILD-TYPE 285  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4B1 MUTATED      7    1
  CYP4B1 WILD-TYPE  285   58
     clus
vv    CYP4B1 MUTATED CYP4B1 WILD-TYPE
  NO               7              285
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CYP4B1 MUTATED                                          0
  CYP4B1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CYP4B1 MUTATED                                       1
  CYP4B1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CYP4B1 MUTATED                                                        2
  CYP4B1 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CYP4B1 MUTATED                                                   1
  CYP4B1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CYP4B1 MUTATED                                                                   2
  CYP4B1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CYP4B1 MUTATED                                                    0
  CYP4B1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CYP4B1 MUTATED                                                  4
  CYP4B1 WILD-TYPE                                               57
D858V9, multiclass
                                                                   clus
vv                                                                  CYP4B1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  CYP4B1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CYP4B1 MUTATED     8   1   0   1
  CYP4B1 WILD-TYPE 303  13  15  23
D858V10, multiclass
    clus
vv   CYP4B1 MUTATED CYP4B1 WILD-TYPE
  R0              8              303
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D858V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CYP4B1 MUTATED       4                         1
  CYP4B1 WILD-TYPE    83                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CYP4B1 MUTATED                                           0     4
  CYP4B1 WILD-TYPE                                         1   239
D858V12, multiclass
                                           clus
vv                                          CYP4B1 MUTATED CYP4B1 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D858V13, binary
                  cls
clus                 0   1
  CYP4B1 MUTATED     0   8
  CYP4B1 WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4B1 MUTATED      0    8
  CYP4B1 WILD-TYPE    4  302
                        clus
vv                       CYP4B1 MUTATED CYP4B1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(859) Variable = EXO1 MUTATION ANALYSIS
D859V1, survival
                sevent
clus2              0   1
  EXO1 MUTATED    12   3
  EXO1 WILD-TYPE 218 136
  EXO1 MUTATED EXO1 WILD-TYPE 
            15            354 
  EXO1 MUTATED EXO1 WILD-TYPE 
             3            136 
$`EXO1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       26.70         6.97        34.68        44.94        21.90        36.16 
TCGA-BR-7707 TCGA-BR-A4J8 TCGA-CG-5733 TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GT 
       35.84        13.51        21.07        22.32        29.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-IN-A6RR 
        6.58        23.84         6.74 

$`EXO1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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 

  EXO1 MUTATED EXO1 WILD-TYPE 
          6.51           0.00 
  EXO1 MUTATED EXO1 WILD-TYPE 
         44.94         122.30 
  EXO1 MUTATED EXO1 WILD-TYPE 
         22.32          14.07 
[1] "6.5 - 44.9 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.4"
D859V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EXO1 MUTATED         0        1        1        0         4         4
  EXO1 WILD-TYPE       2       14       39       30        33        48
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EXO1 MUTATED           0          4          1          0        1
  EXO1 WILD-TYPE         3         66         52         32       37
D859V3, multiclass
            clus
vv           EXO1 MUTATED EXO1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             4             33
  STAGE IIB             4             48
  STAGE III             0              3
  STAGE IIIA            4             66
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EXO1 MUTATED     2   4   8   3
  EXO1 WILD-TYPE  20  88 165  94
D859V4, multiclass
    clus
vv   EXO1 MUTATED EXO1 WILD-TYPE
  T1            2             20
  T2            4             88
  T3            8            165
  T4            3             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
  EXO1 MUTATED     8   4   2   2
  EXO1 WILD-TYPE 110 100  75  75
D859V5, multiclass
    clus
vv   EXO1 MUTATED EXO1 WILD-TYPE
  N0            8            110
  N1            4            100
  N2            2             75
  N3            2             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"
D859V6, binary
                cls
clus               0   1
  EXO1 MUTATED    15   1
  EXO1 WILD-TYPE 331  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXO1 MUTATED     15    1
  EXO1 WILD-TYPE  331   28
   clus
vv  EXO1 MUTATED EXO1 WILD-TYPE
  0           15            331
  1            1             28
[1] 2 2
[1] FALSE
D859V7, binary
                cls
clus               0   1
  EXO1 MUTATED    11   6
  EXO1 WILD-TYPE 134 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXO1 MUTATED     11    6
  EXO1 WILD-TYPE  134  242
        clus
vv       EXO1 MUTATED EXO1 WILD-TYPE
  FEMALE           11            134
  MALE              6            242
[1] 2 2
[1] FALSE
D859V8, binary
                cls
clus               0   1
  EXO1 MUTATED    15   0
  EXO1 WILD-TYPE 277  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXO1 MUTATED     15    0
  EXO1 WILD-TYPE  277   59
     clus
vv    EXO1 MUTATED EXO1 WILD-TYPE
  NO            15            277
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EXO1 MUTATED                                          0
  EXO1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EXO1 MUTATED                                       3
  EXO1 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EXO1 MUTATED                                                        9
  EXO1 WILD-TYPE                                                    149
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EXO1 MUTATED                                                   0
  EXO1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EXO1 MUTATED                                                                   1
  EXO1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EXO1 MUTATED                                                    1
  EXO1 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EXO1 MUTATED                                                  3
  EXO1 WILD-TYPE                                               58
D859V9, multiclass
                                                                   clus
vv                                                                  EXO1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  EXO1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EXO1 MUTATED    14   0   0   3
  EXO1 WILD-TYPE 297  14  15  21
D859V10, multiclass
    clus
vv   EXO1 MUTATED EXO1 WILD-TYPE
  R0           14            297
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D859V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  EXO1 MUTATED       5                         0
  EXO1 WILD-TYPE    82                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EXO1 MUTATED                                           0    11
  EXO1 WILD-TYPE                                         1   232
D859V12, multiclass
                                           clus
vv                                          EXO1 MUTATED EXO1 WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D859V13, binary
                cls
clus               0   1
  EXO1 MUTATED     0  16
  EXO1 WILD-TYPE   4 294
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXO1 MUTATED      0   16
  EXO1 WILD-TYPE    4  294
                        clus
vv                       EXO1 MUTATED EXO1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           16            294
[1] 2 2
[1] FALSE

Clustering(860) Variable = THYN1 MUTATION ANALYSIS
D860V1, survival
                 sevent
clus2               0   1
  THYN1 MUTATED     3   5
  THYN1 WILD-TYPE 227 134
  THYN1 MUTATED THYN1 WILD-TYPE 
              8             361 
  THYN1 MUTATED THYN1 WILD-TYPE 
              5             134 
$`THYN1 MUTATED`
TCGA-CG-4460 TCGA-BR-4257 TCGA-BR-7707 TCGA-CD-8535 TCGA-CD-A48C TCGA-CG-5726 
       21.99         9.67        35.84        12.82        11.61        28.96 
TCGA-F1-6874 TCGA-HJ-7597 
       14.47        26.47 

$`THYN1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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 

  THYN1 MUTATED THYN1 WILD-TYPE 
           9.67            0.00 
  THYN1 MUTATED THYN1 WILD-TYPE 
          35.84          122.30 
  THYN1 MUTATED THYN1 WILD-TYPE 
          18.23           14.17 
[1] "9.7 - 35.8 (18.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D860V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  THYN1 MUTATED         0        1        3        0         0         1
  THYN1 WILD-TYPE       2       14       37       30        37        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  THYN1 MUTATED           0          1          0          0        1
  THYN1 WILD-TYPE         3         69         53         32       37
D860V3, multiclass
            clus
vv           THYN1 MUTATED THYN1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  THYN1 MUTATED     1   3   2   1
  THYN1 WILD-TYPE  21  89 171  96
D860V4, multiclass
    clus
vv   THYN1 MUTATED THYN1 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             2             171
  T4             1              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
  THYN1 MUTATED     4   3   0   0
  THYN1 WILD-TYPE 114 101  77  77
D860V5, multiclass
    clus
vv   THYN1 MUTATED THYN1 WILD-TYPE
  N0             4             114
  N1             3             101
  N2             0              77
  N3             0              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"
D860V6, binary
                 cls
clus                0   1
  THYN1 MUTATED     6   1
  THYN1 WILD-TYPE 340  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THYN1 MUTATED      6    1
  THYN1 WILD-TYPE  340   28
   clus
vv  THYN1 MUTATED THYN1 WILD-TYPE
  0             6             340
  1             1              28
[1] 2 2
[1] FALSE
D860V7, binary
                 cls
clus                0   1
  THYN1 MUTATED     5   3
  THYN1 WILD-TYPE 140 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THYN1 MUTATED      5    3
  THYN1 WILD-TYPE  140  245
        clus
vv       THYN1 MUTATED THYN1 WILD-TYPE
  FEMALE             5             140
  MALE               3             245
[1] 2 2
[1] FALSE
D860V8, binary
                 cls
clus                0   1
  THYN1 MUTATED     7   0
  THYN1 WILD-TYPE 285  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THYN1 MUTATED      7    0
  THYN1 WILD-TYPE  285   59
     clus
vv    THYN1 MUTATED THYN1 WILD-TYPE
  NO              7             285
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  THYN1 MUTATED                                          1
  THYN1 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  THYN1 MUTATED                                       0
  THYN1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  THYN1 MUTATED                                                        4
  THYN1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  THYN1 MUTATED                                                   0
  THYN1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  THYN1 MUTATED                                                                   3
  THYN1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  THYN1 MUTATED                                                    0
  THYN1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  THYN1 MUTATED                                                  0
  THYN1 WILD-TYPE                                               61
D860V9, multiclass
                                                                   clus
vv                                                                  THYN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  THYN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  THYN1 MUTATED     5   0   1   1
  THYN1 WILD-TYPE 306  14  14  23
D860V10, multiclass
    clus
vv   THYN1 MUTATED THYN1 WILD-TYPE
  R0             5             306
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D860V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  THYN1 MUTATED       2                         0
  THYN1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  THYN1 MUTATED                                           0     4
  THYN1 WILD-TYPE                                         1   239
D860V12, multiclass
                                           clus
vv                                          THYN1 MUTATED THYN1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D860V13, binary
                 cls
clus                0   1
  THYN1 MUTATED     0   6
  THYN1 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THYN1 MUTATED      0    6
  THYN1 WILD-TYPE    4  304
                        clus
vv                       THYN1 MUTATED THYN1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(861) Variable = FOXQ1 MUTATION ANALYSIS
D861V1, survival
                 sevent
clus2               0   1
  FOXQ1 MUTATED     2   1
  FOXQ1 WILD-TYPE 228 138
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              3             366 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              1             138 
$`FOXQ1 MUTATED`
TCGA-BR-7707 TCGA-BR-8078 TCGA-CG-4306 
       35.84        29.59         1.02 

$`FOXQ1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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           14.22 
[1] "1.0 - 35.8 (29.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D861V2, 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       2       15       39       30        37        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FOXQ1 MUTATED           0          0          0          0        1
  FOXQ1 WILD-TYPE         3         70         53         32       37
D861V3, multiclass
            clus
vv           FOXQ1 MUTATED FOXQ1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOXQ1 MUTATED     0   1   1   1
  FOXQ1 WILD-TYPE  22  91 172  96
D861V4, multiclass
    clus
vv   FOXQ1 MUTATED FOXQ1 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             1             172
  T4             1              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
  FOXQ1 MUTATED     2   0   1   0
  FOXQ1 WILD-TYPE 116 104  76  77
D861V5, multiclass
    clus
vv   FOXQ1 MUTATED FOXQ1 WILD-TYPE
  N0             2             116
  N1             0             104
  N2             1              76
  N3             0              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"
D861V6, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     2   1
  FOXQ1 WILD-TYPE 344  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      2    1
  FOXQ1 WILD-TYPE  344   28
   clus
vv  FOXQ1 MUTATED FOXQ1 WILD-TYPE
  0             2             344
  1             1              28
[1] 2 2
[1] FALSE
D861V7, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     2   1
  FOXQ1 WILD-TYPE 143 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      2    1
  FOXQ1 WILD-TYPE  143  247
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  FEMALE             2             143
  MALE               1             247
[1] 2 2
[1] FALSE
D861V8, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     2   0
  FOXQ1 WILD-TYPE 290  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      2    0
  FOXQ1 WILD-TYPE  290   59
     clus
vv    FOXQ1 MUTATED FOXQ1 WILD-TYPE
  NO              2             290
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FOXQ1 MUTATED                                          0
  FOXQ1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FOXQ1 MUTATED                                       0
  FOXQ1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FOXQ1 MUTATED                                                        3
  FOXQ1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FOXQ1 MUTATED                                                   0
  FOXQ1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FOXQ1 MUTATED                                                                   0
  FOXQ1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FOXQ1 MUTATED                                                    0
  FOXQ1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FOXQ1 MUTATED                                                  0
  FOXQ1 WILD-TYPE                                               61
D861V9, multiclass
                                                                   clus
vv                                                                  FOXQ1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  FOXQ1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FOXQ1 MUTATED     2   0   1   0
  FOXQ1 WILD-TYPE 309  14  14  24
D861V10, multiclass
    clus
vv   FOXQ1 MUTATED FOXQ1 WILD-TYPE
  R0             2             309
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D861V11, continuous
[1] "Remove cluster labels:" "FOXQ1 MUTATED"         
clus
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              2             341 
     TCGA-CG-4444      TCGA-CG-4460      TCGA-CG-4475      TCGA-CG-4476 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-5727      TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-FP-A8CX 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HF-7131      TCGA-KB-A93G      TCGA-MX-A663      TCGA-B7-5816 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-B7-A5TI      TCGA-BR-4183      TCGA-BR-4184      TCGA-BR-4188 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4191      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4361 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4362      TCGA-BR-4368      TCGA-BR-6452      TCGA-BR-6453 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6709      TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6803      TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7703      TCGA-BR-7704      TCGA-BR-7715      TCGA-BR-7716 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7717      TCGA-BR-7722      TCGA-BR-7723      TCGA-BR-7851 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7901      TCGA-BR-7957      TCGA-BR-7958      TCGA-BR-7959 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8058      TCGA-BR-8059      TCGA-BR-8060      TCGA-BR-8077 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8080      TCGA-BR-8081      TCGA-BR-8284      TCGA-BR-8285 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291      TCGA-BR-8295 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8297      TCGA-BR-8360      TCGA-BR-8361      TCGA-BR-8363 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366      TCGA-BR-8367 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370      TCGA-BR-8371 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8372      TCGA-BR-8373      TCGA-BR-8380      TCGA-BR-8381 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483      TCGA-BR-8484 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487      TCGA-BR-8588 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591      TCGA-BR-8592 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678      TCGA-BR-8679 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683      TCGA-BR-8686 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T      TCGA-BR-A44U 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ      TCGA-BR-A4CR 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV      TCGA-BR-A4IY 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2      TCGA-BR-A4J4 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4J5      TCGA-BR-A4J6      TCGA-BR-A4J8      TCGA-BR-A4PD 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QL 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4QM      TCGA-CD-5804      TCGA-CD-8525      TCGA-CD-8526 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-8531      TCGA-CD-8535      TCGA-CD-A487      TCGA-CG-4301 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4436      TCGA-CG-4437 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-4438      TCGA-CG-4440      TCGA-CG-4441      TCGA-CG-4442 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-4443      TCGA-CG-4449      TCGA-CG-4455      TCGA-CG-4462 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-4465      TCGA-CG-4466      TCGA-CG-4469      TCGA-CG-4474 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-4477      TCGA-CG-5717      TCGA-CG-5718      TCGA-CG-5719 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-5720      TCGA-CG-5721      TCGA-CG-5722      TCGA-CG-5723 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-5724      TCGA-CG-5725      TCGA-CG-5726      TCGA-CG-5728 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CG-5730      TCGA-CG-5732      TCGA-CG-5733      TCGA-CG-5734 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579      TCGA-D7-6518 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526      TCGA-D7-6527 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817      TCGA-D7-6818 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570      TCGA-D7-8572 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575      TCGA-D7-8576 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT      TCGA-D7-A4YU 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY      TCGA-D7-A4Z0 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A6ET      TCGA-D7-A6EV      TCGA-D7-A6EX      TCGA-D7-A6EY 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A6EZ      TCGA-D7-A6F0      TCGA-D7-A6F2      TCGA-D7-A747 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A748      TCGA-D7-A74A      TCGA-D7-A74B      TCGA-EQ-5647 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-EQ-8122      TCGA-F1-6874      TCGA-F1-6875      TCGA-F1-A448 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-F1-A72C      TCGA-FP-7735      TCGA-FP-7829      TCGA-FP-7916 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209      TCGA-FP-8210 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BE      TCGA-FP-A4BF 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-A9TM      TCGA-HF-7132      TCGA-HF-7133      TCGA-HF-7134 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HF-7136      TCGA-HF-A5NB      TCGA-HJ-7597      TCGA-HU-8238 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-8243      TCGA-HU-8244      TCGA-HU-8249      TCGA-HU-8602 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610      TCGA-HU-A4G2 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8      TCGA-HU-A4G9 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF      TCGA-HU-A4GH 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4GJ      TCGA-HU-A4GN      TCGA-HU-A4GP      TCGA-HU-A4GQ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX      TCGA-HU-A4GY 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3      TCGA-HU-A4H4 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8      TCGA-HU-A4HB 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IN-8663      TCGA-IN-A6RI      TCGA-IN-A6RJ      TCGA-IN-A6RL 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IN-A6RN      TCGA-IN-A6RO      TCGA-IN-A6RP      TCGA-IN-A6RR 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IN-A6RS      TCGA-IN-A7NR      TCGA-IN-A7NT      TCGA-IN-A7NU 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IN-AB1V      TCGA-IN-AB1X      TCGA-IP-7968      TCGA-KB-A6F5 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-KB-A6F7      TCGA-KB-A93J      TCGA-MX-A5UG      TCGA-MX-A5UJ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-R5-A7ZI      TCGA-RD-A7BS      TCGA-RD-A7BT      TCGA-RD-A7BW 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-RD-A7C1      TCGA-RD-A8MV      TCGA-RD-A8MW      TCGA-RD-A8N0 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-RD-A8N1      TCGA-RD-A8N2      TCGA-RD-A8N4      TCGA-RD-A8N5 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-RD-A8N6      TCGA-RD-A8N9      TCGA-SW-A7EA      TCGA-SW-A7EB 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-A8DL      TCGA-VQ-A8DT      TCGA-VQ-A8DU      TCGA-VQ-A8DV 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-A8DZ      TCGA-VQ-A8E2      TCGA-VQ-A8E7      TCGA-VQ-A8P2 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-A8P3      TCGA-VQ-A8PE      TCGA-VQ-A8PK      TCGA-VQ-A8PM 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-A8PQ      TCGA-VQ-A91Q      TCGA-VQ-A91U      TCGA-VQ-A91V 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-A92D      TCGA-VQ-A94T      TCGA-VQ-AA64      TCGA-VQ-AA68 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-AA69      TCGA-VQ-AA6A      TCGA-VQ-AA6B      TCGA-VQ-AA6F 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-AA6G      TCGA-VQ-AA6I      TCGA-VQ-AA6J      TCGA-VQ-AA6K 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-ZA-A8F6 
"FOXQ1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FOXQ1 MUTATED       0                         0
  FOXQ1 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FOXQ1 MUTATED                                           0     2
  FOXQ1 WILD-TYPE                                         1   241
D861V12, multiclass
[1] "Remove cluster labels:" "FOXQ1 MUTATED"         
clus
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              2             338 
     TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-FP-A8CX      TCGA-KB-A93G 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-MX-A663      TCGA-B7-5816      TCGA-B7-5818      TCGA-B7-A5TI 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-B7-A5TJ      TCGA-B7-A5TK      TCGA-B7-A5TN      TCGA-BR-4183 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4184      TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4201      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4257      TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4292      TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4362      TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-4369      TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6452 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6453      TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6457      TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6565      TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6707      TCGA-BR-6709      TCGA-BR-6710      TCGA-BR-6801 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-6802      TCGA-BR-6803      TCGA-BR-6852      TCGA-BR-7196 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7704      TCGA-BR-7715 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722      TCGA-BR-7723 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957      TCGA-BR-7958 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059      TCGA-BR-8060 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8077      TCGA-BR-8080      TCGA-BR-8081      TCGA-BR-8284 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8285      TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8295      TCGA-BR-8297      TCGA-BR-8360      TCGA-BR-8361 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373      TCGA-BR-8380 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4J4      TCGA-BR-A4J5      TCGA-BR-A4J6      TCGA-BR-A4J7 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-BR-A4QI      TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5798 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-5799      TCGA-CD-5800      TCGA-CD-5801      TCGA-CD-5802 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-5803      TCGA-CD-5804      TCGA-CD-5813      TCGA-CD-8524 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-8525      TCGA-CD-8526      TCGA-CD-8527      TCGA-CD-8528 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-8529      TCGA-CD-8530      TCGA-CD-8531      TCGA-CD-8532 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-8533      TCGA-CD-8534      TCGA-CD-8535      TCGA-CD-8536 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-A486      TCGA-CD-A487      TCGA-CD-A489      TCGA-CD-A48A 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-A48C      TCGA-CD-A4MG      TCGA-CD-A4MH      TCGA-CD-A4MI 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CD-A4MJ      TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6518      TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-8572      TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-8576      TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A4YU      TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A4Z0      TCGA-D7-A6ET      TCGA-D7-A6EV      TCGA-D7-A6EX 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A6EY      TCGA-D7-A6EZ      TCGA-D7-A6F0      TCGA-D7-A6F2 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-D7-A747      TCGA-D7-A748      TCGA-D7-A74A      TCGA-D7-A74B 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-EQ-5647      TCGA-EQ-8122      TCGA-F1-6874      TCGA-F1-6875 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-F1-A448      TCGA-F1-A72C      TCGA-FP-7735      TCGA-FP-7829 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BE 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-FP-A4BF      TCGA-FP-A9TM      TCGA-HJ-7597      TCGA-HU-8238 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-8243      TCGA-HU-8244      TCGA-HU-8249      TCGA-HU-8602 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610      TCGA-HU-A4G2 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8      TCGA-HU-A4G9 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF      TCGA-HU-A4GH 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4GJ      TCGA-HU-A4GN      TCGA-HU-A4GP      TCGA-HU-A4GQ 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX      TCGA-HU-A4GY 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3      TCGA-HU-A4H4 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8      TCGA-HU-A4HB 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IN-8663      TCGA-IN-A6RI      TCGA-IN-A6RJ      TCGA-IN-A6RL 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IN-A6RN      TCGA-IN-A6RO      TCGA-IN-A6RP      TCGA-IN-A6RR 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IN-A6RS      TCGA-IN-A7NR      TCGA-IN-A7NT      TCGA-IN-A7NU 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-IN-AB1V      TCGA-IN-AB1X      TCGA-IP-7968      TCGA-KB-A93J 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-MX-A5UG      TCGA-MX-A5UJ      TCGA-MX-A666      TCGA-R5-A7O7 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-R5-A7ZE      TCGA-R5-A7ZF      TCGA-R5-A7ZI      TCGA-R5-A7ZR 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-R5-A804      TCGA-R5-A805      TCGA-RD-A7BS      TCGA-RD-A7BT 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-RD-A7BW      TCGA-RD-A7C1      TCGA-RD-A8MV      TCGA-RD-A8MW 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-RD-A8N0      TCGA-RD-A8N1      TCGA-RD-A8N2      TCGA-RD-A8N4 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-RD-A8N5      TCGA-RD-A8N6      TCGA-RD-A8N9      TCGA-SW-A7EA 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-SW-A7EB      TCGA-VQ-A8DL      TCGA-VQ-A8DU      TCGA-VQ-A8DV 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-A8DZ      TCGA-VQ-A8E2      TCGA-VQ-A8E7      TCGA-VQ-A8P2 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-A8P3      TCGA-VQ-A8PE      TCGA-VQ-A8PK      TCGA-VQ-A8PM 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-A8PQ      TCGA-VQ-A91U      TCGA-VQ-A92D      TCGA-VQ-AA64 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-AA68      TCGA-VQ-AA69      TCGA-VQ-AA6A      TCGA-VQ-AA6B 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-AA6F      TCGA-VQ-AA6G      TCGA-VQ-AA6I      TCGA-VQ-AA6J 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-VQ-AA6K      TCGA-ZA-A8F6 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
D861V13, binary
                 cls
clus                0   1
  FOXQ1 MUTATED     0   2
  FOXQ1 WILD-TYPE   4 308
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      0    2
  FOXQ1 WILD-TYPE    4  308
                        clus
vv                       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             2             308
[1] 2 2
[1] FALSE

Clustering(862) Variable = HIVEP1 MUTATION ANALYSIS
D862V1, survival
                  sevent
clus2                0   1
  HIVEP1 MUTATED    17   6
  HIVEP1 WILD-TYPE 213 133
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
              23              346 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
               6              133 
$`HIVEP1 MUTATED`
TCGA-EQ-A4SO TCGA-BR-4257 TCGA-BR-6802 TCGA-BR-7704 TCGA-BR-8078 TCGA-BR-8081 
       16.24         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-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-8371 TCGA-BR-8372 
        0.95        26.33         4.31        14.04        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-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-8529 
       12.39        12.76        12.59        12.53         7.17        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-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-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-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-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 

  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
            1.12             0.00 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
           52.21           122.30 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
           16.24            14.12 
[1] "1.1 - 52.2 (16.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D862V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HIVEP1 MUTATED         0        2        1        2         3         4
  HIVEP1 WILD-TYPE       2       13       39       28        34        48
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIVEP1 MUTATED           0          2          3          3        2
  HIVEP1 WILD-TYPE         3         68         50         29       36
D862V3, multiclass
            clus
vv           HIVEP1 MUTATED HIVEP1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                2               13
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               3               34
  STAGE IIB               4               48
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              3               50
  STAGE IIIC              3               29
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HIVEP1 MUTATED     3   2   8  10
  HIVEP1 WILD-TYPE  19  90 165  87
D862V4, multiclass
    clus
vv   HIVEP1 MUTATED HIVEP1 WILD-TYPE
  T1              3               19
  T2              2               90
  T3              8              165
  T4             10               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
  HIVEP1 MUTATED    10   4   3   5
  HIVEP1 WILD-TYPE 108 100  74  72
D862V5, multiclass
    clus
vv   HIVEP1 MUTATED HIVEP1 WILD-TYPE
  N0             10              108
  N1              4              100
  N2              3               74
  N3              5               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"
D862V6, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED    21   1
  HIVEP1 WILD-TYPE 325  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED     21    1
  HIVEP1 WILD-TYPE  325   28
   clus
vv  HIVEP1 MUTATED HIVEP1 WILD-TYPE
  0             21              325
  1              1               28
[1] 2 2
[1] FALSE
D862V7, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED    13  11
  HIVEP1 WILD-TYPE 132 237
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED     13   11
  HIVEP1 WILD-TYPE  132  237
        clus
vv       HIVEP1 MUTATED HIVEP1 WILD-TYPE
  FEMALE             13              132
  MALE               11              237
[1] 2 2
[1] FALSE
D862V8, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED    20   2
  HIVEP1 WILD-TYPE 272  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED     20    2
  HIVEP1 WILD-TYPE  272   57
     clus
vv    HIVEP1 MUTATED HIVEP1 WILD-TYPE
  NO              20              272
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HIVEP1 MUTATED                                          0
  HIVEP1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HIVEP1 MUTATED                                       3
  HIVEP1 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HIVEP1 MUTATED                                                       10
  HIVEP1 WILD-TYPE                                                    148
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HIVEP1 MUTATED                                                   0
  HIVEP1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HIVEP1 MUTATED                                                                   6
  HIVEP1 WILD-TYPE                                                                62
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HIVEP1 MUTATED                                                    0
  HIVEP1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HIVEP1 MUTATED                                                  4
  HIVEP1 WILD-TYPE                                               57
D862V9, multiclass
                                                                   clus
vv                                                                  HIVEP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  HIVEP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HIVEP1 MUTATED    21   0   0   2
  HIVEP1 WILD-TYPE 290  14  15  22
D862V10, multiclass
    clus
vv   HIVEP1 MUTATED HIVEP1 WILD-TYPE
  R0             21              290
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D862V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  HIVEP1 MUTATED       7                         0
  HIVEP1 WILD-TYPE    80                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HIVEP1 MUTATED                                           0    13
  HIVEP1 WILD-TYPE                                         1   230
D862V12, multiclass
                                           clus
vv                                          HIVEP1 MUTATED HIVEP1 WILD-TYPE
  ASIAN                                                  7               80
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D862V13, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED     0  20
  HIVEP1 WILD-TYPE   4 290
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED      0   20
  HIVEP1 WILD-TYPE    4  290
                        clus
vv                       HIVEP1 MUTATED HIVEP1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             20              290
[1] 2 2
[1] FALSE

Clustering(863) Variable = ZNF687 MUTATION ANALYSIS
D863V1, survival
                  sevent
clus2                0   1
  ZNF687 MUTATED     7   2
  ZNF687 WILD-TYPE 223 137
  ZNF687 MUTATED ZNF687 WILD-TYPE 
               9              360 
  ZNF687 MUTATED ZNF687 WILD-TYPE 
               2              137 
$`ZNF687 MUTATED`
TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-4306 TCGA-CG-5721 
        1.12        28.14        31.96        16.14         1.02         6.02 
TCGA-F1-6874 TCGA-F1-A448 TCGA-VQ-A8P2 
       14.47        21.27        38.14 

$`ZNF687 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  ZNF687 MUTATED ZNF687 WILD-TYPE 
            1.02             0.00 
  ZNF687 MUTATED ZNF687 WILD-TYPE 
           38.14           122.30 
  ZNF687 MUTATED ZNF687 WILD-TYPE 
           16.14            14.12 
[1] "1.0 - 38.1 (16.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D863V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF687 MUTATED         0        0        1        0         1         0
  ZNF687 WILD-TYPE       2       15       39       30        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF687 MUTATED           0          1          2          1        4
  ZNF687 WILD-TYPE         3         69         51         31       34
D863V3, multiclass
            clus
vv           ZNF687 MUTATED ZNF687 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              2               51
  STAGE IIIC              1               31
  STAGE IV                4               34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF687 MUTATED     1   1   4   5
  ZNF687 WILD-TYPE  21  91 169  92
D863V4, multiclass
    clus
vv   ZNF687 MUTATED ZNF687 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              4              169
  T4              5               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
  ZNF687 MUTATED     2   2   3   3
  ZNF687 WILD-TYPE 116 102  74  74
D863V5, multiclass
    clus
vv   ZNF687 MUTATED ZNF687 WILD-TYPE
  N0              2              116
  N1              2              102
  N2              3               74
  N3              3               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"
D863V6, binary
                  cls
clus                 0   1
  ZNF687 MUTATED     9   2
  ZNF687 WILD-TYPE 337  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF687 MUTATED      9    2
  ZNF687 WILD-TYPE  337   27
   clus
vv  ZNF687 MUTATED ZNF687 WILD-TYPE
  0              9              337
  1              2               27
[1] 2 2
[1] FALSE
D863V7, binary
                  cls
clus                 0   1
  ZNF687 MUTATED     4   7
  ZNF687 WILD-TYPE 141 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF687 MUTATED      4    7
  ZNF687 WILD-TYPE  141  241
        clus
vv       ZNF687 MUTATED ZNF687 WILD-TYPE
  FEMALE              4              141
  MALE                7              241
[1] 2 2
[1] FALSE
D863V8, binary
                  cls
clus                 0   1
  ZNF687 MUTATED     6   2
  ZNF687 WILD-TYPE 286  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF687 MUTATED      6    2
  ZNF687 WILD-TYPE  286   57
     clus
vv    ZNF687 MUTATED ZNF687 WILD-TYPE
  NO               6              286
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF687 MUTATED                                          0
  ZNF687 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF687 MUTATED                                       0
  ZNF687 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF687 MUTATED                                                        6
  ZNF687 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF687 MUTATED                                                   2
  ZNF687 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF687 MUTATED                                                                   2
  ZNF687 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF687 MUTATED                                                    0
  ZNF687 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF687 MUTATED                                                  1
  ZNF687 WILD-TYPE                                               60
D863V9, multiclass
                                                                   clus
vv                                                                  ZNF687 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ZNF687 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF687 MUTATED     8   0   1   2
  ZNF687 WILD-TYPE 303  14  14  22
D863V10, multiclass
    clus
vv   ZNF687 MUTATED ZNF687 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D863V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF687 MUTATED       1                         0
  ZNF687 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF687 MUTATED                                           0     8
  ZNF687 WILD-TYPE                                         1   235
D863V12, multiclass
                                           clus
vv                                          ZNF687 MUTATED ZNF687 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D863V13, binary
                  cls
clus                 0   1
  ZNF687 MUTATED     1   7
  ZNF687 WILD-TYPE   3 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF687 MUTATED      1    7
  ZNF687 WILD-TYPE    3  303
                        clus
vv                       ZNF687 MUTATED ZNF687 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(864) Variable = PTPN23 MUTATION ANALYSIS
D864V1, survival
                  sevent
clus2                0   1
  PTPN23 MUTATED    14   3
  PTPN23 WILD-TYPE 216 136
  PTPN23 MUTATED PTPN23 WILD-TYPE 
              17              352 
  PTPN23 MUTATED PTPN23 WILD-TYPE 
               3              136 
$`PTPN23 MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8372 TCGA-BR-8487 
       11.70         6.97        44.94        29.59        31.27         1.12 
TCGA-BR-8591 TCGA-CG-5721 TCGA-CG-5726 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HF-7132 
       28.14         6.02        28.96         5.92        11.08        77.29 
TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4H3 TCGA-MX-A5UJ TCGA-VQ-AA6F 
       30.51        22.68        29.00        19.73        54.12 

$`PTPN23 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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 
           28.14            14.07 
[1] "1.1 - 77.3 (28.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.9"
D864V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPN23 MUTATED         0        1        2        1         3         5
  PTPN23 WILD-TYPE       2       14       38       29        34        47
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN23 MUTATED           0          3          0          4        2
  PTPN23 WILD-TYPE         3         67         53         28       36
D864V3, multiclass
            clus
vv           PTPN23 MUTATED PTPN23 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               5               47
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              4               28
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTPN23 MUTATED     1   3   8   9
  PTPN23 WILD-TYPE  21  89 165  88
D864V4, multiclass
    clus
vv   PTPN23 MUTATED PTPN23 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              8              165
  T4              9               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
  PTPN23 MUTATED     9   6   2   4
  PTPN23 WILD-TYPE 109  98  75  73
D864V5, multiclass
    clus
vv   PTPN23 MUTATED PTPN23 WILD-TYPE
  N0              9              109
  N1              6               98
  N2              2               75
  N3              4               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"
D864V6, binary
                  cls
clus                 0   1
  PTPN23 MUTATED    20   0
  PTPN23 WILD-TYPE 326  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN23 MUTATED     20    0
  PTPN23 WILD-TYPE  326   29
   clus
vv  PTPN23 MUTATED PTPN23 WILD-TYPE
  0             20              326
  1              0               29
[1] 2 2
[1] FALSE
D864V7, binary
                  cls
clus                 0   1
  PTPN23 MUTATED    10  11
  PTPN23 WILD-TYPE 135 237
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN23 MUTATED     10   11
  PTPN23 WILD-TYPE  135  237
        clus
vv       PTPN23 MUTATED PTPN23 WILD-TYPE
  FEMALE             10              135
  MALE               11              237
[1] 2 2
[1] FALSE
D864V8, binary
                  cls
clus                 0   1
  PTPN23 MUTATED    12   4
  PTPN23 WILD-TYPE 280  55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN23 MUTATED     12    4
  PTPN23 WILD-TYPE  280   55
     clus
vv    PTPN23 MUTATED PTPN23 WILD-TYPE
  NO              12              280
  YES              4               55
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PTPN23 MUTATED                                          0
  PTPN23 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PTPN23 MUTATED                                       3
  PTPN23 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTPN23 MUTATED                                                        9
  PTPN23 WILD-TYPE                                                    149
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PTPN23 MUTATED                                                   2
  PTPN23 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTPN23 MUTATED                                                                   5
  PTPN23 WILD-TYPE                                                                63
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PTPN23 MUTATED                                                    0
  PTPN23 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PTPN23 MUTATED                                                  2
  PTPN23 WILD-TYPE                                               59
D864V9, multiclass
                                                                   clus
vv                                                                  PTPN23 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  PTPN23 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PTPN23 MUTATED    16   1   0   3
  PTPN23 WILD-TYPE 295  13  15  21
D864V10, multiclass
    clus
vv   PTPN23 MUTATED PTPN23 WILD-TYPE
  R0             16              295
  R1              1               13
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D864V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PTPN23 MUTATED       2                         1
  PTPN23 WILD-TYPE    85                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPN23 MUTATED                                           0    13
  PTPN23 WILD-TYPE                                         1   230
D864V12, multiclass
                                           clus
vv                                          PTPN23 MUTATED PTPN23 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 13              230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D864V13, binary
                  cls
clus                 0   1
  PTPN23 MUTATED     0  15
  PTPN23 WILD-TYPE   4 295
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN23 MUTATED      0   15
  PTPN23 WILD-TYPE    4  295
                        clus
vv                       PTPN23 MUTATED PTPN23 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             15              295
[1] 2 2
[1] FALSE

Clustering(865) Variable = ADAM7 MUTATION ANALYSIS
D865V1, survival
                 sevent
clus2               0   1
  ADAM7 MUTATED    10   3
  ADAM7 WILD-TYPE 220 136
  ADAM7 MUTATED ADAM7 WILD-TYPE 
             13             356 
  ADAM7 MUTATED ADAM7 WILD-TYPE 
              3             136 
$`ADAM7 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8367 TCGA-BR-8372 TCGA-D7-5579 
       26.70        34.68        35.84        26.33        31.27        20.91 
TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-RD-A7C1 TCGA-SW-A7EA 
       11.08        30.51        24.20         0.10        16.67        19.04 
TCGA-VQ-A8P2 
       38.14 

$`ADAM7 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-8368 
       31.10         0.26        22.19        17.52         0.95         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-D7-6518 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-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-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-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 

  ADAM7 MUTATED ADAM7 WILD-TYPE 
            0.1             0.0 
  ADAM7 MUTATED ADAM7 WILD-TYPE 
          38.14          122.30 
  ADAM7 MUTATED ADAM7 WILD-TYPE 
          26.33           14.04 
[1] "0.1 - 38.1 (26.3)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "2.3"
D865V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADAM7 MUTATED         0        1        4        0         2         1
  ADAM7 WILD-TYPE       2       14       36       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM7 MUTATED           0          3          1          3        0
  ADAM7 WILD-TYPE         3         67         52         29       38
D865V3, multiclass
            clus
vv           ADAM7 MUTATED ADAM7 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               4              36
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             3              29
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ADAM7 MUTATED     1   4   4   6
  ADAM7 WILD-TYPE  21  88 169  91
D865V4, multiclass
    clus
vv   ADAM7 MUTATED ADAM7 WILD-TYPE
  T1             1              21
  T2             4              88
  T3             4             169
  T4             6              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
  ADAM7 MUTATED     9   1   2   3
  ADAM7 WILD-TYPE 109 103  75  74
D865V5, multiclass
    clus
vv   ADAM7 MUTATED ADAM7 WILD-TYPE
  N0             9             109
  N1             1             103
  N2             2              75
  N3             3              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"
D865V6, binary
                 cls
clus                0   1
  ADAM7 MUTATED    16   0
  ADAM7 WILD-TYPE 330  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADAM7 MUTATED     16    0
  ADAM7 WILD-TYPE  330   29
   clus
vv  ADAM7 MUTATED ADAM7 WILD-TYPE
  0            16             330
  1             0              29
[1] 2 2
[1] FALSE
D865V7, binary
                 cls
clus                0   1
  ADAM7 MUTATED     8   8
  ADAM7 WILD-TYPE 137 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADAM7 MUTATED      8    8
  ADAM7 WILD-TYPE  137  240
        clus
vv       ADAM7 MUTATED ADAM7 WILD-TYPE
  FEMALE             8             137
  MALE               8             240
[1] 2 2
[1] FALSE
D865V8, binary
                 cls
clus                0   1
  ADAM7 MUTATED    10   3
  ADAM7 WILD-TYPE 282  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADAM7 MUTATED     10    3
  ADAM7 WILD-TYPE  282   56
     clus
vv    ADAM7 MUTATED ADAM7 WILD-TYPE
  NO             10             282
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ADAM7 MUTATED                                          0
  ADAM7 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ADAM7 MUTATED                                       3
  ADAM7 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ADAM7 MUTATED                                                        7
  ADAM7 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ADAM7 MUTATED                                                   3
  ADAM7 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ADAM7 MUTATED                                                                   1
  ADAM7 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ADAM7 MUTATED                                                    0
  ADAM7 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ADAM7 MUTATED                                                  2
  ADAM7 WILD-TYPE                                               59
D865V9, multiclass
                                                                   clus
vv                                                                  ADAM7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  ADAM7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ADAM7 MUTATED    12   2   0   2
  ADAM7 WILD-TYPE 299  12  15  22
D865V10, multiclass
    clus
vv   ADAM7 MUTATED ADAM7 WILD-TYPE
  R0            12             299
  R1             2              12
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D865V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ADAM7 MUTATED       2                         1
  ADAM7 WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ADAM7 MUTATED                                           0    11
  ADAM7 WILD-TYPE                                         1   232
D865V12, multiclass
                                           clus
vv                                          ADAM7 MUTATED ADAM7 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D865V13, binary
                 cls
clus                0   1
  ADAM7 MUTATED     0  13
  ADAM7 WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADAM7 MUTATED      0   13
  ADAM7 WILD-TYPE    4  297
                        clus
vv                       ADAM7 MUTATED ADAM7 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(866) Variable = NOP2 MUTATION ANALYSIS
D866V1, survival
                sevent
clus2              0   1
  NOP2 MUTATED     6   2
  NOP2 WILD-TYPE 224 137
  NOP2 MUTATED NOP2 WILD-TYPE 
             8            361 
  NOP2 MUTATED NOP2 WILD-TYPE 
             2            137 
$`NOP2 MUTATED`
TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8487 TCGA-CD-A4MI TCGA-HF-7132 TCGA-HU-A4H8 
        3.32        31.27         1.12        11.77        77.29        14.07 
TCGA-VQ-A8P2 TCGA-VQ-AA6G 
       38.14        26.04 

$`NOP2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8371 
       17.52         0.95        26.33         4.31        14.04        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-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-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-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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       38.93        32.94        54.12        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       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 
        20.055         14.270 
[1] "1.1 - 77.3 (20.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.9"
D866V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NOP2 MUTATED         0        0        1        1         2         0
  NOP2 WILD-TYPE       2       15       39       29        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOP2 MUTATED           0          2          1          1        0
  NOP2 WILD-TYPE         3         68         52         31       38
D866V3, multiclass
            clus
vv           NOP2 MUTATED NOP2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOP2 MUTATED     1   1   4   2
  NOP2 WILD-TYPE  21  91 169  95
D866V4, multiclass
    clus
vv   NOP2 MUTATED NOP2 WILD-TYPE
  T1            1             21
  T2            1             91
  T3            4            169
  T4            2             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
  NOP2 MUTATED     2   4   0   2
  NOP2 WILD-TYPE 116 100  77  75
D866V5, multiclass
    clus
vv   NOP2 MUTATED NOP2 WILD-TYPE
  N0            2            116
  N1            4            100
  N2            0             77
  N3            2             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"
D866V6, binary
                cls
clus               0   1
  NOP2 MUTATED     8   0
  NOP2 WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOP2 MUTATED      8    0
  NOP2 WILD-TYPE  338   29
   clus
vv  NOP2 MUTATED NOP2 WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D866V7, binary
                cls
clus               0   1
  NOP2 MUTATED     1   7
  NOP2 WILD-TYPE 144 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOP2 MUTATED      1    7
  NOP2 WILD-TYPE  144  241
        clus
vv       NOP2 MUTATED NOP2 WILD-TYPE
  FEMALE            1            144
  MALE              7            241
[1] 2 2
[1] FALSE
D866V8, binary
                cls
clus               0   1
  NOP2 MUTATED     6   2
  NOP2 WILD-TYPE 286  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOP2 MUTATED      6    2
  NOP2 WILD-TYPE  286   57
     clus
vv    NOP2 MUTATED NOP2 WILD-TYPE
  NO             6            286
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NOP2 MUTATED                                          0
  NOP2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NOP2 MUTATED                                       1
  NOP2 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NOP2 MUTATED                                                        3
  NOP2 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NOP2 MUTATED                                                   2
  NOP2 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NOP2 MUTATED                                                                   1
  NOP2 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NOP2 MUTATED                                                    0
  NOP2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NOP2 MUTATED                                                  1
  NOP2 WILD-TYPE                                               60
D866V9, multiclass
                                                                   clus
vv                                                                  NOP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  NOP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NOP2 MUTATED     7   0   0   0
  NOP2 WILD-TYPE 304  14  15  24
D866V10, multiclass
    clus
vv   NOP2 MUTATED NOP2 WILD-TYPE
  R0            7            304
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D866V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NOP2 MUTATED       2                         0
  NOP2 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NOP2 MUTATED                                           0     5
  NOP2 WILD-TYPE                                         1   238
D866V12, multiclass
                                           clus
vv                                          NOP2 MUTATED NOP2 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D866V13, binary
                cls
clus               0   1
  NOP2 MUTATED     0   5
  NOP2 WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOP2 MUTATED      0    5
  NOP2 WILD-TYPE    4  305
                        clus
vv                       NOP2 MUTATED NOP2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(867) Variable = FAM26E MUTATION ANALYSIS
D867V1, survival
                  sevent
clus2                0   1
  FAM26E MUTATED     2   1
  FAM26E WILD-TYPE 228 138
  FAM26E MUTATED FAM26E WILD-TYPE 
               3              366 
  FAM26E MUTATED FAM26E WILD-TYPE 
               1              138 
$`FAM26E MUTATED`
TCGA-BR-6566 TCGA-D7-A6EY TCGA-HU-8602 
       32.78        11.44        22.32 

$`FAM26E WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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            14.22 
[1] "11.4 - 32.8 (22.3)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.5"
D867V2, 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       2       15       40       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM26E MUTATED           0          0          1          0        0
  FAM26E WILD-TYPE         3         70         52         32       38
D867V3, multiclass
            clus
vv           FAM26E MUTATED FAM26E WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM26E MUTATED     0   0   2   1
  FAM26E WILD-TYPE  22  92 171  96
D867V4, multiclass
    clus
vv   FAM26E MUTATED FAM26E WILD-TYPE
  T1              0               22
  T2              0               92
  T3              2              171
  T4              1               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
  FAM26E MUTATED     2   0   0   1
  FAM26E WILD-TYPE 116 104  77  76
D867V5, multiclass
    clus
vv   FAM26E MUTATED FAM26E WILD-TYPE
  N0              2              116
  N1              0              104
  N2              0               77
  N3              1               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"
D867V6, binary
                  cls
clus                 0   1
  FAM26E MUTATED     3   0
  FAM26E WILD-TYPE 343  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      3    0
  FAM26E WILD-TYPE  343   29
   clus
vv  FAM26E MUTATED FAM26E WILD-TYPE
  0              3              343
  1              0               29
[1] 2 2
[1] FALSE
D867V7, binary
                  cls
clus                 0   1
  FAM26E MUTATED     3   0
  FAM26E WILD-TYPE 142 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      3    0
  FAM26E WILD-TYPE  142  248
        clus
vv       FAM26E MUTATED FAM26E WILD-TYPE
  FEMALE              3              142
  MALE                0              248
[1] 2 2
[1] FALSE
D867V8, binary
                  cls
clus                 0   1
  FAM26E MUTATED     3   0
  FAM26E WILD-TYPE 289  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      3    0
  FAM26E WILD-TYPE  289   59
     clus
vv    FAM26E MUTATED FAM26E WILD-TYPE
  NO               3              289
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM26E MUTATED                                          0
  FAM26E WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM26E MUTATED                                       1
  FAM26E WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM26E MUTATED                                                        1
  FAM26E WILD-TYPE                                                    157
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM26E MUTATED                                                   0
  FAM26E WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM26E MUTATED                                                                   0
  FAM26E WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM26E MUTATED                                                    0
  FAM26E WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM26E MUTATED                                                  1
  FAM26E WILD-TYPE                                               60
D867V9, multiclass
                                                                   clus
vv                                                                  FAM26E MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  FAM26E WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAM26E MUTATED     3   0   0   0
  FAM26E WILD-TYPE 308  14  15  24
D867V10, multiclass
    clus
vv   FAM26E MUTATED FAM26E WILD-TYPE
  R0              3              308
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D867V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAM26E MUTATED       1                         0
  FAM26E WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM26E MUTATED                                           0     2
  FAM26E WILD-TYPE                                         1   241
D867V12, multiclass
                                           clus
vv                                          FAM26E MUTATED FAM26E WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D867V13, binary
                  cls
clus                 0   1
  FAM26E MUTATED     0   3
  FAM26E WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      0    3
  FAM26E WILD-TYPE    4  307
                        clus
vv                       FAM26E MUTATED FAM26E WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(868) Variable = OTX2 MUTATION ANALYSIS
D868V1, survival
                sevent
clus2              0   1
  OTX2 MUTATED     4   2
  OTX2 WILD-TYPE 226 137
  OTX2 MUTATED OTX2 WILD-TYPE 
             6            363 
  OTX2 MUTATED OTX2 WILD-TYPE 
             2            137 
$`OTX2 MUTATED`
TCGA-BR-6452 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5723 TCGA-HU-A4H8 TCGA-VQ-A8P2 
       34.68        16.14         6.58       105.07        14.07        38.14 

$`OTX2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  OTX2 MUTATED OTX2 WILD-TYPE 
          6.58           0.00 
  OTX2 MUTATED OTX2 WILD-TYPE 
        105.07         122.30 
  OTX2 MUTATED OTX2 WILD-TYPE 
         25.41          14.17 
[1] "6.6 - 105.1 (25.4)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.7"
D868V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OTX2 MUTATED         0        0        1        1         2         0
  OTX2 WILD-TYPE       2       15       39       29        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OTX2 MUTATED           0          2          1          0        1
  OTX2 WILD-TYPE         3         68         52         32       37
D868V3, multiclass
            clus
vv           OTX2 MUTATED OTX2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OTX2 MUTATED     1   1   3   3
  OTX2 WILD-TYPE  21  91 170  94
D868V4, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  T1            1             21
  T2            1             91
  T3            3            170
  T4            3             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
  OTX2 MUTATED     3   3   1   1
  OTX2 WILD-TYPE 115 101  76  76
D868V5, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  N0            3            115
  N1            3            101
  N2            1             76
  N3            1             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"
D868V6, binary
                cls
clus               0   1
  OTX2 MUTATED     9   0
  OTX2 WILD-TYPE 337  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      9    0
  OTX2 WILD-TYPE  337   29
   clus
vv  OTX2 MUTATED OTX2 WILD-TYPE
  0            9            337
  1            0             29
[1] 2 2
[1] FALSE
D868V7, binary
                cls
clus               0   1
  OTX2 MUTATED     5   4
  OTX2 WILD-TYPE 140 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      5    4
  OTX2 WILD-TYPE  140  244
        clus
vv       OTX2 MUTATED OTX2 WILD-TYPE
  FEMALE            5            140
  MALE              4            244
[1] 2 2
[1] FALSE
D868V8, binary
                cls
clus               0   1
  OTX2 MUTATED     5   1
  OTX2 WILD-TYPE 287  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      5    1
  OTX2 WILD-TYPE  287   58
     clus
vv    OTX2 MUTATED OTX2 WILD-TYPE
  NO             5            287
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OTX2 MUTATED                                          0
  OTX2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OTX2 MUTATED                                       1
  OTX2 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OTX2 MUTATED                                                        6
  OTX2 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OTX2 MUTATED                                                   1
  OTX2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OTX2 MUTATED                                                                   0
  OTX2 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OTX2 MUTATED                                                    0
  OTX2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OTX2 MUTATED                                                  1
  OTX2 WILD-TYPE                                               60
D868V9, multiclass
                                                                   clus
vv                                                                  OTX2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  OTX2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  OTX2 MUTATED     5   0   0   3
  OTX2 WILD-TYPE 306  14  15  21
D868V10, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  R0            5            306
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D868V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  OTX2 MUTATED       2                         0
  OTX2 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OTX2 MUTATED                                           0     6
  OTX2 WILD-TYPE                                         1   237
D868V12, multiclass
                                           clus
vv                                          OTX2 MUTATED OTX2 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D868V13, binary
                cls
clus               0   1
  OTX2 MUTATED     0   7
  OTX2 WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      0    7
  OTX2 WILD-TYPE    4  303
                        clus
vv                       OTX2 MUTATED OTX2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(869) Variable = TMEM116 MUTATION ANALYSIS
D869V1, survival
                   sevent
clus2                 0   1
  TMEM116 MUTATED     0   3
  TMEM116 WILD-TYPE 230 136
  TMEM116 MUTATED TMEM116 WILD-TYPE 
                3               366 
  TMEM116 MUTATED TMEM116 WILD-TYPE 
                3               136 
$`TMEM116 MUTATED`
TCGA-BR-4184 TCGA-BR-A4QL TCGA-VQ-A91U 
        6.97        16.14         1.71 

$`TMEM116 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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             14.35 
[1] "1.7 - 16.1 (7.0)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "5.8"
D869V2, 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       2       15       40       30        37        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM116 MUTATED           0          2          1          0        0
  TMEM116 WILD-TYPE         3         68         52         32       38
D869V3, multiclass
            clus
vv           TMEM116 MUTATED TMEM116 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                0                37
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM116 MUTATED     0   0   3   0
  TMEM116 WILD-TYPE  22  92 170  97
D869V4, multiclass
    clus
vv   TMEM116 MUTATED TMEM116 WILD-TYPE
  T1               0                22
  T2               0                92
  T3               3               170
  T4               0                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
  TMEM116 MUTATED     0   2   0   1
  TMEM116 WILD-TYPE 118 102  77  76
D869V5, multiclass
    clus
vv   TMEM116 MUTATED TMEM116 WILD-TYPE
  N0               0               118
  N1               2               102
  N2               0                77
  N3               1                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"
D869V6, binary
                   cls
clus                  0   1
  TMEM116 MUTATED     2   0
  TMEM116 WILD-TYPE 344  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM116 MUTATED      2    0
  TMEM116 WILD-TYPE  344   29
   clus
vv  TMEM116 MUTATED TMEM116 WILD-TYPE
  0               2               344
  1               0                29
[1] 2 2
[1] FALSE
D869V7, binary
                   cls
clus                  0   1
  TMEM116 MUTATED     1   2
  TMEM116 WILD-TYPE 144 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM116 MUTATED      1    2
  TMEM116 WILD-TYPE  144  246
        clus
vv       TMEM116 MUTATED TMEM116 WILD-TYPE
  FEMALE               1               144
  MALE                 2               246
[1] 2 2
[1] FALSE
D869V8, binary
                   cls
clus                  0   1
  TMEM116 MUTATED     3   0
  TMEM116 WILD-TYPE 289  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM116 MUTATED      3    0
  TMEM116 WILD-TYPE  289   59
     clus
vv    TMEM116 MUTATED TMEM116 WILD-TYPE
  NO                3               289
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TMEM116 MUTATED                                          0
  TMEM116 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TMEM116 MUTATED                                       0
  TMEM116 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM116 MUTATED                                                        2
  TMEM116 WILD-TYPE                                                    156
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TMEM116 MUTATED                                                   0
  TMEM116 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM116 MUTATED                                                                   1
  TMEM116 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TMEM116 MUTATED                                                    0
  TMEM116 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TMEM116 MUTATED                                                  0
  TMEM116 WILD-TYPE                                               61
D869V9, multiclass
                                                                   clus
vv                                                                  TMEM116 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  TMEM116 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM116 MUTATED     2   0   0   1
  TMEM116 WILD-TYPE 309  14  15  23
D869V10, multiclass
    clus
vv   TMEM116 MUTATED TMEM116 WILD-TYPE
  R0               2               309
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D869V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM116 MUTATED       1                         0
  TMEM116 WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM116 MUTATED                                           0     2
  TMEM116 WILD-TYPE                                         1   241
D869V12, multiclass
                                           clus
vv                                          TMEM116 MUTATED TMEM116 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D869V13, binary
                   cls
clus                  0   1
  TMEM116 MUTATED     0   2
  TMEM116 WILD-TYPE   4 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM116 MUTATED      0    2
  TMEM116 WILD-TYPE    4  308
                        clus
vv                       TMEM116 MUTATED TMEM116 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               2               308
[1] 2 2
[1] FALSE

Clustering(870) Variable = IRS4 MUTATION ANALYSIS
D870V1, survival
                sevent
clus2              0   1
  IRS4 MUTATED    15   5
  IRS4 WILD-TYPE 215 134
  IRS4 MUTATED IRS4 WILD-TYPE 
            20            349 
  IRS4 MUTATED IRS4 WILD-TYPE 
             5            134 
$`IRS4 MUTATED`
TCGA-B7-5818 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8382 TCGA-BR-8680 
       11.70         9.67        34.68        35.84        25.05        31.96 
TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6526 TCGA-FP-7998 TCGA-HU-8602 TCGA-HU-A4GP 
      105.07        21.07        17.19        22.29        22.32         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-IN-A6RJ TCGA-MX-A5UJ 
        0.10         6.51         2.10        29.00        12.46        19.73 
TCGA-VQ-A8DU TCGA-VQ-A8P2 
        5.46        38.14 

$`IRS4 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-A4GU 
       22.75        25.81        11.77        21.37        29.98         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
       20.25         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-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38        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 

  IRS4 MUTATED IRS4 WILD-TYPE 
           0.1            0.0 
  IRS4 MUTATED IRS4 WILD-TYPE 
        105.07         122.30 
  IRS4 MUTATED IRS4 WILD-TYPE 
         20.40          14.07 
[1] "0.1 - 105.1 (20.4)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D870V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IRS4 MUTATED         0        1        2        1         3         1
  IRS4 WILD-TYPE       2       14       38       29        34        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IRS4 MUTATED           0          6          0          6        1
  IRS4 WILD-TYPE         3         64         53         26       37
D870V3, multiclass
            clus
vv           IRS4 MUTATED IRS4 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              2             38
  STAGE II              1             29
  STAGE IIA             3             34
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            6             64
  STAGE IIIB            0             53
  STAGE IIIC            6             26
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IRS4 MUTATED     2   5   5  10
  IRS4 WILD-TYPE  20  87 168  87
D870V4, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  T1            2             20
  T2            5             87
  T3            5            168
  T4           10             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
  IRS4 MUTATED     7   4   6   5
  IRS4 WILD-TYPE 111 100  71  72
D870V5, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  N0            7            111
  N1            4            100
  N2            6             71
  N3            5             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"
D870V6, binary
                cls
clus               0   1
  IRS4 MUTATED    22   1
  IRS4 WILD-TYPE 324  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     22    1
  IRS4 WILD-TYPE  324   28
   clus
vv  IRS4 MUTATED IRS4 WILD-TYPE
  0           22            324
  1            1             28
[1] 2 2
[1] FALSE
D870V7, binary
                cls
clus               0   1
  IRS4 MUTATED    15   9
  IRS4 WILD-TYPE 130 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     15    9
  IRS4 WILD-TYPE  130  239
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  FEMALE           15            130
  MALE              9            239
[1] 2 2
[1] FALSE
D870V8, binary
                cls
clus               0   1
  IRS4 MUTATED    19   1
  IRS4 WILD-TYPE 273  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     19    1
  IRS4 WILD-TYPE  273   58
     clus
vv    IRS4 MUTATED IRS4 WILD-TYPE
  NO            19            273
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IRS4 MUTATED                                          0
  IRS4 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IRS4 MUTATED                                       6
  IRS4 WILD-TYPE                                    64
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IRS4 MUTATED                                                       10
  IRS4 WILD-TYPE                                                    148
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IRS4 MUTATED                                                   1
  IRS4 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IRS4 MUTATED                                                                   1
  IRS4 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IRS4 MUTATED                                                    0
  IRS4 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IRS4 MUTATED                                                  6
  IRS4 WILD-TYPE                                               55
D870V9, multiclass
                                                                   clus
vv                                                                  IRS4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             6
                                                                   clus
vv                                                                  IRS4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IRS4 MUTATED    20   0   0   4
  IRS4 WILD-TYPE 291  14  15  20
D870V10, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  R0           20            291
  R1            0             14
  R2            0             15
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D870V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IRS4 MUTATED       7                         0
  IRS4 WILD-TYPE    80                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IRS4 MUTATED                                           0    15
  IRS4 WILD-TYPE                                         1   228
D870V12, multiclass
                                           clus
vv                                          IRS4 MUTATED IRS4 WILD-TYPE
  ASIAN                                                7             80
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               15            228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D870V13, binary
                cls
clus               0   1
  IRS4 MUTATED     1  19
  IRS4 WILD-TYPE   3 291
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      1   19
  IRS4 WILD-TYPE    3  291
                        clus
vv                       IRS4 MUTATED IRS4 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           19            291
[1] 2 2
[1] FALSE

Clustering(871) Variable = C9ORF152 MUTATION ANALYSIS
D871V1, survival
                    sevent
clus2                  0   1
  C9ORF152 MUTATED     0   3
  C9ORF152 WILD-TYPE 230 136
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
                 3                366 
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
                 3                136 
$`C9ORF152 MUTATED`
TCGA-BR-4257 TCGA-BR-8284 TCGA-D7-A6EZ 
        9.67         8.05        20.32 

$`C9ORF152 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-D7-8573 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-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 

  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
              8.05               0.00 
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
             20.32             122.30 
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
              9.67              14.35 
[1] "8.1 - 20.3 (9.7)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "3.6"
D871V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C9ORF152 MUTATED         0        0        0        0         0         0
  C9ORF152 WILD-TYPE       2       15       40       30        37        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF152 MUTATED           0          1          0          1        0
  C9ORF152 WILD-TYPE         3         69         53         31       38
D871V3, multiclass
[1] "Remove cluster labels:" "C9ORF152 MUTATED"      
clus
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
                 2                370 
        TCGA-CG-4444         TCGA-CG-4460         TCGA-CG-4475 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-5716         TCGA-CG-5727 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-EQ-A4SO         TCGA-F1-6177         TCGA-FP-A8CX 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HF-7131         TCGA-KB-A93G         TCGA-MX-A663 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-B7-A5TI 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-B7-A5TJ         TCGA-B7-A5TK         TCGA-B7-A5TN 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4183         TCGA-BR-4184         TCGA-BR-4253 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4255         TCGA-BR-4267         TCGA-BR-4279 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4280         TCGA-BR-4361         TCGA-BR-4368 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6452         TCGA-BR-6453         TCGA-BR-6454 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6456         TCGA-BR-6457 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6458         TCGA-BR-6563         TCGA-BR-6564 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6565         TCGA-BR-6566         TCGA-BR-6705 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6706         TCGA-BR-6707         TCGA-BR-6709 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6710         TCGA-BR-6801         TCGA-BR-6802 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6803         TCGA-BR-6852         TCGA-BR-7196 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7197         TCGA-BR-7703         TCGA-BR-7704 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7707         TCGA-BR-7715         TCGA-BR-7716 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7717         TCGA-BR-7722         TCGA-BR-7723 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7851         TCGA-BR-7901         TCGA-BR-7957 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7958         TCGA-BR-7959         TCGA-BR-8058 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8059         TCGA-BR-8060         TCGA-BR-8077 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8078         TCGA-BR-8080         TCGA-BR-8081 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8285         TCGA-BR-8286         TCGA-BR-8289 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8291         TCGA-BR-8295         TCGA-BR-8297 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8360         TCGA-BR-8361         TCGA-BR-8363 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8364         TCGA-BR-8365         TCGA-BR-8366 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8367         TCGA-BR-8368         TCGA-BR-8369 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8370         TCGA-BR-8371         TCGA-BR-8372 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8373         TCGA-BR-8380         TCGA-BR-8381 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8382         TCGA-BR-8384         TCGA-BR-8483 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8484         TCGA-BR-8485         TCGA-BR-8486 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8487         TCGA-BR-8588         TCGA-BR-8589 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8590         TCGA-BR-8591         TCGA-BR-8592 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8676         TCGA-BR-8677         TCGA-BR-8678 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8679         TCGA-BR-8680         TCGA-BR-8682 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8683         TCGA-BR-8686         TCGA-BR-8687 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8690         TCGA-BR-A44T         TCGA-BR-A44U 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A452         TCGA-BR-A453         TCGA-BR-A4CQ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4CR         TCGA-BR-A4CS         TCGA-BR-A4IU 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4IV         TCGA-BR-A4IY         TCGA-BR-A4IZ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4J1         TCGA-BR-A4J2         TCGA-BR-A4J4 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4J5         TCGA-BR-A4J6         TCGA-BR-A4J7 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4J8         TCGA-BR-A4PD         TCGA-BR-A4PE 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4QM         TCGA-CD-5798         TCGA-CD-5799 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-5803         TCGA-CD-5813         TCGA-CD-8524 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8525         TCGA-CD-8526         TCGA-CD-8527 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8528         TCGA-CD-8529         TCGA-CD-8530 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8531         TCGA-CD-8532         TCGA-CD-8533 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8534         TCGA-CD-8535         TCGA-CD-8536 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-A486         TCGA-CD-A487         TCGA-CD-A489 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-A48A         TCGA-CD-A48C         TCGA-CD-A4MG 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-A4MH         TCGA-CD-A4MI         TCGA-CD-A4MJ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4442         TCGA-CG-4443 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4462 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5717 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6522         TCGA-D7-6524 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-8570         TCGA-D7-8572         TCGA-D7-8573 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-8574         TCGA-D7-8575         TCGA-D7-8576 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-8578         TCGA-D7-8579         TCGA-D7-A4YT 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A4YU         TCGA-D7-A4YV         TCGA-D7-A4YX 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A4YY         TCGA-D7-A4Z0         TCGA-D7-A6ET 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A6EV         TCGA-D7-A6EX         TCGA-D7-A6EY 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A6F0         TCGA-D7-A6F2         TCGA-D7-A747 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A748         TCGA-D7-A74A         TCGA-D7-A74B 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6874 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-F1-6875         TCGA-F1-A448         TCGA-F1-A72C 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-8210         TCGA-FP-8211         TCGA-FP-8631 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-A4BE         TCGA-FP-A4BF         TCGA-HF-7132 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HF-7133         TCGA-HF-7134         TCGA-HF-7136 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HF-A5NB         TCGA-HJ-7597         TCGA-HU-8243 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-8244         TCGA-HU-8249         TCGA-HU-8602 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-8604         TCGA-HU-8608         TCGA-HU-8610 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4G2         TCGA-HU-A4G3         TCGA-HU-A4G6 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4G8         TCGA-HU-A4G9         TCGA-HU-A4GC 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GD         TCGA-HU-A4GF         TCGA-HU-A4GH 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GJ         TCGA-HU-A4GN         TCGA-HU-A4GP 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GQ         TCGA-HU-A4GT         TCGA-HU-A4GU 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GX         TCGA-HU-A4GY         TCGA-HU-A4H0 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4H2         TCGA-HU-A4H3         TCGA-HU-A4H4 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4H5         TCGA-HU-A4H6         TCGA-HU-A4H8 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4HB         TCGA-HU-A4HD         TCGA-IN-7806 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-8462         TCGA-IN-8663         TCGA-IN-A6RI 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A6RJ         TCGA-IN-A6RL         TCGA-IN-A6RN 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A6RO         TCGA-IN-A6RP         TCGA-IN-A6RR 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A6RS         TCGA-IN-A7NR         TCGA-IN-A7NT 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A7NU         TCGA-IN-AB1V         TCGA-IN-AB1X 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IP-7968         TCGA-KB-A6F5         TCGA-KB-A6F7 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-KB-A93J         TCGA-MX-A5UG         TCGA-MX-A5UJ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-MX-A666         TCGA-R5-A7O7         TCGA-R5-A7ZE 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-R5-A7ZF         TCGA-R5-A7ZI         TCGA-R5-A7ZR 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-R5-A804         TCGA-R5-A805         TCGA-RD-A7BS 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A7BT         TCGA-RD-A7BW         TCGA-RD-A7C1 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A8MV         TCGA-RD-A8MW         TCGA-RD-A8N0 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A8N1         TCGA-RD-A8N2         TCGA-RD-A8N4 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A8N5         TCGA-RD-A8N6         TCGA-RD-A8N9 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-SW-A7EA         TCGA-SW-A7EB         TCGA-VQ-A8DL 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8DT         TCGA-VQ-A8DU         TCGA-VQ-A8DV 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8DZ         TCGA-VQ-A8E2         TCGA-VQ-A8E7 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8P2         TCGA-VQ-A8P3         TCGA-VQ-A8PE 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8PK         TCGA-VQ-A8PM         TCGA-VQ-A8PQ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A91Q         TCGA-VQ-A91U         TCGA-VQ-A91V 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A92D         TCGA-VQ-A94T         TCGA-VQ-AA64 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-AA68         TCGA-VQ-AA69         TCGA-VQ-AA6A 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-AA6B         TCGA-VQ-AA6F         TCGA-VQ-AA6G 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-AA6I         TCGA-VQ-AA6J         TCGA-VQ-AA6K 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-ZA-A8F6 
"C9ORF152 WILD-TYPE" 
                    vv
clus                  T1  T2  T3  T4
  C9ORF152 MUTATED     0   0   1   1
  C9ORF152 WILD-TYPE  22  92 172  96
D871V4, multiclass
[1] "Remove cluster labels:" "C9ORF152 MUTATED"      
clus
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
                 2                382 
        TCGA-CG-4444         TCGA-CG-4460         TCGA-CG-4475 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-5716         TCGA-CG-5727 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-EQ-A4SO         TCGA-F1-6177         TCGA-FP-A8CX 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HF-7131         TCGA-KB-A93G         TCGA-MX-A663 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-B7-A5TI 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-B7-A5TJ         TCGA-B7-A5TK         TCGA-B7-A5TN 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4183         TCGA-BR-4184         TCGA-BR-4201 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4267 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4279         TCGA-BR-4280         TCGA-BR-4292 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4294         TCGA-BR-4357         TCGA-BR-4361 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4363         TCGA-BR-4368         TCGA-BR-4371 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6452         TCGA-BR-6453         TCGA-BR-6454 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6456         TCGA-BR-6457 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6458         TCGA-BR-6563         TCGA-BR-6564 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6565         TCGA-BR-6566         TCGA-BR-6705 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6706         TCGA-BR-6707         TCGA-BR-6709 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6710         TCGA-BR-6801         TCGA-BR-6802 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6803         TCGA-BR-6852         TCGA-BR-7196 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7197         TCGA-BR-7703         TCGA-BR-7704 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7707         TCGA-BR-7715         TCGA-BR-7716 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7717         TCGA-BR-7722         TCGA-BR-7723 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7851         TCGA-BR-7901         TCGA-BR-7957 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7958         TCGA-BR-7959         TCGA-BR-8058 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8059         TCGA-BR-8060         TCGA-BR-8077 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8078         TCGA-BR-8080         TCGA-BR-8081 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8285         TCGA-BR-8286         TCGA-BR-8289 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8291         TCGA-BR-8295         TCGA-BR-8297 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8360         TCGA-BR-8361         TCGA-BR-8363 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8364         TCGA-BR-8365         TCGA-BR-8366 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8367         TCGA-BR-8368         TCGA-BR-8369 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8370         TCGA-BR-8371         TCGA-BR-8372 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8373         TCGA-BR-8380         TCGA-BR-8381 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8382         TCGA-BR-8384         TCGA-BR-8483 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8484         TCGA-BR-8485         TCGA-BR-8486 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8487         TCGA-BR-8588         TCGA-BR-8589 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8590         TCGA-BR-8591         TCGA-BR-8592 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8676         TCGA-BR-8677         TCGA-BR-8678 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8679         TCGA-BR-8680         TCGA-BR-8682 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8683         TCGA-BR-8686         TCGA-BR-8687 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8690         TCGA-BR-A44T         TCGA-BR-A44U 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A452         TCGA-BR-A453         TCGA-BR-A4CQ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4CR         TCGA-BR-A4CS         TCGA-BR-A4IU 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4IV         TCGA-BR-A4IY         TCGA-BR-A4IZ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4J1         TCGA-BR-A4J2         TCGA-BR-A4J4 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4J5         TCGA-BR-A4J6         TCGA-BR-A4J7 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4J8         TCGA-BR-A4PD         TCGA-BR-A4PE 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4QM         TCGA-CD-5798         TCGA-CD-5799 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-5803         TCGA-CD-5804         TCGA-CD-5813 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8524         TCGA-CD-8525         TCGA-CD-8526 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8527         TCGA-CD-8528         TCGA-CD-8529 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8530         TCGA-CD-8531         TCGA-CD-8532 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8533         TCGA-CD-8534         TCGA-CD-8535 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8536         TCGA-CD-A486         TCGA-CD-A487 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-A489         TCGA-CD-A48A         TCGA-CD-A48C 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-A4MG         TCGA-CD-A4MH         TCGA-CD-A4MI 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-A4MJ         TCGA-CG-4300         TCGA-CG-4301 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4442 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4449         TCGA-CG-4455 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4474         TCGA-CG-4477 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5728         TCGA-CG-5730 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-8570         TCGA-D7-8572         TCGA-D7-8573 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-8574         TCGA-D7-8575         TCGA-D7-8576 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-8578         TCGA-D7-8579         TCGA-D7-A4YT 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A4YU         TCGA-D7-A4YV         TCGA-D7-A4YX 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A4YY         TCGA-D7-A4Z0         TCGA-D7-A6ET 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A6EV         TCGA-D7-A6EX         TCGA-D7-A6EY 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A6F0         TCGA-D7-A6F2         TCGA-D7-A747 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A748         TCGA-D7-A74A         TCGA-D7-A74B 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6874 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-F1-6875         TCGA-F1-A448         TCGA-F1-A72C 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-8210         TCGA-FP-8211         TCGA-FP-8631 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-A4BE         TCGA-FP-A4BF         TCGA-FP-A9TM 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HF-7132         TCGA-HF-7133         TCGA-HF-7134 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HF-7136         TCGA-HF-A5NB         TCGA-HJ-7597 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-8238         TCGA-HU-8243         TCGA-HU-8244 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-8249         TCGA-HU-8602         TCGA-HU-8604 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-8608         TCGA-HU-8610         TCGA-HU-A4G2 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4G3         TCGA-HU-A4G6         TCGA-HU-A4G8 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4G9         TCGA-HU-A4GC         TCGA-HU-A4GD 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GF         TCGA-HU-A4GH         TCGA-HU-A4GJ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GN         TCGA-HU-A4GP         TCGA-HU-A4GQ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GT         TCGA-HU-A4GU         TCGA-HU-A4GX 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GY         TCGA-HU-A4H0         TCGA-HU-A4H2 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4H3         TCGA-HU-A4H4         TCGA-HU-A4H5 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4H6         TCGA-HU-A4H8         TCGA-HU-A4HB 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4HD         TCGA-IN-7806         TCGA-IN-7808 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-8462         TCGA-IN-8663         TCGA-IN-A6RI 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A6RJ         TCGA-IN-A6RL         TCGA-IN-A6RN 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A6RO         TCGA-IN-A6RP         TCGA-IN-A6RR 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A6RS         TCGA-IN-A7NR         TCGA-IN-A7NT 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A7NU         TCGA-IN-AB1V         TCGA-IN-AB1X 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IP-7968         TCGA-KB-A6F5         TCGA-KB-A6F7 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-KB-A93J         TCGA-MX-A5UG         TCGA-MX-A5UJ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-MX-A666         TCGA-R5-A7O7         TCGA-R5-A7ZE 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-R5-A7ZF         TCGA-R5-A7ZI         TCGA-R5-A7ZR 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-R5-A804         TCGA-R5-A805         TCGA-RD-A7BS 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A7BT         TCGA-RD-A7BW         TCGA-RD-A7C1 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A8MV         TCGA-RD-A8MW         TCGA-RD-A8N0 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A8N1         TCGA-RD-A8N2         TCGA-RD-A8N4 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A8N5         TCGA-RD-A8N6         TCGA-RD-A8N9 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-SW-A7EA         TCGA-SW-A7EB         TCGA-VQ-A8DL 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8DT         TCGA-VQ-A8DU         TCGA-VQ-A8DV 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8DZ         TCGA-VQ-A8E2         TCGA-VQ-A8E7 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8P2         TCGA-VQ-A8P3         TCGA-VQ-A8PE 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8PK         TCGA-VQ-A8PM         TCGA-VQ-A8PQ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A91Q         TCGA-VQ-A91U         TCGA-VQ-A91V 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A92D         TCGA-VQ-A94T         TCGA-VQ-AA64 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-AA68         TCGA-VQ-AA69         TCGA-VQ-AA6A 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-AA6B         TCGA-VQ-AA6F         TCGA-VQ-AA6G 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-AA6I         TCGA-VQ-AA6J         TCGA-VQ-AA6K 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-ZA-A8F6 
"C9ORF152 WILD-TYPE" 
                    vv
clus                  N0  N1  N2  N3
  C9ORF152 MUTATED     0   0   1   1
  C9ORF152 WILD-TYPE 118 104  76  76
D871V5, multiclass
[1] "Remove cluster labels:" "C9ORF152 MUTATED"      
clus
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
                 2                374 
        TCGA-CG-4444         TCGA-CG-4460         TCGA-CG-4475 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-5716         TCGA-CG-5727 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-EQ-A4SO         TCGA-F1-6177         TCGA-FP-A8CX 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HF-7131         TCGA-KB-A93G         TCGA-MX-A663 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-B7-A5TI 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4183         TCGA-BR-4184         TCGA-BR-4188 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4191         TCGA-BR-4253         TCGA-BR-4255 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4256         TCGA-BR-4267         TCGA-BR-4279 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4280         TCGA-BR-4361         TCGA-BR-4362 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4368         TCGA-BR-6452         TCGA-BR-6453 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6454         TCGA-BR-6455         TCGA-BR-6456 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6457         TCGA-BR-6458         TCGA-BR-6563 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6564         TCGA-BR-6565         TCGA-BR-6566 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6705         TCGA-BR-6706         TCGA-BR-6707 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6709         TCGA-BR-6710         TCGA-BR-6801 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6802         TCGA-BR-6803         TCGA-BR-6852 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7196         TCGA-BR-7197         TCGA-BR-7703 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7704         TCGA-BR-7707         TCGA-BR-7715 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7716         TCGA-BR-7717         TCGA-BR-7722 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7723         TCGA-BR-7851         TCGA-BR-7901 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7957         TCGA-BR-7958         TCGA-BR-7959 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8058         TCGA-BR-8059         TCGA-BR-8060 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8285         TCGA-BR-8286 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8289         TCGA-BR-8291         TCGA-BR-8295 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8297         TCGA-BR-8360         TCGA-BR-8361 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8363         TCGA-BR-8364         TCGA-BR-8365 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8366         TCGA-BR-8367         TCGA-BR-8368 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8369         TCGA-BR-8370         TCGA-BR-8371 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8372         TCGA-BR-8373         TCGA-BR-8380 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8381         TCGA-BR-8382         TCGA-BR-8384 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8483         TCGA-BR-8484         TCGA-BR-8485 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8486         TCGA-BR-8487         TCGA-BR-8588 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8589         TCGA-BR-8590         TCGA-BR-8591 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-8676         TCGA-BR-8677 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8678         TCGA-BR-8679         TCGA-BR-8680 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8682         TCGA-BR-8683         TCGA-BR-8686 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8687         TCGA-BR-8690         TCGA-BR-A44T 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A44U         TCGA-BR-A452         TCGA-BR-A453 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4CQ         TCGA-BR-A4CR         TCGA-BR-A4CS 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4IU         TCGA-BR-A4IV         TCGA-BR-A4IY 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4IZ         TCGA-BR-A4J1         TCGA-BR-A4J2 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4J4         TCGA-BR-A4J5         TCGA-BR-A4J6 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4J8         TCGA-BR-A4PD         TCGA-BR-A4PE 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4QM         TCGA-CD-5798         TCGA-CD-5799 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-5803         TCGA-CD-5804         TCGA-CD-5813 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8524         TCGA-CD-8525         TCGA-CD-8526 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8527         TCGA-CD-8528         TCGA-CD-8529 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8530         TCGA-CD-8531         TCGA-CD-8532 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8533         TCGA-CD-8534         TCGA-CD-8535 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8536         TCGA-CD-A486         TCGA-CD-A487 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-A489         TCGA-CD-A48A         TCGA-CD-A48C 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-A4MG         TCGA-CD-A4MH         TCGA-CD-A4MI 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-A4MJ         TCGA-CG-4300         TCGA-CG-4301 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4442 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4449         TCGA-CG-4455 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4474         TCGA-CG-4477 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5728         TCGA-CG-5730 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-8570         TCGA-D7-8572         TCGA-D7-8573 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-8574         TCGA-D7-8575         TCGA-D7-8576 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-8578         TCGA-D7-8579         TCGA-D7-A4YT 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A4YU         TCGA-D7-A4YV         TCGA-D7-A4YX 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A4YY         TCGA-D7-A4Z0         TCGA-D7-A6ET 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A6EV         TCGA-D7-A6EX         TCGA-D7-A6EY 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A6F0         TCGA-D7-A6F2         TCGA-D7-A747 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A748         TCGA-D7-A74A         TCGA-D7-A74B 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6874 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-F1-6875         TCGA-F1-A448         TCGA-F1-A72C 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-8210         TCGA-FP-8211         TCGA-FP-8631 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-A4BE         TCGA-FP-A4BF         TCGA-FP-A9TM 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HF-7132         TCGA-HF-7133         TCGA-HF-7134 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HF-7136         TCGA-HF-A5NB         TCGA-HJ-7597 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-8238         TCGA-HU-8243         TCGA-HU-8244 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-8249         TCGA-HU-8602         TCGA-HU-8604 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-8608         TCGA-HU-8610         TCGA-HU-A4G2 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4G3         TCGA-HU-A4G6         TCGA-HU-A4G8 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4G9         TCGA-HU-A4GC         TCGA-HU-A4GD 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GF         TCGA-HU-A4GH         TCGA-HU-A4GJ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GN         TCGA-HU-A4GP         TCGA-HU-A4GQ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GT         TCGA-HU-A4GU         TCGA-HU-A4GX 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GY         TCGA-HU-A4H0         TCGA-HU-A4H2 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4H3         TCGA-HU-A4H4         TCGA-HU-A4H5 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4H6         TCGA-HU-A4H8         TCGA-HU-A4HB 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4HD         TCGA-IN-7806         TCGA-IN-7808 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-8462         TCGA-IN-8663         TCGA-IN-A6RI 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A6RJ         TCGA-IN-A6RL         TCGA-IN-A6RN 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A6RO         TCGA-IN-A6RP         TCGA-IN-A6RR 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A6RS         TCGA-IN-A7NR         TCGA-IN-A7NT 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A7NU         TCGA-IN-AB1V         TCGA-IN-AB1X 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IP-7968         TCGA-KB-A6F5         TCGA-KB-A6F7 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-KB-A93J         TCGA-MX-A5UG         TCGA-MX-A5UJ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-R5-A7O7         TCGA-R5-A7ZE         TCGA-R5-A7ZF 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-R5-A7ZI         TCGA-R5-A804         TCGA-R5-A805 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A7BS         TCGA-RD-A7BT         TCGA-RD-A7BW 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A7C1         TCGA-RD-A8MV         TCGA-RD-A8MW 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A8N0         TCGA-RD-A8N1         TCGA-RD-A8N2 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A8N4         TCGA-RD-A8N5         TCGA-RD-A8N6 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A8N9         TCGA-SW-A7EA         TCGA-SW-A7EB 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8DL         TCGA-VQ-A8DT         TCGA-VQ-A8DU 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8DV         TCGA-VQ-A8DZ         TCGA-VQ-A8E2 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8E7         TCGA-VQ-A8P2         TCGA-VQ-A8P3 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8PE         TCGA-VQ-A8PK         TCGA-VQ-A8PM 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8PQ         TCGA-VQ-A91Q         TCGA-VQ-A91U 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A91V         TCGA-VQ-A92D         TCGA-VQ-A94T 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-AA64         TCGA-VQ-AA68         TCGA-VQ-AA69 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-AA6A         TCGA-VQ-AA6B         TCGA-VQ-AA6F 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-AA6G         TCGA-VQ-AA6I         TCGA-VQ-AA6J 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-AA6K         TCGA-ZA-A8F6 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
D871V6, binary
                    cls
clus                   0   1
  C9ORF152 MUTATED     3   0
  C9ORF152 WILD-TYPE 343  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF152 MUTATED      3    0
  C9ORF152 WILD-TYPE  343   29
   clus
vv  C9ORF152 MUTATED C9ORF152 WILD-TYPE
  0                3                343
  1                0                 29
[1] 2 2
[1] FALSE
D871V7, binary
                    cls
clus                   0   1
  C9ORF152 MUTATED     2   1
  C9ORF152 WILD-TYPE 143 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF152 MUTATED      2    1
  C9ORF152 WILD-TYPE  143  247
        clus
vv       C9ORF152 MUTATED C9ORF152 WILD-TYPE
  FEMALE                2                143
  MALE                  1                247
[1] 2 2
[1] FALSE
D871V8, binary
                    cls
clus                   0   1
  C9ORF152 MUTATED     3   0
  C9ORF152 WILD-TYPE 289  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF152 MUTATED      3    0
  C9ORF152 WILD-TYPE  289   59
     clus
vv    C9ORF152 MUTATED C9ORF152 WILD-TYPE
  NO                 3                289
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C9ORF152 MUTATED                                          0
  C9ORF152 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C9ORF152 MUTATED                                       0
  C9ORF152 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C9ORF152 MUTATED                                                        1
  C9ORF152 WILD-TYPE                                                    157
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C9ORF152 MUTATED                                                   0
  C9ORF152 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C9ORF152 MUTATED                                                                   2
  C9ORF152 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C9ORF152 MUTATED                                                    0
  C9ORF152 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C9ORF152 MUTATED                                                  0
  C9ORF152 WILD-TYPE                                               61
D871V9, multiclass
                                                                   clus
vv                                                                  C9ORF152 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 0
                                                                   clus
vv                                                                  C9ORF152 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C9ORF152 MUTATED     2   0   0   1
  C9ORF152 WILD-TYPE 309  14  15  23
D871V10, multiclass
    clus
vv   C9ORF152 MUTATED C9ORF152 WILD-TYPE
  R0                2                309
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D871V11, continuous
[1] "Remove cluster labels:" "C9ORF152 MUTATED"      
clus
  C9ORF152 MUTATED C9ORF152 WILD-TYPE 
                 2                341 
        TCGA-CG-4444         TCGA-CG-4460         TCGA-CG-4475 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-5727         TCGA-EQ-A4SO 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-F1-6177         TCGA-FP-A8CX         TCGA-HF-7131 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-KB-A93G         TCGA-MX-A663         TCGA-B7-5816 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-B7-A5TI         TCGA-BR-4183         TCGA-BR-4184 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4188         TCGA-BR-4191         TCGA-BR-4253 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4255         TCGA-BR-4256         TCGA-BR-4267 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4279         TCGA-BR-4280         TCGA-BR-4361 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-4362         TCGA-BR-4368         TCGA-BR-6452 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6453         TCGA-BR-6454         TCGA-BR-6455 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6456         TCGA-BR-6457         TCGA-BR-6458 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8058         TCGA-BR-8059 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8060         TCGA-BR-8077         TCGA-BR-8078 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8080         TCGA-BR-8081         TCGA-BR-8285 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8297         TCGA-BR-8360 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8361         TCGA-BR-8363         TCGA-BR-8364 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8365         TCGA-BR-8366         TCGA-BR-8367 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8368         TCGA-BR-8369         TCGA-BR-8370 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8371         TCGA-BR-8372         TCGA-BR-8373 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8380         TCGA-BR-8381         TCGA-BR-8382 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8384         TCGA-BR-8483         TCGA-BR-8484 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8485         TCGA-BR-8486         TCGA-BR-8487 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8588         TCGA-BR-8589         TCGA-BR-8590 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8591         TCGA-BR-8592         TCGA-BR-8676 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8677         TCGA-BR-8678         TCGA-BR-8679 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8680         TCGA-BR-8682         TCGA-BR-8683 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-8686         TCGA-BR-8687         TCGA-BR-8690 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A44T         TCGA-BR-A44U         TCGA-BR-A452 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A453         TCGA-BR-A4CQ         TCGA-BR-A4CR 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4CS         TCGA-BR-A4IU         TCGA-BR-A4IV 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4PD 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4PE         TCGA-BR-A4PF         TCGA-BR-A4QI 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-BR-A4QL         TCGA-BR-A4QM         TCGA-CD-5804 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8525         TCGA-CD-8526         TCGA-CD-8531 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CD-8535         TCGA-CD-A487         TCGA-CG-4301 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4436 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4442         TCGA-CG-4443 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4462 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4477         TCGA-CG-5717 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-D7-8570 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-8572         TCGA-D7-8573         TCGA-D7-8574 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-8575         TCGA-D7-8576         TCGA-D7-8578 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-8579         TCGA-D7-A4YT         TCGA-D7-A4YU 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A4YV         TCGA-D7-A4YX         TCGA-D7-A4YY 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A4Z0         TCGA-D7-A6ET         TCGA-D7-A6EV 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A6EX         TCGA-D7-A6EY         TCGA-D7-A6F0 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A6F2         TCGA-D7-A747         TCGA-D7-A748 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-D7-A74A         TCGA-D7-A74B         TCGA-EQ-5647 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-EQ-8122         TCGA-F1-6874         TCGA-F1-6875 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-F1-A448         TCGA-F1-A72C         TCGA-FP-7735 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-8211         TCGA-FP-8631         TCGA-FP-A4BE 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-FP-A4BF         TCGA-FP-A9TM         TCGA-HF-7132 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HF-7133         TCGA-HF-7134         TCGA-HF-7136 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HF-A5NB         TCGA-HJ-7597         TCGA-HU-8238 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-8243         TCGA-HU-8244         TCGA-HU-8249 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-8602         TCGA-HU-8604         TCGA-HU-8608 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-8610         TCGA-HU-A4G2         TCGA-HU-A4G3 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4G6         TCGA-HU-A4G8         TCGA-HU-A4G9 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GC         TCGA-HU-A4GD         TCGA-HU-A4GF 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GH         TCGA-HU-A4GJ         TCGA-HU-A4GN 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GP         TCGA-HU-A4GQ         TCGA-HU-A4GT 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4GU         TCGA-HU-A4GX         TCGA-HU-A4GY 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4H0         TCGA-HU-A4H2         TCGA-HU-A4H3 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4H4         TCGA-HU-A4H5         TCGA-HU-A4H6 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-HU-A4H8         TCGA-HU-A4HB         TCGA-HU-A4HD 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IN-8462 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-8663         TCGA-IN-A6RI         TCGA-IN-A6RJ 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A6RL         TCGA-IN-A6RN         TCGA-IN-A6RO 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A6RP         TCGA-IN-A6RR         TCGA-IN-A6RS 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-A7NR         TCGA-IN-A7NT         TCGA-IN-A7NU 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-IN-AB1V         TCGA-IN-AB1X         TCGA-IP-7968 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-KB-A6F5         TCGA-KB-A6F7         TCGA-KB-A93J 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-MX-A5UG         TCGA-MX-A5UJ         TCGA-R5-A7ZI 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A7BS         TCGA-RD-A7BT         TCGA-RD-A7BW 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A7C1         TCGA-RD-A8MV         TCGA-RD-A8MW 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A8N0         TCGA-RD-A8N1         TCGA-RD-A8N2 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A8N4         TCGA-RD-A8N5         TCGA-RD-A8N6 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-RD-A8N9         TCGA-SW-A7EA         TCGA-SW-A7EB 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8DL         TCGA-VQ-A8DT         TCGA-VQ-A8DU 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8DV         TCGA-VQ-A8DZ         TCGA-VQ-A8E2 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8E7         TCGA-VQ-A8P2         TCGA-VQ-A8P3 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8PE         TCGA-VQ-A8PK         TCGA-VQ-A8PM 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A8PQ         TCGA-VQ-A91Q         TCGA-VQ-A91U 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-A91V         TCGA-VQ-A92D         TCGA-VQ-A94T 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-AA64         TCGA-VQ-AA68         TCGA-VQ-AA69 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-AA6A         TCGA-VQ-AA6B         TCGA-VQ-AA6F 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-AA6G         TCGA-VQ-AA6I         TCGA-VQ-AA6J 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
        TCGA-VQ-AA6K         TCGA-ZA-A8F6 
"C9ORF152 WILD-TYPE" "C9ORF152 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C9ORF152 MUTATED       0                         0
  C9ORF152 WILD-TYPE    87                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C9ORF152 MUTATED                                           0     3
  C9ORF152 WILD-TYPE                                         1   240
D871V12, multiclass
                                           clus
vv                                          C9ORF152 MUTATED C9ORF152 WILD-TYPE
  ASIAN                                                    0                 87
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D871V13, binary
                    cls
clus                   0   1
  C9ORF152 MUTATED     0   3
  C9ORF152 WILD-TYPE   4 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF152 MUTATED      0    3
  C9ORF152 WILD-TYPE    4  307
                        clus
vv                       C9ORF152 MUTATED C9ORF152 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                3                307
[1] 2 2
[1] FALSE

Clustering(872) Variable = YIF1A MUTATION ANALYSIS
D872V1, survival
                 sevent
clus2               0   1
  YIF1A MUTATED     3   1
  YIF1A WILD-TYPE 227 138
  YIF1A MUTATED YIF1A WILD-TYPE 
              4             365 
  YIF1A MUTATED YIF1A WILD-TYPE 
              1             138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-7722 
       36.16        35.24        35.84        33.63        39.78        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-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-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 

  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          14.070 
[1] "18.1 - 38.1 (25.2)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.3"
D872V2, 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       2       15       39       30        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  YIF1A MUTATED           0          2          0          1        1
  YIF1A WILD-TYPE         3         68         53         31       37
D872V3, multiclass
            clus
vv           YIF1A MUTATED YIF1A WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  YIF1A MUTATED     0   1   0   4
  YIF1A WILD-TYPE  22  91 173  93
D872V4, multiclass
    clus
vv   YIF1A MUTATED YIF1A WILD-TYPE
  T1             0              22
  T2             1              91
  T3             0             173
  T4             4              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
  YIF1A MUTATED     2   2   0   1
  YIF1A WILD-TYPE 116 102  77  76
D872V5, multiclass
    clus
vv   YIF1A MUTATED YIF1A WILD-TYPE
  N0             2             116
  N1             2             102
  N2             0              77
  N3             1              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"
D872V6, binary
                 cls
clus                0   1
  YIF1A MUTATED     5   0
  YIF1A WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIF1A MUTATED      5    0
  YIF1A WILD-TYPE  341   29
   clus
vv  YIF1A MUTATED YIF1A WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D872V7, binary
                 cls
clus                0   1
  YIF1A MUTATED     2   3
  YIF1A WILD-TYPE 143 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIF1A MUTATED      2    3
  YIF1A WILD-TYPE  143  245
        clus
vv       YIF1A MUTATED YIF1A WILD-TYPE
  FEMALE             2             143
  MALE               3             245
[1] 2 2
[1] FALSE
D872V8, binary
                 cls
clus                0   1
  YIF1A MUTATED     3   1
  YIF1A WILD-TYPE 289  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIF1A MUTATED      3    1
  YIF1A WILD-TYPE  289   58
     clus
vv    YIF1A MUTATED YIF1A WILD-TYPE
  NO              3             289
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  YIF1A MUTATED                                          0
  YIF1A WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  YIF1A MUTATED                                       0
  YIF1A WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  YIF1A MUTATED                                                        3
  YIF1A WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  YIF1A MUTATED                                                   1
  YIF1A WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  YIF1A MUTATED                                                                   1
  YIF1A WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  YIF1A MUTATED                                                    0
  YIF1A WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  YIF1A MUTATED                                                  0
  YIF1A WILD-TYPE                                               61
D872V9, multiclass
                                                                   clus
vv                                                                  YIF1A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  YIF1A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  YIF1A MUTATED     4   0   0   1
  YIF1A WILD-TYPE 307  14  15  23
D872V10, multiclass
    clus
vv   YIF1A MUTATED YIF1A WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D872V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  YIF1A MUTATED       0                         0
  YIF1A WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  YIF1A MUTATED                                           0     5
  YIF1A WILD-TYPE                                         1   238
D872V12, multiclass
                                           clus
vv                                          YIF1A MUTATED YIF1A WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D872V13, binary
                 cls
clus                0   1
  YIF1A MUTATED     0   4
  YIF1A WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIF1A MUTATED      0    4
  YIF1A WILD-TYPE    4  306
                        clus
vv                       YIF1A MUTATED YIF1A WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(873) Variable = RUSC1 MUTATION ANALYSIS
D873V1, survival
                 sevent
clus2               0   1
  RUSC1 MUTATED    14   4
  RUSC1 WILD-TYPE 216 135
  RUSC1 MUTATED RUSC1 WILD-TYPE 
             18             351 
  RUSC1 MUTATED RUSC1 WILD-TYPE 
              4             135 
$`RUSC1 MUTATED`
TCGA-B7-5816 TCGA-B7-A5TJ TCGA-BR-4201 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CD-8536 
       26.70        11.01        30.90         1.12        16.14        12.43 
TCGA-CG-5721 TCGA-D7-5579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A6EY TCGA-D7-A74A 
        6.02        20.91        14.27         5.92        11.44        19.96 
TCGA-F1-6874 TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4GX TCGA-MX-A5UJ 
       14.47        22.82        22.68         6.51        20.25        19.73 

$`RUSC1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        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-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-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-D7-6518 TCGA-D7-6519 
       21.07         7.99        25.71        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-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       14.66        21.14        20.91        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-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       15.65         8.38         4.34         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-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-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-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 

  RUSC1 MUTATED RUSC1 WILD-TYPE 
           1.12            0.00 
  RUSC1 MUTATED RUSC1 WILD-TYPE 
           30.9           122.3 
  RUSC1 MUTATED RUSC1 WILD-TYPE 
         15.305          14.070 
[1] "1.1 - 30.9 (15.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D873V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RUSC1 MUTATED         0        0        1        1         3         4
  RUSC1 WILD-TYPE       2       15       39       29        34        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RUSC1 MUTATED           0          4          2          1        1
  RUSC1 WILD-TYPE         3         66         51         31       37
D873V3, multiclass
            clus
vv           RUSC1 MUTATED RUSC1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RUSC1 MUTATED     0   3  11   4
  RUSC1 WILD-TYPE  22  89 162  93
D873V4, multiclass
    clus
vv   RUSC1 MUTATED RUSC1 WILD-TYPE
  T1             0              22
  T2             3              89
  T3            11             162
  T4             4              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
  RUSC1 MUTATED     6   4   4   3
  RUSC1 WILD-TYPE 112 100  73  74
D873V5, multiclass
    clus
vv   RUSC1 MUTATED RUSC1 WILD-TYPE
  N0             6             112
  N1             4             100
  N2             4              73
  N3             3              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"
D873V6, binary
                 cls
clus                0   1
  RUSC1 MUTATED    19   0
  RUSC1 WILD-TYPE 327  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC1 MUTATED     19    0
  RUSC1 WILD-TYPE  327   29
   clus
vv  RUSC1 MUTATED RUSC1 WILD-TYPE
  0            19             327
  1             0              29
[1] 2 2
[1] FALSE
D873V7, binary
                 cls
clus                0   1
  RUSC1 MUTATED    13   6
  RUSC1 WILD-TYPE 132 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC1 MUTATED     13    6
  RUSC1 WILD-TYPE  132  242
        clus
vv       RUSC1 MUTATED RUSC1 WILD-TYPE
  FEMALE            13             132
  MALE               6             242
[1] 2 2
[1] FALSE
D873V8, binary
                 cls
clus                0   1
  RUSC1 MUTATED    18   0
  RUSC1 WILD-TYPE 274  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC1 MUTATED     18    0
  RUSC1 WILD-TYPE  274   59
     clus
vv    RUSC1 MUTATED RUSC1 WILD-TYPE
  NO             18             274
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RUSC1 MUTATED                                          0
  RUSC1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RUSC1 MUTATED                                       3
  RUSC1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RUSC1 MUTATED                                                        5
  RUSC1 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RUSC1 MUTATED                                                   1
  RUSC1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RUSC1 MUTATED                                                                   3
  RUSC1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RUSC1 MUTATED                                                    0
  RUSC1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RUSC1 MUTATED                                                  7
  RUSC1 WILD-TYPE                                               54
D873V9, multiclass
                                                                   clus
vv                                                                  RUSC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              7
                                                                   clus
vv                                                                  RUSC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RUSC1 MUTATED    14   1   0   2
  RUSC1 WILD-TYPE 297  13  15  22
D873V10, multiclass
    clus
vv   RUSC1 MUTATED RUSC1 WILD-TYPE
  R0            14             297
  R1             1              13
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D873V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RUSC1 MUTATED       5                         0
  RUSC1 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RUSC1 MUTATED                                           0    13
  RUSC1 WILD-TYPE                                         1   230
D873V12, multiclass
                                           clus
vv                                          RUSC1 MUTATED RUSC1 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D873V13, binary
                 cls
clus                0   1
  RUSC1 MUTATED     0  18
  RUSC1 WILD-TYPE   4 292
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC1 MUTATED      0   18
  RUSC1 WILD-TYPE    4  292
                        clus
vv                       RUSC1 MUTATED RUSC1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            18             292
[1] 2 2
[1] FALSE

Clustering(874) Variable = CNTLN MUTATION ANALYSIS
D874V1, survival
                 sevent
clus2               0   1
  CNTLN MUTATED    21  11
  CNTLN WILD-TYPE 209 128
  CNTLN MUTATED CNTLN WILD-TYPE 
             32             337 
  CNTLN MUTATED CNTLN WILD-TYPE 
             11             128 
$`CNTLN MUTATED`
TCGA-MX-A663 TCGA-B7-5818 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6566 
        9.86        11.70         6.61        34.68        15.95        32.78 
TCGA-BR-6852 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 
       44.94        31.10         4.31        31.27         1.12        31.96 
TCGA-BR-A4PF TCGA-CG-4465 TCGA-CG-5723 TCGA-CG-5726 TCGA-D7-6528 TCGA-D7-8570 
        1.15         9.01       105.07        28.96        15.22        24.72 
TCGA-D7-A4YV TCGA-FP-7916 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8602 
        5.92        14.07        52.21        30.51        26.47        22.32 
TCGA-HU-A4GD TCGA-HU-A4GQ TCGA-IN-A6RR TCGA-SW-A7EA TCGA-VQ-A8DU TCGA-VQ-A8P2 
       22.75         0.10         6.74        19.04         5.46        38.14 
TCGA-VQ-A91U TCGA-VQ-A91V 
        1.71        42.64 

$`CNTLN WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15        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-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-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-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-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-5724 TCGA-CG-5725 
        1.02         0.99         6.02         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-D7-6815 
       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-D7-8572 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-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-HU-8238 TCGA-HU-8243 
        5.52         6.21        77.29        63.06         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-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-A7EB 
      116.38        71.38        57.44         8.94        35.61         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-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 

  CNTLN MUTATED CNTLN WILD-TYPE 
            0.1             0.0 
  CNTLN MUTATED CNTLN WILD-TYPE 
         105.07          122.30 
  CNTLN MUTATED CNTLN WILD-TYPE 
          20.68           14.04 
[1] "0.1 - 105.1 (20.7)" "0.0 - 122.3 (14.0)"
[1] "hr=" "1.3"
D874V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNTLN MUTATED         1        2        5        1         6         4
  CNTLN WILD-TYPE       1       13       35       29        31        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNTLN MUTATED           1          6          2          5        2
  CNTLN WILD-TYPE         2         64         51         27       36
D874V3, multiclass
            clus
vv           CNTLN MUTATED CNTLN WILD-TYPE
  STAGE I                1               1
  STAGE IA               2              13
  STAGE IB               5              35
  STAGE II               1              29
  STAGE IIA              6              31
  STAGE IIB              4              48
  STAGE III              1               2
  STAGE IIIA             6              64
  STAGE IIIB             2              51
  STAGE IIIC             5              27
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CNTLN MUTATED     3   8  12  12
  CNTLN WILD-TYPE  19  84 161  85
D874V4, multiclass
    clus
vv   CNTLN MUTATED CNTLN WILD-TYPE
  T1             3              19
  T2             8              84
  T3            12             161
  T4            12              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
  CNTLN MUTATED    15  10   6   5
  CNTLN WILD-TYPE 103  94  71  72
D874V5, multiclass
    clus
vv   CNTLN MUTATED CNTLN WILD-TYPE
  N0            15             103
  N1            10              94
  N2             6              71
  N3             5              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"
D874V6, binary
                 cls
clus                0   1
  CNTLN MUTATED    31   2
  CNTLN WILD-TYPE 315  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTLN MUTATED     31    2
  CNTLN WILD-TYPE  315   27
   clus
vv  CNTLN MUTATED CNTLN WILD-TYPE
  0            31             315
  1             2              27
[1] 2 2
[1] FALSE
D874V7, binary
                 cls
clus                0   1
  CNTLN MUTATED    16  20
  CNTLN WILD-TYPE 129 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTLN MUTATED     16   20
  CNTLN WILD-TYPE  129  228
        clus
vv       CNTLN MUTATED CNTLN WILD-TYPE
  FEMALE            16             129
  MALE              20             228
[1] 2 2
[1] FALSE
D874V8, binary
                 cls
clus                0   1
  CNTLN MUTATED    29   3
  CNTLN WILD-TYPE 263  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTLN MUTATED     29    3
  CNTLN WILD-TYPE  263   56
     clus
vv    CNTLN MUTATED CNTLN WILD-TYPE
  NO             29             263
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CNTLN MUTATED                                          1
  CNTLN WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CNTLN MUTATED                                       5
  CNTLN WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CNTLN MUTATED                                                       16
  CNTLN WILD-TYPE                                                    142
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CNTLN MUTATED                                                   2
  CNTLN WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CNTLN MUTATED                                                                   4
  CNTLN WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CNTLN MUTATED                                                    0
  CNTLN WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CNTLN MUTATED                                                  8
  CNTLN WILD-TYPE                                               53
D874V9, multiclass
                                                                   clus
vv                                                                  CNTLN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              8
                                                                   clus
vv                                                                  CNTLN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               53
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CNTLN MUTATED    30   1   1   3
  CNTLN WILD-TYPE 281  13  14  21
D874V10, multiclass
    clus
vv   CNTLN MUTATED CNTLN WILD-TYPE
  R0            30             281
  R1             1              13
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D874V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CNTLN MUTATED       6                         1
  CNTLN WILD-TYPE    81                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CNTLN MUTATED                                           0    23
  CNTLN WILD-TYPE                                         1   220
D874V12, multiclass
                                           clus
vv                                          CNTLN MUTATED CNTLN WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                23             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D874V13, binary
                 cls
clus                0   1
  CNTLN MUTATED     0  27
  CNTLN WILD-TYPE   4 283
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTLN MUTATED      0   27
  CNTLN WILD-TYPE    4  283
                        clus
vv                       CNTLN MUTATED CNTLN WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            27             283
[1] 2 2
[1] FALSE

Clustering(875) Variable = NUAK1 MUTATION ANALYSIS
D875V1, survival
                 sevent
clus2               0   1
  NUAK1 MUTATED    12   5
  NUAK1 WILD-TYPE 218 134
  NUAK1 MUTATED NUAK1 WILD-TYPE 
             17             352 
  NUAK1 MUTATED NUAK1 WILD-TYPE 
              5             134 
$`NUAK1 MUTATED`
TCGA-B7-A5TI TCGA-BR-4256 TCGA-BR-6566 TCGA-BR-7901 TCGA-BR-8078 TCGA-BR-8081 
       19.56         9.34        32.78         3.45        29.59        32.25 
TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-8536 TCGA-CG-4469 TCGA-CG-5723 TCGA-CG-5726 
       31.96        16.14        12.43         7.07       105.07        28.96 
TCGA-D7-A4YU TCGA-HU-8602 TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-VQ-A8P2 
       16.44        22.32         2.10        23.84        38.14 

$`NUAK1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
       20.25         0.26        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-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 

  NUAK1 MUTATED NUAK1 WILD-TYPE 
            2.1             0.0 
  NUAK1 MUTATED NUAK1 WILD-TYPE 
         105.07          122.30 
  NUAK1 MUTATED NUAK1 WILD-TYPE 
         22.320          14.055 
[1] "2.1 - 105.1 (22.3)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D875V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NUAK1 MUTATED         0        1        0        2         1         5
  NUAK1 WILD-TYPE       2       14       40       28        36        47
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUAK1 MUTATED           0          1          2          2        2
  NUAK1 WILD-TYPE         3         69         51         30       36
D875V3, multiclass
            clus
vv           NUAK1 MUTATED NUAK1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               2              28
  STAGE IIA              1              36
  STAGE IIB              5              47
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NUAK1 MUTATED     1   2   7   7
  NUAK1 WILD-TYPE  21  90 166  90
D875V4, multiclass
    clus
vv   NUAK1 MUTATED NUAK1 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             7             166
  T4             7              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
  NUAK1 MUTATED     6   4   2   5
  NUAK1 WILD-TYPE 112 100  75  72
D875V5, multiclass
    clus
vv   NUAK1 MUTATED NUAK1 WILD-TYPE
  N0             6             112
  N1             4             100
  N2             2              75
  N3             5              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"
D875V6, binary
                 cls
clus                0   1
  NUAK1 MUTATED    16   1
  NUAK1 WILD-TYPE 330  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUAK1 MUTATED     16    1
  NUAK1 WILD-TYPE  330   28
   clus
vv  NUAK1 MUTATED NUAK1 WILD-TYPE
  0            16             330
  1             1              28
[1] 2 2
[1] FALSE
D875V7, binary
                 cls
clus                0   1
  NUAK1 MUTATED     7  11
  NUAK1 WILD-TYPE 138 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUAK1 MUTATED      7   11
  NUAK1 WILD-TYPE  138  237
        clus
vv       NUAK1 MUTATED NUAK1 WILD-TYPE
  FEMALE             7             138
  MALE              11             237
[1] 2 2
[1] FALSE
D875V8, binary
                 cls
clus                0   1
  NUAK1 MUTATED    14   1
  NUAK1 WILD-TYPE 278  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUAK1 MUTATED     14    1
  NUAK1 WILD-TYPE  278   58
     clus
vv    NUAK1 MUTATED NUAK1 WILD-TYPE
  NO             14             278
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NUAK1 MUTATED                                          0
  NUAK1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NUAK1 MUTATED                                       3
  NUAK1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NUAK1 MUTATED                                                        9
  NUAK1 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NUAK1 MUTATED                                                   1
  NUAK1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NUAK1 MUTATED                                                                   2
  NUAK1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NUAK1 MUTATED                                                    0
  NUAK1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NUAK1 MUTATED                                                  3
  NUAK1 WILD-TYPE                                               58
D875V9, multiclass
                                                                   clus
vv                                                                  NUAK1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  NUAK1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NUAK1 MUTATED    14   1   0   2
  NUAK1 WILD-TYPE 297  13  15  22
D875V10, multiclass
    clus
vv   NUAK1 MUTATED NUAK1 WILD-TYPE
  R0            14             297
  R1             1              13
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D875V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NUAK1 MUTATED       5                         0
  NUAK1 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NUAK1 MUTATED                                           0    10
  NUAK1 WILD-TYPE                                         1   233
D875V12, multiclass
                                           clus
vv                                          NUAK1 MUTATED NUAK1 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D875V13, binary
                 cls
clus                0   1
  NUAK1 MUTATED     0  14
  NUAK1 WILD-TYPE   4 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUAK1 MUTATED      0   14
  NUAK1 WILD-TYPE    4  296
                        clus
vv                       NUAK1 MUTATED NUAK1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(876) Variable = GCG MUTATION ANALYSIS
D876V1, survival
               sevent
clus2             0   1
  GCG MUTATED     6   1
  GCG WILD-TYPE 224 138
  GCG MUTATED GCG WILD-TYPE 
            7           362 
  GCG MUTATED GCG WILD-TYPE 
            1           138 
$`GCG MUTATED`
TCGA-B7-5816 TCGA-BR-6706 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 TCGA-VQ-A8DT 
       26.70        18.05         1.12        31.96         6.02        48.79 
TCGA-VQ-A8P2 
       38.14 

$`GCG WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  GCG MUTATED GCG WILD-TYPE 
         1.12          0.00 
  GCG MUTATED GCG WILD-TYPE 
        48.79        122.30 
  GCG MUTATED GCG WILD-TYPE 
        26.70         14.12 
[1] "1.1 - 48.8 (26.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.4"
D876V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GCG MUTATED         0        0        0        0         1         1
  GCG WILD-TYPE       2       15       40       30        36        51
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GCG MUTATED           0          2          1          0        2
  GCG WILD-TYPE         3         68         52         32       36
D876V3, multiclass
            clus
vv           GCG MUTATED GCG WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             0            40
  STAGE II             0            30
  STAGE IIA            1            36
  STAGE IIB            1            51
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           1            52
  STAGE IIIC           0            32
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  GCG MUTATED     0   0   3   4
  GCG WILD-TYPE  22  92 170  93
D876V4, multiclass
    clus
vv   GCG MUTATED GCG WILD-TYPE
  T1           0            22
  T2           0            92
  T3           3           170
  T4           4            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
  GCG MUTATED     2   3   1   1
  GCG WILD-TYPE 116 101  76  76
D876V5, multiclass
    clus
vv   GCG MUTATED GCG WILD-TYPE
  N0           2           116
  N1           3           101
  N2           1            76
  N3           1            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"
D876V6, binary
               cls
clus              0   1
  GCG MUTATED     6   1
  GCG WILD-TYPE 340  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  GCG MUTATED      6    1
  GCG WILD-TYPE  340   28
   clus
vv  GCG MUTATED GCG WILD-TYPE
  0           6           340
  1           1            28
[1] 2 2
[1] FALSE
D876V7, binary
               cls
clus              0   1
  GCG MUTATED     2   5
  GCG WILD-TYPE 143 243
[1] "tbl2"
               cls
clus            [,1] [,2]
  GCG MUTATED      2    5
  GCG WILD-TYPE  143  243
        clus
vv       GCG MUTATED GCG WILD-TYPE
  FEMALE           2           143
  MALE             5           243
[1] 2 2
[1] FALSE
D876V8, binary
               cls
clus              0   1
  GCG MUTATED     5   2
  GCG WILD-TYPE 287  57
[1] "tbl2"
               cls
clus            [,1] [,2]
  GCG MUTATED      5    2
  GCG WILD-TYPE  287   57
     clus
vv    GCG MUTATED GCG WILD-TYPE
  NO            5           287
  YES           2            57
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GCG MUTATED                                          0
  GCG WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GCG MUTATED                                       1
  GCG WILD-TYPE                                    69
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GCG MUTATED                                                        2
  GCG WILD-TYPE                                                    156
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GCG MUTATED                                                   1
  GCG WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GCG MUTATED                                                                   2
  GCG WILD-TYPE                                                                66
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GCG MUTATED                                                    0
  GCG WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GCG MUTATED                                                  1
  GCG WILD-TYPE                                               60
D876V9, multiclass
                                                                   clus
vv                                                                  GCG MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            1
                                                                   clus
vv                                                                  GCG WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  GCG MUTATED     7   0   0   0
  GCG WILD-TYPE 304  14  15  24
D876V10, multiclass
    clus
vv   GCG MUTATED GCG WILD-TYPE
  R0           7           304
  R1           0            14
  R2           0            15
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D876V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  GCG MUTATED       1                         0
  GCG WILD-TYPE    86                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GCG MUTATED                                           0     4
  GCG WILD-TYPE                                         1   239
D876V12, multiclass
                                           clus
vv                                          GCG MUTATED GCG WILD-TYPE
  ASIAN                                               1            86
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               4           239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D876V13, binary
               cls
clus              0   1
  GCG MUTATED     0   4
  GCG WILD-TYPE   4 306
[1] "tbl2"
               cls
clus            [,1] [,2]
  GCG MUTATED      0    4
  GCG WILD-TYPE    4  306
                        clus
vv                       GCG MUTATED GCG WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           4           306
[1] 2 2
[1] FALSE

Clustering(877) Variable = VPS4B MUTATION ANALYSIS
D877V1, survival
                 sevent
clus2               0   1
  VPS4B MUTATED     6   1
  VPS4B WILD-TYPE 224 138
  VPS4B MUTATED VPS4B WILD-TYPE 
              7             362 
  VPS4B MUTATED VPS4B WILD-TYPE 
              1             138 
$`VPS4B MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-8680 TCGA-CG-5721 TCGA-D7-8574 TCGA-R5-A7ZI 
       21.99        34.68        31.96         6.02        17.19        74.53 
TCGA-VQ-A8P2 
       38.14 

$`VPS4B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-D7-6528 
       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-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-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 

  VPS4B MUTATED VPS4B WILD-TYPE 
           6.02            0.00 
  VPS4B MUTATED VPS4B WILD-TYPE 
          74.53          122.30 
  VPS4B MUTATED VPS4B WILD-TYPE 
          31.96           14.07 
[1] "6.0 - 74.5 (32.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "4.3"
D877V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VPS4B MUTATED         0        0        1        0         1         0
  VPS4B WILD-TYPE       2       15       39       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPS4B MUTATED           0          2          0          0        4
  VPS4B WILD-TYPE         3         68         53         32       34
D877V3, multiclass
            clus
vv           VPS4B MUTATED VPS4B WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VPS4B MUTATED     0   2   1   5
  VPS4B WILD-TYPE  22  90 172  92
D877V4, multiclass
    clus
vv   VPS4B MUTATED VPS4B WILD-TYPE
  T1             0              22
  T2             2              90
  T3             1             172
  T4             5              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
  VPS4B MUTATED     2   4   1   1
  VPS4B WILD-TYPE 116 100  76  76
D877V5, multiclass
    clus
vv   VPS4B MUTATED VPS4B WILD-TYPE
  N0             2             116
  N1             4             100
  N2             1              76
  N3             1              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"
D877V6, binary
                 cls
clus                0   1
  VPS4B MUTATED     5   3
  VPS4B WILD-TYPE 341  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS4B MUTATED      5    3
  VPS4B WILD-TYPE  341   26
   clus
vv  VPS4B MUTATED VPS4B WILD-TYPE
  0             5             341
  1             3              26
[1] 2 2
[1] FALSE
D877V7, binary
                 cls
clus                0   1
  VPS4B MUTATED     3   5
  VPS4B WILD-TYPE 142 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS4B MUTATED      3    5
  VPS4B WILD-TYPE  142  243
        clus
vv       VPS4B MUTATED VPS4B WILD-TYPE
  FEMALE             3             142
  MALE               5             243
[1] 2 2
[1] FALSE
D877V8, binary
                 cls
clus                0   1
  VPS4B MUTATED     6   1
  VPS4B WILD-TYPE 286  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS4B MUTATED      6    1
  VPS4B WILD-TYPE  286   58
     clus
vv    VPS4B MUTATED VPS4B WILD-TYPE
  NO              6             286
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  VPS4B MUTATED                                          0
  VPS4B WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  VPS4B MUTATED                                       1
  VPS4B WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  VPS4B MUTATED                                                        2
  VPS4B WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  VPS4B MUTATED                                                   1
  VPS4B WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  VPS4B MUTATED                                                                   3
  VPS4B WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  VPS4B MUTATED                                                    0
  VPS4B WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  VPS4B MUTATED                                                  1
  VPS4B WILD-TYPE                                               60
D877V9, multiclass
                                                                   clus
vv                                                                  VPS4B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  VPS4B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  VPS4B MUTATED     7   0   1   0
  VPS4B WILD-TYPE 304  14  14  24
D877V10, multiclass
    clus
vv   VPS4B MUTATED VPS4B WILD-TYPE
  R0             7             304
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D877V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  VPS4B MUTATED       1                         0
  VPS4B WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  VPS4B MUTATED                                           0     4
  VPS4B WILD-TYPE                                         1   239
D877V12, multiclass
                                           clus
vv                                          VPS4B MUTATED VPS4B WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D877V13, binary
                 cls
clus                0   1
  VPS4B MUTATED     1   3
  VPS4B WILD-TYPE   3 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS4B MUTATED      1    3
  VPS4B WILD-TYPE    3  307
                        clus
vv                       VPS4B MUTATED VPS4B WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(878) Variable = C12ORF40 MUTATION ANALYSIS
D878V1, survival
                    sevent
clus2                  0   1
  C12ORF40 MUTATED     2   2
  C12ORF40 WILD-TYPE 228 137
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                 4                365 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                 2                137 
$`C12ORF40 MUTATED`
TCGA-CG-4460 TCGA-BR-8590 TCGA-CG-4443 TCGA-F1-A72C 
       21.99         9.34        29.98        11.38 

$`C12ORF40 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
              9.34               0.00 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
             29.98             122.30 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
            16.685             14.270 
[1] "9.3 - 30.0 (16.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D878V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C12ORF40 MUTATED         1        1        1        0         1         0
  C12ORF40 WILD-TYPE       1       14       39       30        36        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF40 MUTATED           0          0          0          1        1
  C12ORF40 WILD-TYPE         3         70         53         31       37
D878V3, multiclass
            clus
vv           C12ORF40 MUTATED C12ORF40 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  1                 14
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                0                 53
  STAGE IIIC                1                 31
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C12ORF40 MUTATED     2   1   1   2
  C12ORF40 WILD-TYPE  20  91 172  95
D878V4, multiclass
    clus
vv   C12ORF40 MUTATED C12ORF40 WILD-TYPE
  T1                2                 20
  T2                1                 91
  T3                1                172
  T4                2                 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
  C12ORF40 MUTATED     3   3   1   0
  C12ORF40 WILD-TYPE 115 101  76  77
D878V5, multiclass
    clus
vv   C12ORF40 MUTATED C12ORF40 WILD-TYPE
  N0                3                115
  N1                3                101
  N2                1                 76
  N3                0                 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"
D878V6, binary
                    cls
clus                   0   1
  C12ORF40 MUTATED     5   1
  C12ORF40 WILD-TYPE 341  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF40 MUTATED      5    1
  C12ORF40 WILD-TYPE  341   28
   clus
vv  C12ORF40 MUTATED C12ORF40 WILD-TYPE
  0                5                341
  1                1                 28
[1] 2 2
[1] FALSE
D878V7, binary
                    cls
clus                   0   1
  C12ORF40 MUTATED     3   4
  C12ORF40 WILD-TYPE 142 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF40 MUTATED      3    4
  C12ORF40 WILD-TYPE  142  244
        clus
vv       C12ORF40 MUTATED C12ORF40 WILD-TYPE
  FEMALE                3                142
  MALE                  4                244
[1] 2 2
[1] FALSE
D878V8, binary
                    cls
clus                   0   1
  C12ORF40 MUTATED     5   0
  C12ORF40 WILD-TYPE 287  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF40 MUTATED      5    0
  C12ORF40 WILD-TYPE  287   59
     clus
vv    C12ORF40 MUTATED C12ORF40 WILD-TYPE
  NO                 5                287
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C12ORF40 MUTATED                                          0
  C12ORF40 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C12ORF40 MUTATED                                       0
  C12ORF40 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C12ORF40 MUTATED                                                        4
  C12ORF40 WILD-TYPE                                                    154
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C12ORF40 MUTATED                                                   0
  C12ORF40 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C12ORF40 MUTATED                                                                   3
  C12ORF40 WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C12ORF40 MUTATED                                                    0
  C12ORF40 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C12ORF40 MUTATED                                                  0
  C12ORF40 WILD-TYPE                                               61
D878V9, multiclass
                                                                   clus
vv                                                                  C12ORF40 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 0
                                                                   clus
vv                                                                  C12ORF40 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C12ORF40 MUTATED     5   0   1   1
  C12ORF40 WILD-TYPE 306  14  14  23
D878V10, multiclass
    clus
vv   C12ORF40 MUTATED C12ORF40 WILD-TYPE
  R0                5                306
  R1                0                 14
  R2                1                 14
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D878V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C12ORF40 MUTATED       1                         1
  C12ORF40 WILD-TYPE    86                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C12ORF40 MUTATED                                           0     3
  C12ORF40 WILD-TYPE                                         1   240
D878V12, multiclass
                                           clus
vv                                          C12ORF40 MUTATED C12ORF40 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D878V13, binary
                    cls
clus                   0   1
  C12ORF40 MUTATED     0   5
  C12ORF40 WILD-TYPE   4 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF40 MUTATED      0    5
  C12ORF40 WILD-TYPE    4  305
                        clus
vv                       C12ORF40 MUTATED C12ORF40 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                5                305
[1] 2 2
[1] FALSE

Clustering(879) Variable = NHSL2 MUTATION ANALYSIS
D879V1, survival
                 sevent
clus2               0   1
  NHSL2 MUTATED     5   1
  NHSL2 WILD-TYPE 225 138
  NHSL2 MUTATED NHSL2 WILD-TYPE 
              6             363 
  NHSL2 MUTATED NHSL2 WILD-TYPE 
              1             138 
$`NHSL2 MUTATED`
TCGA-BR-6452 TCGA-CD-A4MG TCGA-CG-5723 TCGA-D7-6528 TCGA-FP-A4BE TCGA-HU-A4GX 
       34.68         6.58       105.07        15.22        11.08        20.25 

$`NHSL2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-D7-6815 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-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 

  NHSL2 MUTATED NHSL2 WILD-TYPE 
           6.58            0.00 
  NHSL2 MUTATED NHSL2 WILD-TYPE 
         105.07          122.30 
  NHSL2 MUTATED NHSL2 WILD-TYPE 
         17.735          14.170 
[1] "6.6 - 105.1 (17.7)" "0.0 - 122.3 (14.2)"
[1] "hr=" "3"  
D879V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NHSL2 MUTATED         0        0        1        1         3         0
  NHSL2 WILD-TYPE       2       15       39       29        34        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NHSL2 MUTATED           0          0          0          1        0
  NHSL2 WILD-TYPE         3         70         53         31       38
D879V3, multiclass
            clus
vv           NHSL2 MUTATED NHSL2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NHSL2 MUTATED     0   2   3   1
  NHSL2 WILD-TYPE  22  90 170  96
D879V4, multiclass
    clus
vv   NHSL2 MUTATED NHSL2 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             3             170
  T4             1              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
  NHSL2 MUTATED     4   1   1   0
  NHSL2 WILD-TYPE 114 103  76  77
D879V5, multiclass
    clus
vv   NHSL2 MUTATED NHSL2 WILD-TYPE
  N0             4             114
  N1             1             103
  N2             1              76
  N3             0              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"
D879V6, binary
                 cls
clus                0   1
  NHSL2 MUTATED     6   0
  NHSL2 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NHSL2 MUTATED      6    0
  NHSL2 WILD-TYPE  340   29
   clus
vv  NHSL2 MUTATED NHSL2 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D879V7, binary
                 cls
clus                0   1
  NHSL2 MUTATED     3   3
  NHSL2 WILD-TYPE 142 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NHSL2 MUTATED      3    3
  NHSL2 WILD-TYPE  142  245
        clus
vv       NHSL2 MUTATED NHSL2 WILD-TYPE
  FEMALE             3             142
  MALE               3             245
[1] 2 2
[1] FALSE
D879V8, binary
                 cls
clus                0   1
  NHSL2 MUTATED     5   1
  NHSL2 WILD-TYPE 287  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NHSL2 MUTATED      5    1
  NHSL2 WILD-TYPE  287   58
     clus
vv    NHSL2 MUTATED NHSL2 WILD-TYPE
  NO              5             287
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NHSL2 MUTATED                                          0
  NHSL2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NHSL2 MUTATED                                       2
  NHSL2 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NHSL2 MUTATED                                                        3
  NHSL2 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NHSL2 MUTATED                                                   0
  NHSL2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NHSL2 MUTATED                                                                   0
  NHSL2 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NHSL2 MUTATED                                                    0
  NHSL2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NHSL2 MUTATED                                                  1
  NHSL2 WILD-TYPE                                               60
D879V9, multiclass
                                                                   clus
vv                                                                  NHSL2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  NHSL2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NHSL2 MUTATED     5   0   0   0
  NHSL2 WILD-TYPE 306  14  15  24
D879V10, multiclass
    clus
vv   NHSL2 MUTATED NHSL2 WILD-TYPE
  R0             5             306
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D879V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NHSL2 MUTATED       2                         1
  NHSL2 WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NHSL2 MUTATED                                           0     2
  NHSL2 WILD-TYPE                                         1   241
D879V12, multiclass
                                           clus
vv                                          NHSL2 MUTATED NHSL2 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D879V13, binary
                 cls
clus                0   1
  NHSL2 MUTATED     0   5
  NHSL2 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NHSL2 MUTATED      0    5
  NHSL2 WILD-TYPE    4  305
                        clus
vv                       NHSL2 MUTATED NHSL2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(880) Variable = MYO9B MUTATION ANALYSIS
D880V1, survival
                 sevent
clus2               0   1
  MYO9B MUTATED    11   9
  MYO9B WILD-TYPE 219 130
  MYO9B MUTATED MYO9B WILD-TYPE 
             20             349 
  MYO9B MUTATED MYO9B WILD-TYPE 
              9             130 
$`MYO9B MUTATED`
TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-7704 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8382 
        6.97         9.67        35.24        32.25         0.26        25.05 
TCGA-BR-8680 TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-6528 
       31.96         1.02         6.02        28.96        21.07        15.22 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-HJ-7597 TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-HU-A4H8 
        5.92        36.43        26.47        22.68         6.58        14.07 
TCGA-IN-7806 TCGA-VQ-A8P2 
       36.36        38.14 

$`MYO9B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-A4HB 
       12.95        29.00        23.84        23.80        21.17        15.68 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       33.40         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 

  MYO9B MUTATED MYO9B WILD-TYPE 
           0.26            0.00 
  MYO9B MUTATED MYO9B WILD-TYPE 
          38.14          122.30 
  MYO9B MUTATED MYO9B WILD-TYPE 
         21.875          14.070 
[1] "0.3 - 38.1 (21.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D880V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYO9B MUTATED         0        1        4        1         0         6
  MYO9B WILD-TYPE       2       14       36       29        37        46
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MYO9B MUTATED           0          3          0          1        3
  MYO9B WILD-TYPE         3         67         53         31       35
D880V3, multiclass
            clus
vv           MYO9B MUTATED MYO9B WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               4              36
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              6              46
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYO9B MUTATED     2   4   8   5
  MYO9B WILD-TYPE  20  88 165  92
D880V4, multiclass
    clus
vv   MYO9B MUTATED MYO9B WILD-TYPE
  T1             2              20
  T2             4              88
  T3             8             165
  T4             5              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
  MYO9B MUTATED     6   9   3   1
  MYO9B WILD-TYPE 112  95  74  76
D880V5, multiclass
    clus
vv   MYO9B MUTATED MYO9B WILD-TYPE
  N0             6             112
  N1             9              95
  N2             3              74
  N3             1              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"
D880V6, binary
                 cls
clus                0   1
  MYO9B MUTATED    16   2
  MYO9B WILD-TYPE 330  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO9B MUTATED     16    2
  MYO9B WILD-TYPE  330   27
   clus
vv  MYO9B MUTATED MYO9B WILD-TYPE
  0            16             330
  1             2              27
[1] 2 2
[1] FALSE
D880V7, binary
                 cls
clus                0   1
  MYO9B MUTATED    10  10
  MYO9B WILD-TYPE 135 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO9B MUTATED     10   10
  MYO9B WILD-TYPE  135  238
        clus
vv       MYO9B MUTATED MYO9B WILD-TYPE
  FEMALE            10             135
  MALE              10             238
[1] 2 2
[1] FALSE
D880V8, binary
                 cls
clus                0   1
  MYO9B MUTATED    17   1
  MYO9B WILD-TYPE 275  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO9B MUTATED     17    1
  MYO9B WILD-TYPE  275   58
     clus
vv    MYO9B MUTATED MYO9B WILD-TYPE
  NO             17             275
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MYO9B MUTATED                                          1
  MYO9B WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MYO9B MUTATED                                       3
  MYO9B WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MYO9B MUTATED                                                        7
  MYO9B WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MYO9B MUTATED                                                   1
  MYO9B WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MYO9B MUTATED                                                                   4
  MYO9B WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MYO9B MUTATED                                                    0
  MYO9B WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MYO9B MUTATED                                                  4
  MYO9B WILD-TYPE                                               57
D880V9, multiclass
                                                                   clus
vv                                                                  MYO9B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  MYO9B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYO9B MUTATED    16   0   1   2
  MYO9B WILD-TYPE 295  14  14  22
D880V10, multiclass
    clus
vv   MYO9B MUTATED MYO9B WILD-TYPE
  R0            16             295
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D880V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MYO9B MUTATED       4                         0
  MYO9B WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MYO9B MUTATED                                           0    12
  MYO9B WILD-TYPE                                         1   231
D880V12, multiclass
                                           clus
vv                                          MYO9B MUTATED MYO9B WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D880V13, binary
                 cls
clus                0   1
  MYO9B MUTATED     0  15
  MYO9B WILD-TYPE   4 295
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO9B MUTATED      0   15
  MYO9B WILD-TYPE    4  295
                        clus
vv                       MYO9B MUTATED MYO9B WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            15             295
[1] 2 2
[1] FALSE

Clustering(881) Variable = PCLO MUTATION ANALYSIS
D881V1, survival
                sevent
clus2              0   1
  PCLO MUTATED    48  24
  PCLO WILD-TYPE 182 115
  PCLO MUTATED PCLO WILD-TYPE 
            72            297 
  PCLO MUTATED PCLO WILD-TYPE 
            24            115 
$`PCLO MUTATED`
TCGA-FP-A8CX TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-4280 
        0.23        11.70         6.97        30.90         9.34         6.61 
TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-8059 
       34.68        19.33         9.21        35.24        28.73        14.43 
TCGA-BR-8078 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8483 TCGA-BR-8484 
       29.59         7.40        31.10         4.31         5.39        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-8690 
       20.22         1.12        27.12        28.14        31.96        10.68 
TCGA-BR-A452 TCGA-BR-A4PF TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A4MG TCGA-CD-A4MI 
        7.53         1.15        12.07        12.82         6.58        11.77 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4455 
       27.02        15.95         1.02         7.99         4.01        12.03 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5721 TCGA-CG-5734 TCGA-D7-6527 
       18.97         7.07        36.00         6.02         7.99        10.26 
TCGA-D7-6822 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4Z0 TCGA-F1-A448 TCGA-FP-A4BE 
       12.33        20.91        16.44        14.76        21.27        11.08 
TCGA-HF-7132 TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GH 
       77.29        22.82        22.68        24.20        22.75        11.77 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H4 
        8.98         0.10         6.58        20.25        29.00        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A7NT TCGA-R5-A7ZE 
       23.80        14.07         3.45         3.39        10.62        18.21 
TCGA-R5-A7ZI TCGA-R5-A805 TCGA-RD-A7BT TCGA-VQ-A8P2 TCGA-VQ-AA68 TCGA-VQ-AA6I 
       74.53         9.24         8.61        38.14        43.66        16.14 

$`PCLO WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G 
       47.05        21.99        22.98        79.07        16.24        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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 
        13.445         14.470 
[1] "0.1 - 77.3 (13.4)"  "0.0 - 122.3 (14.5)"
[1] "hr=" "1.1"
D881V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCLO MUTATED         1        4        9        8         6        10
  PCLO WILD-TYPE       1       11       31       22        31        42
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCLO MUTATED           2         10          8          8        8
  PCLO WILD-TYPE         1         60         45         24       30
D881V3, multiclass
            clus
vv           PCLO MUTATED PCLO WILD-TYPE
  STAGE I               1              1
  STAGE IA              4             11
  STAGE IB              9             31
  STAGE II              8             22
  STAGE IIA             6             31
  STAGE IIB            10             42
  STAGE III             2              1
  STAGE IIIA           10             60
  STAGE IIIB            8             45
  STAGE IIIC            8             24
  STAGE IV              8             30
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PCLO MUTATED     7  20  30  20
  PCLO WILD-TYPE  15  72 143  77
D881V4, multiclass
    clus
vv   PCLO MUTATED PCLO WILD-TYPE
  T1            7             15
  T2           20             72
  T3           30            143
  T4           20             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
  PCLO MUTATED   22 27 14 14
  PCLO WILD-TYPE 96 77 63 63
D881V5, multiclass
    clus
vv   PCLO MUTATED PCLO WILD-TYPE
  N0           22             96
  N1           27             77
  N2           14             63
  N3           14             63
[1] 4 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
  PCLO MUTATED    72   5
  PCLO WILD-TYPE 274  24
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCLO MUTATED     72    5
  PCLO WILD-TYPE  274   24
   clus
vv  PCLO MUTATED PCLO WILD-TYPE
  0           72            274
  1            5             24
[1] 2 2
[1] FALSE
D881V7, binary
                cls
clus               0   1
  PCLO MUTATED    32  48
  PCLO WILD-TYPE 113 200
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCLO MUTATED     32   48
  PCLO WILD-TYPE  113  200
        clus
vv       PCLO MUTATED PCLO WILD-TYPE
  FEMALE           32            113
  MALE             48            200
[1] 2 2
[1] FALSE
D881V8, binary
                cls
clus               0   1
  PCLO MUTATED    57   9
  PCLO WILD-TYPE 235  50
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCLO MUTATED     57    9
  PCLO WILD-TYPE  235   50
     clus
vv    PCLO MUTATED PCLO WILD-TYPE
  NO            57            235
  YES            9             50
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PCLO MUTATED                                          1
  PCLO WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PCLO MUTATED                                      11
  PCLO WILD-TYPE                                    59
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PCLO MUTATED                                                       33
  PCLO WILD-TYPE                                                    125
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PCLO MUTATED                                                   5
  PCLO WILD-TYPE                                                16
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PCLO MUTATED                                                                  15
  PCLO WILD-TYPE                                                                53
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PCLO MUTATED                                                    2
  PCLO WILD-TYPE                                                  3
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PCLO MUTATED                                                 13
  PCLO WILD-TYPE                                               48
D881V9, multiclass
                                                                   clus
vv                                                                  PCLO MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       11
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      33
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           15
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            13
                                                                   clus
vv                                                                  PCLO WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         59
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       125
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             16
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             53
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              48
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PCLO MUTATED    61   1   3   9
  PCLO WILD-TYPE 250  13  12  15
D881V10, multiclass
    clus
vv   PCLO MUTATED PCLO WILD-TYPE
  R0           61            250
  R1            1             13
  R2            3             12
  RX            9             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D881V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PCLO MUTATED      20                         2
  PCLO WILD-TYPE    67                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PCLO MUTATED                                           1    44
  PCLO WILD-TYPE                                         0   199
D881V12, multiclass
                                           clus
vv                                          PCLO MUTATED PCLO WILD-TYPE
  ASIAN                                               20             67
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                               44            199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D881V13, binary
                cls
clus               0   1
  PCLO MUTATED     2  62
  PCLO WILD-TYPE   2 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCLO MUTATED      2   62
  PCLO WILD-TYPE    2  248
                        clus
vv                       PCLO MUTATED PCLO WILD-TYPE
  HISPANIC OR LATINO                2              2
  NOT HISPANIC OR LATINO           62            248
[1] 2 2
[1] FALSE

Clustering(882) Variable = KCNK13 MUTATION ANALYSIS
D882V1, survival
                  sevent
clus2                0   1
  KCNK13 MUTATED     6   4
  KCNK13 WILD-TYPE 224 135
  KCNK13 MUTATED KCNK13 WILD-TYPE 
              10              359 
  KCNK13 MUTATED KCNK13 WILD-TYPE 
               4              135 
$`KCNK13 MUTATED`
TCGA-BR-8486 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-D7-6520 
       20.22        28.14        31.96         6.58        11.77        18.84 
TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HU-A4GQ TCGA-HU-A4GU 
        5.92        11.08         0.10         6.58 

$`KCNK13 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39        25.18         9.21         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-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-D7-6521 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-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-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-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-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 

  KCNK13 MUTATED KCNK13 WILD-TYPE 
             0.1              0.0 
  KCNK13 MUTATED KCNK13 WILD-TYPE 
           31.96           122.30 
  KCNK13 MUTATED KCNK13 WILD-TYPE 
          11.425           14.430 
[1] "0.1 - 32.0 (11.4)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.3"
D882V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNK13 MUTATED         0        1        0        0         2         2
  KCNK13 WILD-TYPE       2       14       40       30        35        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNK13 MUTATED           0          3          0          2        1
  KCNK13 WILD-TYPE         3         67         53         30       37
D882V3, multiclass
            clus
vv           KCNK13 MUTATED KCNK13 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KCNK13 MUTATED     1   1   5   4
  KCNK13 WILD-TYPE  21  91 168  93
D882V4, multiclass
    clus
vv   KCNK13 MUTATED KCNK13 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              5              168
  T4              4               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
  KCNK13 MUTATED     4   3   3   1
  KCNK13 WILD-TYPE 114 101  74  76
D882V5, multiclass
    clus
vv   KCNK13 MUTATED KCNK13 WILD-TYPE
  N0              4              114
  N1              3              101
  N2              3               74
  N3              1               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"
D882V6, binary
                  cls
clus                 0   1
  KCNK13 MUTATED    10   1
  KCNK13 WILD-TYPE 336  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNK13 MUTATED     10    1
  KCNK13 WILD-TYPE  336   28
   clus
vv  KCNK13 MUTATED KCNK13 WILD-TYPE
  0             10              336
  1              1               28
[1] 2 2
[1] FALSE
D882V7, binary
                  cls
clus                 0   1
  KCNK13 MUTATED     3   8
  KCNK13 WILD-TYPE 142 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNK13 MUTATED      3    8
  KCNK13 WILD-TYPE  142  240
        clus
vv       KCNK13 MUTATED KCNK13 WILD-TYPE
  FEMALE              3              142
  MALE                8              240
[1] 2 2
[1] FALSE
D882V8, binary
                  cls
clus                 0   1
  KCNK13 MUTATED     9   1
  KCNK13 WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNK13 MUTATED      9    1
  KCNK13 WILD-TYPE  283   58
     clus
vv    KCNK13 MUTATED KCNK13 WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KCNK13 MUTATED                                          0
  KCNK13 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KCNK13 MUTATED                                       2
  KCNK13 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNK13 MUTATED                                                        5
  KCNK13 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KCNK13 MUTATED                                                   0
  KCNK13 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNK13 MUTATED                                                                   0
  KCNK13 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KCNK13 MUTATED                                                    0
  KCNK13 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KCNK13 MUTATED                                                  4
  KCNK13 WILD-TYPE                                               57
D882V9, multiclass
                                                                   clus
vv                                                                  KCNK13 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  KCNK13 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KCNK13 MUTATED     8   0   0   1
  KCNK13 WILD-TYPE 303  14  15  23
D882V10, multiclass
    clus
vv   KCNK13 MUTATED KCNK13 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D882V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KCNK13 MUTATED       5                         1
  KCNK13 WILD-TYPE    82                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNK13 MUTATED                                           0     5
  KCNK13 WILD-TYPE                                         1   238
D882V12, multiclass
                                           clus
vv                                          KCNK13 MUTATED KCNK13 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D882V13, binary
                  cls
clus                 0   1
  KCNK13 MUTATED     0  11
  KCNK13 WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCNK13 MUTATED      0   11
  KCNK13 WILD-TYPE    4  299
                        clus
vv                       KCNK13 MUTATED KCNK13 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(883) Variable = SHMT2 MUTATION ANALYSIS
D883V1, survival
                 sevent
clus2               0   1
  SHMT2 MUTATED     7   2
  SHMT2 WILD-TYPE 223 137
  SHMT2 MUTATED SHMT2 WILD-TYPE 
              9             360 
  SHMT2 MUTATED SHMT2 WILD-TYPE 
              2             137 
$`SHMT2 MUTATED`
TCGA-CG-4460 TCGA-BR-4201 TCGA-BR-8372 TCGA-BR-8373 TCGA-CD-5798 TCGA-CD-A4MJ 
       21.99        30.90        31.27        14.79        13.41        12.62 
TCGA-CG-5723 TCGA-HU-A4GU TCGA-VQ-A8P2 
      105.07         6.58        38.14 

$`SHMT2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-8381 
       26.33         4.31        14.04         3.32        11.80         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-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-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-F1-6875 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-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 

  SHMT2 MUTATED SHMT2 WILD-TYPE 
           6.58            0.00 
  SHMT2 MUTATED SHMT2 WILD-TYPE 
         105.07          122.30 
  SHMT2 MUTATED SHMT2 WILD-TYPE 
          21.99           14.12 
[1] "6.6 - 105.1 (22.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.4"
D883V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SHMT2 MUTATED         0        0        1        2         0         1
  SHMT2 WILD-TYPE       2       15       39       28        37        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SHMT2 MUTATED           0          2          0          1        1
  SHMT2 WILD-TYPE         3         68         53         31       37
D883V3, multiclass
            clus
vv           SHMT2 MUTATED SHMT2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              0              37
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SHMT2 MUTATED     1   3   2   4
  SHMT2 WILD-TYPE  21  89 171  93
D883V4, multiclass
    clus
vv   SHMT2 MUTATED SHMT2 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             2             171
  T4             4              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
  SHMT2 MUTATED     2   5   0   1
  SHMT2 WILD-TYPE 116  99  77  76
D883V5, multiclass
    clus
vv   SHMT2 MUTATED SHMT2 WILD-TYPE
  N0             2             116
  N1             5              99
  N2             0              77
  N3             1              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"
D883V6, binary
                 cls
clus                0   1
  SHMT2 MUTATED     9   1
  SHMT2 WILD-TYPE 337  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHMT2 MUTATED      9    1
  SHMT2 WILD-TYPE  337   28
   clus
vv  SHMT2 MUTATED SHMT2 WILD-TYPE
  0             9             337
  1             1              28
[1] 2 2
[1] FALSE
D883V7, binary
                 cls
clus                0   1
  SHMT2 MUTATED     4   6
  SHMT2 WILD-TYPE 141 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHMT2 MUTATED      4    6
  SHMT2 WILD-TYPE  141  242
        clus
vv       SHMT2 MUTATED SHMT2 WILD-TYPE
  FEMALE             4             141
  MALE               6             242
[1] 2 2
[1] FALSE
D883V8, binary
                 cls
clus                0   1
  SHMT2 MUTATED     8   1
  SHMT2 WILD-TYPE 284  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHMT2 MUTATED      8    1
  SHMT2 WILD-TYPE  284   58
     clus
vv    SHMT2 MUTATED SHMT2 WILD-TYPE
  NO              8             284
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SHMT2 MUTATED                                          0
  SHMT2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SHMT2 MUTATED                                       1
  SHMT2 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SHMT2 MUTATED                                                        5
  SHMT2 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SHMT2 MUTATED                                                   2
  SHMT2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SHMT2 MUTATED                                                                   2
  SHMT2 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SHMT2 MUTATED                                                    0
  SHMT2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SHMT2 MUTATED                                                  0
  SHMT2 WILD-TYPE                                               61
D883V9, multiclass
                                                                   clus
vv                                                                  SHMT2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  SHMT2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SHMT2 MUTATED     5   0   1   2
  SHMT2 WILD-TYPE 306  14  14  22
D883V10, multiclass
    clus
vv   SHMT2 MUTATED SHMT2 WILD-TYPE
  R0             5             306
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D883V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SHMT2 MUTATED       3                         0
  SHMT2 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SHMT2 MUTATED                                           0     5
  SHMT2 WILD-TYPE                                         1   238
D883V12, multiclass
                                           clus
vv                                          SHMT2 MUTATED SHMT2 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D883V13, binary
                 cls
clus                0   1
  SHMT2 MUTATED     0   7
  SHMT2 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHMT2 MUTATED      0    7
  SHMT2 WILD-TYPE    4  303
                        clus
vv                       SHMT2 MUTATED SHMT2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(884) Variable = TBC1D22B MUTATION ANALYSIS
D884V1, survival
                    sevent
clus2                  0   1
  TBC1D22B MUTATED     5   1
  TBC1D22B WILD-TYPE 225 138
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
                 6                363 
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
                 1                138 
$`TBC1D22B MUTATED`
TCGA-BR-8487 TCGA-HF-7134 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-VQ-A8P2 
        1.12        52.21        22.32         0.10         6.58        38.14 

$`TBC1D22B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         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 

  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
               0.1                0.0 
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
             52.21             122.30 
  TBC1D22B MUTATED TBC1D22B WILD-TYPE 
             14.45              14.27 
[1] "0.1 - 52.2 (14.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.2"
D884V2, 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       2       14       40       30        36        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBC1D22B MUTATED           0          1          0          1        0
  TBC1D22B WILD-TYPE         3         69         53         31       38
D884V3, multiclass
            clus
vv           TBC1D22B MUTATED TBC1D22B WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                0                 53
  STAGE IIIC                1                 31
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TBC1D22B MUTATED     1   0   3   3
  TBC1D22B WILD-TYPE  21  92 170  94
D884V4, multiclass
    clus
vv   TBC1D22B MUTATED TBC1D22B WILD-TYPE
  T1                1                 21
  T2                0                 92
  T3                3                170
  T4                3                 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
  TBC1D22B MUTATED     3   2   1   0
  TBC1D22B WILD-TYPE 115 102  76  77
D884V5, multiclass
    clus
vv   TBC1D22B MUTATED TBC1D22B WILD-TYPE
  N0                3                115
  N1                2                102
  N2                1                 76
  N3                0                 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"
D884V6, binary
                    cls
clus                   0   1
  TBC1D22B MUTATED     6   0
  TBC1D22B WILD-TYPE 340  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D22B MUTATED      6    0
  TBC1D22B WILD-TYPE  340   29
   clus
vv  TBC1D22B MUTATED TBC1D22B WILD-TYPE
  0                6                340
  1                0                 29
[1] 2 2
[1] FALSE
D884V7, binary
                    cls
clus                   0   1
  TBC1D22B MUTATED     3   4
  TBC1D22B WILD-TYPE 142 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D22B MUTATED      3    4
  TBC1D22B WILD-TYPE  142  244
        clus
vv       TBC1D22B MUTATED TBC1D22B WILD-TYPE
  FEMALE                3                142
  MALE                  4                244
[1] 2 2
[1] FALSE
D884V8, binary
                    cls
clus                   0   1
  TBC1D22B MUTATED     5   1
  TBC1D22B WILD-TYPE 287  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D22B MUTATED      5    1
  TBC1D22B WILD-TYPE  287   58
     clus
vv    TBC1D22B MUTATED TBC1D22B WILD-TYPE
  NO                 5                287
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TBC1D22B MUTATED                                          0
  TBC1D22B WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TBC1D22B MUTATED                                       2
  TBC1D22B WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TBC1D22B MUTATED                                                        2
  TBC1D22B WILD-TYPE                                                    156
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TBC1D22B MUTATED                                                   1
  TBC1D22B WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TBC1D22B MUTATED                                                                   1
  TBC1D22B WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TBC1D22B MUTATED                                                    0
  TBC1D22B WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TBC1D22B MUTATED                                                  1
  TBC1D22B WILD-TYPE                                               60
D884V9, multiclass
                                                                   clus
vv                                                                  TBC1D22B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  TBC1D22B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  TBC1D22B MUTATED     6   0   0   1
  TBC1D22B WILD-TYPE 305  14  15  23
D884V10, multiclass
    clus
vv   TBC1D22B MUTATED TBC1D22B WILD-TYPE
  R0                6                305
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D884V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  TBC1D22B MUTATED       3                         0
  TBC1D22B WILD-TYPE    84                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TBC1D22B MUTATED                                           0     3
  TBC1D22B WILD-TYPE                                         1   240
D884V12, multiclass
                                           clus
vv                                          TBC1D22B MUTATED TBC1D22B WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D884V13, binary
                    cls
clus                   0   1
  TBC1D22B MUTATED     0   5
  TBC1D22B WILD-TYPE   4 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D22B MUTATED      0    5
  TBC1D22B WILD-TYPE    4  305
                        clus
vv                       TBC1D22B MUTATED TBC1D22B WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                5                305
[1] 2 2
[1] FALSE

Clustering(885) Variable = TACC2 MUTATION ANALYSIS
D885V1, survival
                 sevent
clus2               0   1
  TACC2 MUTATED    18  13
  TACC2 WILD-TYPE 212 126
  TACC2 MUTATED TACC2 WILD-TYPE 
             31             338 
  TACC2 MUTATED TACC2 WILD-TYPE 
             13             126 
$`TACC2 MUTATED`
TCGA-CG-4460 TCGA-FP-A8CX TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4201 
       21.99         0.23        26.70         6.97         7.43        30.90 
TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6706 TCGA-BR-8081 TCGA-BR-8360 
        9.67         6.61        34.68        18.05        32.25         6.18 
TCGA-BR-8363 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A44U TCGA-CG-4305 TCGA-CG-4465 
        0.26         1.12        31.96        13.87        15.95         9.01 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6520 TCGA-D7-6526 TCGA-FP-7829 
        6.02       105.07        21.07        18.84        17.19        19.53 
TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4H5 
       11.08        77.29        22.32        11.77         0.10        23.80 
TCGA-IN-A6RL 
       13.35 

$`TACC2 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-KB-A93G TCGA-MX-A663 
       47.05        22.98        79.07        16.24        20.15         9.86 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-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-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4267 
        4.64        18.35         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-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-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-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-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-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-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-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-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-D7-6521 
       25.71        12.66        20.91        19.13        20.55        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-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-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-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        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-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-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-A6RS TCGA-IN-A7NR 
       12.46        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 

  TACC2 MUTATED TACC2 WILD-TYPE 
            0.1             0.0 
  TACC2 MUTATED TACC2 WILD-TYPE 
         105.07          122.30 
  TACC2 MUTATED TACC2 WILD-TYPE 
          15.95           14.22 
[1] "0.1 - 105.1 (15.9)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D885V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TACC2 MUTATED         1        1        3        3         4         4
  TACC2 WILD-TYPE       1       14       37       27        33        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TACC2 MUTATED           1          6          1          2        4
  TACC2 WILD-TYPE         2         64         52         30       34
D885V3, multiclass
            clus
vv           TACC2 MUTATED TACC2 WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               3              27
  STAGE IIA              4              33
  STAGE IIB              4              48
  STAGE III              1               2
  STAGE IIIA             6              64
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TACC2 MUTATED     2  11   9   9
  TACC2 WILD-TYPE  20  81 164  88
D885V4, multiclass
    clus
vv   TACC2 MUTATED TACC2 WILD-TYPE
  T1             2              20
  T2            11              81
  T3             9             164
  T4             9              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
  TACC2 MUTATED    11  12   5   3
  TACC2 WILD-TYPE 107  92  72  74
D885V5, multiclass
    clus
vv   TACC2 MUTATED TACC2 WILD-TYPE
  N0            11             107
  N1            12              92
  N2             5              72
  N3             3              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"
D885V6, binary
                 cls
clus                0   1
  TACC2 MUTATED    27   3
  TACC2 WILD-TYPE 319  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACC2 MUTATED     27    3
  TACC2 WILD-TYPE  319   26
   clus
vv  TACC2 MUTATED TACC2 WILD-TYPE
  0            27             319
  1             3              26
[1] 2 2
[1] FALSE
D885V7, binary
                 cls
clus                0   1
  TACC2 MUTATED    14  19
  TACC2 WILD-TYPE 131 229
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACC2 MUTATED     14   19
  TACC2 WILD-TYPE  131  229
        clus
vv       TACC2 MUTATED TACC2 WILD-TYPE
  FEMALE            14             131
  MALE              19             229
[1] 2 2
[1] FALSE
D885V8, binary
                 cls
clus                0   1
  TACC2 MUTATED    27   3
  TACC2 WILD-TYPE 265  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACC2 MUTATED     27    3
  TACC2 WILD-TYPE  265   56
     clus
vv    TACC2 MUTATED TACC2 WILD-TYPE
  NO             27             265
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TACC2 MUTATED                                          1
  TACC2 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TACC2 MUTATED                                       3
  TACC2 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TACC2 MUTATED                                                       16
  TACC2 WILD-TYPE                                                    142
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TACC2 MUTATED                                                   2
  TACC2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TACC2 MUTATED                                                                   5
  TACC2 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TACC2 MUTATED                                                    1
  TACC2 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TACC2 MUTATED                                                  5
  TACC2 WILD-TYPE                                               56
D885V9, multiclass
                                                                   clus
vv                                                                  TACC2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              5
                                                                   clus
vv                                                                  TACC2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TACC2 MUTATED    26   0   2   5
  TACC2 WILD-TYPE 285  14  13  19
D885V10, multiclass
    clus
vv   TACC2 MUTATED TACC2 WILD-TYPE
  R0            26             285
  R1             0              14
  R2             2              13
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D885V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TACC2 MUTATED       5                         2
  TACC2 WILD-TYPE    82                         7
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TACC2 MUTATED                                           0    18
  TACC2 WILD-TYPE                                         1   225
D885V12, multiclass
                                           clus
vv                                          TACC2 MUTATED TACC2 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             2               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                18             225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D885V13, binary
                 cls
clus                0   1
  TACC2 MUTATED     0  25
  TACC2 WILD-TYPE   4 285
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TACC2 MUTATED      0   25
  TACC2 WILD-TYPE    4  285
                        clus
vv                       TACC2 MUTATED TACC2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            25             285
[1] 2 2
[1] FALSE

Clustering(886) Variable = EXOC3L2 MUTATION ANALYSIS
D886V1, survival
                   sevent
clus2                 0   1
  EXOC3L2 MUTATED     2   1
  EXOC3L2 WILD-TYPE 228 138
  EXOC3L2 MUTATED EXOC3L2 WILD-TYPE 
                3               366 
  EXOC3L2 MUTATED EXOC3L2 WILD-TYPE 
                1               138 
$`EXOC3L2 MUTATED`
TCGA-BR-4280 TCGA-BR-8680 TCGA-HU-A4H8 
        6.61        31.96        14.07 

$`EXOC3L2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  EXOC3L2 MUTATED EXOC3L2 WILD-TYPE 
             6.61              0.00 
  EXOC3L2 MUTATED EXOC3L2 WILD-TYPE 
            31.96            122.30 
  EXOC3L2 MUTATED EXOC3L2 WILD-TYPE 
            14.07             14.35 
[1] "6.6 - 32.0 (14.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D886V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EXOC3L2 MUTATED         0        0        1        0         0         0
  EXOC3L2 WILD-TYPE       2       15       39       30        37        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EXOC3L2 MUTATED           1          0          0          0        1
  EXOC3L2 WILD-TYPE         2         70         53         32       37
D886V3, multiclass
            clus
vv           EXOC3L2 MUTATED EXOC3L2 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                0                37
  STAGE IIB                0                52
  STAGE III                1                 2
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  EXOC3L2 MUTATED     1   1   0   1
  EXOC3L2 WILD-TYPE  21  91 173  96
D886V4, multiclass
    clus
vv   EXOC3L2 MUTATED EXOC3L2 WILD-TYPE
  T1               1                21
  T2               1                91
  T3               0               173
  T4               1                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
  EXOC3L2 MUTATED     0   2   1   0
  EXOC3L2 WILD-TYPE 118 102  76  77
D886V5, multiclass
    clus
vv   EXOC3L2 MUTATED EXOC3L2 WILD-TYPE
  N0               0               118
  N1               2               102
  N2               1                76
  N3               0                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"
D886V6, binary
                   cls
clus                  0   1
  EXOC3L2 MUTATED     2   1
  EXOC3L2 WILD-TYPE 344  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOC3L2 MUTATED      2    1
  EXOC3L2 WILD-TYPE  344   28
   clus
vv  EXOC3L2 MUTATED EXOC3L2 WILD-TYPE
  0               2               344
  1               1                28
[1] 2 2
[1] FALSE
D886V7, binary
                   cls
clus                  0   1
  EXOC3L2 MUTATED     1   2
  EXOC3L2 WILD-TYPE 144 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOC3L2 MUTATED      1    2
  EXOC3L2 WILD-TYPE  144  246
        clus
vv       EXOC3L2 MUTATED EXOC3L2 WILD-TYPE
  FEMALE               1               144
  MALE                 2               246
[1] 2 2
[1] FALSE
D886V8, binary
                   cls
clus                  0   1
  EXOC3L2 MUTATED     3   0
  EXOC3L2 WILD-TYPE 289  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOC3L2 MUTATED      3    0
  EXOC3L2 WILD-TYPE  289   59
     clus
vv    EXOC3L2 MUTATED EXOC3L2 WILD-TYPE
  NO                3               289
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EXOC3L2 MUTATED                                          0
  EXOC3L2 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EXOC3L2 MUTATED                                       0
  EXOC3L2 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EXOC3L2 MUTATED                                                        1
  EXOC3L2 WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EXOC3L2 MUTATED                                                   0
  EXOC3L2 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EXOC3L2 MUTATED                                                                   0
  EXOC3L2 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EXOC3L2 MUTATED                                                    0
  EXOC3L2 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EXOC3L2 MUTATED                                                  2
  EXOC3L2 WILD-TYPE                                               59
D886V9, multiclass
                                                                   clus
vv                                                                  EXOC3L2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  EXOC3L2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  EXOC3L2 MUTATED     2   0   0   1
  EXOC3L2 WILD-TYPE 309  14  15  23
D886V10, multiclass
    clus
vv   EXOC3L2 MUTATED EXOC3L2 WILD-TYPE
  R0               2               309
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D886V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  EXOC3L2 MUTATED       2                         0
  EXOC3L2 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EXOC3L2 MUTATED                                           0     1
  EXOC3L2 WILD-TYPE                                         1   242
D886V12, multiclass
                                           clus
vv                                          EXOC3L2 MUTATED EXOC3L2 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   1               242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D886V13, binary
                   cls
clus                  0   1
  EXOC3L2 MUTATED     0   3
  EXOC3L2 WILD-TYPE   4 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOC3L2 MUTATED      0    3
  EXOC3L2 WILD-TYPE    4  307
                        clus
vv                       EXOC3L2 MUTATED EXOC3L2 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               3               307
[1] 2 2
[1] FALSE

Clustering(887) Variable = BAG4 MUTATION ANALYSIS
D887V1, survival
                sevent
clus2              0   1
  BAG4 MUTATED     2   1
  BAG4 WILD-TYPE 228 138
  BAG4 MUTATED BAG4 WILD-TYPE 
             3            366 
  BAG4 MUTATED BAG4 WILD-TYPE 
             1            138 
$`BAG4 MUTATED`
TCGA-D7-A4YV TCGA-HF-7132 TCGA-MX-A5UJ 
        5.92        77.29        19.73 

$`BAG4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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          14.22 
[1] "5.9 - 77.3 (19.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D887V2, 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       2       15       39       29        37        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BAG4 MUTATED           0          1          0          0        0
  BAG4 WILD-TYPE         3         69         53         32       38
D887V3, multiclass
            clus
vv           BAG4 MUTATED BAG4 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             0             37
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BAG4 MUTATED     1   2   2   0
  BAG4 WILD-TYPE  21  90 171  97
D887V4, multiclass
    clus
vv   BAG4 MUTATED BAG4 WILD-TYPE
  T1            1             21
  T2            2             90
  T3            2            171
  T4            0             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
  BAG4 MUTATED     1   2   1   0
  BAG4 WILD-TYPE 117 102  76  77
D887V5, multiclass
    clus
vv   BAG4 MUTATED BAG4 WILD-TYPE
  N0            1            117
  N1            2            102
  N2            1             76
  N3            0             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"
D887V6, binary
                cls
clus               0   1
  BAG4 MUTATED     5   0
  BAG4 WILD-TYPE 341  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      5    0
  BAG4 WILD-TYPE  341   29
   clus
vv  BAG4 MUTATED BAG4 WILD-TYPE
  0            5            341
  1            0             29
[1] 2 2
[1] FALSE
D887V7, binary
                cls
clus               0   1
  BAG4 MUTATED     3   2
  BAG4 WILD-TYPE 142 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      3    2
  BAG4 WILD-TYPE  142  246
        clus
vv       BAG4 MUTATED BAG4 WILD-TYPE
  FEMALE            3            142
  MALE              2            246
[1] 2 2
[1] FALSE
D887V8, binary
                cls
clus               0   1
  BAG4 MUTATED     2   1
  BAG4 WILD-TYPE 290  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      2    1
  BAG4 WILD-TYPE  290   58
     clus
vv    BAG4 MUTATED BAG4 WILD-TYPE
  NO             2            290
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BAG4 MUTATED                                          0
  BAG4 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BAG4 MUTATED                                       0
  BAG4 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BAG4 MUTATED                                                        1
  BAG4 WILD-TYPE                                                    157
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BAG4 MUTATED                                                   1
  BAG4 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BAG4 MUTATED                                                                   1
  BAG4 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BAG4 MUTATED                                                    0
  BAG4 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BAG4 MUTATED                                                  2
  BAG4 WILD-TYPE                                               59
D887V9, multiclass
                                                                   clus
vv                                                                  BAG4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  BAG4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BAG4 MUTATED     4   0   0   1
  BAG4 WILD-TYPE 307  14  15  23
D887V10, multiclass
    clus
vv   BAG4 MUTATED BAG4 WILD-TYPE
  R0            4            307
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D887V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BAG4 MUTATED       0                         0
  BAG4 WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BAG4 MUTATED                                           0     3
  BAG4 WILD-TYPE                                         1   240
D887V12, multiclass
                                           clus
vv                                          BAG4 MUTATED BAG4 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D887V13, binary
                cls
clus               0   1
  BAG4 MUTATED     0   3
  BAG4 WILD-TYPE   4 307
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      0    3
  BAG4 WILD-TYPE    4  307
                        clus
vv                       BAG4 MUTATED BAG4 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            3            307
[1] 2 2
[1] FALSE

Clustering(888) Variable = SLC26A8 MUTATION ANALYSIS
D888V1, survival
                   sevent
clus2                 0   1
  SLC26A8 MUTATED     6   4
  SLC26A8 WILD-TYPE 224 135
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               10               359 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
                4               135 
$`SLC26A8 MUTATED`
TCGA-BR-4257 TCGA-BR-8360 TCGA-CD-8535 TCGA-CG-4437 TCGA-CG-5721 TCGA-D7-A6EY 
        9.67         6.18        12.82         8.05         6.02        11.44 
TCGA-EQ-5647 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-VQ-A8P2 
        0.62        22.32         0.10        38.14 

$`SLC26A8 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
              0.1               0.0 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
            38.14            122.30 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
             8.86             14.66 
[1] "0.1 - 38.1 (8.9)"   "0.0 - 122.3 (14.7)"
[1] "hr=" "1.7"
D888V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC26A8 MUTATED         0        0        0        1         1         1
  SLC26A8 WILD-TYPE       2       15       40       29        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC26A8 MUTATED           0          2          1          1        2
  SLC26A8 WILD-TYPE         3         68         52         31       36
D888V3, multiclass
            clus
vv           SLC26A8 MUTATED SLC26A8 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC26A8 MUTATED     0   1   3   5
  SLC26A8 WILD-TYPE  22  91 170  92
D888V4, multiclass
    clus
vv   SLC26A8 MUTATED SLC26A8 WILD-TYPE
  T1               0                22
  T2               1                91
  T3               3               170
  T4               5                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
  SLC26A8 MUTATED     2   4   1   2
  SLC26A8 WILD-TYPE 116 100  76  75
D888V5, multiclass
    clus
vv   SLC26A8 MUTATED SLC26A8 WILD-TYPE
  N0               2               116
  N1               4               100
  N2               1                76
  N3               2                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"
D888V6, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED     9   1
  SLC26A8 WILD-TYPE 337  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED      9    1
  SLC26A8 WILD-TYPE  337   28
   clus
vv  SLC26A8 MUTATED SLC26A8 WILD-TYPE
  0               9               337
  1               1                28
[1] 2 2
[1] FALSE
D888V7, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED     4   6
  SLC26A8 WILD-TYPE 141 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED      4    6
  SLC26A8 WILD-TYPE  141  242
        clus
vv       SLC26A8 MUTATED SLC26A8 WILD-TYPE
  FEMALE               4               141
  MALE                 6               242
[1] 2 2
[1] FALSE
D888V8, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED     9   1
  SLC26A8 WILD-TYPE 283  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED      9    1
  SLC26A8 WILD-TYPE  283   58
     clus
vv    SLC26A8 MUTATED SLC26A8 WILD-TYPE
  NO                9               283
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC26A8 MUTATED                                          0
  SLC26A8 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC26A8 MUTATED                                       1
  SLC26A8 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC26A8 MUTATED                                                        3
  SLC26A8 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC26A8 MUTATED                                                   1
  SLC26A8 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC26A8 MUTATED                                                                   3
  SLC26A8 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC26A8 MUTATED                                                    0
  SLC26A8 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC26A8 MUTATED                                                  2
  SLC26A8 WILD-TYPE                                               59
D888V9, multiclass
                                                                   clus
vv                                                                  SLC26A8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  SLC26A8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC26A8 MUTATED     8   0   1   1
  SLC26A8 WILD-TYPE 303  14  14  23
D888V10, multiclass
    clus
vv   SLC26A8 MUTATED SLC26A8 WILD-TYPE
  R0               8               303
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D888V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC26A8 MUTATED       3                         0
  SLC26A8 WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC26A8 MUTATED                                           0     5
  SLC26A8 WILD-TYPE                                         1   238
D888V12, multiclass
                                           clus
vv                                          SLC26A8 MUTATED SLC26A8 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D888V13, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED     0   7
  SLC26A8 WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED      0    7
  SLC26A8 WILD-TYPE    4  303
                        clus
vv                       SLC26A8 MUTATED SLC26A8 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(889) Variable = MBOAT2 MUTATION ANALYSIS
D889V1, survival
                  sevent
clus2                0   1
  MBOAT2 MUTATED     2   0
  MBOAT2 WILD-TYPE 228 139
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               2              367 
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               0              139 
$`MBOAT2 MUTATED`
TCGA-HF-7132 TCGA-HU-A4GT 
       77.29         6.51 

$`MBOAT2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
            6.51             0.00 
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
           77.29           122.30 
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
           41.90            14.27 
[1] "6.5 - 77.3 (41.9)"  "0.0 - 122.3 (14.3)"
[1] "Remove cluster labels:" "MBOAT2 MUTATED"        
D889V2, continuous
[1] "Remove cluster labels:" "MBOAT2 MUTATED"        
clus
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               2              384 
      TCGA-CG-4444       TCGA-CG-4460       TCGA-CG-4475       TCGA-CG-4476 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5716       TCGA-CG-5727       TCGA-EQ-A4SO       TCGA-F1-6177 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-A8CX       TCGA-KB-A93G       TCGA-MX-A663       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-4187 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4188       TCGA-BR-4191       TCGA-BR-4201       TCGA-BR-4253 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4255       TCGA-BR-4256       TCGA-BR-4257       TCGA-BR-4267 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4294       TCGA-BR-4357 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4361       TCGA-BR-4362       TCGA-BR-4363       TCGA-BR-4366 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4368       TCGA-BR-4369       TCGA-BR-4370       TCGA-BR-4371 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6452       TCGA-BR-6453       TCGA-BR-6454       TCGA-BR-6455 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6456       TCGA-BR-6457       TCGA-BR-6458       TCGA-BR-6563 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6564       TCGA-BR-6565       TCGA-BR-6566       TCGA-BR-6705 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6706       TCGA-BR-6707       TCGA-BR-6709       TCGA-BR-6710 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803       TCGA-BR-6852 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703       TCGA-BR-7704 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7707       TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7722       TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7957       TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8059       TCGA-BR-8060       TCGA-BR-8077       TCGA-BR-8078 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8080       TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8285 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8286       TCGA-BR-8289       TCGA-BR-8291       TCGA-BR-8295 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8297       TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8364       TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8368       TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8372       TCGA-BR-8373       TCGA-BR-8380       TCGA-BR-8381 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8382       TCGA-BR-8384       TCGA-BR-8483       TCGA-BR-8484 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8485       TCGA-BR-8486       TCGA-BR-8487       TCGA-BR-8588 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8589       TCGA-BR-8590       TCGA-BR-8591       TCGA-BR-8592 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8676       TCGA-BR-8677       TCGA-BR-8678       TCGA-BR-8679 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8680       TCGA-BR-8682       TCGA-BR-8683       TCGA-BR-8686 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8687       TCGA-BR-8690       TCGA-BR-A44T       TCGA-BR-A44U 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A452       TCGA-BR-A453       TCGA-BR-A4CQ       TCGA-BR-A4CR 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4CS       TCGA-BR-A4IU       TCGA-BR-A4IV       TCGA-BR-A4IY 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4IZ       TCGA-BR-A4J1       TCGA-BR-A4J2       TCGA-BR-A4J4 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4J5       TCGA-BR-A4J6       TCGA-BR-A4J7       TCGA-BR-A4J8 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4PD       TCGA-BR-A4PE       TCGA-BR-A4PF       TCGA-BR-A4QI 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4QL       TCGA-BR-A4QM       TCGA-CD-5798       TCGA-CD-5799 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-5802       TCGA-CD-5803       TCGA-CD-5804       TCGA-CD-5813 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8524       TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8527 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8528       TCGA-CD-8529       TCGA-CD-8530       TCGA-CD-8531 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8532       TCGA-CD-8533       TCGA-CD-8534       TCGA-CD-8535 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8536       TCGA-CD-A486       TCGA-CD-A487       TCGA-CD-A489 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A48A       TCGA-CD-A48C       TCGA-CD-A4MG       TCGA-CD-A4MH 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A4MI       TCGA-CD-A4MJ       TCGA-CG-4300       TCGA-CG-4301 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4304       TCGA-CG-4305       TCGA-CG-4306       TCGA-CG-4436 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4437       TCGA-CG-4438       TCGA-CG-4440       TCGA-CG-4441 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4442       TCGA-CG-4443       TCGA-CG-4449       TCGA-CG-4455 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466       TCGA-CG-4469 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4474       TCGA-CG-4477       TCGA-CG-5717       TCGA-CG-5718 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5719       TCGA-CG-5720       TCGA-CG-5721       TCGA-CG-5722 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5723       TCGA-CG-5724       TCGA-CG-5725       TCGA-CG-5726 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5728       TCGA-CG-5730       TCGA-CG-5732       TCGA-CG-5733 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5734       TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6518       TCGA-D7-6519       TCGA-D7-6520       TCGA-D7-6521 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6522       TCGA-D7-6524       TCGA-D7-6525       TCGA-D7-6526 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6527       TCGA-D7-6528       TCGA-D7-6815       TCGA-D7-6817 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6818       TCGA-D7-6820       TCGA-D7-6822       TCGA-D7-8570 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-8572       TCGA-D7-8573       TCGA-D7-8574       TCGA-D7-8575 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-8576       TCGA-D7-8578       TCGA-D7-8579       TCGA-D7-A4YT 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A4YU       TCGA-D7-A4YV       TCGA-D7-A4YX       TCGA-D7-A4YY 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A4Z0       TCGA-D7-A6ET       TCGA-D7-A6EV       TCGA-D7-A6EX 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A6EY       TCGA-D7-A6EZ       TCGA-D7-A6F0       TCGA-D7-A6F2 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A747       TCGA-D7-A748       TCGA-D7-A74A       TCGA-D7-A74B 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-EQ-5647       TCGA-EQ-8122       TCGA-F1-6874       TCGA-F1-6875 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-F1-A448       TCGA-F1-A72C       TCGA-FP-7735       TCGA-FP-7829 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-7916       TCGA-FP-7998       TCGA-FP-8099       TCGA-FP-8209 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-8210       TCGA-FP-8211       TCGA-FP-8631       TCGA-FP-A4BE 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-A4BF       TCGA-FP-A9TM       TCGA-HF-A5NB       TCGA-HJ-7597 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-8238       TCGA-HU-8243       TCGA-HU-8244       TCGA-HU-8249 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-8602       TCGA-HU-8604       TCGA-HU-8608       TCGA-HU-8610 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6       TCGA-HU-A4G8 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD       TCGA-HU-A4GF 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GH       TCGA-HU-A4GJ       TCGA-HU-A4GN       TCGA-HU-A4GP 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GQ       TCGA-HU-A4GU       TCGA-HU-A4GX       TCGA-HU-A4GY 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3       TCGA-HU-A4H4 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8       TCGA-HU-A4HB 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808       TCGA-IN-8462 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-8663       TCGA-IN-A6RI       TCGA-IN-A6RJ       TCGA-IN-A6RL 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-A6RN       TCGA-IN-A6RO       TCGA-IN-A6RP       TCGA-IN-A6RR 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-A6RS       TCGA-IN-A7NR       TCGA-IN-A7NT       TCGA-IN-A7NU 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-AB1V       TCGA-IN-AB1X       TCGA-IP-7968       TCGA-KB-A6F5 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-KB-A6F7       TCGA-KB-A93J       TCGA-MX-A5UG       TCGA-MX-A5UJ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-MX-A666       TCGA-R5-A7O7       TCGA-R5-A7ZE       TCGA-R5-A7ZF 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-R5-A7ZI       TCGA-R5-A7ZR       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" 
                  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       2       15       40       29        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MBOAT2 MUTATED           0          0          0          0        0
  MBOAT2 WILD-TYPE         3         70         53         32       38
D889V3, multiclass
[1] "Remove cluster labels:" "MBOAT2 MUTATED"        
clus
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               2              370 
      TCGA-CG-4444       TCGA-CG-4460       TCGA-CG-4475       TCGA-CG-4476 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5716       TCGA-CG-5727       TCGA-EQ-A4SO       TCGA-F1-6177 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-A8CX       TCGA-HF-7131       TCGA-KB-A93G       TCGA-MX-A663 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-B7-A5TI       TCGA-B7-A5TJ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-B7-A5TK       TCGA-B7-A5TN       TCGA-BR-4183       TCGA-BR-4184 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4267       TCGA-BR-4279 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4280       TCGA-BR-4361       TCGA-BR-4368       TCGA-BR-6452 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6453       TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6457       TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6565       TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6707       TCGA-BR-6709       TCGA-BR-6710       TCGA-BR-6801 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6802       TCGA-BR-6803       TCGA-BR-6852       TCGA-BR-7196 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7197       TCGA-BR-7703       TCGA-BR-7704       TCGA-BR-7707 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717       TCGA-BR-7722 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901       TCGA-BR-7957 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058       TCGA-BR-8059 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8060       TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8285       TCGA-BR-8286 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8289       TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8297 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8373       TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8384       TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8486       TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8590       TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8677       TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8682       TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8690       TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A453       TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4IU       TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4J1       TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J5 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4J6       TCGA-BR-A4J7       TCGA-BR-A4J8       TCGA-BR-A4PD 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4PE       TCGA-BR-A4PF       TCGA-BR-A4QI       TCGA-BR-A4QL 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4QM       TCGA-CD-5798       TCGA-CD-5799       TCGA-CD-5800 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-5801       TCGA-CD-5802       TCGA-CD-5803       TCGA-CD-5813 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8524       TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8527 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8528       TCGA-CD-8529       TCGA-CD-8530       TCGA-CD-8531 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8532       TCGA-CD-8533       TCGA-CD-8534       TCGA-CD-8535 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8536       TCGA-CD-A486       TCGA-CD-A487       TCGA-CD-A489 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A48A       TCGA-CD-A48C       TCGA-CD-A4MG       TCGA-CD-A4MH 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A4MI       TCGA-CD-A4MJ       TCGA-CG-4300       TCGA-CG-4301 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4304       TCGA-CG-4305       TCGA-CG-4306       TCGA-CG-4436 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4437       TCGA-CG-4438       TCGA-CG-4440       TCGA-CG-4441 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4442       TCGA-CG-4443       TCGA-CG-4449       TCGA-CG-4455 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466       TCGA-CG-4469 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4474       TCGA-CG-4477       TCGA-CG-5717       TCGA-CG-5718 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5719       TCGA-CG-5720       TCGA-CG-5721       TCGA-CG-5722 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5723       TCGA-CG-5724       TCGA-CG-5725       TCGA-CG-5726 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5728       TCGA-CG-5730       TCGA-CG-5732       TCGA-CG-5733 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5734       TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6518       TCGA-D7-6520       TCGA-D7-6522       TCGA-D7-6524 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6525       TCGA-D7-6526       TCGA-D7-6527       TCGA-D7-6528 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6815       TCGA-D7-6817       TCGA-D7-6818       TCGA-D7-6820 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6822       TCGA-D7-8570       TCGA-D7-8572       TCGA-D7-8573 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-8574       TCGA-D7-8575       TCGA-D7-8576       TCGA-D7-8578 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-8579       TCGA-D7-A4YT       TCGA-D7-A4YU       TCGA-D7-A4YV 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A4YX       TCGA-D7-A4YY       TCGA-D7-A4Z0       TCGA-D7-A6ET 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A6EV       TCGA-D7-A6EX       TCGA-D7-A6EY       TCGA-D7-A6EZ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A6F0       TCGA-D7-A6F2       TCGA-D7-A747       TCGA-D7-A748 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-A74A       TCGA-D7-A74B       TCGA-EQ-5647       TCGA-EQ-8122 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-F1-6874       TCGA-F1-6875       TCGA-F1-A448       TCGA-F1-A72C 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-7735       TCGA-FP-7829       TCGA-FP-7916       TCGA-FP-7998 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-8099       TCGA-FP-8209       TCGA-FP-8210       TCGA-FP-8211 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-8631       TCGA-FP-A4BE       TCGA-FP-A4BF       TCGA-HF-7133 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HF-7134       TCGA-HF-7136       TCGA-HF-A5NB       TCGA-HJ-7597 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-8243       TCGA-HU-8244       TCGA-HU-8249       TCGA-HU-8602 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-8604       TCGA-HU-8608       TCGA-HU-8610       TCGA-HU-A4G2 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4G3       TCGA-HU-A4G6       TCGA-HU-A4G8       TCGA-HU-A4G9 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GC       TCGA-HU-A4GD       TCGA-HU-A4GF       TCGA-HU-A4GH 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GJ       TCGA-HU-A4GN       TCGA-HU-A4GP       TCGA-HU-A4GQ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GU       TCGA-HU-A4GX       TCGA-HU-A4GY       TCGA-HU-A4H0 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4H2       TCGA-HU-A4H3       TCGA-HU-A4H4       TCGA-HU-A4H5 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4H6       TCGA-HU-A4H8       TCGA-HU-A4HB       TCGA-HU-A4HD 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-7806       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-MX-A666       TCGA-R5-A7O7 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-R5-A7ZE       TCGA-R5-A7ZF       TCGA-R5-A7ZI       TCGA-R5-A7ZR 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-R5-A804       TCGA-R5-A805       TCGA-RD-A7BS       TCGA-RD-A7BT 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A7BW       TCGA-RD-A7C1       TCGA-RD-A8MV       TCGA-RD-A8MW 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A8N0       TCGA-RD-A8N1       TCGA-RD-A8N2       TCGA-RD-A8N4 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A8N5       TCGA-RD-A8N6       TCGA-RD-A8N9       TCGA-SW-A7EA 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-SW-A7EB       TCGA-VQ-A8DL       TCGA-VQ-A8DT       TCGA-VQ-A8DU 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A8DV       TCGA-VQ-A8DZ       TCGA-VQ-A8E2       TCGA-VQ-A8E7 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A8P2       TCGA-VQ-A8P3       TCGA-VQ-A8PE       TCGA-VQ-A8PK 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A8PM       TCGA-VQ-A8PQ       TCGA-VQ-A91Q       TCGA-VQ-A91U 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A91V       TCGA-VQ-A92D       TCGA-VQ-A94T       TCGA-VQ-AA64 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-AA68       TCGA-VQ-AA69       TCGA-VQ-AA6A       TCGA-VQ-AA6B 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-AA6F       TCGA-VQ-AA6G       TCGA-VQ-AA6I       TCGA-VQ-AA6J 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-AA6K       TCGA-ZA-A8F6 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
                  vv
clus                T1  T2  T3  T4
  MBOAT2 MUTATED     1   1   1   0
  MBOAT2 WILD-TYPE  21  91 172  97
D889V4, multiclass
    clus
vv   MBOAT2 MUTATED MBOAT2 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              1              172
  T4              0               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
  MBOAT2 MUTATED     1   1   0   0
  MBOAT2 WILD-TYPE 117 103  77  77
D889V5, multiclass
[1] "Remove cluster labels:" "MBOAT2 MUTATED"        
clus
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               2              374 
      TCGA-CG-4444       TCGA-CG-4460       TCGA-CG-4475       TCGA-CG-4476 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5716       TCGA-CG-5727       TCGA-EQ-A4SO       TCGA-F1-6177 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-FP-A8CX       TCGA-HF-7131       TCGA-KB-A93G       TCGA-MX-A663 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-B7-A5TI       TCGA-BR-4183 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4184       TCGA-BR-4188       TCGA-BR-4191       TCGA-BR-4253 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4255       TCGA-BR-4256       TCGA-BR-4267       TCGA-BR-4279 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4280       TCGA-BR-4361       TCGA-BR-4362       TCGA-BR-4368 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6452       TCGA-BR-6453       TCGA-BR-6454       TCGA-BR-6455 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6456       TCGA-BR-6457       TCGA-BR-6458       TCGA-BR-6563 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6564       TCGA-BR-6565       TCGA-BR-6566       TCGA-BR-6705 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6706       TCGA-BR-6707       TCGA-BR-6709       TCGA-BR-6710 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803       TCGA-BR-6852 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7196       TCGA-BR-7197       TCGA-BR-7703       TCGA-BR-7704 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7707       TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7722       TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-7957       TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8059       TCGA-BR-8060       TCGA-BR-8077       TCGA-BR-8078 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8080       TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8285 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8286       TCGA-BR-8289       TCGA-BR-8291       TCGA-BR-8295 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8297       TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8364       TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8368       TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8372       TCGA-BR-8373       TCGA-BR-8380       TCGA-BR-8381 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8382       TCGA-BR-8384       TCGA-BR-8483       TCGA-BR-8484 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8485       TCGA-BR-8486       TCGA-BR-8487       TCGA-BR-8588 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8589       TCGA-BR-8590       TCGA-BR-8591       TCGA-BR-8592 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8676       TCGA-BR-8677       TCGA-BR-8678       TCGA-BR-8679 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8680       TCGA-BR-8682       TCGA-BR-8683       TCGA-BR-8686 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-8687       TCGA-BR-8690       TCGA-BR-A44T       TCGA-BR-A44U 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A452       TCGA-BR-A453       TCGA-BR-A4CQ       TCGA-BR-A4CR 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4CS       TCGA-BR-A4IU       TCGA-BR-A4IV       TCGA-BR-A4IY 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4IZ       TCGA-BR-A4J1       TCGA-BR-A4J2       TCGA-BR-A4J4 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4J5       TCGA-BR-A4J6       TCGA-BR-A4J8       TCGA-BR-A4PD 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4PE       TCGA-BR-A4PF       TCGA-BR-A4QI       TCGA-BR-A4QL 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-A4QM       TCGA-CD-5798       TCGA-CD-5799       TCGA-CD-5800 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-5801       TCGA-CD-5802       TCGA-CD-5803       TCGA-CD-5804 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-5813       TCGA-CD-8524       TCGA-CD-8525       TCGA-CD-8526 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8527       TCGA-CD-8528       TCGA-CD-8529       TCGA-CD-8530 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8531       TCGA-CD-8532       TCGA-CD-8533       TCGA-CD-8534 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8535       TCGA-CD-8536       TCGA-CD-A486       TCGA-CD-A487 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A489       TCGA-CD-A48A       TCGA-CD-A48C       TCGA-CD-A4MG 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A4MH       TCGA-CD-A4MI       TCGA-CD-A4MJ       TCGA-CG-4300 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305       TCGA-CG-4306 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4436       TCGA-CG-4437       TCGA-CG-4438       TCGA-CG-4440 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4441       TCGA-CG-4442       TCGA-CG-4443       TCGA-CG-4449 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4455       TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4469       TCGA-CG-4474       TCGA-CG-4477       TCGA-CG-5717 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5718       TCGA-CG-5719       TCGA-CG-5720       TCGA-CG-5721 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5722       TCGA-CG-5723       TCGA-CG-5724       TCGA-CG-5725 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5726       TCGA-CG-5728       TCGA-CG-5730       TCGA-CG-5732 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5733       TCGA-CG-5734       TCGA-D7-5577       TCGA-D7-5578 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-5579       TCGA-D7-6518       TCGA-D7-6519       TCGA-D7-6520 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6521       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-FP-A9TM       TCGA-HF-7133 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HF-7134       TCGA-HF-7136       TCGA-HF-A5NB       TCGA-HJ-7597 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-8238       TCGA-HU-8243       TCGA-HU-8244       TCGA-HU-8249 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-8602       TCGA-HU-8604       TCGA-HU-8608       TCGA-HU-8610 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6       TCGA-HU-A4G8 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD       TCGA-HU-A4GF 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GH       TCGA-HU-A4GJ       TCGA-HU-A4GN       TCGA-HU-A4GP 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GQ       TCGA-HU-A4GU       TCGA-HU-A4GX       TCGA-HU-A4GY 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3       TCGA-HU-A4H4 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8       TCGA-HU-A4HB 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808       TCGA-IN-8462 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-8663       TCGA-IN-A6RI       TCGA-IN-A6RJ       TCGA-IN-A6RL 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-A6RN       TCGA-IN-A6RO       TCGA-IN-A6RP       TCGA-IN-A6RR 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-A6RS       TCGA-IN-A7NR       TCGA-IN-A7NT       TCGA-IN-A7NU 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-AB1V       TCGA-IN-AB1X       TCGA-IP-7968       TCGA-KB-A6F5 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-KB-A6F7       TCGA-KB-A93J       TCGA-MX-A5UG       TCGA-MX-A5UJ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-R5-A7O7       TCGA-R5-A7ZE       TCGA-R5-A7ZF       TCGA-R5-A7ZI 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-R5-A804       TCGA-R5-A805       TCGA-RD-A7BS       TCGA-RD-A7BT 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A7BW       TCGA-RD-A7C1       TCGA-RD-A8MV       TCGA-RD-A8MW 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A8N0       TCGA-RD-A8N1       TCGA-RD-A8N2       TCGA-RD-A8N4 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A8N5       TCGA-RD-A8N6       TCGA-RD-A8N9       TCGA-SW-A7EA 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-SW-A7EB       TCGA-VQ-A8DL       TCGA-VQ-A8DT       TCGA-VQ-A8DU 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A8DV       TCGA-VQ-A8DZ       TCGA-VQ-A8E2       TCGA-VQ-A8E7 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A8P2       TCGA-VQ-A8P3       TCGA-VQ-A8PE       TCGA-VQ-A8PK 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A8PM       TCGA-VQ-A8PQ       TCGA-VQ-A91Q       TCGA-VQ-A91U 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-A91V       TCGA-VQ-A92D       TCGA-VQ-A94T       TCGA-VQ-AA64 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-AA68       TCGA-VQ-AA69       TCGA-VQ-AA6A       TCGA-VQ-AA6B 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-AA6F       TCGA-VQ-AA6G       TCGA-VQ-AA6I       TCGA-VQ-AA6J 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-AA6K       TCGA-ZA-A8F6 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
D889V6, binary
                  cls
clus                 0   1
  MBOAT2 MUTATED     3   0
  MBOAT2 WILD-TYPE 343  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MBOAT2 MUTATED      3    0
  MBOAT2 WILD-TYPE  343   29
   clus
vv  MBOAT2 MUTATED MBOAT2 WILD-TYPE
  0              3              343
  1              0               29
[1] 2 2
[1] FALSE
D889V7, binary
                  cls
clus                 0   1
  MBOAT2 MUTATED     2   1
  MBOAT2 WILD-TYPE 143 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MBOAT2 MUTATED      2    1
  MBOAT2 WILD-TYPE  143  247
        clus
vv       MBOAT2 MUTATED MBOAT2 WILD-TYPE
  FEMALE              2              143
  MALE                1              247
[1] 2 2
[1] FALSE
D889V8, binary
                  cls
clus                 0   1
  MBOAT2 MUTATED     1   1
  MBOAT2 WILD-TYPE 291  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MBOAT2 MUTATED      1    1
  MBOAT2 WILD-TYPE  291   58
     clus
vv    MBOAT2 MUTATED MBOAT2 WILD-TYPE
  NO               1              291
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MBOAT2 MUTATED                                          0
  MBOAT2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MBOAT2 MUTATED                                       0
  MBOAT2 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MBOAT2 MUTATED                                                        1
  MBOAT2 WILD-TYPE                                                    157
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MBOAT2 MUTATED                                                   1
  MBOAT2 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MBOAT2 MUTATED                                                                   0
  MBOAT2 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MBOAT2 MUTATED                                                    0
  MBOAT2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MBOAT2 MUTATED                                                  1
  MBOAT2 WILD-TYPE                                               60
D889V9, multiclass
                                                                   clus
vv                                                                  MBOAT2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  MBOAT2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MBOAT2 MUTATED     2   0   0   1
  MBOAT2 WILD-TYPE 309  14  15  23
D889V10, multiclass
    clus
vv   MBOAT2 MUTATED MBOAT2 WILD-TYPE
  R0              2              309
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D889V11, continuous
[1] "Remove cluster labels:" "MBOAT2 MUTATED"        
clus
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               2              341 
      TCGA-CG-4444       TCGA-CG-4460       TCGA-CG-4475       TCGA-CG-4476 
"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-B7-5816 
"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-5804 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8531       TCGA-CD-8535 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A487       TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4436       TCGA-CG-4437       TCGA-CG-4438       TCGA-CG-4440 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4441       TCGA-CG-4442       TCGA-CG-4443       TCGA-CG-4449 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4455       TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-4469       TCGA-CG-4474       TCGA-CG-4477       TCGA-CG-5717 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5718       TCGA-CG-5719       TCGA-CG-5720       TCGA-CG-5721 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5722       TCGA-CG-5723       TCGA-CG-5724       TCGA-CG-5725 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5726       TCGA-CG-5728       TCGA-CG-5730       TCGA-CG-5732 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CG-5733       TCGA-CG-5734       TCGA-D7-5577       TCGA-D7-5578 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-5579       TCGA-D7-6518       TCGA-D7-6519       TCGA-D7-6520 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6521       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-FP-A9TM       TCGA-HF-7133 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HF-7134       TCGA-HF-7136       TCGA-HF-A5NB       TCGA-HJ-7597 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-8238       TCGA-HU-8243       TCGA-HU-8244       TCGA-HU-8249 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-8602       TCGA-HU-8604       TCGA-HU-8608       TCGA-HU-8610 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6       TCGA-HU-A4G8 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD       TCGA-HU-A4GF 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GH       TCGA-HU-A4GJ       TCGA-HU-A4GN       TCGA-HU-A4GP 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GQ       TCGA-HU-A4GU       TCGA-HU-A4GX       TCGA-HU-A4GY 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3       TCGA-HU-A4H4 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8       TCGA-HU-A4HB 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808       TCGA-IN-8462 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-8663       TCGA-IN-A6RI       TCGA-IN-A6RJ       TCGA-IN-A6RL 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-A6RN       TCGA-IN-A6RO       TCGA-IN-A6RP       TCGA-IN-A6RR 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-A6RS       TCGA-IN-A7NR       TCGA-IN-A7NT       TCGA-IN-A7NU 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-AB1V       TCGA-IN-AB1X       TCGA-IP-7968       TCGA-KB-A6F5 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-KB-A6F7       TCGA-KB-A93J       TCGA-MX-A5UG       TCGA-MX-A5UJ 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-R5-A7ZI       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               ASIAN BLACK OR AFRICAN AMERICAN
  MBOAT2 MUTATED       1                         0
  MBOAT2 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MBOAT2 MUTATED                                           0     1
  MBOAT2 WILD-TYPE                                         1   242
D889V12, multiclass
[1] "Remove cluster labels:" "MBOAT2 MUTATED"        
clus
  MBOAT2 MUTATED MBOAT2 WILD-TYPE 
               2              338 
      TCGA-EQ-A4SO       TCGA-F1-6177       TCGA-FP-A8CX       TCGA-KB-A93G 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-MX-A663       TCGA-B7-5816       TCGA-B7-5818       TCGA-B7-A5TI 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-B7-A5TJ       TCGA-B7-A5TK       TCGA-B7-A5TN       TCGA-BR-4183 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4184       TCGA-BR-4187       TCGA-BR-4188       TCGA-BR-4191 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4201       TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4257       TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4294       TCGA-BR-4357       TCGA-BR-4361       TCGA-BR-4362 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4363       TCGA-BR-4366       TCGA-BR-4368       TCGA-BR-4369 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-BR-4370       TCGA-BR-4371       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-5804       TCGA-CD-5813 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8524       TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8527 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8528       TCGA-CD-8529       TCGA-CD-8530       TCGA-CD-8531 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8532       TCGA-CD-8533       TCGA-CD-8534       TCGA-CD-8535 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-8536       TCGA-CD-A486       TCGA-CD-A487       TCGA-CD-A489 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A48A       TCGA-CD-A48C       TCGA-CD-A4MG       TCGA-CD-A4MH 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-CD-A4MI       TCGA-CD-A4MJ       TCGA-D7-5577       TCGA-D7-5578 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-5579       TCGA-D7-6518       TCGA-D7-6519       TCGA-D7-6520 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-D7-6521       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-FP-A9TM       TCGA-HJ-7597 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-8238       TCGA-HU-8243       TCGA-HU-8244       TCGA-HU-8249 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-8602       TCGA-HU-8604       TCGA-HU-8608       TCGA-HU-8610 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6       TCGA-HU-A4G8 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD       TCGA-HU-A4GF 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GH       TCGA-HU-A4GJ       TCGA-HU-A4GN       TCGA-HU-A4GP 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4GQ       TCGA-HU-A4GU       TCGA-HU-A4GX       TCGA-HU-A4GY 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3       TCGA-HU-A4H4 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8       TCGA-HU-A4HB 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808       TCGA-IN-8462 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-8663       TCGA-IN-A6RI       TCGA-IN-A6RJ       TCGA-IN-A6RL 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-A6RN       TCGA-IN-A6RO       TCGA-IN-A6RP       TCGA-IN-A6RR 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-A6RS       TCGA-IN-A7NR       TCGA-IN-A7NT       TCGA-IN-A7NU 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-IN-AB1V       TCGA-IN-AB1X       TCGA-IP-7968       TCGA-KB-A93J 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-MX-A5UG       TCGA-MX-A5UJ       TCGA-MX-A666       TCGA-R5-A7O7 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-R5-A7ZE       TCGA-R5-A7ZF       TCGA-R5-A7ZI       TCGA-R5-A7ZR 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-R5-A804       TCGA-R5-A805       TCGA-RD-A7BS       TCGA-RD-A7BT 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A7BW       TCGA-RD-A7C1       TCGA-RD-A8MV       TCGA-RD-A8MW 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A8N0       TCGA-RD-A8N1       TCGA-RD-A8N2       TCGA-RD-A8N4 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-RD-A8N5       TCGA-RD-A8N6       TCGA-RD-A8N9       TCGA-SW-A7EA 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-SW-A7EB       TCGA-VQ-A8DL       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-A91U       TCGA-VQ-A92D       TCGA-VQ-AA64 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-AA68       TCGA-VQ-AA69       TCGA-VQ-AA6A       TCGA-VQ-AA6B 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-AA6F       TCGA-VQ-AA6G       TCGA-VQ-AA6I       TCGA-VQ-AA6J 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
      TCGA-VQ-AA6K       TCGA-ZA-A8F6 
"MBOAT2 WILD-TYPE" "MBOAT2 WILD-TYPE" 
D889V13, binary
                  cls
clus                 0   1
  MBOAT2 MUTATED     0   2
  MBOAT2 WILD-TYPE   4 308
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MBOAT2 MUTATED      0    2
  MBOAT2 WILD-TYPE    4  308
                        clus
vv                       MBOAT2 MUTATED MBOAT2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              2              308
[1] 2 2
[1] FALSE

Clustering(890) Variable = GIMAP7 MUTATION ANALYSIS
D890V1, survival
                  sevent
clus2                0   1
  GIMAP7 MUTATED     4   1
  GIMAP7 WILD-TYPE 226 138
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
               5              364 
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
               1              138 
$`GIMAP7 MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7703 TCGA-CG-5726 TCGA-HU-8602 
       34.68        32.78        36.16        28.96        22.32 

$`GIMAP7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
           22.32             0.00 
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
           36.16           122.30 
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
           32.78            14.07 
[1] "22.3 - 36.2 (32.8)" "0.0 - 122.3 (14.1)"
[1] "hr=" "3.3"
D890V2, 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       2       13       40       30        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GIMAP7 MUTATED           0          0          0          0        0
  GIMAP7 WILD-TYPE         3         70         53         32       38
D890V3, multiclass
            clus
vv           GIMAP7 MUTATED GIMAP7 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                2               13
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GIMAP7 MUTATED     2   0   2   1
  GIMAP7 WILD-TYPE  20  92 171  96
D890V4, multiclass
    clus
vv   GIMAP7 MUTATED GIMAP7 WILD-TYPE
  T1              2               20
  T2              0               92
  T3              2              171
  T4              1               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
  GIMAP7 MUTATED     5   0   0   0
  GIMAP7 WILD-TYPE 113 104  77  77
D890V5, multiclass
    clus
vv   GIMAP7 MUTATED GIMAP7 WILD-TYPE
  N0              5              113
  N1              0              104
  N2              0               77
  N3              0               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"
D890V6, binary
                  cls
clus                 0   1
  GIMAP7 MUTATED     5   0
  GIMAP7 WILD-TYPE 341  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP7 MUTATED      5    0
  GIMAP7 WILD-TYPE  341   29
   clus
vv  GIMAP7 MUTATED GIMAP7 WILD-TYPE
  0              5              341
  1              0               29
[1] 2 2
[1] FALSE
D890V7, binary
                  cls
clus                 0   1
  GIMAP7 MUTATED     3   2
  GIMAP7 WILD-TYPE 142 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP7 MUTATED      3    2
  GIMAP7 WILD-TYPE  142  246
        clus
vv       GIMAP7 MUTATED GIMAP7 WILD-TYPE
  FEMALE              3              142
  MALE                2              246
[1] 2 2
[1] FALSE
D890V8, binary
                  cls
clus                 0   1
  GIMAP7 MUTATED     4   0
  GIMAP7 WILD-TYPE 288  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP7 MUTATED      4    0
  GIMAP7 WILD-TYPE  288   59
     clus
vv    GIMAP7 MUTATED GIMAP7 WILD-TYPE
  NO               4              288
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GIMAP7 MUTATED                                          0
  GIMAP7 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GIMAP7 MUTATED                                       1
  GIMAP7 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GIMAP7 MUTATED                                                        2
  GIMAP7 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GIMAP7 MUTATED                                                   0
  GIMAP7 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GIMAP7 MUTATED                                                                   1
  GIMAP7 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GIMAP7 MUTATED                                                    1
  GIMAP7 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GIMAP7 MUTATED                                                  0
  GIMAP7 WILD-TYPE                                               61
D890V9, multiclass
                                                                   clus
vv                                                                  GIMAP7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  GIMAP7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GIMAP7 MUTATED     5   0   0   0
  GIMAP7 WILD-TYPE 306  14  15  24
D890V10, multiclass
    clus
vv   GIMAP7 MUTATED GIMAP7 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D890V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GIMAP7 MUTATED       1                         0
  GIMAP7 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GIMAP7 MUTATED                                           0     3
  GIMAP7 WILD-TYPE                                         1   240
D890V12, multiclass
                                           clus
vv                                          GIMAP7 MUTATED GIMAP7 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D890V13, binary
                  cls
clus                 0   1
  GIMAP7 MUTATED     0   4
  GIMAP7 WILD-TYPE   4 306
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP7 MUTATED      0    4
  GIMAP7 WILD-TYPE    4  306
                        clus
vv                       GIMAP7 MUTATED GIMAP7 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              306
[1] 2 2
[1] FALSE

Clustering(891) Variable = C2CD3 MUTATION ANALYSIS
D891V1, survival
                 sevent
clus2               0   1
  C2CD3 MUTATED    12   9
  C2CD3 WILD-TYPE 218 130
  C2CD3 MUTATED C2CD3 WILD-TYPE 
             21             348 
  C2CD3 MUTATED C2CD3 WILD-TYPE 
              9             130 
$`C2CD3 MUTATED`
TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8589 
       30.90         4.08        31.10         4.31         1.12        27.12 
TCGA-BR-8680 TCGA-BR-A452 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CG-4477 TCGA-CG-5721 
       31.96         7.53        11.61         6.58        30.97         6.02 
TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GX TCGA-HU-A4H8 TCGA-RD-A7BS 
       11.44        22.32        24.20        20.25        14.07        11.05 
TCGA-VQ-A8DL TCGA-VQ-A92D TCGA-VQ-AA6K 
        0.92        66.81        12.43 

$`C2CD3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       18.35         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-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-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-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-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-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5722 
        7.07         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-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-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-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-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-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-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-ZA-A8F6 
       32.94        54.12        26.04        16.14        27.55        17.26 

  C2CD3 MUTATED C2CD3 WILD-TYPE 
           0.92            0.00 
  C2CD3 MUTATED C2CD3 WILD-TYPE 
          66.81          122.30 
  C2CD3 MUTATED C2CD3 WILD-TYPE 
          12.43           14.45 
[1] "0.9 - 66.8 (12.4)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D891V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C2CD3 MUTATED         0        1        5        0         3         2
  C2CD3 WILD-TYPE       2       14       35       30        34        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C2CD3 MUTATED           0          3          2          3        2
  C2CD3 WILD-TYPE         3         67         51         29       36
D891V3, multiclass
            clus
vv           C2CD3 MUTATED C2CD3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               5              35
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  C2CD3 MUTATED     3   5   7   8
  C2CD3 WILD-TYPE  19  87 166  89
D891V4, multiclass
    clus
vv   C2CD3 MUTATED C2CD3 WILD-TYPE
  T1             3              19
  T2             5              87
  T3             7             166
  T4             8              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
  C2CD3 MUTATED     9   7   3   2
  C2CD3 WILD-TYPE 109  97  74  75
D891V5, multiclass
    clus
vv   C2CD3 MUTATED C2CD3 WILD-TYPE
  N0             9             109
  N1             7              97
  N2             3              74
  N3             2              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"
D891V6, binary
                 cls
clus                0   1
  C2CD3 MUTATED    22   1
  C2CD3 WILD-TYPE 324  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C2CD3 MUTATED     22    1
  C2CD3 WILD-TYPE  324   28
   clus
vv  C2CD3 MUTATED C2CD3 WILD-TYPE
  0            22             324
  1             1              28
[1] 2 2
[1] FALSE
D891V7, binary
                 cls
clus                0   1
  C2CD3 MUTATED    13  10
  C2CD3 WILD-TYPE 132 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C2CD3 MUTATED     13   10
  C2CD3 WILD-TYPE  132  238
        clus
vv       C2CD3 MUTATED C2CD3 WILD-TYPE
  FEMALE            13             132
  MALE              10             238
[1] 2 2
[1] FALSE
D891V8, binary
                 cls
clus                0   1
  C2CD3 MUTATED    18   3
  C2CD3 WILD-TYPE 274  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C2CD3 MUTATED     18    3
  C2CD3 WILD-TYPE  274   56
     clus
vv    C2CD3 MUTATED C2CD3 WILD-TYPE
  NO             18             274
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C2CD3 MUTATED                                          1
  C2CD3 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C2CD3 MUTATED                                       4
  C2CD3 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C2CD3 MUTATED                                                        8
  C2CD3 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C2CD3 MUTATED                                                   0
  C2CD3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C2CD3 MUTATED                                                                   3
  C2CD3 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C2CD3 MUTATED                                                    0
  C2CD3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C2CD3 MUTATED                                                  7
  C2CD3 WILD-TYPE                                               54
D891V9, multiclass
                                                                   clus
vv                                                                  C2CD3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              7
                                                                   clus
vv                                                                  C2CD3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  C2CD3 MUTATED    17   1   0   3
  C2CD3 WILD-TYPE 294  13  15  21
D891V10, multiclass
    clus
vv   C2CD3 MUTATED C2CD3 WILD-TYPE
  R0            17             294
  R1             1              13
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D891V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  C2CD3 MUTATED       8                         0
  C2CD3 WILD-TYPE    79                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C2CD3 MUTATED                                           0    12
  C2CD3 WILD-TYPE                                         1   231
D891V12, multiclass
                                           clus
vv                                          C2CD3 MUTATED C2CD3 WILD-TYPE
  ASIAN                                                 8              79
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D891V13, binary
                 cls
clus                0   1
  C2CD3 MUTATED     0  17
  C2CD3 WILD-TYPE   4 293
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C2CD3 MUTATED      0   17
  C2CD3 WILD-TYPE    4  293
                        clus
vv                       C2CD3 MUTATED C2CD3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            17             293
[1] 2 2
[1] FALSE

Clustering(892) Variable = TAF1D MUTATION ANALYSIS
D892V1, survival
                 sevent
clus2               0   1
  TAF1D MUTATED     6   1
  TAF1D WILD-TYPE 224 138
  TAF1D MUTATED TAF1D WILD-TYPE 
              7             362 
  TAF1D MUTATED TAF1D WILD-TYPE 
              1             138 
$`TAF1D MUTATED`
TCGA-CG-4437 TCGA-CG-5721 TCGA-D7-A4YY TCGA-EQ-5647 TCGA-HF-A5NB TCGA-HU-A4GN 
        8.05         6.02        13.78         0.62        30.51        29.98 
TCGA-HU-A4HD 
       33.40 

$`TAF1D WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  TAF1D MUTATED TAF1D WILD-TYPE 
           0.62            0.00 
  TAF1D MUTATED TAF1D WILD-TYPE 
           33.4           122.3 
  TAF1D MUTATED TAF1D WILD-TYPE 
          13.78           14.35 
[1] "0.6 - 33.4 (13.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.6"
D892V2, 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       2       15       40       29        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAF1D MUTATED           0          1          1          1        2
  TAF1D WILD-TYPE         3         69         52         31       36
D892V3, multiclass
            clus
vv           TAF1D MUTATED TAF1D WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TAF1D MUTATED     0   2   2   3
  TAF1D WILD-TYPE  22  90 171  94
D892V4, multiclass
    clus
vv   TAF1D MUTATED TAF1D WILD-TYPE
  T1             0              22
  T2             2              90
  T3             2             171
  T4             3              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
  TAF1D MUTATED     0   3   1   3
  TAF1D WILD-TYPE 118 101  76  74
D892V5, multiclass
    clus
vv   TAF1D MUTATED TAF1D WILD-TYPE
  N0             0             118
  N1             3             101
  N2             1              76
  N3             3              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"
D892V6, binary
                 cls
clus                0   1
  TAF1D MUTATED     6   1
  TAF1D WILD-TYPE 340  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1D MUTATED      6    1
  TAF1D WILD-TYPE  340   28
   clus
vv  TAF1D MUTATED TAF1D WILD-TYPE
  0             6             340
  1             1              28
[1] 2 2
[1] FALSE
D892V7, binary
                 cls
clus                0   1
  TAF1D MUTATED     2   5
  TAF1D WILD-TYPE 143 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1D MUTATED      2    5
  TAF1D WILD-TYPE  143  243
        clus
vv       TAF1D MUTATED TAF1D WILD-TYPE
  FEMALE             2             143
  MALE               5             243
[1] 2 2
[1] FALSE
D892V8, binary
                 cls
clus                0   1
  TAF1D MUTATED     5   2
  TAF1D WILD-TYPE 287  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1D MUTATED      5    2
  TAF1D WILD-TYPE  287   57
     clus
vv    TAF1D MUTATED TAF1D WILD-TYPE
  NO              5             287
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TAF1D MUTATED                                          0
  TAF1D WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TAF1D MUTATED                                       0
  TAF1D WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TAF1D MUTATED                                                        2
  TAF1D WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TAF1D MUTATED                                                   1
  TAF1D WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TAF1D MUTATED                                                                   2
  TAF1D WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TAF1D MUTATED                                                    0
  TAF1D WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TAF1D MUTATED                                                  2
  TAF1D WILD-TYPE                                               59
D892V9, multiclass
                                                                   clus
vv                                                                  TAF1D MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  TAF1D WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TAF1D MUTATED     5   1   1   0
  TAF1D WILD-TYPE 306  13  14  24
D892V10, multiclass
    clus
vv   TAF1D MUTATED TAF1D WILD-TYPE
  R0             5             306
  R1             1              13
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D892V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TAF1D MUTATED       2                         0
  TAF1D WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TAF1D MUTATED                                           0     2
  TAF1D WILD-TYPE                                         1   241
D892V12, multiclass
                                           clus
vv                                          TAF1D MUTATED TAF1D WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D892V13, binary
                 cls
clus                0   1
  TAF1D MUTATED     0   4
  TAF1D WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1D MUTATED      0    4
  TAF1D WILD-TYPE    4  306
                        clus
vv                       TAF1D MUTATED TAF1D WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(893) Variable = CEP120 MUTATION ANALYSIS
D893V1, survival
                  sevent
clus2                0   1
  CEP120 MUTATED     7   4
  CEP120 WILD-TYPE 223 135
  CEP120 MUTATED CEP120 WILD-TYPE 
              11              358 
  CEP120 MUTATED CEP120 WILD-TYPE 
               4              135 
$`CEP120 MUTATED`
TCGA-BR-4184 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 
        6.97        29.59         9.60         1.12        31.96         6.02 
TCGA-CG-5726 TCGA-CG-5733 TCGA-HU-8602 TCGA-R5-A7ZI TCGA-VQ-A8P2 
       28.96        21.07        22.32        74.53        38.14 

$`CEP120 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-D7-6528 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-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 

  CEP120 MUTATED CEP120 WILD-TYPE 
            1.12             0.00 
  CEP120 MUTATED CEP120 WILD-TYPE 
           74.53           122.30 
  CEP120 MUTATED CEP120 WILD-TYPE 
           22.32            14.12 
[1] "1.1 - 74.5 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D893V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CEP120 MUTATED         0        1        0        0         1         2
  CEP120 WILD-TYPE       2       14       40       30        36        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP120 MUTATED           0          4          0          1        3
  CEP120 WILD-TYPE         3         66         53         31       35
D893V3, multiclass
            clus
vv           CEP120 MUTATED CEP120 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CEP120 MUTATED     1   1   2   8
  CEP120 WILD-TYPE  21  91 171  89
D893V4, multiclass
    clus
vv   CEP120 MUTATED CEP120 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              2              171
  T4              8               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
  CEP120 MUTATED     5   4   2   1
  CEP120 WILD-TYPE 113 100  75  76
D893V5, multiclass
    clus
vv   CEP120 MUTATED CEP120 WILD-TYPE
  N0              5              113
  N1              4              100
  N2              2               75
  N3              1               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"
D893V6, binary
                  cls
clus                 0   1
  CEP120 MUTATED     9   2
  CEP120 WILD-TYPE 337  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP120 MUTATED      9    2
  CEP120 WILD-TYPE  337   27
   clus
vv  CEP120 MUTATED CEP120 WILD-TYPE
  0              9              337
  1              2               27
[1] 2 2
[1] FALSE
D893V7, binary
                  cls
clus                 0   1
  CEP120 MUTATED     7   5
  CEP120 WILD-TYPE 138 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP120 MUTATED      7    5
  CEP120 WILD-TYPE  138  243
        clus
vv       CEP120 MUTATED CEP120 WILD-TYPE
  FEMALE              7              138
  MALE                5              243
[1] 2 2
[1] FALSE
D893V8, binary
                  cls
clus                 0   1
  CEP120 MUTATED     9   1
  CEP120 WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP120 MUTATED      9    1
  CEP120 WILD-TYPE  283   58
     clus
vv    CEP120 MUTATED CEP120 WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CEP120 MUTATED                                          0
  CEP120 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CEP120 MUTATED                                       2
  CEP120 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CEP120 MUTATED                                                        4
  CEP120 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CEP120 MUTATED                                                   2
  CEP120 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CEP120 MUTATED                                                                   3
  CEP120 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CEP120 MUTATED                                                    0
  CEP120 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CEP120 MUTATED                                                  1
  CEP120 WILD-TYPE                                               60
D893V9, multiclass
                                                                   clus
vv                                                                  CEP120 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  CEP120 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CEP120 MUTATED    10   0   0   2
  CEP120 WILD-TYPE 301  14  15  22
D893V10, multiclass
    clus
vv   CEP120 MUTATED CEP120 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D893V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CEP120 MUTATED       2                         0
  CEP120 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CEP120 MUTATED                                           0     7
  CEP120 WILD-TYPE                                         1   236
D893V12, multiclass
                                           clus
vv                                          CEP120 MUTATED CEP120 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D893V13, binary
                  cls
clus                 0   1
  CEP120 MUTATED     1   7
  CEP120 WILD-TYPE   3 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP120 MUTATED      1    7
  CEP120 WILD-TYPE    3  303
                        clus
vv                       CEP120 MUTATED CEP120 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(894) Variable = OR2M5 MUTATION ANALYSIS
D894V1, survival
                 sevent
clus2               0   1
  OR2M5 MUTATED     7   6
  OR2M5 WILD-TYPE 223 133
  OR2M5 MUTATED OR2M5 WILD-TYPE 
             13             356 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
              6             133 
$`OR2M5 MUTATED`
TCGA-B7-A5TJ TCGA-BR-4257 TCGA-BR-7723 TCGA-BR-8384 TCGA-BR-8686 TCGA-BR-8687 
       11.01         9.67        28.73         3.72        20.88         8.22 
TCGA-CD-A48C TCGA-D7-6527 TCGA-D7-A4YU TCGA-HU-A4G3 TCGA-HU-A4G9 TCGA-IN-A7NU 
       11.61        10.26        16.44         5.59        24.20        11.70 
TCGA-VQ-A8P2 
       38.14 

$`OR2M5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15         9.86        26.70        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-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-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-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        7.36        25.05         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-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-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-D7-6528 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-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-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
       21.07         0.76        24.30        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-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59         6.51        10.62        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 

  OR2M5 MUTATED OR2M5 WILD-TYPE 
           3.72            0.00 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
          38.14          122.30 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
          11.61           14.45 
[1] "3.7 - 38.1 (11.6)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.4"
D894V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OR2M5 MUTATED         0        1        1        1         0         4
  OR2M5 WILD-TYPE       2       14       39       29        37        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR2M5 MUTATED           0          1          4          2        0
  OR2M5 WILD-TYPE         3         69         49         30       38
D894V3, multiclass
            clus
vv           OR2M5 MUTATED OR2M5 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             4              49
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR2M5 MUTATED     1   3   4   6
  OR2M5 WILD-TYPE  21  89 169  91
D894V4, multiclass
    clus
vv   OR2M5 MUTATED OR2M5 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             4             169
  T4             6              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
  OR2M5 MUTATED     3   4   3   3
  OR2M5 WILD-TYPE 115 100  74  74
D894V5, multiclass
    clus
vv   OR2M5 MUTATED OR2M5 WILD-TYPE
  N0             3             115
  N1             4             100
  N2             3              74
  N3             3              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"
D894V6, binary
                 cls
clus                0   1
  OR2M5 MUTATED    15   0
  OR2M5 WILD-TYPE 331  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED     15    0
  OR2M5 WILD-TYPE  331   29
   clus
vv  OR2M5 MUTATED OR2M5 WILD-TYPE
  0            15             331
  1             0              29
[1] 2 2
[1] FALSE
D894V7, binary
                 cls
clus                0   1
  OR2M5 MUTATED     4  11
  OR2M5 WILD-TYPE 141 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      4   11
  OR2M5 WILD-TYPE  141  237
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  FEMALE             4             141
  MALE              11             237
[1] 2 2
[1] FALSE
D894V8, binary
                 cls
clus                0   1
  OR2M5 MUTATED    12   2
  OR2M5 WILD-TYPE 280  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED     12    2
  OR2M5 WILD-TYPE  280   57
     clus
vv    OR2M5 MUTATED OR2M5 WILD-TYPE
  NO             12             280
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OR2M5 MUTATED                                          0
  OR2M5 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OR2M5 MUTATED                                       0
  OR2M5 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OR2M5 MUTATED                                                        6
  OR2M5 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OR2M5 MUTATED                                                   1
  OR2M5 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OR2M5 MUTATED                                                                   3
  OR2M5 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OR2M5 MUTATED                                                    1
  OR2M5 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OR2M5 MUTATED                                                  4
  OR2M5 WILD-TYPE                                               57
D894V9, multiclass
                                                                   clus
vv                                                                  OR2M5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  OR2M5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR2M5 MUTATED    11   1   0   1
  OR2M5 WILD-TYPE 300  13  15  23
D894V10, multiclass
    clus
vv   OR2M5 MUTATED OR2M5 WILD-TYPE
  R0            11             300
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D894V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OR2M5 MUTATED       4                         0
  OR2M5 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OR2M5 MUTATED                                           0    10
  OR2M5 WILD-TYPE                                         1   233
D894V12, multiclass
                                           clus
vv                                          OR2M5 MUTATED OR2M5 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D894V13, binary
                 cls
clus                0   1
  OR2M5 MUTATED     0  13
  OR2M5 WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      0   13
  OR2M5 WILD-TYPE    4  297
                        clus
vv                       OR2M5 MUTATED OR2M5 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(895) Variable = ANKMY2 MUTATION ANALYSIS
D895V1, survival
                  sevent
clus2                0   1
  ANKMY2 MUTATED     3   1
  ANKMY2 WILD-TYPE 227 138
  ANKMY2 MUTATED ANKMY2 WILD-TYPE 
               4              365 
  ANKMY2 MUTATED ANKMY2 WILD-TYPE 
               1              138 
$`ANKMY2 MUTATED`
TCGA-BR-6705 TCGA-BR-8680 TCGA-D7-A4YT TCGA-VQ-A8P2 
       25.61        31.96        14.27        38.14 

$`ANKMY2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  ANKMY2 MUTATED ANKMY2 WILD-TYPE 
           14.27             0.00 
  ANKMY2 MUTATED ANKMY2 WILD-TYPE 
           38.14           122.30 
  ANKMY2 MUTATED ANKMY2 WILD-TYPE 
          28.785           14.070 
[1] "14.3 - 38.1 (28.8)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.3"
D895V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKMY2 MUTATED         0        0        0        0         0         0
  ANKMY2 WILD-TYPE       2       15       40       30        37        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKMY2 MUTATED           0          2          1          0        1
  ANKMY2 WILD-TYPE         3         68         52         32       37
D895V3, multiclass
            clus
vv           ANKMY2 MUTATED ANKMY2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ANKMY2 MUTATED     0   1   1   2
  ANKMY2 WILD-TYPE  22  91 172  95
D895V4, multiclass
    clus
vv   ANKMY2 MUTATED ANKMY2 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              1              172
  T4              2               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
  ANKMY2 MUTATED     0   1   1   2
  ANKMY2 WILD-TYPE 118 103  76  75
D895V5, multiclass
    clus
vv   ANKMY2 MUTATED ANKMY2 WILD-TYPE
  N0              0              118
  N1              1              103
  N2              1               76
  N3              2               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"
D895V6, binary
                  cls
clus                 0   1
  ANKMY2 MUTATED     3   1
  ANKMY2 WILD-TYPE 343  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKMY2 MUTATED      3    1
  ANKMY2 WILD-TYPE  343   28
   clus
vv  ANKMY2 MUTATED ANKMY2 WILD-TYPE
  0              3              343
  1              1               28
[1] 2 2
[1] FALSE
D895V7, binary
                  cls
clus                 0   1
  ANKMY2 MUTATED     1   3
  ANKMY2 WILD-TYPE 144 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKMY2 MUTATED      1    3
  ANKMY2 WILD-TYPE  144  245
        clus
vv       ANKMY2 MUTATED ANKMY2 WILD-TYPE
  FEMALE              1              144
  MALE                3              245
[1] 2 2
[1] FALSE
D895V8, binary
                  cls
clus                 0   1
  ANKMY2 MUTATED     3   1
  ANKMY2 WILD-TYPE 289  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKMY2 MUTATED      3    1
  ANKMY2 WILD-TYPE  289   58
     clus
vv    ANKMY2 MUTATED ANKMY2 WILD-TYPE
  NO               3              289
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ANKMY2 MUTATED                                          0
  ANKMY2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ANKMY2 MUTATED                                       0
  ANKMY2 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANKMY2 MUTATED                                                        1
  ANKMY2 WILD-TYPE                                                    157
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ANKMY2 MUTATED                                                   1
  ANKMY2 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANKMY2 MUTATED                                                                   0
  ANKMY2 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ANKMY2 MUTATED                                                    0
  ANKMY2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ANKMY2 MUTATED                                                  2
  ANKMY2 WILD-TYPE                                               59
D895V9, multiclass
                                                                   clus
vv                                                                  ANKMY2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  ANKMY2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ANKMY2 MUTATED     4   0   0   0
  ANKMY2 WILD-TYPE 307  14  15  24
D895V10, multiclass
    clus
vv   ANKMY2 MUTATED ANKMY2 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D895V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ANKMY2 MUTATED       1                         0
  ANKMY2 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANKMY2 MUTATED                                           0     3
  ANKMY2 WILD-TYPE                                         1   240
D895V12, multiclass
                                           clus
vv                                          ANKMY2 MUTATED ANKMY2 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D895V13, binary
                  cls
clus                 0   1
  ANKMY2 MUTATED     0   3
  ANKMY2 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKMY2 MUTATED      0    3
  ANKMY2 WILD-TYPE    4  307
                        clus
vv                       ANKMY2 MUTATED ANKMY2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(896) Variable = TYRO3 MUTATION ANALYSIS
D896V1, survival
                 sevent
clus2               0   1
  TYRO3 MUTATED     8   3
  TYRO3 WILD-TYPE 222 136
  TYRO3 MUTATED TYRO3 WILD-TYPE 
             11             358 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
              3             136 
$`TYRO3 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.58         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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  TYRO3 MUTATED TYRO3 WILD-TYPE 
            0.1             0.0 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
          38.14          122.30 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
          14.47           14.22 
[1] "0.1 - 38.1 (14.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D896V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TYRO3 MUTATED         0        0        1        1         3         0
  TYRO3 WILD-TYPE       2       15       39       29        34        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TYRO3 MUTATED           0          2          1          2        1
  TYRO3 WILD-TYPE         3         68         52         30       37
D896V3, multiclass
            clus
vv           TYRO3 MUTATED TYRO3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TYRO3 MUTATED     0   2   3   6
  TYRO3 WILD-TYPE  22  90 170  91
D896V4, multiclass
    clus
vv   TYRO3 MUTATED TYRO3 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             3             170
  T4             6              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
  TYRO3 MUTATED     5   4   2   0
  TYRO3 WILD-TYPE 113 100  75  77
D896V5, multiclass
    clus
vv   TYRO3 MUTATED TYRO3 WILD-TYPE
  N0             5             113
  N1             4             100
  N2             2              75
  N3             0              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"
D896V6, binary
                 cls
clus                0   1
  TYRO3 MUTATED    11   0
  TYRO3 WILD-TYPE 335  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED     11    0
  TYRO3 WILD-TYPE  335   29
   clus
vv  TYRO3 MUTATED TYRO3 WILD-TYPE
  0            11             335
  1             0              29
[1] 2 2
[1] FALSE
D896V7, binary
                 cls
clus                0   1
  TYRO3 MUTATED     3   8
  TYRO3 WILD-TYPE 142 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      3    8
  TYRO3 WILD-TYPE  142  240
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  FEMALE             3             142
  MALE               8             240
[1] 2 2
[1] FALSE
D896V8, binary
                 cls
clus                0   1
  TYRO3 MUTATED    10   1
  TYRO3 WILD-TYPE 282  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED     10    1
  TYRO3 WILD-TYPE  282   58
     clus
vv    TYRO3 MUTATED TYRO3 WILD-TYPE
  NO             10             282
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TYRO3 MUTATED                                          0
  TYRO3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TYRO3 MUTATED                                       3
  TYRO3 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TYRO3 MUTATED                                                        3
  TYRO3 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TYRO3 MUTATED                                                   1
  TYRO3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TYRO3 MUTATED                                                                   3
  TYRO3 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TYRO3 MUTATED                                                    0
  TYRO3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TYRO3 MUTATED                                                  1
  TYRO3 WILD-TYPE                                               60
D896V9, multiclass
                                                                   clus
vv                                                                  TYRO3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  TYRO3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TYRO3 MUTATED    10   0   0   0
  TYRO3 WILD-TYPE 301  14  15  24
D896V10, multiclass
    clus
vv   TYRO3 MUTATED TYRO3 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D896V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TYRO3 MUTATED       4                         0
  TYRO3 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TYRO3 MUTATED                                           0     5
  TYRO3 WILD-TYPE                                         1   238
D896V12, multiclass
                                           clus
vv                                          TYRO3 MUTATED TYRO3 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D896V13, binary
                 cls
clus                0   1
  TYRO3 MUTATED     0   7
  TYRO3 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      0    7
  TYRO3 WILD-TYPE    4  303
                        clus
vv                       TYRO3 MUTATED TYRO3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(897) Variable = VASH1 MUTATION ANALYSIS
D897V1, survival
                 sevent
clus2               0   1
  VASH1 MUTATED     6   1
  VASH1 WILD-TYPE 224 138
  VASH1 MUTATED VASH1 WILD-TYPE 
              7             362 
  VASH1 MUTATED VASH1 WILD-TYPE 
              1             138 
$`VASH1 MUTATED`
TCGA-BR-6705 TCGA-BR-6852 TCGA-BR-8680 TCGA-CD-A4MJ TCGA-CG-4305 TCGA-HU-A4G9 
       25.61        44.94        31.96        12.62        15.95        24.20 
TCGA-HU-A4GU 
        6.58 

$`VASH1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  VASH1 MUTATED VASH1 WILD-TYPE 
           6.58            0.00 
  VASH1 MUTATED VASH1 WILD-TYPE 
          44.94          122.30 
  VASH1 MUTATED VASH1 WILD-TYPE 
          24.20           14.12 
[1] "6.6 - 44.9 (24.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.3"
D897V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VASH1 MUTATED         0        1        1        1         1         1
  VASH1 WILD-TYPE       2       14       39       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VASH1 MUTATED           0          0          1          0        1
  VASH1 WILD-TYPE         3         70         52         32       37
D897V3, multiclass
            clus
vv           VASH1 MUTATED VASH1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VASH1 MUTATED     1   2   3   1
  VASH1 WILD-TYPE  21  90 170  96
D897V4, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             3             170
  T4             1              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
  VASH1 MUTATED     3   2   1   1
  VASH1 WILD-TYPE 115 102  76  76
D897V5, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  N0             3             115
  N1             2             102
  N2             1              76
  N3             1              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"
D897V6, binary
                 cls
clus                0   1
  VASH1 MUTATED     6   1
  VASH1 WILD-TYPE 340  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      6    1
  VASH1 WILD-TYPE  340   28
   clus
vv  VASH1 MUTATED VASH1 WILD-TYPE
  0             6             340
  1             1              28
[1] 2 2
[1] FALSE
D897V7, binary
                 cls
clus                0   1
  VASH1 MUTATED     3   4
  VASH1 WILD-TYPE 142 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      3    4
  VASH1 WILD-TYPE  142  244
        clus
vv       VASH1 MUTATED VASH1 WILD-TYPE
  FEMALE             3             142
  MALE               4             244
[1] 2 2
[1] FALSE
D897V8, binary
                 cls
clus                0   1
  VASH1 MUTATED     7   0
  VASH1 WILD-TYPE 285  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      7    0
  VASH1 WILD-TYPE  285   59
     clus
vv    VASH1 MUTATED VASH1 WILD-TYPE
  NO              7             285
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  VASH1 MUTATED                                          0
  VASH1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  VASH1 MUTATED                                       1
  VASH1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  VASH1 MUTATED                                                        4
  VASH1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  VASH1 MUTATED                                                   0
  VASH1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  VASH1 MUTATED                                                                   0
  VASH1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  VASH1 MUTATED                                                    0
  VASH1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  VASH1 MUTATED                                                  2
  VASH1 WILD-TYPE                                               59
D897V9, multiclass
                                                                   clus
vv                                                                  VASH1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  VASH1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  VASH1 MUTATED     6   0   0   0
  VASH1 WILD-TYPE 305  14  15  24
D897V10, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D897V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  VASH1 MUTATED       4                         0
  VASH1 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  VASH1 MUTATED                                           0     2
  VASH1 WILD-TYPE                                         1   241
D897V12, multiclass
                                           clus
vv                                          VASH1 MUTATED VASH1 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D897V13, binary
                 cls
clus                0   1
  VASH1 MUTATED     0   6
  VASH1 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      0    6
  VASH1 WILD-TYPE    4  304
                        clus
vv                       VASH1 MUTATED VASH1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(898) Variable = MCM4 MUTATION ANALYSIS
D898V1, survival
                sevent
clus2              0   1
  MCM4 MUTATED     7   4
  MCM4 WILD-TYPE 223 135
  MCM4 MUTATED MCM4 WILD-TYPE 
            11            358 
  MCM4 MUTATED MCM4 WILD-TYPE 
             4            135 
$`MCM4 MUTATED`
TCGA-BR-4257 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-7707 TCGA-BR-8680 TCGA-CD-A4MG 
        9.67        32.78        18.05        35.84        31.96         6.58 
TCGA-CG-5726 TCGA-HU-A4G8 TCGA-HU-A4GT TCGA-HU-A4GX TCGA-VQ-A8P2 
       28.96        22.68         6.51        20.25        38.14 

$`MCM4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-6705 
       13.68        19.33        39.12        26.10         9.17        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-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-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-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-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-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 

  MCM4 MUTATED MCM4 WILD-TYPE 
          6.51           0.00 
  MCM4 MUTATED MCM4 WILD-TYPE 
         38.14         122.30 
  MCM4 MUTATED MCM4 WILD-TYPE 
         22.68          14.07 
[1] "6.5 - 38.1 (22.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D898V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MCM4 MUTATED         0        1        2        0         3         1
  MCM4 WILD-TYPE       2       14       38       30        34        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MCM4 MUTATED           0          2          0          1        3
  MCM4 WILD-TYPE         3         68         53         31       35
D898V3, multiclass
            clus
vv           MCM4 MUTATED MCM4 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             3             34
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MCM4 MUTATED     2   2   5   5
  MCM4 WILD-TYPE  20  90 168  92
D898V4, multiclass
    clus
vv   MCM4 MUTATED MCM4 WILD-TYPE
  T1            2             20
  T2            2             90
  T3            5            168
  T4            5             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
  MCM4 MUTATED     6   3   4   0
  MCM4 WILD-TYPE 112 101  73  77
D898V5, multiclass
    clus
vv   MCM4 MUTATED MCM4 WILD-TYPE
  N0            6            112
  N1            3            101
  N2            4             73
  N3            0             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"
D898V6, binary
                cls
clus               0   1
  MCM4 MUTATED    13   2
  MCM4 WILD-TYPE 333  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM4 MUTATED     13    2
  MCM4 WILD-TYPE  333   27
   clus
vv  MCM4 MUTATED MCM4 WILD-TYPE
  0           13            333
  1            2             27
[1] 2 2
[1] FALSE
D898V7, binary
                cls
clus               0   1
  MCM4 MUTATED     9   6
  MCM4 WILD-TYPE 136 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM4 MUTATED      9    6
  MCM4 WILD-TYPE  136  242
        clus
vv       MCM4 MUTATED MCM4 WILD-TYPE
  FEMALE            9            136
  MALE              6            242
[1] 2 2
[1] FALSE
D898V8, binary
                cls
clus               0   1
  MCM4 MUTATED     9   1
  MCM4 WILD-TYPE 283  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM4 MUTATED      9    1
  MCM4 WILD-TYPE  283   58
     clus
vv    MCM4 MUTATED MCM4 WILD-TYPE
  NO             9            283
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MCM4 MUTATED                                          0
  MCM4 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MCM4 MUTATED                                       4
  MCM4 WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MCM4 MUTATED                                                        6
  MCM4 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MCM4 MUTATED                                                   1
  MCM4 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MCM4 MUTATED                                                                   2
  MCM4 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MCM4 MUTATED                                                    0
  MCM4 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MCM4 MUTATED                                                  2
  MCM4 WILD-TYPE                                               59
D898V9, multiclass
                                                                   clus
vv                                                                  MCM4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  MCM4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MCM4 MUTATED     9   0   1   3
  MCM4 WILD-TYPE 302  14  14  21
D898V10, multiclass
    clus
vv   MCM4 MUTATED MCM4 WILD-TYPE
  R0            9            302
  R1            0             14
  R2            1             14
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D898V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MCM4 MUTATED       5                         0
  MCM4 WILD-TYPE    82                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MCM4 MUTATED                                           0     7
  MCM4 WILD-TYPE                                         1   236
D898V12, multiclass
                                           clus
vv                                          MCM4 MUTATED MCM4 WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D898V13, binary
                cls
clus               0   1
  MCM4 MUTATED     0  11
  MCM4 WILD-TYPE   4 299
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM4 MUTATED      0   11
  MCM4 WILD-TYPE    4  299
                        clus
vv                       MCM4 MUTATED MCM4 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           11            299
[1] 2 2
[1] FALSE

Clustering(899) Variable = PPP1R12C MUTATION ANALYSIS
D899V1, survival
                    sevent
clus2                  0   1
  PPP1R12C MUTATED     5   2
  PPP1R12C WILD-TYPE 225 137
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 7                362 
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 2                137 
$`PPP1R12C MUTATED`
TCGA-BR-7703 TCGA-BR-8487 TCGA-BR-8680 TCGA-D7-A6EY TCGA-HU-A4G8 TCGA-VQ-A8P2 
       36.16         1.12        31.96        11.44        22.68        38.14 
TCGA-VQ-AA6I 
       16.14 

$`PPP1R12C WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-AA6J 
       28.41        38.93        32.94        54.12        26.04        27.55 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       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              14.12 
[1] "1.1 - 38.1 (22.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D899V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPP1R12C MUTATED         0        1        0        0         1         2
  PPP1R12C WILD-TYPE       2       14       40       30        36        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R12C MUTATED           0          2          2          0        1
  PPP1R12C WILD-TYPE         3         68         51         32       37
D899V3, multiclass
            clus
vv           PPP1R12C MUTATED PPP1R12C WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                2                 51
  STAGE IIIC                0                 32
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PPP1R12C MUTATED     1   0   4   4
  PPP1R12C WILD-TYPE  21  92 169  93
D899V4, multiclass
    clus
vv   PPP1R12C MUTATED PPP1R12C WILD-TYPE
  T1                1                 21
  T2                0                 92
  T3                4                169
  T4                4                 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
  PPP1R12C MUTATED     4   2   1   2
  PPP1R12C WILD-TYPE 114 102  76  75
D899V5, multiclass
    clus
vv   PPP1R12C MUTATED PPP1R12C WILD-TYPE
  N0                4                114
  N1                2                102
  N2                1                 76
  N3                2                 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"
D899V6, binary
                    cls
clus                   0   1
  PPP1R12C MUTATED     8   1
  PPP1R12C WILD-TYPE 338  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      8    1
  PPP1R12C WILD-TYPE  338   28
   clus
vv  PPP1R12C MUTATED PPP1R12C WILD-TYPE
  0                8                338
  1                1                 28
[1] 2 2
[1] FALSE
D899V7, binary
                    cls
clus                   0   1
  PPP1R12C MUTATED     4   5
  PPP1R12C WILD-TYPE 141 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      4    5
  PPP1R12C WILD-TYPE  141  243
        clus
vv       PPP1R12C MUTATED PPP1R12C WILD-TYPE
  FEMALE                4                141
  MALE                  5                243
[1] 2 2
[1] FALSE
D899V8, binary
                    cls
clus                   0   1
  PPP1R12C MUTATED     7   1
  PPP1R12C WILD-TYPE 285  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      7    1
  PPP1R12C WILD-TYPE  285   58
     clus
vv    PPP1R12C MUTATED PPP1R12C WILD-TYPE
  NO                 7                285
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PPP1R12C MUTATED                                          0
  PPP1R12C WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PPP1R12C MUTATED                                       1
  PPP1R12C WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPP1R12C MUTATED                                                        2
  PPP1R12C WILD-TYPE                                                    156
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PPP1R12C MUTATED                                                   1
  PPP1R12C WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPP1R12C MUTATED                                                                   2
  PPP1R12C WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PPP1R12C MUTATED                                                    1
  PPP1R12C WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PPP1R12C MUTATED                                                  2
  PPP1R12C WILD-TYPE                                               59
D899V9, multiclass
                                                                   clus
vv                                                                  PPP1R12C MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  PPP1R12C WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  PPP1R12C MUTATED     7   0   0   1
  PPP1R12C WILD-TYPE 304  14  15  23
D899V10, multiclass
    clus
vv   PPP1R12C MUTATED PPP1R12C WILD-TYPE
  R0                7                304
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D899V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  PPP1R12C MUTATED       2                         0
  PPP1R12C WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPP1R12C MUTATED                                           0     7
  PPP1R12C WILD-TYPE                                         1   236
D899V12, multiclass
                                           clus
vv                                          PPP1R12C MUTATED PPP1R12C WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D899V13, binary
                    cls
clus                   0   1
  PPP1R12C MUTATED     0   7
  PPP1R12C WILD-TYPE   4 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      0    7
  PPP1R12C WILD-TYPE    4  303
                        clus
vv                       PPP1R12C MUTATED PPP1R12C WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                7                303
[1] 2 2
[1] FALSE

Clustering(900) Variable = PRB1 MUTATION ANALYSIS
D900V1, survival
                sevent
clus2              0   1
  PRB1 MUTATED     0   3
  PRB1 WILD-TYPE 230 136
  PRB1 MUTATED PRB1 WILD-TYPE 
             3            366 
  PRB1 MUTATED PRB1 WILD-TYPE 
             3            136 
$`PRB1 MUTATED`
TCGA-BR-4201 TCGA-BR-4280 TCGA-CD-A4MG 
       30.90         6.61         6.58 

$`PRB1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  PRB1 MUTATED PRB1 WILD-TYPE 
          6.58           0.00 
  PRB1 MUTATED PRB1 WILD-TYPE 
          30.9          122.3 
  PRB1 MUTATED PRB1 WILD-TYPE 
          6.61          14.35 
[1] "6.6 - 30.9 (6.6)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "3.4"
D900V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRB1 MUTATED         0        0        0        0         1         0
  PRB1 WILD-TYPE       2       15       40       30        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRB1 MUTATED           1          0          0          0        0
  PRB1 WILD-TYPE         2         70         53         32       38
D900V3, multiclass
[1] "Remove cluster labels:" "PRB1 MUTATED"          
clus
  PRB1 MUTATED PRB1 WILD-TYPE 
             2            370 
    TCGA-CG-4444     TCGA-CG-4460     TCGA-CG-4475     TCGA-CG-4476 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5716     TCGA-CG-5727     TCGA-EQ-A4SO     TCGA-F1-6177 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FP-A8CX     TCGA-HF-7131     TCGA-KB-A93G     TCGA-MX-A663 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-B7-5816     TCGA-B7-5818     TCGA-B7-A5TI     TCGA-B7-A5TJ 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-B7-A5TK     TCGA-B7-A5TN     TCGA-BR-4183     TCGA-BR-4184 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-4253     TCGA-BR-4255     TCGA-BR-4267     TCGA-BR-4279 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-4361     TCGA-BR-4368     TCGA-BR-6452     TCGA-BR-6453 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6454     TCGA-BR-6455     TCGA-BR-6456     TCGA-BR-6457 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6458     TCGA-BR-6563     TCGA-BR-6564     TCGA-BR-6565 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6566     TCGA-BR-6705     TCGA-BR-6706     TCGA-BR-6707 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6709     TCGA-BR-6710     TCGA-BR-6801     TCGA-BR-6802 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6803     TCGA-BR-6852     TCGA-BR-7196     TCGA-BR-7197 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7703     TCGA-BR-7704     TCGA-BR-7707     TCGA-BR-7715 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7716     TCGA-BR-7717     TCGA-BR-7722     TCGA-BR-7723 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7851     TCGA-BR-7901     TCGA-BR-7957     TCGA-BR-7958 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7959     TCGA-BR-8058     TCGA-BR-8059     TCGA-BR-8060 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8077     TCGA-BR-8078     TCGA-BR-8080     TCGA-BR-8081 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8284     TCGA-BR-8285     TCGA-BR-8286     TCGA-BR-8289 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8291     TCGA-BR-8295     TCGA-BR-8297     TCGA-BR-8360 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8361     TCGA-BR-8363     TCGA-BR-8364     TCGA-BR-8365 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8366     TCGA-BR-8367     TCGA-BR-8368     TCGA-BR-8369 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8370     TCGA-BR-8371     TCGA-BR-8372     TCGA-BR-8373 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8380     TCGA-BR-8381     TCGA-BR-8382     TCGA-BR-8384 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8483     TCGA-BR-8484     TCGA-BR-8485     TCGA-BR-8486 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8487     TCGA-BR-8588     TCGA-BR-8589     TCGA-BR-8590 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8591     TCGA-BR-8592     TCGA-BR-8676     TCGA-BR-8677 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8678     TCGA-BR-8679     TCGA-BR-8680     TCGA-BR-8682 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8683     TCGA-BR-8686     TCGA-BR-8687     TCGA-BR-8690 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A44T     TCGA-BR-A44U     TCGA-BR-A452     TCGA-BR-A453 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4CQ     TCGA-BR-A4CR     TCGA-BR-A4CS     TCGA-BR-A4IU 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4IV     TCGA-BR-A4IY     TCGA-BR-A4IZ     TCGA-BR-A4J1 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4J2     TCGA-BR-A4J4     TCGA-BR-A4J5     TCGA-BR-A4J6 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4J7     TCGA-BR-A4J8     TCGA-BR-A4PD     TCGA-BR-A4PE 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4PF     TCGA-BR-A4QI     TCGA-BR-A4QL     TCGA-BR-A4QM 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-5798     TCGA-CD-5799     TCGA-CD-5800     TCGA-CD-5801 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-5802     TCGA-CD-5803     TCGA-CD-5813     TCGA-CD-8524 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-8525     TCGA-CD-8526     TCGA-CD-8527     TCGA-CD-8528 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-8529     TCGA-CD-8530     TCGA-CD-8531     TCGA-CD-8532 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-8533     TCGA-CD-8534     TCGA-CD-8535     TCGA-CD-8536 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-A486     TCGA-CD-A487     TCGA-CD-A489     TCGA-CD-A48A 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-A48C     TCGA-CD-A4MH     TCGA-CD-A4MI     TCGA-CD-A4MJ 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4300     TCGA-CG-4301     TCGA-CG-4304     TCGA-CG-4305 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4306     TCGA-CG-4436     TCGA-CG-4437     TCGA-CG-4438 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4440     TCGA-CG-4441     TCGA-CG-4442     TCGA-CG-4443 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4449     TCGA-CG-4455     TCGA-CG-4462     TCGA-CG-4465 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4466     TCGA-CG-4469     TCGA-CG-4474     TCGA-CG-4477 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5717     TCGA-CG-5718     TCGA-CG-5719     TCGA-CG-5720 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5721     TCGA-CG-5722     TCGA-CG-5723     TCGA-CG-5724 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5725     TCGA-CG-5726     TCGA-CG-5728     TCGA-CG-5730 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5732     TCGA-CG-5733     TCGA-CG-5734     TCGA-D7-5577 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-5578     TCGA-D7-5579     TCGA-D7-6518     TCGA-D7-6520 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-6522     TCGA-D7-6524     TCGA-D7-6525     TCGA-D7-6526 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-6527     TCGA-D7-6528     TCGA-D7-6815     TCGA-D7-6817 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-6818     TCGA-D7-6820     TCGA-D7-6822     TCGA-D7-8570 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-8572     TCGA-D7-8573     TCGA-D7-8574     TCGA-D7-8575 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-8576     TCGA-D7-8578     TCGA-D7-8579     TCGA-D7-A4YT 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A4YU     TCGA-D7-A4YV     TCGA-D7-A4YX     TCGA-D7-A4YY 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A4Z0     TCGA-D7-A6ET     TCGA-D7-A6EV     TCGA-D7-A6EX 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A6EY     TCGA-D7-A6EZ     TCGA-D7-A6F0     TCGA-D7-A6F2 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A747     TCGA-D7-A748     TCGA-D7-A74A     TCGA-D7-A74B 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-EQ-5647     TCGA-EQ-8122     TCGA-F1-6874     TCGA-F1-6875 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-F1-A448     TCGA-F1-A72C     TCGA-FP-7735     TCGA-FP-7829 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FP-7916     TCGA-FP-7998     TCGA-FP-8099     TCGA-FP-8209 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FP-8210     TCGA-FP-8211     TCGA-FP-8631     TCGA-FP-A4BE 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FP-A4BF     TCGA-HF-7132     TCGA-HF-7133     TCGA-HF-7134 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HF-7136     TCGA-HF-A5NB     TCGA-HJ-7597     TCGA-HU-8243 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-8244     TCGA-HU-8249     TCGA-HU-8602     TCGA-HU-8604 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-8608     TCGA-HU-8610     TCGA-HU-A4G2     TCGA-HU-A4G3 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4G6     TCGA-HU-A4G8     TCGA-HU-A4G9     TCGA-HU-A4GC 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4GD     TCGA-HU-A4GF     TCGA-HU-A4GH     TCGA-HU-A4GJ 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4GN     TCGA-HU-A4GP     TCGA-HU-A4GQ     TCGA-HU-A4GT 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4GU     TCGA-HU-A4GX     TCGA-HU-A4GY     TCGA-HU-A4H0 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4H2     TCGA-HU-A4H3     TCGA-HU-A4H4     TCGA-HU-A4H5 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4H6     TCGA-HU-A4H8     TCGA-HU-A4HB     TCGA-HU-A4HD 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-7806     TCGA-IN-8462     TCGA-IN-8663     TCGA-IN-A6RI 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-A6RJ     TCGA-IN-A6RL     TCGA-IN-A6RN     TCGA-IN-A6RO 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-A6RP     TCGA-IN-A6RR     TCGA-IN-A6RS     TCGA-IN-A7NR 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-A7NT     TCGA-IN-A7NU     TCGA-IN-AB1V     TCGA-IN-AB1X 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IP-7968     TCGA-KB-A6F5     TCGA-KB-A6F7     TCGA-KB-A93J 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-MX-A5UG     TCGA-MX-A5UJ     TCGA-MX-A666     TCGA-R5-A7O7 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-R5-A7ZE     TCGA-R5-A7ZF     TCGA-R5-A7ZI     TCGA-R5-A7ZR 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-R5-A804     TCGA-R5-A805     TCGA-RD-A7BS     TCGA-RD-A7BT 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-RD-A7BW     TCGA-RD-A7C1     TCGA-RD-A8MV     TCGA-RD-A8MW 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-RD-A8N0     TCGA-RD-A8N1     TCGA-RD-A8N2     TCGA-RD-A8N4 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-RD-A8N5     TCGA-RD-A8N6     TCGA-RD-A8N9     TCGA-SW-A7EA 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-SW-A7EB     TCGA-VQ-A8DL     TCGA-VQ-A8DT     TCGA-VQ-A8DU 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A8DV     TCGA-VQ-A8DZ     TCGA-VQ-A8E2     TCGA-VQ-A8E7 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A8P2     TCGA-VQ-A8P3     TCGA-VQ-A8PE     TCGA-VQ-A8PK 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A8PM     TCGA-VQ-A8PQ     TCGA-VQ-A91Q     TCGA-VQ-A91U 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A91V     TCGA-VQ-A92D     TCGA-VQ-A94T     TCGA-VQ-AA64 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-AA68     TCGA-VQ-AA69     TCGA-VQ-AA6A     TCGA-VQ-AA6B 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-AA6F     TCGA-VQ-AA6G     TCGA-VQ-AA6I     TCGA-VQ-AA6J 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-AA6K     TCGA-ZA-A8F6 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
                vv
clus              T1  T2  T3  T4
  PRB1 MUTATED     0   2   1   0
  PRB1 WILD-TYPE  22  90 172  97
D900V4, multiclass
    clus
vv   PRB1 MUTATED PRB1 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            1            172
  T4            0             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
  PRB1 MUTATED     1   1   0   0
  PRB1 WILD-TYPE 117 103  77  77
D900V5, multiclass
[1] "Remove cluster labels:" "PRB1 MUTATED"          
clus
  PRB1 MUTATED PRB1 WILD-TYPE 
             2            374 
    TCGA-CG-4444     TCGA-CG-4460     TCGA-CG-4475     TCGA-CG-4476 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5716     TCGA-CG-5727     TCGA-EQ-A4SO     TCGA-F1-6177 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FP-A8CX     TCGA-HF-7131     TCGA-KB-A93G     TCGA-MX-A663 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-B7-5816     TCGA-B7-5818     TCGA-B7-A5TI     TCGA-BR-4183 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-4184     TCGA-BR-4188     TCGA-BR-4191     TCGA-BR-4253 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-4255     TCGA-BR-4256     TCGA-BR-4267     TCGA-BR-4279 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-4361     TCGA-BR-4362     TCGA-BR-4368     TCGA-BR-6452 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6453     TCGA-BR-6454     TCGA-BR-6455     TCGA-BR-6456 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6457     TCGA-BR-6458     TCGA-BR-6563     TCGA-BR-6564 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6565     TCGA-BR-6566     TCGA-BR-6705     TCGA-BR-6706 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6707     TCGA-BR-6709     TCGA-BR-6710     TCGA-BR-6801 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6802     TCGA-BR-6803     TCGA-BR-6852     TCGA-BR-7196 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7197     TCGA-BR-7703     TCGA-BR-7704     TCGA-BR-7707 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7715     TCGA-BR-7716     TCGA-BR-7717     TCGA-BR-7722 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7723     TCGA-BR-7851     TCGA-BR-7901     TCGA-BR-7957 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7958     TCGA-BR-7959     TCGA-BR-8058     TCGA-BR-8059 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8060     TCGA-BR-8077     TCGA-BR-8078     TCGA-BR-8080 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8081     TCGA-BR-8284     TCGA-BR-8285     TCGA-BR-8286 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8289     TCGA-BR-8291     TCGA-BR-8295     TCGA-BR-8297 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8360     TCGA-BR-8361     TCGA-BR-8363     TCGA-BR-8364 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8365     TCGA-BR-8366     TCGA-BR-8367     TCGA-BR-8368 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8369     TCGA-BR-8370     TCGA-BR-8371     TCGA-BR-8372 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8373     TCGA-BR-8380     TCGA-BR-8381     TCGA-BR-8382 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8384     TCGA-BR-8483     TCGA-BR-8484     TCGA-BR-8485 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8486     TCGA-BR-8487     TCGA-BR-8588     TCGA-BR-8589 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8590     TCGA-BR-8591     TCGA-BR-8592     TCGA-BR-8676 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8677     TCGA-BR-8678     TCGA-BR-8679     TCGA-BR-8680 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8682     TCGA-BR-8683     TCGA-BR-8686     TCGA-BR-8687 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8690     TCGA-BR-A44T     TCGA-BR-A44U     TCGA-BR-A452 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A453     TCGA-BR-A4CQ     TCGA-BR-A4CR     TCGA-BR-A4CS 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4IU     TCGA-BR-A4IV     TCGA-BR-A4IY     TCGA-BR-A4IZ 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4J1     TCGA-BR-A4J2     TCGA-BR-A4J4     TCGA-BR-A4J5 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4J6     TCGA-BR-A4J8     TCGA-BR-A4PD     TCGA-BR-A4PE 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4PF     TCGA-BR-A4QI     TCGA-BR-A4QL     TCGA-BR-A4QM 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-5798     TCGA-CD-5799     TCGA-CD-5800     TCGA-CD-5801 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-5802     TCGA-CD-5803     TCGA-CD-5804     TCGA-CD-5813 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-8524     TCGA-CD-8525     TCGA-CD-8526     TCGA-CD-8527 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-8528     TCGA-CD-8529     TCGA-CD-8530     TCGA-CD-8531 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-8532     TCGA-CD-8533     TCGA-CD-8534     TCGA-CD-8535 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-8536     TCGA-CD-A486     TCGA-CD-A487     TCGA-CD-A489 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-A48A     TCGA-CD-A48C     TCGA-CD-A4MH     TCGA-CD-A4MI 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-A4MJ     TCGA-CG-4300     TCGA-CG-4301     TCGA-CG-4304 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4305     TCGA-CG-4306     TCGA-CG-4436     TCGA-CG-4437 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4438     TCGA-CG-4440     TCGA-CG-4441     TCGA-CG-4442 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4443     TCGA-CG-4449     TCGA-CG-4455     TCGA-CG-4462 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4465     TCGA-CG-4466     TCGA-CG-4469     TCGA-CG-4474 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4477     TCGA-CG-5717     TCGA-CG-5718     TCGA-CG-5719 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5720     TCGA-CG-5721     TCGA-CG-5722     TCGA-CG-5723 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5724     TCGA-CG-5725     TCGA-CG-5726     TCGA-CG-5728 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5730     TCGA-CG-5732     TCGA-CG-5733     TCGA-CG-5734 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-5577     TCGA-D7-5578     TCGA-D7-5579     TCGA-D7-6518 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-6519     TCGA-D7-6520     TCGA-D7-6521     TCGA-D7-6522 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-6524     TCGA-D7-6525     TCGA-D7-6526     TCGA-D7-6527 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-6528     TCGA-D7-6815     TCGA-D7-6817     TCGA-D7-6818 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-6820     TCGA-D7-6822     TCGA-D7-8570     TCGA-D7-8572 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-8573     TCGA-D7-8574     TCGA-D7-8575     TCGA-D7-8576 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-8578     TCGA-D7-8579     TCGA-D7-A4YT     TCGA-D7-A4YU 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A4YV     TCGA-D7-A4YX     TCGA-D7-A4YY     TCGA-D7-A4Z0 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A6ET     TCGA-D7-A6EV     TCGA-D7-A6EX     TCGA-D7-A6EY 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A6EZ     TCGA-D7-A6F0     TCGA-D7-A6F2     TCGA-D7-A747 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A748     TCGA-D7-A74A     TCGA-D7-A74B     TCGA-EQ-5647 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-EQ-8122     TCGA-F1-6874     TCGA-F1-6875     TCGA-F1-A448 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-F1-A72C     TCGA-FP-7735     TCGA-FP-7829     TCGA-FP-7916 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FP-7998     TCGA-FP-8099     TCGA-FP-8209     TCGA-FP-8210 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FP-8211     TCGA-FP-8631     TCGA-FP-A4BE     TCGA-FP-A4BF 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FP-A9TM     TCGA-HF-7132     TCGA-HF-7133     TCGA-HF-7134 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HF-7136     TCGA-HF-A5NB     TCGA-HJ-7597     TCGA-HU-8238 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-8243     TCGA-HU-8244     TCGA-HU-8249     TCGA-HU-8602 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-8604     TCGA-HU-8608     TCGA-HU-8610     TCGA-HU-A4G2 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4G3     TCGA-HU-A4G6     TCGA-HU-A4G8     TCGA-HU-A4G9 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4GC     TCGA-HU-A4GD     TCGA-HU-A4GF     TCGA-HU-A4GH 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4GJ     TCGA-HU-A4GN     TCGA-HU-A4GP     TCGA-HU-A4GQ 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4GT     TCGA-HU-A4GU     TCGA-HU-A4GX     TCGA-HU-A4GY 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4H0     TCGA-HU-A4H2     TCGA-HU-A4H3     TCGA-HU-A4H4 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4H5     TCGA-HU-A4H6     TCGA-HU-A4H8     TCGA-HU-A4HB 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4HD     TCGA-IN-7806     TCGA-IN-7808     TCGA-IN-8462 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-8663     TCGA-IN-A6RI     TCGA-IN-A6RJ     TCGA-IN-A6RL 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-A6RN     TCGA-IN-A6RO     TCGA-IN-A6RP     TCGA-IN-A6RR 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-A6RS     TCGA-IN-A7NR     TCGA-IN-A7NT     TCGA-IN-A7NU 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-AB1V     TCGA-IN-AB1X     TCGA-IP-7968     TCGA-KB-A6F5 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-KB-A6F7     TCGA-KB-A93J     TCGA-MX-A5UG     TCGA-MX-A5UJ 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-R5-A7O7     TCGA-R5-A7ZE     TCGA-R5-A7ZF     TCGA-R5-A7ZI 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-R5-A804     TCGA-R5-A805     TCGA-RD-A7BS     TCGA-RD-A7BT 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-RD-A7BW     TCGA-RD-A7C1     TCGA-RD-A8MV     TCGA-RD-A8MW 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-RD-A8N0     TCGA-RD-A8N1     TCGA-RD-A8N2     TCGA-RD-A8N4 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-RD-A8N5     TCGA-RD-A8N6     TCGA-RD-A8N9     TCGA-SW-A7EA 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-SW-A7EB     TCGA-VQ-A8DL     TCGA-VQ-A8DT     TCGA-VQ-A8DU 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A8DV     TCGA-VQ-A8DZ     TCGA-VQ-A8E2     TCGA-VQ-A8E7 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A8P2     TCGA-VQ-A8P3     TCGA-VQ-A8PE     TCGA-VQ-A8PK 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A8PM     TCGA-VQ-A8PQ     TCGA-VQ-A91Q     TCGA-VQ-A91U 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A91V     TCGA-VQ-A92D     TCGA-VQ-A94T     TCGA-VQ-AA64 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-AA68     TCGA-VQ-AA69     TCGA-VQ-AA6A     TCGA-VQ-AA6B 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-AA6F     TCGA-VQ-AA6G     TCGA-VQ-AA6I     TCGA-VQ-AA6J 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-AA6K     TCGA-ZA-A8F6 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
D900V6, binary
                cls
clus               0   1
  PRB1 MUTATED     3   0
  PRB1 WILD-TYPE 343  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB1 MUTATED      3    0
  PRB1 WILD-TYPE  343   29
   clus
vv  PRB1 MUTATED PRB1 WILD-TYPE
  0            3            343
  1            0             29
[1] 2 2
[1] FALSE
D900V7, binary
                cls
clus               0   1
  PRB1 MUTATED     2   1
  PRB1 WILD-TYPE 143 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB1 MUTATED      2    1
  PRB1 WILD-TYPE  143  247
        clus
vv       PRB1 MUTATED PRB1 WILD-TYPE
  FEMALE            2            143
  MALE              1            247
[1] 2 2
[1] FALSE
D900V8, binary
                cls
clus               0   1
  PRB1 MUTATED     3   0
  PRB1 WILD-TYPE 289  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB1 MUTATED      3    0
  PRB1 WILD-TYPE  289   59
     clus
vv    PRB1 MUTATED PRB1 WILD-TYPE
  NO             3            289
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PRB1 MUTATED                                          0
  PRB1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PRB1 MUTATED                                       1
  PRB1 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRB1 MUTATED                                                        2
  PRB1 WILD-TYPE                                                    156
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PRB1 MUTATED                                                   0
  PRB1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRB1 MUTATED                                                                   0
  PRB1 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PRB1 MUTATED                                                    0
  PRB1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PRB1 MUTATED                                                  0
  PRB1 WILD-TYPE                                               61
D900V9, multiclass
                                                                   clus
vv                                                                  PRB1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  PRB1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PRB1 MUTATED     0   0   0   2
  PRB1 WILD-TYPE 311  14  15  22
D900V10, multiclass
[1] "Remove cluster labels:" "PRB1 MUTATED"          
clus
  PRB1 MUTATED PRB1 WILD-TYPE 
             2            362 
    TCGA-CG-4444     TCGA-CG-4460     TCGA-CG-4475     TCGA-CG-4476 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5716     TCGA-CG-5727     TCGA-EQ-A4SO     TCGA-F1-6177 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FP-A8CX     TCGA-HF-7131     TCGA-KB-A93G     TCGA-MX-A663 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-B7-5816     TCGA-B7-5818     TCGA-BR-4183     TCGA-BR-4184 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-4187     TCGA-BR-4188     TCGA-BR-4191     TCGA-BR-4253 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-4255     TCGA-BR-4256     TCGA-BR-4257     TCGA-BR-4267 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-4279     TCGA-BR-4292     TCGA-BR-4294     TCGA-BR-4357 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-4361     TCGA-BR-4362     TCGA-BR-4363     TCGA-BR-4366 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-4368     TCGA-BR-4369     TCGA-BR-4370     TCGA-BR-4371 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6452     TCGA-BR-6453     TCGA-BR-6454     TCGA-BR-6455 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6456     TCGA-BR-6457     TCGA-BR-6458     TCGA-BR-6563 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6564     TCGA-BR-6565     TCGA-BR-6566     TCGA-BR-6705 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6706     TCGA-BR-6707     TCGA-BR-6709     TCGA-BR-6710 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6801     TCGA-BR-6802     TCGA-BR-6803     TCGA-BR-6852 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7196     TCGA-BR-7197     TCGA-BR-7703     TCGA-BR-7704 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7707     TCGA-BR-7715     TCGA-BR-7716     TCGA-BR-7717 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7722     TCGA-BR-7723     TCGA-BR-7851     TCGA-BR-7901 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7957     TCGA-BR-7958     TCGA-BR-7959     TCGA-BR-8058 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8059     TCGA-BR-8060     TCGA-BR-8077     TCGA-BR-8078 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8080     TCGA-BR-8081     TCGA-BR-8284     TCGA-BR-8285 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8286     TCGA-BR-8289     TCGA-BR-8291     TCGA-BR-8295 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8297     TCGA-BR-8360     TCGA-BR-8361     TCGA-BR-8363 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8364     TCGA-BR-8365     TCGA-BR-8366     TCGA-BR-8367 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8368     TCGA-BR-8369     TCGA-BR-8370     TCGA-BR-8371 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8372     TCGA-BR-8373     TCGA-BR-8380     TCGA-BR-8381 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8382     TCGA-BR-8384     TCGA-BR-8483     TCGA-BR-8484 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8485     TCGA-BR-8486     TCGA-BR-8487     TCGA-BR-8588 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8589     TCGA-BR-8590     TCGA-BR-8591     TCGA-BR-8592 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8676     TCGA-BR-8677     TCGA-BR-8678     TCGA-BR-8679 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8680     TCGA-BR-8682     TCGA-BR-8683     TCGA-BR-8686 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8687     TCGA-BR-8690     TCGA-BR-A44T     TCGA-BR-A44U 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A452     TCGA-BR-A453     TCGA-BR-A4CQ     TCGA-BR-A4CR 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4CS     TCGA-BR-A4IU     TCGA-BR-A4IV     TCGA-BR-A4IY 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4IZ     TCGA-BR-A4J1     TCGA-BR-A4J2     TCGA-BR-A4J4 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4J5     TCGA-BR-A4J6     TCGA-BR-A4J7     TCGA-BR-A4J8 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4PD     TCGA-BR-A4PE     TCGA-BR-A4PF     TCGA-BR-A4QI 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4QL     TCGA-BR-A4QM     TCGA-CD-5800     TCGA-CD-5801 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-5804     TCGA-CD-8524     TCGA-CD-8525     TCGA-CD-8526 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-8527     TCGA-CD-8528     TCGA-CD-8529     TCGA-CD-8530 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-8531     TCGA-CD-8532     TCGA-CD-8533     TCGA-CD-8534 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-8535     TCGA-CD-8536     TCGA-CD-A487     TCGA-CG-4300 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4301     TCGA-CG-4304     TCGA-CG-4305     TCGA-CG-4306 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4436     TCGA-CG-4437     TCGA-CG-4438     TCGA-CG-4440 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4441     TCGA-CG-4442     TCGA-CG-4443     TCGA-CG-4449 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4455     TCGA-CG-4462     TCGA-CG-4465     TCGA-CG-4466 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4469     TCGA-CG-4474     TCGA-CG-4477     TCGA-CG-5717 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5718     TCGA-CG-5719     TCGA-CG-5720     TCGA-CG-5721 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5722     TCGA-CG-5723     TCGA-CG-5724     TCGA-CG-5725 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5726     TCGA-CG-5728     TCGA-CG-5730     TCGA-CG-5732 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5733     TCGA-CG-5734     TCGA-D7-5577     TCGA-D7-5578 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-5579     TCGA-D7-6518     TCGA-D7-6519     TCGA-D7-6520 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-6521     TCGA-D7-6522     TCGA-D7-6524     TCGA-D7-6525 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-6526     TCGA-D7-6527     TCGA-D7-6528     TCGA-D7-6815 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-6817     TCGA-D7-6818     TCGA-D7-6820     TCGA-D7-6822 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-8570     TCGA-D7-8572     TCGA-D7-8573     TCGA-D7-8574 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-8575     TCGA-D7-8576     TCGA-D7-8578     TCGA-D7-8579 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A4YT     TCGA-D7-A4YU     TCGA-D7-A4YV     TCGA-D7-A4YX 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A4YY     TCGA-D7-A4Z0     TCGA-D7-A6ET     TCGA-D7-A6EV 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A6EX     TCGA-D7-A6EY     TCGA-D7-A6EZ     TCGA-D7-A6F0 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A6F2     TCGA-D7-A747     TCGA-D7-A748     TCGA-D7-A74A 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A74B     TCGA-EQ-5647     TCGA-F1-6874     TCGA-F1-6875 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-F1-A448     TCGA-F1-A72C     TCGA-FP-7735     TCGA-FP-7829 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FP-7998     TCGA-FP-8099     TCGA-FP-8209     TCGA-FP-8211 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FP-8631     TCGA-FP-A4BE     TCGA-FP-A4BF     TCGA-FP-A9TM 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HF-7132     TCGA-HF-7133     TCGA-HF-7134     TCGA-HF-7136 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HF-A5NB     TCGA-HJ-7597     TCGA-HU-8238     TCGA-HU-8243 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-8244     TCGA-HU-8249     TCGA-HU-8602     TCGA-HU-8604 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-8608     TCGA-HU-8610     TCGA-HU-A4G2     TCGA-HU-A4G3 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4G6     TCGA-HU-A4G9     TCGA-HU-A4GC     TCGA-HU-A4GD 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4GF     TCGA-HU-A4GH     TCGA-HU-A4GJ     TCGA-HU-A4GN 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4GP     TCGA-HU-A4GQ     TCGA-HU-A4GT     TCGA-HU-A4GU 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4GX     TCGA-HU-A4GY     TCGA-HU-A4H0     TCGA-HU-A4H2 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4H3     TCGA-HU-A4H4     TCGA-HU-A4H5     TCGA-HU-A4H6 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4H8     TCGA-HU-A4HB     TCGA-HU-A4HD     TCGA-IN-7806 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-8462     TCGA-IN-8663     TCGA-IN-A6RI     TCGA-IN-A6RJ 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-A6RL     TCGA-IN-A6RN     TCGA-IN-A6RO     TCGA-IN-A6RP 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-A6RR     TCGA-IN-A6RS     TCGA-IN-A7NR     TCGA-IN-A7NT 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-A7NU     TCGA-IN-AB1V     TCGA-IN-AB1X     TCGA-IP-7968 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-KB-A6F5     TCGA-KB-A6F7     TCGA-KB-A93J     TCGA-MX-A5UG 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-MX-A5UJ     TCGA-R5-A7ZI     TCGA-RD-A7BS     TCGA-RD-A7BT 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-RD-A7BW     TCGA-RD-A7C1     TCGA-RD-A8MV     TCGA-RD-A8MW 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-RD-A8N0     TCGA-RD-A8N1     TCGA-RD-A8N2     TCGA-RD-A8N4 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-RD-A8N5     TCGA-RD-A8N6     TCGA-RD-A8N9     TCGA-SW-A7EA 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-SW-A7EB     TCGA-VQ-A8DL     TCGA-VQ-A8DT     TCGA-VQ-A8DU 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A8DV     TCGA-VQ-A8DZ     TCGA-VQ-A8E2     TCGA-VQ-A8E7 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A8P2     TCGA-VQ-A8P3     TCGA-VQ-A8PE     TCGA-VQ-A8PK 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A8PM     TCGA-VQ-A8PQ     TCGA-VQ-A91Q     TCGA-VQ-A91U 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A91V     TCGA-VQ-A92D     TCGA-VQ-A94T     TCGA-VQ-AA64 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-AA68     TCGA-VQ-AA69     TCGA-VQ-AA6A     TCGA-VQ-AA6B 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-AA6F     TCGA-VQ-AA6G     TCGA-VQ-AA6I     TCGA-VQ-AA6J 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-AA6K     TCGA-ZA-A8F6 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
D900V11, continuous
[1] "Remove cluster labels:" "PRB1 MUTATED"          
clus
  PRB1 MUTATED PRB1 WILD-TYPE 
             1            342 
    TCGA-CG-4444     TCGA-CG-4460     TCGA-CG-4475     TCGA-CG-4476 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5727     TCGA-EQ-A4SO     TCGA-F1-6177     TCGA-FP-A8CX 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HF-7131     TCGA-KB-A93G     TCGA-MX-A663     TCGA-B7-5816 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-B7-A5TI     TCGA-BR-4183     TCGA-BR-4184     TCGA-BR-4188 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-4191     TCGA-BR-4253     TCGA-BR-4255     TCGA-BR-4256 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-4267     TCGA-BR-4279     TCGA-BR-4361     TCGA-BR-4362 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-4368     TCGA-BR-6452     TCGA-BR-6453     TCGA-BR-6454 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6455     TCGA-BR-6456     TCGA-BR-6457     TCGA-BR-6458 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6563     TCGA-BR-6564     TCGA-BR-6565     TCGA-BR-6566 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6705     TCGA-BR-6706     TCGA-BR-6707     TCGA-BR-6709 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6710     TCGA-BR-6801     TCGA-BR-6802     TCGA-BR-6803 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-6852     TCGA-BR-7196     TCGA-BR-7197     TCGA-BR-7703 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7704     TCGA-BR-7707     TCGA-BR-7715     TCGA-BR-7716 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7717     TCGA-BR-7722     TCGA-BR-7723     TCGA-BR-7851 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-7901     TCGA-BR-7957     TCGA-BR-7958     TCGA-BR-7959 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8058     TCGA-BR-8059     TCGA-BR-8060     TCGA-BR-8077 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8078     TCGA-BR-8080     TCGA-BR-8081     TCGA-BR-8284 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8285     TCGA-BR-8286     TCGA-BR-8289     TCGA-BR-8291 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8295     TCGA-BR-8297     TCGA-BR-8360     TCGA-BR-8361 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8363     TCGA-BR-8364     TCGA-BR-8365     TCGA-BR-8366 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8367     TCGA-BR-8368     TCGA-BR-8369     TCGA-BR-8370 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8371     TCGA-BR-8372     TCGA-BR-8373     TCGA-BR-8380 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8381     TCGA-BR-8382     TCGA-BR-8384     TCGA-BR-8483 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8484     TCGA-BR-8485     TCGA-BR-8486     TCGA-BR-8487 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8588     TCGA-BR-8589     TCGA-BR-8590     TCGA-BR-8591 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8592     TCGA-BR-8676     TCGA-BR-8677     TCGA-BR-8678 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8679     TCGA-BR-8680     TCGA-BR-8682     TCGA-BR-8683 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-8686     TCGA-BR-8687     TCGA-BR-8690     TCGA-BR-A44T 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A44U     TCGA-BR-A452     TCGA-BR-A453     TCGA-BR-A4CQ 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4CR     TCGA-BR-A4CS     TCGA-BR-A4IU     TCGA-BR-A4IV 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4IY     TCGA-BR-A4IZ     TCGA-BR-A4J1     TCGA-BR-A4J2 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4J4     TCGA-BR-A4J5     TCGA-BR-A4J6     TCGA-BR-A4J8 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4PD     TCGA-BR-A4PE     TCGA-BR-A4PF     TCGA-BR-A4QI 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-BR-A4QL     TCGA-BR-A4QM     TCGA-CD-5804     TCGA-CD-8525 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CD-8526     TCGA-CD-8531     TCGA-CD-8535     TCGA-CD-A487 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4301     TCGA-CG-4304     TCGA-CG-4305     TCGA-CG-4436 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4437     TCGA-CG-4438     TCGA-CG-4440     TCGA-CG-4441 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4442     TCGA-CG-4443     TCGA-CG-4449     TCGA-CG-4455 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4462     TCGA-CG-4465     TCGA-CG-4466     TCGA-CG-4469 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-4474     TCGA-CG-4477     TCGA-CG-5717     TCGA-CG-5718 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5719     TCGA-CG-5720     TCGA-CG-5721     TCGA-CG-5722 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5723     TCGA-CG-5724     TCGA-CG-5725     TCGA-CG-5726 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5728     TCGA-CG-5730     TCGA-CG-5732     TCGA-CG-5733 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-CG-5734     TCGA-D7-5577     TCGA-D7-5578     TCGA-D7-5579 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-6518     TCGA-D7-6519     TCGA-D7-6520     TCGA-D7-6521 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-6522     TCGA-D7-6524     TCGA-D7-6525     TCGA-D7-6526 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-6527     TCGA-D7-6528     TCGA-D7-6815     TCGA-D7-6817 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-6818     TCGA-D7-6820     TCGA-D7-6822     TCGA-D7-8570 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-8572     TCGA-D7-8573     TCGA-D7-8574     TCGA-D7-8575 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-8576     TCGA-D7-8578     TCGA-D7-8579     TCGA-D7-A4YT 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A4YU     TCGA-D7-A4YV     TCGA-D7-A4YX     TCGA-D7-A4YY 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A4Z0     TCGA-D7-A6ET     TCGA-D7-A6EV     TCGA-D7-A6EX 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A6EY     TCGA-D7-A6EZ     TCGA-D7-A6F0     TCGA-D7-A6F2 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-D7-A747     TCGA-D7-A748     TCGA-D7-A74A     TCGA-D7-A74B 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-EQ-5647     TCGA-EQ-8122     TCGA-F1-6874     TCGA-F1-6875 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-F1-A448     TCGA-F1-A72C     TCGA-FP-7735     TCGA-FP-7829 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FP-7916     TCGA-FP-7998     TCGA-FP-8099     TCGA-FP-8209 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FP-8210     TCGA-FP-8211     TCGA-FP-8631     TCGA-FP-A4BE 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-FP-A4BF     TCGA-FP-A9TM     TCGA-HF-7132     TCGA-HF-7133 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HF-7134     TCGA-HF-7136     TCGA-HF-A5NB     TCGA-HJ-7597 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-8238     TCGA-HU-8243     TCGA-HU-8244     TCGA-HU-8249 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-8602     TCGA-HU-8604     TCGA-HU-8608     TCGA-HU-8610 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4G2     TCGA-HU-A4G3     TCGA-HU-A4G6     TCGA-HU-A4G8 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4G9     TCGA-HU-A4GC     TCGA-HU-A4GD     TCGA-HU-A4GF 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4GH     TCGA-HU-A4GJ     TCGA-HU-A4GN     TCGA-HU-A4GP 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4GQ     TCGA-HU-A4GT     TCGA-HU-A4GU     TCGA-HU-A4GX 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4GY     TCGA-HU-A4H0     TCGA-HU-A4H2     TCGA-HU-A4H3 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4H4     TCGA-HU-A4H5     TCGA-HU-A4H6     TCGA-HU-A4H8 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-HU-A4HB     TCGA-HU-A4HD     TCGA-IN-7806     TCGA-IN-7808 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-8462     TCGA-IN-8663     TCGA-IN-A6RI     TCGA-IN-A6RJ 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-A6RL     TCGA-IN-A6RN     TCGA-IN-A6RO     TCGA-IN-A6RP 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-A6RR     TCGA-IN-A6RS     TCGA-IN-A7NR     TCGA-IN-A7NT 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-IN-A7NU     TCGA-IN-AB1V     TCGA-IN-AB1X     TCGA-IP-7968 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-KB-A6F5     TCGA-KB-A6F7     TCGA-KB-A93J     TCGA-MX-A5UG 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-MX-A5UJ     TCGA-R5-A7ZI     TCGA-RD-A7BS     TCGA-RD-A7BT 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-RD-A7BW     TCGA-RD-A7C1     TCGA-RD-A8MV     TCGA-RD-A8MW 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-RD-A8N0     TCGA-RD-A8N1     TCGA-RD-A8N2     TCGA-RD-A8N4 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-RD-A8N5     TCGA-RD-A8N6     TCGA-RD-A8N9     TCGA-SW-A7EA 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-SW-A7EB     TCGA-VQ-A8DL     TCGA-VQ-A8DT     TCGA-VQ-A8DU 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A8DV     TCGA-VQ-A8DZ     TCGA-VQ-A8E2     TCGA-VQ-A8E7 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A8P2     TCGA-VQ-A8P3     TCGA-VQ-A8PE     TCGA-VQ-A8PK 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A8PM     TCGA-VQ-A8PQ     TCGA-VQ-A91Q     TCGA-VQ-A91U 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-A91V     TCGA-VQ-A92D     TCGA-VQ-A94T     TCGA-VQ-AA64 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-AA68     TCGA-VQ-AA69     TCGA-VQ-AA6A     TCGA-VQ-AA6B 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-AA6F     TCGA-VQ-AA6G     TCGA-VQ-AA6I     TCGA-VQ-AA6J 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
    TCGA-VQ-AA6K     TCGA-ZA-A8F6 
"PRB1 WILD-TYPE" "PRB1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PRB1 MUTATED       1                         0
  PRB1 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRB1 MUTATED                                           0     2
  PRB1 WILD-TYPE                                         1   241
D900V12, multiclass
                                           clus
vv                                          PRB1 MUTATED PRB1 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D900V13, binary
                cls
clus               0   1
  PRB1 MUTATED     0   3
  PRB1 WILD-TYPE   4 307
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB1 MUTATED      0    3
  PRB1 WILD-TYPE    4  307
                        clus
vv                       PRB1 MUTATED PRB1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            3            307
[1] 2 2
[1] FALSE

Clustering(901) Variable = TPD52L1 MUTATION ANALYSIS
D901V1, survival
                   sevent
clus2                 0   1
  TPD52L1 MUTATED     6   3
  TPD52L1 WILD-TYPE 224 136
  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
                9               360 
  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
                3               136 
$`TPD52L1 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8060 TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A4J5 
        6.97        34.68        11.44        31.96        10.68        28.34 
TCGA-CG-4306 TCGA-HF-7132 TCGA-HU-A4GX 
        1.02        77.29        20.25 

$`TPD52L1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       20.88         8.22        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-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         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-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 

  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
             1.02              0.00 
  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
            77.29            122.30 
  TPD52L1 MUTATED TPD52L1 WILD-TYPE 
            20.25             14.22 
[1] "1.0 - 77.3 (20.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D901V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TPD52L1 MUTATED         0        0        1        1         1         1
  TPD52L1 WILD-TYPE       2       15       39       29        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TPD52L1 MUTATED           0          2          1          1        2
  TPD52L1 WILD-TYPE         3         68         52         31       36
D901V3, multiclass
            clus
vv           TPD52L1 MUTATED TPD52L1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TPD52L1 MUTATED     0   3   4   3
  TPD52L1 WILD-TYPE  22  89 169  94
D901V4, multiclass
    clus
vv   TPD52L1 MUTATED TPD52L1 WILD-TYPE
  T1               0                22
  T2               3                89
  T3               4               169
  T4               3                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
  TPD52L1 MUTATED     2   3   4   1
  TPD52L1 WILD-TYPE 116 101  73  76
D901V5, multiclass
    clus
vv   TPD52L1 MUTATED TPD52L1 WILD-TYPE
  N0               2               116
  N1               3               101
  N2               4                73
  N3               1                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"
D901V6, binary
                   cls
clus                  0   1
  TPD52L1 MUTATED     7   2
  TPD52L1 WILD-TYPE 339  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TPD52L1 MUTATED      7    2
  TPD52L1 WILD-TYPE  339   27
   clus
vv  TPD52L1 MUTATED TPD52L1 WILD-TYPE
  0               7               339
  1               2                27
[1] 2 2
[1] FALSE
D901V7, binary
                   cls
clus                  0   1
  TPD52L1 MUTATED     4   6
  TPD52L1 WILD-TYPE 141 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TPD52L1 MUTATED      4    6
  TPD52L1 WILD-TYPE  141  242
        clus
vv       TPD52L1 MUTATED TPD52L1 WILD-TYPE
  FEMALE               4               141
  MALE                 6               242
[1] 2 2
[1] FALSE
D901V8, binary
                   cls
clus                  0   1
  TPD52L1 MUTATED     7   1
  TPD52L1 WILD-TYPE 285  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TPD52L1 MUTATED      7    1
  TPD52L1 WILD-TYPE  285   58
     clus
vv    TPD52L1 MUTATED TPD52L1 WILD-TYPE
  NO                7               285
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TPD52L1 MUTATED                                          0
  TPD52L1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TPD52L1 MUTATED                                       1
  TPD52L1 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TPD52L1 MUTATED                                                        5
  TPD52L1 WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TPD52L1 MUTATED                                                   2
  TPD52L1 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TPD52L1 MUTATED                                                                   1
  TPD52L1 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TPD52L1 MUTATED                                                    0
  TPD52L1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TPD52L1 MUTATED                                                  1
  TPD52L1 WILD-TYPE                                               60
D901V9, multiclass
                                                                   clus
vv                                                                  TPD52L1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  TPD52L1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TPD52L1 MUTATED     8   0   1   1
  TPD52L1 WILD-TYPE 303  14  14  23
D901V10, multiclass
    clus
vv   TPD52L1 MUTATED TPD52L1 WILD-TYPE
  R0               8               303
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D901V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TPD52L1 MUTATED       3                         0
  TPD52L1 WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TPD52L1 MUTATED                                           0     4
  TPD52L1 WILD-TYPE                                         1   239
D901V12, multiclass
                                           clus
vv                                          TPD52L1 MUTATED TPD52L1 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D901V13, binary
                   cls
clus                  0   1
  TPD52L1 MUTATED     0   7
  TPD52L1 WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TPD52L1 MUTATED      0    7
  TPD52L1 WILD-TYPE    4  303
                        clus
vv                       TPD52L1 MUTATED TPD52L1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(902) Variable = IGFALS MUTATION ANALYSIS
D902V1, survival
                  sevent
clus2                0   1
  IGFALS MUTATED     6   3
  IGFALS WILD-TYPE 224 136
  IGFALS MUTATED IGFALS WILD-TYPE 
               9              360 
  IGFALS MUTATED IGFALS WILD-TYPE 
               3              136 
$`IGFALS MUTATED`
TCGA-CG-4460 TCGA-BR-8081 TCGA-BR-8366 TCGA-BR-A4QL TCGA-CG-4438 TCGA-CG-5721 
       21.99        32.25         0.95        16.14        54.08         6.02 
TCGA-CG-5726 TCGA-D7-6820 TCGA-HU-A4GU 
       28.96        11.31         6.58 

$`IGFALS WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-D7-6822 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-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 

  IGFALS MUTATED IGFALS WILD-TYPE 
            0.95             0.00 
  IGFALS MUTATED IGFALS WILD-TYPE 
           54.08           122.30 
  IGFALS MUTATED IGFALS WILD-TYPE 
           16.14            14.22 
[1] "0.9 - 54.1 (16.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D902V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IGFALS MUTATED         0        1        0        0         1         3
  IGFALS WILD-TYPE       2       14       40       30        36        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGFALS MUTATED           0          0          1          0        3
  IGFALS WILD-TYPE         3         70         52         32       35
D902V3, multiclass
            clus
vv           IGFALS MUTATED IGFALS WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IGFALS MUTATED     1   1   3   4
  IGFALS WILD-TYPE  21  91 170  93
D902V4, multiclass
    clus
vv   IGFALS MUTATED IGFALS WILD-TYPE
  T1              1               21
  T2              1               91
  T3              3              170
  T4              4               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
  IGFALS MUTATED     3   4   1   1
  IGFALS WILD-TYPE 115 100  76  76
D902V5, multiclass
    clus
vv   IGFALS MUTATED IGFALS WILD-TYPE
  N0              3              115
  N1              4              100
  N2              1               76
  N3              1               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"
D902V6, binary
                  cls
clus                 0   1
  IGFALS MUTATED     8   1
  IGFALS WILD-TYPE 338  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFALS MUTATED      8    1
  IGFALS WILD-TYPE  338   28
   clus
vv  IGFALS MUTATED IGFALS WILD-TYPE
  0              8              338
  1              1               28
[1] 2 2
[1] FALSE
D902V7, binary
                  cls
clus                 0   1
  IGFALS MUTATED     4   5
  IGFALS WILD-TYPE 141 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFALS MUTATED      4    5
  IGFALS WILD-TYPE  141  243
        clus
vv       IGFALS MUTATED IGFALS WILD-TYPE
  FEMALE              4              141
  MALE                5              243
[1] 2 2
[1] FALSE
D902V8, binary
                  cls
clus                 0   1
  IGFALS MUTATED     7   0
  IGFALS WILD-TYPE 285  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFALS MUTATED      7    0
  IGFALS WILD-TYPE  285   59
     clus
vv    IGFALS MUTATED IGFALS WILD-TYPE
  NO               7              285
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IGFALS MUTATED                                          0
  IGFALS WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IGFALS MUTATED                                       1
  IGFALS WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IGFALS MUTATED                                                        3
  IGFALS WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IGFALS MUTATED                                                   0
  IGFALS WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IGFALS MUTATED                                                                   4
  IGFALS WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IGFALS MUTATED                                                    0
  IGFALS WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IGFALS MUTATED                                                  1
  IGFALS WILD-TYPE                                               60
D902V9, multiclass
                                                                   clus
vv                                                                  IGFALS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  IGFALS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IGFALS MUTATED     8   0   1   0
  IGFALS WILD-TYPE 303  14  14  24
D902V10, multiclass
    clus
vv   IGFALS MUTATED IGFALS WILD-TYPE
  R0              8              303
  R1              0               14
  R2              1               14
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D902V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  IGFALS MUTATED       1                         0
  IGFALS WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IGFALS MUTATED                                           0     4
  IGFALS WILD-TYPE                                         1   239
D902V12, multiclass
                                           clus
vv                                          IGFALS MUTATED IGFALS WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D902V13, binary
                  cls
clus                 0   1
  IGFALS MUTATED     0   5
  IGFALS WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFALS MUTATED      0    5
  IGFALS WILD-TYPE    4  305
                        clus
vv                       IGFALS MUTATED IGFALS WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(903) Variable = PAPOLB MUTATION ANALYSIS
D903V1, survival
                  sevent
clus2                0   1
  PAPOLB MUTATED     6   7
  PAPOLB WILD-TYPE 224 132
  PAPOLB MUTATED PAPOLB WILD-TYPE 
              13              356 
  PAPOLB MUTATED PAPOLB WILD-TYPE 
               7              132 
$`PAPOLB MUTATED`
TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-A4J1 TCGA-CG-4441 TCGA-CG-5726 TCGA-D7-6524 
       32.78        30.90         0.72        14.01        28.96        17.85 
TCGA-D7-A6EY TCGA-D7-A747 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-IN-AB1X TCGA-SW-A7EB 
       11.44         8.38        22.68         0.10        13.51         5.79 
TCGA-VQ-A91Q 
       20.81 

$`PAPOLB WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        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-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-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 
       11.24        11.31        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-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-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-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-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 

  PAPOLB MUTATED PAPOLB WILD-TYPE 
             0.1              0.0 
  PAPOLB MUTATED PAPOLB WILD-TYPE 
           32.78           122.30 
  PAPOLB MUTATED PAPOLB WILD-TYPE 
           14.01            14.35 
[1] "0.1 - 32.8 (14.0)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.6"
D903V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAPOLB MUTATED         0        1        0        1         2         2
  PAPOLB WILD-TYPE       2       14       40       29        35        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAPOLB MUTATED           0          4          1          1        1
  PAPOLB WILD-TYPE         3         66         52         31       37
D903V3, multiclass
            clus
vv           PAPOLB MUTATED PAPOLB WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PAPOLB MUTATED     1   2   8   2
  PAPOLB WILD-TYPE  21  90 165  95
D903V4, multiclass
    clus
vv   PAPOLB MUTATED PAPOLB WILD-TYPE
  T1              1               21
  T2              2               90
  T3              8              165
  T4              2               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
  PAPOLB MUTATED     3   4   4   2
  PAPOLB WILD-TYPE 115 100  73  75
D903V5, multiclass
    clus
vv   PAPOLB MUTATED PAPOLB WILD-TYPE
  N0              3              115
  N1              4              100
  N2              4               73
  N3              2               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"
D903V6, binary
                  cls
clus                 0   1
  PAPOLB MUTATED    14   0
  PAPOLB WILD-TYPE 332  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPOLB MUTATED     14    0
  PAPOLB WILD-TYPE  332   29
   clus
vv  PAPOLB MUTATED PAPOLB WILD-TYPE
  0             14              332
  1              0               29
[1] 2 2
[1] FALSE
D903V7, binary
                  cls
clus                 0   1
  PAPOLB MUTATED     5   9
  PAPOLB WILD-TYPE 140 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPOLB MUTATED      5    9
  PAPOLB WILD-TYPE  140  239
        clus
vv       PAPOLB MUTATED PAPOLB WILD-TYPE
  FEMALE              5              140
  MALE                9              239
[1] 2 2
[1] FALSE
D903V8, binary
                  cls
clus                 0   1
  PAPOLB MUTATED     9   1
  PAPOLB WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPOLB MUTATED      9    1
  PAPOLB WILD-TYPE  283   58
     clus
vv    PAPOLB MUTATED PAPOLB WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PAPOLB MUTATED                                          0
  PAPOLB WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PAPOLB MUTATED                                       3
  PAPOLB WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAPOLB MUTATED                                                        5
  PAPOLB WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PAPOLB MUTATED                                                   1
  PAPOLB WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAPOLB MUTATED                                                                   2
  PAPOLB WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PAPOLB MUTATED                                                    0
  PAPOLB WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PAPOLB MUTATED                                                  3
  PAPOLB WILD-TYPE                                               58
D903V9, multiclass
                                                                   clus
vv                                                                  PAPOLB MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  PAPOLB WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PAPOLB MUTATED    11   1   0   1
  PAPOLB WILD-TYPE 300  13  15  23
D903V10, multiclass
    clus
vv   PAPOLB MUTATED PAPOLB WILD-TYPE
  R0             11              300
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D903V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PAPOLB MUTATED       3                         0
  PAPOLB WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAPOLB MUTATED                                           0     8
  PAPOLB WILD-TYPE                                         1   235
D903V12, multiclass
                                           clus
vv                                          PAPOLB MUTATED PAPOLB WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D903V13, binary
                  cls
clus                 0   1
  PAPOLB MUTATED     0  11
  PAPOLB WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPOLB MUTATED      0   11
  PAPOLB WILD-TYPE    4  299
                        clus
vv                       PAPOLB MUTATED PAPOLB WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(904) Variable = SMAD2 MUTATION ANALYSIS
D904V1, survival
                 sevent
clus2               0   1
  SMAD2 MUTATED     5   2
  SMAD2 WILD-TYPE 225 137
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              7             362 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              2             137 
$`SMAD2 MUTATED`
TCGA-CG-4444 TCGA-BR-6452 TCGA-BR-A4QL TCGA-CG-4462 TCGA-F1-A448 TCGA-HU-8604 
       47.05        34.68        16.14         0.00        21.27        22.82 
TCGA-HU-A4H3 
       29.00 

$`SMAD2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-4465 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         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-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-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-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 

  SMAD2 MUTATED SMAD2 WILD-TYPE 
            0.0             0.1 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          47.05          122.30 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          22.82           14.07 
[1] "0.0 - 47.0 (22.8)"  "0.1 - 122.3 (14.1)"
[1] "hr=" "1.8"
D904V2, 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       2       15       40       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMAD2 MUTATED           0          1          2          1        1
  SMAD2 WILD-TYPE         3         69         51         31       37
D904V3, multiclass
            clus
vv           SMAD2 MUTATED SMAD2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMAD2 MUTATED     0   2   5   2
  SMAD2 WILD-TYPE  22  90 168  95
D904V4, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             5             168
  T4             2              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
  SMAD2 MUTATED     3   0   1   4
  SMAD2 WILD-TYPE 115 104  76  73
D904V5, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  N0             3             115
  N1             0             104
  N2             1              76
  N3             4              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"
D904V6, binary
                 cls
clus                0   1
  SMAD2 MUTATED     8   1
  SMAD2 WILD-TYPE 338  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      8    1
  SMAD2 WILD-TYPE  338   28
   clus
vv  SMAD2 MUTATED SMAD2 WILD-TYPE
  0             8             338
  1             1              28
[1] 2 2
[1] FALSE
D904V7, binary
                 cls
clus                0   1
  SMAD2 MUTATED     6   3
  SMAD2 WILD-TYPE 139 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      6    3
  SMAD2 WILD-TYPE  139  245
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  FEMALE             6             139
  MALE               3             245
[1] 2 2
[1] FALSE
D904V8, binary
                 cls
clus                0   1
  SMAD2 MUTATED     4   2
  SMAD2 WILD-TYPE 288  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      4    2
  SMAD2 WILD-TYPE  288   57
     clus
vv    SMAD2 MUTATED SMAD2 WILD-TYPE
  NO              4             288
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SMAD2 MUTATED                                          0
  SMAD2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SMAD2 MUTATED                                       3
  SMAD2 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMAD2 MUTATED                                                        3
  SMAD2 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SMAD2 MUTATED                                                   1
  SMAD2 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMAD2 MUTATED                                                                   1
  SMAD2 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SMAD2 MUTATED                                                    0
  SMAD2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SMAD2 MUTATED                                                  1
  SMAD2 WILD-TYPE                                               60
D904V9, multiclass
                                                                   clus
vv                                                                  SMAD2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  SMAD2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SMAD2 MUTATED     7   0   1   1
  SMAD2 WILD-TYPE 304  14  14  23
D904V10, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D904V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SMAD2 MUTATED       2                         0
  SMAD2 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMAD2 MUTATED                                           0     5
  SMAD2 WILD-TYPE                                         1   238
D904V12, multiclass
                                           clus
vv                                          SMAD2 MUTATED SMAD2 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D904V13, binary
                 cls
clus                0   1
  SMAD2 MUTATED     1   6
  SMAD2 WILD-TYPE   3 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      1    6
  SMAD2 WILD-TYPE    3  304
                        clus
vv                       SMAD2 MUTATED SMAD2 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(905) Variable = ZMYND19 MUTATION ANALYSIS
D905V1, survival
                   sevent
clus2                 0   1
  ZMYND19 MUTATED     4   2
  ZMYND19 WILD-TYPE 226 137
  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
                6               363 
  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
                2               137 
$`ZMYND19 MUTATED`
TCGA-BR-6452 TCGA-BR-8590 TCGA-CD-A4MG TCGA-CG-5723 TCGA-HU-A4H8 TCGA-R5-A7ZI 
       34.68         9.34         6.58       105.07        14.07        74.53 

$`ZMYND19 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
             6.58              0.00 
  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
           105.07            122.30 
  ZMYND19 MUTATED ZMYND19 WILD-TYPE 
           24.375            14.270 
[1] "6.6 - 105.1 (24.4)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.8"
D905V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZMYND19 MUTATED         0        0        2        1         2         0
  ZMYND19 WILD-TYPE       2       15       38       29        35        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZMYND19 MUTATED           0          0          0          1        1
  ZMYND19 WILD-TYPE         3         70         53         31       37
D905V3, multiclass
            clus
vv           ZMYND19 MUTATED ZMYND19 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 1                29
  STAGE IIA                2                35
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZMYND19 MUTATED     1   2   2   2
  ZMYND19 WILD-TYPE  21  90 171  95
D905V4, multiclass
    clus
vv   ZMYND19 MUTATED ZMYND19 WILD-TYPE
  T1               1                21
  T2               2                90
  T3               2               171
  T4               2                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
  ZMYND19 MUTATED     3   3   1   0
  ZMYND19 WILD-TYPE 115 101  76  77
D905V5, multiclass
    clus
vv   ZMYND19 MUTATED ZMYND19 WILD-TYPE
  N0               3               115
  N1               3               101
  N2               1                76
  N3               0                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"
D905V6, binary
                   cls
clus                  0   1
  ZMYND19 MUTATED     7   1
  ZMYND19 WILD-TYPE 339  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZMYND19 MUTATED      7    1
  ZMYND19 WILD-TYPE  339   28
   clus
vv  ZMYND19 MUTATED ZMYND19 WILD-TYPE
  0               7               339
  1               1                28
[1] 2 2
[1] FALSE
D905V7, binary
                   cls
clus                  0   1
  ZMYND19 MUTATED     3   5
  ZMYND19 WILD-TYPE 142 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZMYND19 MUTATED      3    5
  ZMYND19 WILD-TYPE  142  243
        clus
vv       ZMYND19 MUTATED ZMYND19 WILD-TYPE
  FEMALE               3               142
  MALE                 5               243
[1] 2 2
[1] FALSE
D905V8, binary
                   cls
clus                  0   1
  ZMYND19 MUTATED     6   0
  ZMYND19 WILD-TYPE 286  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZMYND19 MUTATED      6    0
  ZMYND19 WILD-TYPE  286   59
     clus
vv    ZMYND19 MUTATED ZMYND19 WILD-TYPE
  NO                6               286
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZMYND19 MUTATED                                          0
  ZMYND19 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZMYND19 MUTATED                                       2
  ZMYND19 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZMYND19 MUTATED                                                        4
  ZMYND19 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZMYND19 MUTATED                                                   0
  ZMYND19 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZMYND19 MUTATED                                                                   1
  ZMYND19 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZMYND19 MUTATED                                                    0
  ZMYND19 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZMYND19 MUTATED                                                  1
  ZMYND19 WILD-TYPE                                               60
D905V9, multiclass
                                                                   clus
vv                                                                  ZMYND19 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  ZMYND19 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZMYND19 MUTATED     6   0   0   1
  ZMYND19 WILD-TYPE 305  14  15  23
D905V10, multiclass
    clus
vv   ZMYND19 MUTATED ZMYND19 WILD-TYPE
  R0               6               305
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D905V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ZMYND19 MUTATED       2                         0
  ZMYND19 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZMYND19 MUTATED                                           0     4
  ZMYND19 WILD-TYPE                                         1   239
D905V12, multiclass
                                           clus
vv                                          ZMYND19 MUTATED ZMYND19 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D905V13, binary
                   cls
clus                  0   1
  ZMYND19 MUTATED     1   5
  ZMYND19 WILD-TYPE   3 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZMYND19 MUTATED      1    5
  ZMYND19 WILD-TYPE    3  305
                        clus
vv                       ZMYND19 MUTATED ZMYND19 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(906) Variable = UBE2Q1 MUTATION ANALYSIS
D906V1, survival
                  sevent
clus2                0   1
  UBE2Q1 MUTATED     2   3
  UBE2Q1 WILD-TYPE 228 136
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
               5              364 
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
               3              136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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            14.35 
[1] "6.0 - 54.1 (7.0)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "2.1"
D906V2, 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       2       15       40       30        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UBE2Q1 MUTATED           0          1          1          0        3
  UBE2Q1 WILD-TYPE         3         69         52         32       35
D906V3, multiclass
            clus
vv           UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UBE2Q1 MUTATED     0   0   3   3
  UBE2Q1 WILD-TYPE  22  92 170  94
D906V4, multiclass
    clus
vv   UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  T1              0               22
  T2              0               92
  T3              3              170
  T4              3               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
  UBE2Q1 MUTATED     1   3   2   1
  UBE2Q1 WILD-TYPE 117 101  75  76
D906V5, multiclass
    clus
vv   UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  N0              1              117
  N1              3              101
  N2              2               75
  N3              1               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"
D906V6, binary
                  cls
clus                 0   1
  UBE2Q1 MUTATED     6   0
  UBE2Q1 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2Q1 MUTATED      6    0
  UBE2Q1 WILD-TYPE  340   29
   clus
vv  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D906V7, binary
                  cls
clus                 0   1
  UBE2Q1 MUTATED     3   4
  UBE2Q1 WILD-TYPE 142 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2Q1 MUTATED      3    4
  UBE2Q1 WILD-TYPE  142  244
        clus
vv       UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  FEMALE              3              142
  MALE                4              244
[1] 2 2
[1] FALSE
D906V8, binary
                  cls
clus                 0   1
  UBE2Q1 MUTATED     4   0
  UBE2Q1 WILD-TYPE 288  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2Q1 MUTATED      4    0
  UBE2Q1 WILD-TYPE  288   59
     clus
vv    UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  NO               4              288
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  UBE2Q1 MUTATED                                          0
  UBE2Q1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  UBE2Q1 MUTATED                                       1
  UBE2Q1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UBE2Q1 MUTATED                                                        4
  UBE2Q1 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  UBE2Q1 MUTATED                                                   0
  UBE2Q1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UBE2Q1 MUTATED                                                                   2
  UBE2Q1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  UBE2Q1 MUTATED                                                    0
  UBE2Q1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  UBE2Q1 MUTATED                                                  0
  UBE2Q1 WILD-TYPE                                               61
D906V9, multiclass
                                                                   clus
vv                                                                  UBE2Q1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  UBE2Q1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  UBE2Q1 MUTATED     3   0   0   3
  UBE2Q1 WILD-TYPE 308  14  15  21
D906V10, multiclass
    clus
vv   UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  R0              3              308
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D906V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  UBE2Q1 MUTATED       1                         0
  UBE2Q1 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UBE2Q1 MUTATED                                           0     4
  UBE2Q1 WILD-TYPE                                         1   239
D906V12, multiclass
                                           clus
vv                                          UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D906V13, binary
                  cls
clus                 0   1
  UBE2Q1 MUTATED     0   5
  UBE2Q1 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2Q1 MUTATED      0    5
  UBE2Q1 WILD-TYPE    4  305
                        clus
vv                       UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(907) Variable = RYR2 MUTATION ANALYSIS
D907V1, survival
                sevent
clus2              0   1
  RYR2 MUTATED    51  18
  RYR2 WILD-TYPE 179 121
  RYR2 MUTATED RYR2 WILD-TYPE 
            69            300 
  RYR2 MUTATED RYR2 WILD-TYPE 
            18            121 
$`RYR2 MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-B7-5816 
       47.05        21.99        16.24         0.23        20.15        26.70 
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6452 
       19.56         9.44         6.97        30.90         9.67        34.68 
TCGA-BR-6802 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-8059 TCGA-BR-8081 TCGA-BR-8289 
       30.90        35.24        35.84        14.43        32.25         2.66 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 
        6.18        31.10         0.26         4.31        31.27        25.05 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A4CQ TCGA-CD-5801 
        1.12        27.12        31.96         9.86        34.98        13.18 
TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 
       12.76        12.39        15.39        12.07        12.82        12.43 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4449 TCGA-CG-5719 
        6.58        11.77        15.95         1.02        19.07         1.02 
TCGA-CG-5721 TCGA-CG-5728 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6526 
        6.02        65.10         4.01        12.66        18.84        17.19 
TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-EQ-8122 
       15.22        12.33        20.91         5.92        13.78         7.99 
TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GH TCGA-HU-A4GQ 
        5.52        30.51        22.32        22.68        11.77         0.10 
TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H8 TCGA-IN-7806 TCGA-KB-A93J TCGA-MX-A5UJ 
       20.25        12.95        14.07        36.36        36.95        19.73 
TCGA-VQ-A8P2 TCGA-VQ-AA64 TCGA-ZA-A8F6 
       38.14        18.41        17.26 

$`RYR2 WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-MX-A663 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       22.98        79.07         9.86        11.70        11.01         9.47 
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-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-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       40.21        31.20        44.94        21.90         9.21        36.16 
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-8291 
       29.59         9.60         8.05         0.56        29.42        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-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8384 
       14.04         3.32        11.80        14.79         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-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-5802 TCGA-CD-5803 
        5.13        13.41        13.02        13.15        13.35        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       12.10        12.39        12.59        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
       12.30        12.59        11.64         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-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-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-5720 TCGA-CG-5722 TCGA-CG-5723 
       30.97         6.97        36.00         0.99         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       12.03        15.02        28.96        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 
       25.71        20.91        19.13        20.55        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.85        13.35        10.26        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-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A4Z0 
       14.66        21.14        14.27        16.44        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-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-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-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-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-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-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-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 

  RYR2 MUTATED RYR2 WILD-TYPE 
           0.1            0.0 
  RYR2 MUTATED RYR2 WILD-TYPE 
          65.1          122.3 
  RYR2 MUTATED RYR2 WILD-TYPE 
        15.390         14.055 
[1] "0.1 - 65.1 (15.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D907V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RYR2 MUTATED         1        1       10        9         4         9
  RYR2 WILD-TYPE       1       14       30       21        33        43
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RYR2 MUTATED           1         14          6          9        8
  RYR2 WILD-TYPE         2         56         47         23       30
D907V3, multiclass
            clus
vv           RYR2 MUTATED RYR2 WILD-TYPE
  STAGE I               1              1
  STAGE IA              1             14
  STAGE IB             10             30
  STAGE II              9             21
  STAGE IIA             4             33
  STAGE IIB             9             43
  STAGE III             1              2
  STAGE IIIA           14             56
  STAGE IIIB            6             47
  STAGE IIIC            9             23
  STAGE IV              8             30
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RYR2 MUTATED     3  17  28  26
  RYR2 WILD-TYPE  19  75 145  71
D907V4, multiclass
    clus
vv   RYR2 MUTATED RYR2 WILD-TYPE
  T1            3             19
  T2           17             75
  T3           28            145
  T4           26             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
  RYR2 MUTATED   25 22 16  9
  RYR2 WILD-TYPE 93 82 61 68
D907V5, multiclass
    clus
vv   RYR2 MUTATED RYR2 WILD-TYPE
  N0           25             93
  N1           22             82
  N2           16             61
  N3            9             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"
D907V6, binary
                cls
clus               0   1
  RYR2 MUTATED    64   6
  RYR2 WILD-TYPE 282  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED     64    6
  RYR2 WILD-TYPE  282   23
   clus
vv  RYR2 MUTATED RYR2 WILD-TYPE
  0           64            282
  1            6             23
[1] 2 2
[1] FALSE
D907V7, binary
                cls
clus               0   1
  RYR2 MUTATED    33  44
  RYR2 WILD-TYPE 112 204
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED     33   44
  RYR2 WILD-TYPE  112  204
        clus
vv       RYR2 MUTATED RYR2 WILD-TYPE
  FEMALE           33            112
  MALE             44            204
[1] 2 2
[1] FALSE
D907V8, binary
                cls
clus               0   1
  RYR2 MUTATED    56  10
  RYR2 WILD-TYPE 236  49
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED     56   10
  RYR2 WILD-TYPE  236   49
     clus
vv    RYR2 MUTATED RYR2 WILD-TYPE
  NO            56            236
  YES           10             49
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RYR2 MUTATED                                          3
  RYR2 WILD-TYPE                                        5
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RYR2 MUTATED                                      11
  RYR2 WILD-TYPE                                    59
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RYR2 MUTATED                                                       31
  RYR2 WILD-TYPE                                                    127
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RYR2 MUTATED                                                   3
  RYR2 WILD-TYPE                                                18
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RYR2 MUTATED                                                                  15
  RYR2 WILD-TYPE                                                                53
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RYR2 MUTATED                                                    0
  RYR2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RYR2 MUTATED                                                 13
  RYR2 WILD-TYPE                                               48
D907V9, multiclass
                                                                   clus
vv                                                                  RYR2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       11
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      31
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           15
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            13
                                                                   clus
vv                                                                  RYR2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         59
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       127
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             53
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              48
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RYR2 MUTATED    57   3   3   8
  RYR2 WILD-TYPE 254  11  12  16
D907V10, multiclass
    clus
vv   RYR2 MUTATED RYR2 WILD-TYPE
  R0           57            254
  R1            3             11
  R2            3             12
  RX            8             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D907V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RYR2 MUTATED      18                         1
  RYR2 WILD-TYPE    69                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RYR2 MUTATED                                           0    47
  RYR2 WILD-TYPE                                         1   196
D907V12, multiclass
                                           clus
vv                                          RYR2 MUTATED RYR2 WILD-TYPE
  ASIAN                                               18             69
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               47            196
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D907V13, binary
                cls
clus               0   1
  RYR2 MUTATED     0  62
  RYR2 WILD-TYPE   4 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED      0   62
  RYR2 WILD-TYPE    4  248
                        clus
vv                       RYR2 MUTATED RYR2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           62            248
[1] 2 2
[1] FALSE

Clustering(908) Variable = STAU1 MUTATION ANALYSIS
D908V1, survival
                 sevent
clus2               0   1
  STAU1 MUTATED     4   4
  STAU1 WILD-TYPE 226 135
  STAU1 MUTATED STAU1 WILD-TYPE 
              8             361 
  STAU1 MUTATED STAU1 WILD-TYPE 
              4             135 
$`STAU1 MUTATED`
TCGA-BR-4184 TCGA-BR-8680 TCGA-CG-4306 TCGA-CG-5733 TCGA-D7-A6EY TCGA-HF-7132 
        6.97        31.96         1.02        21.07        11.44        77.29 
TCGA-HU-A4GT TCGA-MX-A5UJ 
        6.51        19.73 

$`STAU1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  STAU1 MUTATED STAU1 WILD-TYPE 
           1.02            0.00 
  STAU1 MUTATED STAU1 WILD-TYPE 
          77.29          122.30 
  STAU1 MUTATED STAU1 WILD-TYPE 
         15.585          14.270 
[1] "1.0 - 77.3 (15.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D908V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STAU1 MUTATED         0        0        0        1         1         0
  STAU1 WILD-TYPE       2       15       40       29        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STAU1 MUTATED           0          3          1          0        3
  STAU1 WILD-TYPE         3         67         52         32       35
D908V3, multiclass
            clus
vv           STAU1 MUTATED STAU1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STAU1 MUTATED     0   2   5   2
  STAU1 WILD-TYPE  22  90 168  95
D908V4, multiclass
    clus
vv   STAU1 MUTATED STAU1 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             5             168
  T4             2              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
  STAU1 MUTATED     1   3   5   1
  STAU1 WILD-TYPE 117 101  72  76
D908V5, multiclass
    clus
vv   STAU1 MUTATED STAU1 WILD-TYPE
  N0             1             117
  N1             3             101
  N2             5              72
  N3             1              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"
D908V6, binary
                 cls
clus                0   1
  STAU1 MUTATED     7   2
  STAU1 WILD-TYPE 339  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      7    2
  STAU1 WILD-TYPE  339   27
   clus
vv  STAU1 MUTATED STAU1 WILD-TYPE
  0             7             339
  1             2              27
[1] 2 2
[1] FALSE
D908V7, binary
                 cls
clus                0   1
  STAU1 MUTATED     6   4
  STAU1 WILD-TYPE 139 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      6    4
  STAU1 WILD-TYPE  139  244
        clus
vv       STAU1 MUTATED STAU1 WILD-TYPE
  FEMALE             6             139
  MALE               4             244
[1] 2 2
[1] FALSE
D908V8, binary
                 cls
clus                0   1
  STAU1 MUTATED     6   1
  STAU1 WILD-TYPE 286  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      6    1
  STAU1 WILD-TYPE  286   58
     clus
vv    STAU1 MUTATED STAU1 WILD-TYPE
  NO              6             286
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  STAU1 MUTATED                                          0
  STAU1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  STAU1 MUTATED                                       0
  STAU1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  STAU1 MUTATED                                                        4
  STAU1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  STAU1 MUTATED                                                   1
  STAU1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  STAU1 MUTATED                                                                   1
  STAU1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  STAU1 MUTATED                                                    0
  STAU1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  STAU1 MUTATED                                                  4
  STAU1 WILD-TYPE                                               57
D908V9, multiclass
                                                                   clus
vv                                                                  STAU1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  STAU1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STAU1 MUTATED     6   0   1   3
  STAU1 WILD-TYPE 305  14  14  21
D908V10, multiclass
    clus
vv   STAU1 MUTATED STAU1 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D908V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  STAU1 MUTATED       2                         0
  STAU1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  STAU1 MUTATED                                           0     5
  STAU1 WILD-TYPE                                         1   238
D908V12, multiclass
                                           clus
vv                                          STAU1 MUTATED STAU1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D908V13, binary
                 cls
clus                0   1
  STAU1 MUTATED     0   7
  STAU1 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      0    7
  STAU1 WILD-TYPE    4  303
                        clus
vv                       STAU1 MUTATED STAU1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(909) Variable = DLL1 MUTATION ANALYSIS
D909V1, survival
                sevent
clus2              0   1
  DLL1 MUTATED     9   4
  DLL1 WILD-TYPE 221 135
  DLL1 MUTATED DLL1 WILD-TYPE 
            13            356 
  DLL1 MUTATED DLL1 WILD-TYPE 
             4            135 
$`DLL1 MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-8382 TCGA-BR-8680 TCGA-CD-8527 
       19.56         6.97        32.78        25.05        31.96         7.17 
TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-6518 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-HU-A4GT 
        6.02       105.07        19.13        16.44         5.92         6.51 
TCGA-HU-A4GX 
       20.25 

$`DLL1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-D7-6519 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-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       21.14        20.91        14.27        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-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 

  DLL1 MUTATED DLL1 WILD-TYPE 
          5.92           0.00 
  DLL1 MUTATED DLL1 WILD-TYPE 
        105.07         122.30 
  DLL1 MUTATED DLL1 WILD-TYPE 
         19.13          14.12 
[1] "5.9 - 105.1 (19.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D909V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DLL1 MUTATED         0        0        0        2         2         1
  DLL1 WILD-TYPE       2       15       40       28        35        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DLL1 MUTATED           0          3          1          3        2
  DLL1 WILD-TYPE         3         67         52         29       36
D909V3, multiclass
            clus
vv           DLL1 MUTATED DLL1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              2             28
  STAGE IIA             2             35
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            1             52
  STAGE IIIC            3             29
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DLL1 MUTATED     0   3   6   5
  DLL1 WILD-TYPE  22  89 167  92
D909V4, multiclass
    clus
vv   DLL1 MUTATED DLL1 WILD-TYPE
  T1            0             22
  T2            3             89
  T3            6            167
  T4            5             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
  DLL1 MUTATED     2   7   2   4
  DLL1 WILD-TYPE 116  97  75  73
D909V5, multiclass
    clus
vv   DLL1 MUTATED DLL1 WILD-TYPE
  N0            2            116
  N1            7             97
  N2            2             75
  N3            4             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"
D909V6, binary
                cls
clus               0   1
  DLL1 MUTATED    13   1
  DLL1 WILD-TYPE 333  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLL1 MUTATED     13    1
  DLL1 WILD-TYPE  333   28
   clus
vv  DLL1 MUTATED DLL1 WILD-TYPE
  0           13            333
  1            1             28
[1] 2 2
[1] FALSE
D909V7, binary
                cls
clus               0   1
  DLL1 MUTATED     7   8
  DLL1 WILD-TYPE 138 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLL1 MUTATED      7    8
  DLL1 WILD-TYPE  138  240
        clus
vv       DLL1 MUTATED DLL1 WILD-TYPE
  FEMALE            7            138
  MALE              8            240
[1] 2 2
[1] FALSE
D909V8, binary
                cls
clus               0   1
  DLL1 MUTATED    13   1
  DLL1 WILD-TYPE 279  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLL1 MUTATED     13    1
  DLL1 WILD-TYPE  279   58
     clus
vv    DLL1 MUTATED DLL1 WILD-TYPE
  NO            13            279
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DLL1 MUTATED                                          0
  DLL1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DLL1 MUTATED                                       3
  DLL1 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DLL1 MUTATED                                                        6
  DLL1 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DLL1 MUTATED                                                   0
  DLL1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DLL1 MUTATED                                                                   2
  DLL1 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DLL1 MUTATED                                                    0
  DLL1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DLL1 MUTATED                                                  4
  DLL1 WILD-TYPE                                               57
D909V9, multiclass
                                                                   clus
vv                                                                  DLL1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  DLL1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DLL1 MUTATED    10   2   0   2
  DLL1 WILD-TYPE 301  12  15  22
D909V10, multiclass
    clus
vv   DLL1 MUTATED DLL1 WILD-TYPE
  R0           10            301
  R1            2             12
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D909V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DLL1 MUTATED       4                         0
  DLL1 WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DLL1 MUTATED                                           0     8
  DLL1 WILD-TYPE                                         1   235
D909V12, multiclass
                                           clus
vv                                          DLL1 MUTATED DLL1 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D909V13, binary
                cls
clus               0   1
  DLL1 MUTATED     0  12
  DLL1 WILD-TYPE   4 298
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLL1 MUTATED      0   12
  DLL1 WILD-TYPE    4  298
                        clus
vv                       DLL1 MUTATED DLL1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           12            298
[1] 2 2
[1] FALSE

Clustering(910) Variable = E2F7 MUTATION ANALYSIS
D910V1, survival
                sevent
clus2              0   1
  E2F7 MUTATED    13   4
  E2F7 WILD-TYPE 217 135
  E2F7 MUTATED E2F7 WILD-TYPE 
            17            352 
  E2F7 MUTATED E2F7 WILD-TYPE 
             4            135 
$`E2F7 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8485 TCGA-BR-8487 
       30.90        34.68        29.59         0.26         9.21         1.12 
TCGA-BR-8680 TCGA-CD-5801 TCGA-CG-5721 TCGA-D7-6522 TCGA-D7-6822 TCGA-D7-A4YU 
       31.96        13.18         6.02        18.61        12.33        16.44 
TCGA-D7-A4YX TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4GN TCGA-VQ-A8DZ 
       36.43        77.29        30.51        29.98        13.02 

$`E2F7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8486 TCGA-BR-8588 
       25.05         3.72         5.39        25.18        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-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-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-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.54        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-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
       14.27         5.92        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-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-A8E2 TCGA-VQ-A8E7 
        0.92        48.79         5.46        13.25        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 

  E2F7 MUTATED E2F7 WILD-TYPE 
          0.26           0.00 
  E2F7 MUTATED E2F7 WILD-TYPE 
         77.29         122.30 
  E2F7 MUTATED E2F7 WILD-TYPE 
         18.61          14.12 
[1] "0.3 - 77.3 (18.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2"  
D910V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  E2F7 MUTATED         0        0        3        1         3         3
  E2F7 WILD-TYPE       2       15       37       29        34        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  E2F7 MUTATED           0          1          1          2        4
  E2F7 WILD-TYPE         3         69         52         30       34
D910V3, multiclass
            clus
vv           E2F7 MUTATED E2F7 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              3             37
  STAGE II              1             29
  STAGE IIA             3             34
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            2             30
  STAGE IV              4             34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  E2F7 MUTATED     1   6   5   8
  E2F7 WILD-TYPE  21  86 168  89
D910V4, multiclass
    clus
vv   E2F7 MUTATED E2F7 WILD-TYPE
  T1            1             21
  T2            6             86
  T3            5            168
  T4            8             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
  E2F7 MUTATED     7   5   2   4
  E2F7 WILD-TYPE 111  99  75  73
D910V5, multiclass
    clus
vv   E2F7 MUTATED E2F7 WILD-TYPE
  N0            7            111
  N1            5             99
  N2            2             75
  N3            4             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"
D910V6, binary
                cls
clus               0   1
  E2F7 MUTATED    18   2
  E2F7 WILD-TYPE 328  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED     18    2
  E2F7 WILD-TYPE  328   27
   clus
vv  E2F7 MUTATED E2F7 WILD-TYPE
  0           18            328
  1            2             27
[1] 2 2
[1] FALSE
D910V7, binary
                cls
clus               0   1
  E2F7 MUTATED     9  11
  E2F7 WILD-TYPE 136 237
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED      9   11
  E2F7 WILD-TYPE  136  237
        clus
vv       E2F7 MUTATED E2F7 WILD-TYPE
  FEMALE            9            136
  MALE             11            237
[1] 2 2
[1] FALSE
D910V8, binary
                cls
clus               0   1
  E2F7 MUTATED    16   2
  E2F7 WILD-TYPE 276  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED     16    2
  E2F7 WILD-TYPE  276   57
     clus
vv    E2F7 MUTATED E2F7 WILD-TYPE
  NO            16            276
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  E2F7 MUTATED                                          1
  E2F7 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  E2F7 MUTATED                                       1
  E2F7 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  E2F7 MUTATED                                                       10
  E2F7 WILD-TYPE                                                    148
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  E2F7 MUTATED                                                   2
  E2F7 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  E2F7 MUTATED                                                                   2
  E2F7 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  E2F7 MUTATED                                                    0
  E2F7 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  E2F7 MUTATED                                                  4
  E2F7 WILD-TYPE                                               57
D910V9, multiclass
                                                                   clus
vv                                                                  E2F7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  E2F7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  E2F7 MUTATED    15   1   1   3
  E2F7 WILD-TYPE 296  13  14  21
D910V10, multiclass
    clus
vv   E2F7 MUTATED E2F7 WILD-TYPE
  R0           15            296
  R1            1             13
  R2            1             14
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D910V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  E2F7 MUTATED       3                         1
  E2F7 WILD-TYPE    84                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  E2F7 MUTATED                                           0    13
  E2F7 WILD-TYPE                                         1   230
D910V12, multiclass
                                           clus
vv                                          E2F7 MUTATED E2F7 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               13            230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D910V13, binary
                cls
clus               0   1
  E2F7 MUTATED     0  16
  E2F7 WILD-TYPE   4 294
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED      0   16
  E2F7 WILD-TYPE    4  294
                        clus
vv                       E2F7 MUTATED E2F7 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           16            294
[1] 2 2
[1] FALSE

Clustering(911) Variable = MYOCD MUTATION ANALYSIS
D911V1, survival
                 sevent
clus2               0   1
  MYOCD MUTATED     9   6
  MYOCD WILD-TYPE 221 133
  MYOCD MUTATED MYOCD WILD-TYPE 
             15             354 
  MYOCD MUTATED MYOCD WILD-TYPE 
              6             133 
$`MYOCD MUTATED`
TCGA-BR-4201 TCGA-BR-6802 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8591 TCGA-BR-8686 
       30.90        30.90         0.26         0.95        28.14        20.88 
TCGA-BR-A4J4 TCGA-BR-A4QL TCGA-CD-8529 TCGA-CG-5721 TCGA-D7-A4YV TCGA-D7-A6EY 
        0.53        16.14        12.30         6.02         5.92        11.44 
TCGA-F1-6874 TCGA-HU-A4GX TCGA-VQ-A8E2 
       14.47        20.25        43.36 

$`MYOCD WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 
        6.18        31.10        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-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-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD 
       14.17        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-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-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-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-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-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 

  MYOCD MUTATED MYOCD WILD-TYPE 
           0.26            0.00 
  MYOCD MUTATED MYOCD WILD-TYPE 
          43.36          122.30 
  MYOCD MUTATED MYOCD WILD-TYPE 
          14.47           14.22 
[1] "0.3 - 43.4 (14.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D911V2, 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       1       15       38       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MYOCD MUTATED           0          1          5          2        2
  MYOCD WILD-TYPE         3         69         48         30       36
D911V3, multiclass
            clus
vv           MYOCD MUTATED MYOCD WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             5              48
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYOCD MUTATED     1   3   6   6
  MYOCD WILD-TYPE  21  89 167  91
D911V4, multiclass
    clus
vv   MYOCD MUTATED MYOCD WILD-TYPE
  T1             1              21
  T2             3              89
  T3             6             167
  T4             6              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
  MYOCD MUTATED     4   5   4   3
  MYOCD WILD-TYPE 114  99  73  74
D911V5, multiclass
    clus
vv   MYOCD MUTATED MYOCD WILD-TYPE
  N0             4             114
  N1             5              99
  N2             4              73
  N3             3              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"
D911V6, binary
                 cls
clus                0   1
  MYOCD MUTATED    15   1
  MYOCD WILD-TYPE 331  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYOCD MUTATED     15    1
  MYOCD WILD-TYPE  331   28
   clus
vv  MYOCD MUTATED MYOCD WILD-TYPE
  0            15             331
  1             1              28
[1] 2 2
[1] FALSE
D911V7, binary
                 cls
clus                0   1
  MYOCD MUTATED     8   9
  MYOCD WILD-TYPE 137 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYOCD MUTATED      8    9
  MYOCD WILD-TYPE  137  239
        clus
vv       MYOCD MUTATED MYOCD WILD-TYPE
  FEMALE             8             137
  MALE               9             239
[1] 2 2
[1] FALSE
D911V8, binary
                 cls
clus                0   1
  MYOCD MUTATED    13   2
  MYOCD WILD-TYPE 279  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYOCD MUTATED     13    2
  MYOCD WILD-TYPE  279   57
     clus
vv    MYOCD MUTATED MYOCD WILD-TYPE
  NO             13             279
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MYOCD MUTATED                                          0
  MYOCD WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MYOCD MUTATED                                       1
  MYOCD WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MYOCD MUTATED                                                        9
  MYOCD WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MYOCD MUTATED                                                   1
  MYOCD WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MYOCD MUTATED                                                                   2
  MYOCD WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MYOCD MUTATED                                                    0
  MYOCD WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MYOCD MUTATED                                                  4
  MYOCD WILD-TYPE                                               57
D911V9, multiclass
                                                                   clus
vv                                                                  MYOCD MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  MYOCD WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYOCD MUTATED    15   0   0   2
  MYOCD WILD-TYPE 296  14  15  22
D911V10, multiclass
    clus
vv   MYOCD MUTATED MYOCD WILD-TYPE
  R0            15             296
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D911V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MYOCD MUTATED       5                         1
  MYOCD WILD-TYPE    82                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MYOCD MUTATED                                           0    10
  MYOCD WILD-TYPE                                         1   233
D911V12, multiclass
                                           clus
vv                                          MYOCD MUTATED MYOCD WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D911V13, binary
                 cls
clus                0   1
  MYOCD MUTATED     0  15
  MYOCD WILD-TYPE   4 295
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYOCD MUTATED      0   15
  MYOCD WILD-TYPE    4  295
                        clus
vv                       MYOCD MUTATED MYOCD WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            15             295
[1] 2 2
[1] FALSE

Clustering(912) Variable = EVI2B MUTATION ANALYSIS
D912V1, survival
                 sevent
clus2               0   1
  EVI2B MUTATED     8   1
  EVI2B WILD-TYPE 222 138
  EVI2B MUTATED EVI2B WILD-TYPE 
              9             360 
  EVI2B MUTATED EVI2B WILD-TYPE 
              1             138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-4441 
       15.95         1.02         7.99         8.05        54.08        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-D7-6818 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-D7-8576 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-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-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-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 

  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           14.45 
[1] "0.6 - 38.1 (12.8)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "3.2"
D912V2, 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       2       15       39       30        37        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EVI2B MUTATED           0          4          0          0        2
  EVI2B WILD-TYPE         3         66         53         32       36
D912V3, multiclass
            clus
vv           EVI2B MUTATED EVI2B WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EVI2B MUTATED     1   1   3   4
  EVI2B WILD-TYPE  21  91 170  93
D912V4, multiclass
    clus
vv   EVI2B MUTATED EVI2B WILD-TYPE
  T1             1              21
  T2             1              91
  T3             3             170
  T4             4              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
  EVI2B MUTATED     2   4   1   2
  EVI2B WILD-TYPE 116 100  76  75
D912V5, multiclass
    clus
vv   EVI2B MUTATED EVI2B WILD-TYPE
  N0             2             116
  N1             4             100
  N2             1              76
  N3             2              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"
D912V6, binary
                 cls
clus                0   1
  EVI2B MUTATED     6   2
  EVI2B WILD-TYPE 340  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2B MUTATED      6    2
  EVI2B WILD-TYPE  340   27
   clus
vv  EVI2B MUTATED EVI2B WILD-TYPE
  0             6             340
  1             2              27
[1] 2 2
[1] FALSE
D912V7, binary
                 cls
clus                0   1
  EVI2B MUTATED     2   7
  EVI2B WILD-TYPE 143 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2B MUTATED      2    7
  EVI2B WILD-TYPE  143  241
        clus
vv       EVI2B MUTATED EVI2B WILD-TYPE
  FEMALE             2             143
  MALE               7             241
[1] 2 2
[1] FALSE
D912V8, binary
                 cls
clus                0   1
  EVI2B MUTATED     4   3
  EVI2B WILD-TYPE 288  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2B MUTATED      4    3
  EVI2B WILD-TYPE  288   56
     clus
vv    EVI2B MUTATED EVI2B WILD-TYPE
  NO              4             288
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EVI2B MUTATED                                          0
  EVI2B WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EVI2B MUTATED                                       1
  EVI2B WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EVI2B MUTATED                                                        2
  EVI2B WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EVI2B MUTATED                                                   2
  EVI2B WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EVI2B MUTATED                                                                   2
  EVI2B WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EVI2B MUTATED                                                    0
  EVI2B WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EVI2B MUTATED                                                  2
  EVI2B WILD-TYPE                                               59
D912V9, multiclass
                                                                   clus
vv                                                                  EVI2B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  EVI2B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EVI2B MUTATED     8   0   1   0
  EVI2B WILD-TYPE 303  14  14  24
D912V10, multiclass
    clus
vv   EVI2B MUTATED EVI2B WILD-TYPE
  R0             8             303
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D912V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EVI2B MUTATED       3                         0
  EVI2B WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EVI2B MUTATED                                           0     5
  EVI2B WILD-TYPE                                         1   238
D912V12, multiclass
                                           clus
vv                                          EVI2B MUTATED EVI2B WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D912V13, binary
                 cls
clus                0   1
  EVI2B MUTATED     0   7
  EVI2B WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EVI2B MUTATED      0    7
  EVI2B WILD-TYPE    4  303
                        clus
vv                       EVI2B MUTATED EVI2B WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(913) Variable = NRIP3 MUTATION ANALYSIS
D913V1, survival
                 sevent
clus2               0   1
  NRIP3 MUTATED     2   2
  NRIP3 WILD-TYPE 228 137
  NRIP3 MUTATED NRIP3 WILD-TYPE 
              4             365 
  NRIP3 MUTATED NRIP3 WILD-TYPE 
              2             137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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          14.170 
[1] "8.1 - 32.0 (30.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D913V2, 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       2       14       39       30        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NRIP3 MUTATED           0          0          0          2        1
  NRIP3 WILD-TYPE         3         70         53         30       37
D913V3, multiclass
            clus
vv           NRIP3 MUTATED NRIP3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NRIP3 MUTATED     2   1   0   3
  NRIP3 WILD-TYPE  20  91 173  94
D913V4, multiclass
    clus
vv   NRIP3 MUTATED NRIP3 WILD-TYPE
  T1             2              20
  T2             1              91
  T3             0             173
  T4             3              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
  NRIP3 MUTATED     2   0   1   2
  NRIP3 WILD-TYPE 116 104  76  75
D913V5, multiclass
    clus
vv   NRIP3 MUTATED NRIP3 WILD-TYPE
  N0             2             116
  N1             0             104
  N2             1              76
  N3             2              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"
D913V6, binary
                 cls
clus                0   1
  NRIP3 MUTATED     6   1
  NRIP3 WILD-TYPE 340  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NRIP3 MUTATED      6    1
  NRIP3 WILD-TYPE  340   28
   clus
vv  NRIP3 MUTATED NRIP3 WILD-TYPE
  0             6             340
  1             1              28
[1] 2 2
[1] FALSE
D913V7, binary
                 cls
clus                0   1
  NRIP3 MUTATED     3   4
  NRIP3 WILD-TYPE 142 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NRIP3 MUTATED      3    4
  NRIP3 WILD-TYPE  142  244
        clus
vv       NRIP3 MUTATED NRIP3 WILD-TYPE
  FEMALE             3             142
  MALE               4             244
[1] 2 2
[1] FALSE
D913V8, binary
                 cls
clus                0   1
  NRIP3 MUTATED     3   0
  NRIP3 WILD-TYPE 289  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NRIP3 MUTATED      3    0
  NRIP3 WILD-TYPE  289   59
     clus
vv    NRIP3 MUTATED NRIP3 WILD-TYPE
  NO              3             289
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NRIP3 MUTATED                                          0
  NRIP3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NRIP3 MUTATED                                       0
  NRIP3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NRIP3 MUTATED                                                        3
  NRIP3 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NRIP3 MUTATED                                                   0
  NRIP3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NRIP3 MUTATED                                                                   3
  NRIP3 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NRIP3 MUTATED                                                    0
  NRIP3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NRIP3 MUTATED                                                  1
  NRIP3 WILD-TYPE                                               60
D913V9, multiclass
                                                                   clus
vv                                                                  NRIP3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  NRIP3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NRIP3 MUTATED     5   0   0   2
  NRIP3 WILD-TYPE 306  14  15  22
D913V10, multiclass
    clus
vv   NRIP3 MUTATED NRIP3 WILD-TYPE
  R0             5             306
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D913V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NRIP3 MUTATED       1                         0
  NRIP3 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NRIP3 MUTATED                                           0     4
  NRIP3 WILD-TYPE                                         1   239
D913V12, multiclass
                                           clus
vv                                          NRIP3 MUTATED NRIP3 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D913V13, binary
                 cls
clus                0   1
  NRIP3 MUTATED     0   5
  NRIP3 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NRIP3 MUTATED      0    5
  NRIP3 WILD-TYPE    4  305
                        clus
vv                       NRIP3 MUTATED NRIP3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(914) Variable = ABCA7 MUTATION ANALYSIS
D914V1, survival
                 sevent
clus2               0   1
  ABCA7 MUTATED    14   4
  ABCA7 WILD-TYPE 216 135
  ABCA7 MUTATED ABCA7 WILD-TYPE 
             18             351 
  ABCA7 MUTATED ABCA7 WILD-TYPE 
              4             135 
$`ABCA7 MUTATED`
TCGA-EQ-A4SO TCGA-B7-A5TI TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8369 TCGA-BR-8680 
       16.24        19.56        29.59         6.18        14.04        31.96 
TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 TCGA-D7-A6EY TCGA-F1-6874 TCGA-HF-A5NB 
        6.58         1.02         6.02        11.44        14.47        30.51 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-R5-A7ZI TCGA-VQ-A8P2 
       22.32        22.68        24.20         0.10        74.53        38.14 

$`ABCA7 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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 
          17.90           14.07 
[1] "0.1 - 74.5 (17.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D914V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCA7 MUTATED         0        1        1        0         2         3
  ABCA7 WILD-TYPE       2       14       39       30        35        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABCA7 MUTATED           0          3          3          3        4
  ABCA7 WILD-TYPE         3         67         50         29       34
D914V3, multiclass
            clus
vv           ABCA7 MUTATED ABCA7 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             3              50
  STAGE IIIC             3              29
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCA7 MUTATED     1   1   7  11
  ABCA7 WILD-TYPE  21  91 166  86
D914V4, multiclass
    clus
vv   ABCA7 MUTATED ABCA7 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             7             166
  T4            11              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
  ABCA7 MUTATED     7   6   3   4
  ABCA7 WILD-TYPE 111  98  74  73
D914V5, multiclass
    clus
vv   ABCA7 MUTATED ABCA7 WILD-TYPE
  N0             7             111
  N1             6              98
  N2             3              74
  N3             4              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"
D914V6, binary
                 cls
clus                0   1
  ABCA7 MUTATED    16   3
  ABCA7 WILD-TYPE 330  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA7 MUTATED     16    3
  ABCA7 WILD-TYPE  330   26
   clus
vv  ABCA7 MUTATED ABCA7 WILD-TYPE
  0            16             330
  1             3              26
[1] 2 2
[1] FALSE
D914V7, binary
                 cls
clus                0   1
  ABCA7 MUTATED     9  11
  ABCA7 WILD-TYPE 136 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA7 MUTATED      9   11
  ABCA7 WILD-TYPE  136  237
        clus
vv       ABCA7 MUTATED ABCA7 WILD-TYPE
  FEMALE             9             136
  MALE              11             237
[1] 2 2
[1] FALSE
D914V8, binary
                 cls
clus                0   1
  ABCA7 MUTATED    14   4
  ABCA7 WILD-TYPE 278  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA7 MUTATED     14    4
  ABCA7 WILD-TYPE  278   55
     clus
vv    ABCA7 MUTATED ABCA7 WILD-TYPE
  NO             14             278
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ABCA7 MUTATED                                          0
  ABCA7 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ABCA7 MUTATED                                       5
  ABCA7 WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCA7 MUTATED                                                        5
  ABCA7 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ABCA7 MUTATED                                                   2
  ABCA7 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCA7 MUTATED                                                                   3
  ABCA7 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ABCA7 MUTATED                                                    0
  ABCA7 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ABCA7 MUTATED                                                  4
  ABCA7 WILD-TYPE                                               57
D914V9, multiclass
                                                                   clus
vv                                                                  ABCA7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  ABCA7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCA7 MUTATED    13   2   1   1
  ABCA7 WILD-TYPE 298  12  14  23
D914V10, multiclass
    clus
vv   ABCA7 MUTATED ABCA7 WILD-TYPE
  R0            13             298
  R1             2              12
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D914V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCA7 MUTATED       6                         0
  ABCA7 WILD-TYPE    81                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCA7 MUTATED                                           0    10
  ABCA7 WILD-TYPE                                         1   233
D914V12, multiclass
                                           clus
vv                                          ABCA7 MUTATED ABCA7 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D914V13, binary
                 cls
clus                0   1
  ABCA7 MUTATED     1  14
  ABCA7 WILD-TYPE   3 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA7 MUTATED      1   14
  ABCA7 WILD-TYPE    3  296
                        clus
vv                       ABCA7 MUTATED ABCA7 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(915) Variable = CWF19L2 MUTATION ANALYSIS
D915V1, survival
                   sevent
clus2                 0   1
  CWF19L2 MUTATED    10   1
  CWF19L2 WILD-TYPE 220 138
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               11               358 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
                1               138 
$`CWF19L2 MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-8572 
       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-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-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-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 

  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
             6.02              0.00 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
            74.53            122.30 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
            19.73             14.22 
[1] "6.0 - 74.5 (19.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "5.6"
D915V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CWF19L2 MUTATED         1        0        3        1         1         1
  CWF19L2 WILD-TYPE       1       15       37       29        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CWF19L2 MUTATED           0          1          1          1        3
  CWF19L2 WILD-TYPE         3         69         52         31       35
D915V3, multiclass
            clus
vv           CWF19L2 MUTATED CWF19L2 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 3                37
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 3                35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CWF19L2 MUTATED     1   3   4   5
  CWF19L2 WILD-TYPE  21  89 169  92
D915V4, multiclass
    clus
vv   CWF19L2 MUTATED CWF19L2 WILD-TYPE
  T1               1                21
  T2               3                89
  T3               4               169
  T4               5                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
  CWF19L2 MUTATED     6   3   2   2
  CWF19L2 WILD-TYPE 112 101  75  75
D915V5, multiclass
    clus
vv   CWF19L2 MUTATED CWF19L2 WILD-TYPE
  N0               6               112
  N1               3               101
  N2               2                75
  N3               2                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"
D915V6, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED    10   2
  CWF19L2 WILD-TYPE 336  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED     10    2
  CWF19L2 WILD-TYPE  336   27
   clus
vv  CWF19L2 MUTATED CWF19L2 WILD-TYPE
  0              10               336
  1               2                27
[1] 2 2
[1] FALSE
D915V7, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED     7   7
  CWF19L2 WILD-TYPE 138 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED      7    7
  CWF19L2 WILD-TYPE  138  241
        clus
vv       CWF19L2 MUTATED CWF19L2 WILD-TYPE
  FEMALE               7               138
  MALE                 7               241
[1] 2 2
[1] FALSE
D915V8, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED    10   1
  CWF19L2 WILD-TYPE 282  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED     10    1
  CWF19L2 WILD-TYPE  282   58
     clus
vv    CWF19L2 MUTATED CWF19L2 WILD-TYPE
  NO               10               282
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CWF19L2 MUTATED                                          0
  CWF19L2 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CWF19L2 MUTATED                                       2
  CWF19L2 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CWF19L2 MUTATED                                                        7
  CWF19L2 WILD-TYPE                                                    151
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CWF19L2 MUTATED                                                   0
  CWF19L2 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CWF19L2 MUTATED                                                                   2
  CWF19L2 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CWF19L2 MUTATED                                                    1
  CWF19L2 WILD-TYPE                                                  4
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CWF19L2 MUTATED                                                  2
  CWF19L2 WILD-TYPE                                               59
D915V9, multiclass
                                                                   clus
vv                                                                  CWF19L2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  CWF19L2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CWF19L2 MUTATED    11   0   1   1
  CWF19L2 WILD-TYPE 300  14  14  23
D915V10, multiclass
    clus
vv   CWF19L2 MUTATED CWF19L2 WILD-TYPE
  R0              11               300
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D915V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CWF19L2 MUTATED       4                         1
  CWF19L2 WILD-TYPE    83                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CWF19L2 MUTATED                                           0     6
  CWF19L2 WILD-TYPE                                         1   237
D915V12, multiclass
                                           clus
vv                                          CWF19L2 MUTATED CWF19L2 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D915V13, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED     1  10
  CWF19L2 WILD-TYPE   3 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED      1   10
  CWF19L2 WILD-TYPE    3  300
                        clus
vv                       CWF19L2 MUTATED CWF19L2 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              10               300
[1] 2 2
[1] FALSE

Clustering(916) Variable = FIBP MUTATION ANALYSIS
D916V1, survival
                sevent
clus2              0   1
  FIBP MUTATED     8   1
  FIBP WILD-TYPE 222 138
  FIBP MUTATED FIBP WILD-TYPE 
             9            360 
  FIBP MUTATED FIBP WILD-TYPE 
             1            138 
$`FIBP MUTATED`
TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8382 TCGA-BR-8487 TCGA-CD-5802 TCGA-HF-A5NB 
       34.68        31.10        25.05         1.12        13.35        30.51 
TCGA-HU-A4G8 TCGA-HU-A4GU TCGA-VQ-A8P2 
       22.68         6.58        38.14 

$`FIBP WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  FIBP MUTATED FIBP WILD-TYPE 
          1.12           0.00 
  FIBP MUTATED FIBP WILD-TYPE 
         38.14         122.30 
  FIBP MUTATED FIBP WILD-TYPE 
         25.05          14.12 
[1] "1.1 - 38.1 (25.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "4.4"
D916V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FIBP MUTATED         0        0        0        1         2         3
  FIBP WILD-TYPE       2       15       40       29        35        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FIBP MUTATED           0          1          0          3        0
  FIBP WILD-TYPE         3         69         53         29       38
D916V3, multiclass
            clus
vv           FIBP MUTATED FIBP WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            3             29
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FIBP MUTATED     0   0   6   5
  FIBP WILD-TYPE  22  92 167  92
D916V4, multiclass
    clus
vv   FIBP MUTATED FIBP WILD-TYPE
  T1            0             22
  T2            0             92
  T3            6            167
  T4            5             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
  FIBP MUTATED     4   3   1   2
  FIBP WILD-TYPE 114 101  76  75
D916V5, multiclass
    clus
vv   FIBP MUTATED FIBP WILD-TYPE
  N0            4            114
  N1            3            101
  N2            1             76
  N3            2             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"
D916V6, binary
                cls
clus               0   1
  FIBP MUTATED    10   0
  FIBP WILD-TYPE 336  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  FIBP MUTATED     10    0
  FIBP WILD-TYPE  336   29
   clus
vv  FIBP MUTATED FIBP WILD-TYPE
  0           10            336
  1            0             29
[1] 2 2
[1] FALSE
D916V7, binary
                cls
clus               0   1
  FIBP MUTATED     7   4
  FIBP WILD-TYPE 138 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  FIBP MUTATED      7    4
  FIBP WILD-TYPE  138  244
        clus
vv       FIBP MUTATED FIBP WILD-TYPE
  FEMALE            7            138
  MALE              4            244
[1] 2 2
[1] FALSE
D916V8, binary
                cls
clus               0   1
  FIBP MUTATED     7   3
  FIBP WILD-TYPE 285  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  FIBP MUTATED      7    3
  FIBP WILD-TYPE  285   56
     clus
vv    FIBP MUTATED FIBP WILD-TYPE
  NO             7            285
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FIBP MUTATED                                          0
  FIBP WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FIBP MUTATED                                       2
  FIBP WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FIBP MUTATED                                                        6
  FIBP WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FIBP MUTATED                                                   2
  FIBP WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FIBP MUTATED                                                                   1
  FIBP WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FIBP MUTATED                                                    0
  FIBP WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FIBP MUTATED                                                  0
  FIBP WILD-TYPE                                               61
D916V9, multiclass
                                                                   clus
vv                                                                  FIBP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  FIBP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FIBP MUTATED     7   1   0   1
  FIBP WILD-TYPE 304  13  15  23
D916V10, multiclass
    clus
vv   FIBP MUTATED FIBP WILD-TYPE
  R0            7            304
  R1            1             13
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D916V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FIBP MUTATED       3                         0
  FIBP WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FIBP MUTATED                                           0     7
  FIBP WILD-TYPE                                         1   236
D916V12, multiclass
                                           clus
vv                                          FIBP MUTATED FIBP WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D916V13, binary
                cls
clus               0   1
  FIBP MUTATED     0   9
  FIBP WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  FIBP MUTATED      0    9
  FIBP WILD-TYPE    4  301
                        clus
vv                       FIBP MUTATED FIBP WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(917) Variable = PLEKHH3 MUTATION ANALYSIS
D917V1, survival
                   sevent
clus2                 0   1
  PLEKHH3 MUTATED     8   0
  PLEKHH3 WILD-TYPE 222 139
  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE 
                8               361 
  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE 
                0               139 
$`PLEKHH3 MUTATED`
TCGA-CG-5727 TCGA-BR-7707 TCGA-BR-8360 TCGA-BR-8487 TCGA-CG-4305 TCGA-CG-5721 
       79.07        35.84         6.18         1.12        15.95         6.02 
TCGA-CG-5723 TCGA-F1-A448 
      105.07        21.27 

$`PLEKHH3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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 

  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE 
             1.12              0.00 
  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE 
           105.07            122.30 
  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE 
            18.61             14.17 
[1] "1.1 - 105.1 (18.6)" "0.0 - 122.3 (14.2)"
[1] "hr="     "2.7e+07"
D917V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PLEKHH3 MUTATED         1        0        2        3         2         0
  PLEKHH3 WILD-TYPE       1       15       38       27        35        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHH3 MUTATED           0          0          1          0        1
  PLEKHH3 WILD-TYPE         3         70         52         32       37
D917V3, multiclass
            clus
vv           PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 3                27
  STAGE IIA                2                35
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               1                52
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHH3 MUTATED     1   4   4   1
  PLEKHH3 WILD-TYPE  21  88 169  96
D917V4, multiclass
    clus
vv   PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  T1               1                21
  T2               4                88
  T3               4               169
  T4               1                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
  PLEKHH3 MUTATED     5   4   0   1
  PLEKHH3 WILD-TYPE 113 100  77  76
D917V5, multiclass
    clus
vv   PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  N0               5               113
  N1               4               100
  N2               0                77
  N3               1                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"
D917V6, binary
                   cls
clus                  0   1
  PLEKHH3 MUTATED     9   0
  PLEKHH3 WILD-TYPE 337  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH3 MUTATED      9    0
  PLEKHH3 WILD-TYPE  337   29
   clus
vv  PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  0               9               337
  1               0                29
[1] 2 2
[1] FALSE
D917V7, binary
                   cls
clus                  0   1
  PLEKHH3 MUTATED     2   8
  PLEKHH3 WILD-TYPE 143 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH3 MUTATED      2    8
  PLEKHH3 WILD-TYPE  143  240
        clus
vv       PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  FEMALE               2               143
  MALE                 8               240
[1] 2 2
[1] FALSE
D917V8, binary
                   cls
clus                  0   1
  PLEKHH3 MUTATED     8   1
  PLEKHH3 WILD-TYPE 284  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH3 MUTATED      8    1
  PLEKHH3 WILD-TYPE  284   58
     clus
vv    PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  NO                8               284
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PLEKHH3 MUTATED                                          0
  PLEKHH3 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PLEKHH3 MUTATED                                       0
  PLEKHH3 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLEKHH3 MUTATED                                                        5
  PLEKHH3 WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PLEKHH3 MUTATED                                                   1
  PLEKHH3 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PLEKHH3 MUTATED                                                                   4
  PLEKHH3 WILD-TYPE                                                                64
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PLEKHH3 MUTATED                                                    0
  PLEKHH3 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PLEKHH3 MUTATED                                                  0
  PLEKHH3 WILD-TYPE                                               61
D917V9, multiclass
                                                                   clus
vv                                                                  PLEKHH3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  PLEKHH3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PLEKHH3 MUTATED    10   0   0   0
  PLEKHH3 WILD-TYPE 301  14  15  24
D917V10, multiclass
    clus
vv   PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  R0              10               301
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D917V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PLEKHH3 MUTATED       0                         1
  PLEKHH3 WILD-TYPE    87                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PLEKHH3 MUTATED                                           0     4
  PLEKHH3 WILD-TYPE                                         1   239
D917V12, multiclass
                                           clus
vv                                          PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  ASIAN                                                   0                87
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D917V13, binary
                   cls
clus                  0   1
  PLEKHH3 MUTATED     1   4
  PLEKHH3 WILD-TYPE   3 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH3 MUTATED      1    4
  PLEKHH3 WILD-TYPE    3  306
                        clus
vv                       PLEKHH3 MUTATED PLEKHH3 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO               4               306
[1] 2 2
[1] FALSE

Clustering(918) Variable = MAP7D2 MUTATION ANALYSIS
D918V1, survival
                  sevent
clus2                0   1
  MAP7D2 MUTATED     3   1
  MAP7D2 WILD-TYPE 227 138
  MAP7D2 MUTATED MAP7D2 WILD-TYPE 
               4              365 
  MAP7D2 MUTATED MAP7D2 WILD-TYPE 
               1              138 
$`MAP7D2 MUTATED`
TCGA-BR-A4J2 TCGA-EQ-5647 TCGA-IN-A7NT TCGA-VQ-A8P2 
       14.17         0.62        10.62        38.14 

$`MAP7D2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8122 TCGA-F1-6874 TCGA-F1-6875 
        4.34        19.96         7.13         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-A7NU 
       19.53         6.44         6.74        12.59         6.51        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 

  MAP7D2 MUTATED MAP7D2 WILD-TYPE 
            0.62             0.00 
  MAP7D2 MUTATED MAP7D2 WILD-TYPE 
           38.14           122.30 
  MAP7D2 MUTATED MAP7D2 WILD-TYPE 
          12.395           14.430 
[1] "0.6 - 38.1 (12.4)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.3"
D918V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP7D2 MUTATED         0        0        0        0         0         2
  MAP7D2 WILD-TYPE       2       15       40       30        37        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP7D2 MUTATED           0          1          0          0        1
  MAP7D2 WILD-TYPE         3         69         53         32       37
D918V3, multiclass
            clus
vv           MAP7D2 MUTATED MAP7D2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP7D2 MUTATED     0   0   1   3
  MAP7D2 WILD-TYPE  22  92 172  94
D918V4, multiclass
    clus
vv   MAP7D2 MUTATED MAP7D2 WILD-TYPE
  T1              0               22
  T2              0               92
  T3              1              172
  T4              3               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
  MAP7D2 MUTATED     1   3   0   1
  MAP7D2 WILD-TYPE 117 101  77  76
D918V5, multiclass
    clus
vv   MAP7D2 MUTATED MAP7D2 WILD-TYPE
  N0              1              117
  N1              3              101
  N2              0               77
  N3              1               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"
D918V6, binary
                  cls
clus                 0   1
  MAP7D2 MUTATED     4   1
  MAP7D2 WILD-TYPE 342  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D2 MUTATED      4    1
  MAP7D2 WILD-TYPE  342   28
   clus
vv  MAP7D2 MUTATED MAP7D2 WILD-TYPE
  0              4              342
  1              1               28
[1] 2 2
[1] FALSE
D918V7, binary
                  cls
clus                 0   1
  MAP7D2 MUTATED     3   2
  MAP7D2 WILD-TYPE 142 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D2 MUTATED      3    2
  MAP7D2 WILD-TYPE  142  246
        clus
vv       MAP7D2 MUTATED MAP7D2 WILD-TYPE
  FEMALE              3              142
  MALE                2              246
[1] 2 2
[1] FALSE
D918V8, binary
                  cls
clus                 0   1
  MAP7D2 MUTATED     3   1
  MAP7D2 WILD-TYPE 289  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D2 MUTATED      3    1
  MAP7D2 WILD-TYPE  289   58
     clus
vv    MAP7D2 MUTATED MAP7D2 WILD-TYPE
  NO               3              289
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MAP7D2 MUTATED                                          0
  MAP7D2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MAP7D2 MUTATED                                       1
  MAP7D2 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP7D2 MUTATED                                                        3
  MAP7D2 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MAP7D2 MUTATED                                                   1
  MAP7D2 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP7D2 MUTATED                                                                   0
  MAP7D2 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MAP7D2 MUTATED                                                    0
  MAP7D2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MAP7D2 MUTATED                                                  0
  MAP7D2 WILD-TYPE                                               61
D918V9, multiclass
                                                                   clus
vv                                                                  MAP7D2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  MAP7D2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP7D2 MUTATED     3   0   1   1
  MAP7D2 WILD-TYPE 308  14  14  23
D918V10, multiclass
    clus
vv   MAP7D2 MUTATED MAP7D2 WILD-TYPE
  R0              3              308
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D918V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAP7D2 MUTATED       1                         0
  MAP7D2 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP7D2 MUTATED                                           0     4
  MAP7D2 WILD-TYPE                                         1   239
D918V12, multiclass
                                           clus
vv                                          MAP7D2 MUTATED MAP7D2 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D918V13, binary
                  cls
clus                 0   1
  MAP7D2 MUTATED     0   4
  MAP7D2 WILD-TYPE   4 306
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D2 MUTATED      0    4
  MAP7D2 WILD-TYPE    4  306
                        clus
vv                       MAP7D2 MUTATED MAP7D2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              306
[1] 2 2
[1] FALSE

Clustering(919) Variable = ZDHHC7 MUTATION ANALYSIS
D919V1, survival
                  sevent
clus2                0   1
  ZDHHC7 MUTATED     5   1
  ZDHHC7 WILD-TYPE 225 138
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               6              363 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               1              138 
$`ZDHHC7 MUTATED`
TCGA-BR-6452 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MI TCGA-HF-7132 TCGA-HU-A4G8 
       34.68         1.12        28.14        11.77        77.29        22.68 

$`ZDHHC7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
            1.12             0.00 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
           77.29           122.30 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
           25.41            14.17 
[1] "1.1 - 77.3 (25.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3.3"
D919V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZDHHC7 MUTATED         0        0        1        1         2         1
  ZDHHC7 WILD-TYPE       2       15       39       29        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZDHHC7 MUTATED           0          1          0          1        0
  ZDHHC7 WILD-TYPE         3         69         53         31       38
D919V3, multiclass
            clus
vv           ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZDHHC7 MUTATED     0   2   4   1
  ZDHHC7 WILD-TYPE  22  90 169  96
D919V4, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              4              169
  T4              1               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
  ZDHHC7 MUTATED     3   3   0   1
  ZDHHC7 WILD-TYPE 115 101  77  76
D919V5, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  N0              3              115
  N1              3              101
  N2              0               77
  N3              1               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"
D919V6, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     7   0
  ZDHHC7 WILD-TYPE 339  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      7    0
  ZDHHC7 WILD-TYPE  339   29
   clus
vv  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  0              7              339
  1              0               29
[1] 2 2
[1] FALSE
D919V7, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     3   4
  ZDHHC7 WILD-TYPE 142 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      3    4
  ZDHHC7 WILD-TYPE  142  244
        clus
vv       ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  FEMALE              3              142
  MALE                4              244
[1] 2 2
[1] FALSE
D919V8, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     5   1
  ZDHHC7 WILD-TYPE 287  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      5    1
  ZDHHC7 WILD-TYPE  287   58
     clus
vv    ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  NO               5              287
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZDHHC7 MUTATED                                          0
  ZDHHC7 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZDHHC7 MUTATED                                       1
  ZDHHC7 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZDHHC7 MUTATED                                                        4
  ZDHHC7 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZDHHC7 MUTATED                                                   1
  ZDHHC7 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZDHHC7 MUTATED                                                                   1
  ZDHHC7 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZDHHC7 MUTATED                                                    0
  ZDHHC7 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZDHHC7 MUTATED                                                  0
  ZDHHC7 WILD-TYPE                                               61
D919V9, multiclass
                                                                   clus
vv                                                                  ZDHHC7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  ZDHHC7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZDHHC7 MUTATED     5   0   0   0
  ZDHHC7 WILD-TYPE 306  14  15  24
D919V10, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D919V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZDHHC7 MUTATED       2                         0
  ZDHHC7 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZDHHC7 MUTATED                                           0     3
  ZDHHC7 WILD-TYPE                                         1   240
D919V12, multiclass
                                           clus
vv                                          ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D919V13, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     0   5
  ZDHHC7 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      0    5
  ZDHHC7 WILD-TYPE    4  305
                        clus
vv                       ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(920) Variable = HTRA2 MUTATION ANALYSIS
D920V1, survival
                 sevent
clus2               0   1
  HTRA2 MUTATED     7   0
  HTRA2 WILD-TYPE 223 139
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              7             362 
  HTRA2 MUTATED HTRA2 WILD-TYPE 
              0             139 
$`HTRA2 MUTATED`
TCGA-BR-6802 TCGA-BR-8487 TCGA-BR-8589 TCGA-CG-4437 TCGA-HF-A5NB TCGA-HU-8602 
       30.90         1.12        27.12         8.05        30.51        22.32 
TCGA-HU-A4G8 
       22.68 

$`HTRA2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  HTRA2 MUTATED HTRA2 WILD-TYPE 
           1.12            0.00 
  HTRA2 MUTATED HTRA2 WILD-TYPE 
           30.9           122.3 
  HTRA2 MUTATED HTRA2 WILD-TYPE 
          22.68           14.12 
[1] "1.1 - 30.9 (22.7)"  "0.0 - 122.3 (14.1)"
[1] "hr="     "9300000"
D920V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HTRA2 MUTATED         0        0        0        1         1         2
  HTRA2 WILD-TYPE       2       15       40       29        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HTRA2 MUTATED           0          1          1          1        0
  HTRA2 WILD-TYPE         3         69         52         31       38
D920V3, multiclass
            clus
vv           HTRA2 MUTATED HTRA2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HTRA2 MUTATED     0   1   3   3
  HTRA2 WILD-TYPE  22  91 170  94
D920V4, multiclass
    clus
vv   HTRA2 MUTATED HTRA2 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             3             170
  T4             3              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
  HTRA2 MUTATED     2   3   1   1
  HTRA2 WILD-TYPE 116 101  76  76
D920V5, multiclass
    clus
vv   HTRA2 MUTATED HTRA2 WILD-TYPE
  N0             2             116
  N1             3             101
  N2             1              76
  N3             1              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"
D920V6, binary
                 cls
clus                0   1
  HTRA2 MUTATED     7   0
  HTRA2 WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA2 MUTATED      7    0
  HTRA2 WILD-TYPE  339   29
   clus
vv  HTRA2 MUTATED HTRA2 WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D920V7, binary
                 cls
clus                0   1
  HTRA2 MUTATED     4   3
  HTRA2 WILD-TYPE 141 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA2 MUTATED      4    3
  HTRA2 WILD-TYPE  141  245
        clus
vv       HTRA2 MUTATED HTRA2 WILD-TYPE
  FEMALE             4             141
  MALE               3             245
[1] 2 2
[1] FALSE
D920V8, binary
                 cls
clus                0   1
  HTRA2 MUTATED     6   1
  HTRA2 WILD-TYPE 286  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA2 MUTATED      6    1
  HTRA2 WILD-TYPE  286   58
     clus
vv    HTRA2 MUTATED HTRA2 WILD-TYPE
  NO              6             286
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HTRA2 MUTATED                                          0
  HTRA2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HTRA2 MUTATED                                       2
  HTRA2 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HTRA2 MUTATED                                                        3
  HTRA2 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HTRA2 MUTATED                                                   1
  HTRA2 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HTRA2 MUTATED                                                                   1
  HTRA2 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HTRA2 MUTATED                                                    0
  HTRA2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HTRA2 MUTATED                                                  0
  HTRA2 WILD-TYPE                                               61
D920V9, multiclass
                                                                   clus
vv                                                                  HTRA2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  HTRA2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HTRA2 MUTATED     5   1   0   0
  HTRA2 WILD-TYPE 306  13  15  24
D920V10, multiclass
    clus
vv   HTRA2 MUTATED HTRA2 WILD-TYPE
  R0             5             306
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D920V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HTRA2 MUTATED       2                         0
  HTRA2 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HTRA2 MUTATED                                           0     3
  HTRA2 WILD-TYPE                                         1   240
D920V12, multiclass
                                           clus
vv                                          HTRA2 MUTATED HTRA2 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D920V13, binary
                 cls
clus                0   1
  HTRA2 MUTATED     0   5
  HTRA2 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA2 MUTATED      0    5
  HTRA2 WILD-TYPE    4  305
                        clus
vv                       HTRA2 MUTATED HTRA2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(921) Variable = INSIG2 MUTATION ANALYSIS
D921V1, survival
                  sevent
clus2                0   1
  INSIG2 MUTATED     5   1
  INSIG2 WILD-TYPE 225 138
  INSIG2 MUTATED INSIG2 WILD-TYPE 
               6              363 
  INSIG2 MUTATED INSIG2 WILD-TYPE 
               1              138 
$`INSIG2 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8360 TCGA-CD-A4MI TCGA-HF-7132 TCGA-HF-A5NB 
       34.68        29.59         6.18        11.77        77.29        30.51 

$`INSIG2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  INSIG2 MUTATED INSIG2 WILD-TYPE 
            6.18             0.00 
  INSIG2 MUTATED INSIG2 WILD-TYPE 
           77.29           122.30 
  INSIG2 MUTATED INSIG2 WILD-TYPE 
           30.05            14.17 
[1] "6.2 - 77.3 (30.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3.5"
D921V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  INSIG2 MUTATED         0        0        0        1         2         1
  INSIG2 WILD-TYPE       2       15       40       29        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INSIG2 MUTATED           0          1          0          1        0
  INSIG2 WILD-TYPE         3         69         53         31       38
D921V3, multiclass
            clus
vv           INSIG2 MUTATED INSIG2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  INSIG2 MUTATED     1   1   3   2
  INSIG2 WILD-TYPE  21  91 170  95
D921V4, multiclass
    clus
vv   INSIG2 MUTATED INSIG2 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              3              170
  T4              2               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
  INSIG2 MUTATED     3   2   0   1
  INSIG2 WILD-TYPE 115 102  77  76
D921V5, multiclass
    clus
vv   INSIG2 MUTATED INSIG2 WILD-TYPE
  N0              3              115
  N1              2              102
  N2              0               77
  N3              1               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"
D921V6, binary
                  cls
clus                 0   1
  INSIG2 MUTATED     7   0
  INSIG2 WILD-TYPE 339  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INSIG2 MUTATED      7    0
  INSIG2 WILD-TYPE  339   29
   clus
vv  INSIG2 MUTATED INSIG2 WILD-TYPE
  0              7              339
  1              0               29
[1] 2 2
[1] FALSE
D921V7, binary
                  cls
clus                 0   1
  INSIG2 MUTATED     4   3
  INSIG2 WILD-TYPE 141 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INSIG2 MUTATED      4    3
  INSIG2 WILD-TYPE  141  245
        clus
vv       INSIG2 MUTATED INSIG2 WILD-TYPE
  FEMALE              4              141
  MALE                3              245
[1] 2 2
[1] FALSE
D921V8, binary
                  cls
clus                 0   1
  INSIG2 MUTATED     4   2
  INSIG2 WILD-TYPE 288  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INSIG2 MUTATED      4    2
  INSIG2 WILD-TYPE  288   57
     clus
vv    INSIG2 MUTATED INSIG2 WILD-TYPE
  NO               4              288
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  INSIG2 MUTATED                                          0
  INSIG2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  INSIG2 MUTATED                                       0
  INSIG2 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  INSIG2 MUTATED                                                        4
  INSIG2 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  INSIG2 MUTATED                                                   2
  INSIG2 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  INSIG2 MUTATED                                                                   1
  INSIG2 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  INSIG2 MUTATED                                                    0
  INSIG2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  INSIG2 MUTATED                                                  0
  INSIG2 WILD-TYPE                                               61
D921V9, multiclass
                                                                   clus
vv                                                                  INSIG2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  INSIG2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  INSIG2 MUTATED     4   1   0   1
  INSIG2 WILD-TYPE 307  13  15  23
D921V10, multiclass
    clus
vv   INSIG2 MUTATED INSIG2 WILD-TYPE
  R0              4              307
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D921V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  INSIG2 MUTATED       1                         0
  INSIG2 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INSIG2 MUTATED                                           0     4
  INSIG2 WILD-TYPE                                         1   239
D921V12, multiclass
                                           clus
vv                                          INSIG2 MUTATED INSIG2 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D921V13, binary
                  cls
clus                 0   1
  INSIG2 MUTATED     0   5
  INSIG2 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INSIG2 MUTATED      0    5
  INSIG2 WILD-TYPE    4  305
                        clus
vv                       INSIG2 MUTATED INSIG2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(922) Variable = CLSTN1 MUTATION ANALYSIS
D922V1, survival
                  sevent
clus2                0   1
  CLSTN1 MUTATED     6   3
  CLSTN1 WILD-TYPE 224 136
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
               9              360 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
               3              136 
$`CLSTN1 MUTATED`
TCGA-BR-6566 TCGA-BR-7723 TCGA-BR-8363 TCGA-CD-8536 TCGA-CG-5733 TCGA-D7-8570 
       32.78        28.73         0.26        12.43        21.07        24.72 
TCGA-FP-A4BE TCGA-HU-8602 TCGA-VQ-A8P2 
       11.08        22.32        38.14 

$`CLSTN1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-D7-8572 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-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-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 

  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
            0.26             0.00 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
           38.14           122.30 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
           22.32            14.12 
[1] "0.3 - 38.1 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D922V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CLSTN1 MUTATED         0        0        1        1         2         1
  CLSTN1 WILD-TYPE       2       15       39       29        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLSTN1 MUTATED           0          2          2          0        1
  CLSTN1 WILD-TYPE         3         68         51         32       37
D922V3, multiclass
            clus
vv           CLSTN1 MUTATED CLSTN1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              2               51
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CLSTN1 MUTATED     0   2   5   3
  CLSTN1 WILD-TYPE  22  90 168  94
D922V4, multiclass
    clus
vv   CLSTN1 MUTATED CLSTN1 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              5              168
  T4              3               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
  CLSTN1 MUTATED     5   1   2   2
  CLSTN1 WILD-TYPE 113 103  75  75
D922V5, multiclass
    clus
vv   CLSTN1 MUTATED CLSTN1 WILD-TYPE
  N0              5              113
  N1              1              103
  N2              2               75
  N3              2               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"
D922V6, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED    10   0
  CLSTN1 WILD-TYPE 336  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED     10    0
  CLSTN1 WILD-TYPE  336   29
   clus
vv  CLSTN1 MUTATED CLSTN1 WILD-TYPE
  0             10              336
  1              0               29
[1] 2 2
[1] FALSE
D922V7, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED     5   5
  CLSTN1 WILD-TYPE 140 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED      5    5
  CLSTN1 WILD-TYPE  140  243
        clus
vv       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  FEMALE              5              140
  MALE                5              243
[1] 2 2
[1] FALSE
D922V8, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED     7   2
  CLSTN1 WILD-TYPE 285  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED      7    2
  CLSTN1 WILD-TYPE  285   57
     clus
vv    CLSTN1 MUTATED CLSTN1 WILD-TYPE
  NO               7              285
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CLSTN1 MUTATED                                          0
  CLSTN1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CLSTN1 MUTATED                                       1
  CLSTN1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CLSTN1 MUTATED                                                        6
  CLSTN1 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CLSTN1 MUTATED                                                   1
  CLSTN1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CLSTN1 MUTATED                                                                   1
  CLSTN1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CLSTN1 MUTATED                                                    0
  CLSTN1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CLSTN1 MUTATED                                                  1
  CLSTN1 WILD-TYPE                                               60
D922V9, multiclass
                                                                   clus
vv                                                                  CLSTN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  CLSTN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CLSTN1 MUTATED     9   0   0   1
  CLSTN1 WILD-TYPE 302  14  15  23
D922V10, multiclass
    clus
vv   CLSTN1 MUTATED CLSTN1 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D922V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CLSTN1 MUTATED       2                         1
  CLSTN1 WILD-TYPE    85                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CLSTN1 MUTATED                                           0     6
  CLSTN1 WILD-TYPE                                         1   237
D922V12, multiclass
                                           clus
vv                                          CLSTN1 MUTATED CLSTN1 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D922V13, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED     0   8
  CLSTN1 WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED      0    8
  CLSTN1 WILD-TYPE    4  302
                        clus
vv                       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(923) Variable = HNF1B MUTATION ANALYSIS
D923V1, survival
                 sevent
clus2               0   1
  HNF1B MUTATED     2   2
  HNF1B WILD-TYPE 228 137
  HNF1B MUTATED HNF1B WILD-TYPE 
              4             365 
  HNF1B MUTATED HNF1B WILD-TYPE 
              2             137 
$`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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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 

  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          14.270 
[1] "6.6 - 26.7 (14.5)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D923V2, 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       2       15       40       30        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HNF1B MUTATED           0          0          1          0        0
  HNF1B WILD-TYPE         3         70         52         32       38
D923V3, multiclass
            clus
vv           HNF1B MUTATED HNF1B WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HNF1B MUTATED     0   0   2   2
  HNF1B WILD-TYPE  22  92 171  95
D923V4, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  T1             0              22
  T2             0              92
  T3             2             171
  T4             2              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
  HNF1B MUTATED     3   1   0   1
  HNF1B WILD-TYPE 115 103  77  76
D923V5, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  N0             3             115
  N1             1             103
  N2             0              77
  N3             1              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"
D923V6, binary
                 cls
clus                0   1
  HNF1B MUTATED     5   0
  HNF1B WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      5    0
  HNF1B WILD-TYPE  341   29
   clus
vv  HNF1B MUTATED HNF1B WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D923V7, binary
                 cls
clus                0   1
  HNF1B MUTATED     3   2
  HNF1B WILD-TYPE 142 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      3    2
  HNF1B WILD-TYPE  142  246
        clus
vv       HNF1B MUTATED HNF1B WILD-TYPE
  FEMALE             3             142
  MALE               2             246
[1] 2 2
[1] FALSE
D923V8, binary
                 cls
clus                0   1
  HNF1B MUTATED     4   0
  HNF1B WILD-TYPE 288  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      4    0
  HNF1B WILD-TYPE  288   59
     clus
vv    HNF1B MUTATED HNF1B WILD-TYPE
  NO              4             288
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HNF1B MUTATED                                          0
  HNF1B WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HNF1B MUTATED                                       2
  HNF1B WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HNF1B MUTATED                                                        3
  HNF1B WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HNF1B MUTATED                                                   0
  HNF1B WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HNF1B MUTATED                                                                   0
  HNF1B WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HNF1B MUTATED                                                    0
  HNF1B WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HNF1B MUTATED                                                  0
  HNF1B WILD-TYPE                                               61
D923V9, multiclass
                                                                   clus
vv                                                                  HNF1B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  HNF1B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HNF1B MUTATED     3   0   0   1
  HNF1B WILD-TYPE 308  14  15  23
D923V10, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D923V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HNF1B MUTATED       2                         0
  HNF1B WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HNF1B MUTATED                                           0     3
  HNF1B WILD-TYPE                                         1   240
D923V12, multiclass
                                           clus
vv                                          HNF1B MUTATED HNF1B WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D923V13, binary
                 cls
clus                0   1
  HNF1B MUTATED     0   5
  HNF1B WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      0    5
  HNF1B WILD-TYPE    4  305
                        clus
vv                       HNF1B MUTATED HNF1B WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(924) Variable = IBTK MUTATION ANALYSIS
D924V1, survival
                sevent
clus2              0   1
  IBTK MUTATED     9   6
  IBTK WILD-TYPE 221 133
  IBTK MUTATED IBTK WILD-TYPE 
            15            354 
  IBTK MUTATED IBTK WILD-TYPE 
             6            133 
$`IBTK MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8360 
       26.70         6.97        34.68        30.90        44.94         6.18 
TCGA-BR-8680 TCGA-CD-A4MI TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-A6EY TCGA-FP-A4BE 
       31.96        11.77       105.07        21.07        11.44        11.08 
TCGA-HU-8602 TCGA-HU-A4GQ TCGA-VQ-A91U 
       22.32         0.10         1.71 

$`IBTK WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-D7-6528 
       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-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-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-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 

  IBTK MUTATED IBTK WILD-TYPE 
           0.1            0.0 
  IBTK MUTATED IBTK WILD-TYPE 
        105.07         122.30 
  IBTK MUTATED IBTK WILD-TYPE 
         21.07          14.22 
[1] "0.1 - 105.1 (21.1)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D924V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IBTK MUTATED         0        0        1        1         4         2
  IBTK WILD-TYPE       2       15       39       29        33        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IBTK MUTATED           0          5          1          2        2
  IBTK WILD-TYPE         3         65         52         30       36
D924V3, multiclass
            clus
vv           IBTK MUTATED IBTK WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             4             33
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            5             65
  STAGE IIIB            1             52
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IBTK MUTATED     0   3   9   6
  IBTK WILD-TYPE  22  89 164  91
D924V4, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  T1            0             22
  T2            3             89
  T3            9            164
  T4            6             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
  IBTK MUTATED     7   4   5   2
  IBTK WILD-TYPE 111 100  72  75
D924V5, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  N0            7            111
  N1            4            100
  N2            5             72
  N3            2             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"
D924V6, binary
                cls
clus               0   1
  IBTK MUTATED    17   1
  IBTK WILD-TYPE 329  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     17    1
  IBTK WILD-TYPE  329   28
   clus
vv  IBTK MUTATED IBTK WILD-TYPE
  0           17            329
  1            1             28
[1] 2 2
[1] FALSE
D924V7, binary
                cls
clus               0   1
  IBTK MUTATED     8  11
  IBTK WILD-TYPE 137 237
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED      8   11
  IBTK WILD-TYPE  137  237
        clus
vv       IBTK MUTATED IBTK WILD-TYPE
  FEMALE            8            137
  MALE             11            237
[1] 2 2
[1] FALSE
D924V8, binary
                cls
clus               0   1
  IBTK MUTATED    14   1
  IBTK WILD-TYPE 278  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     14    1
  IBTK WILD-TYPE  278   58
     clus
vv    IBTK MUTATED IBTK WILD-TYPE
  NO            14            278
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IBTK MUTATED                                          0
  IBTK WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IBTK MUTATED                                       3
  IBTK WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IBTK MUTATED                                                        9
  IBTK WILD-TYPE                                                    149
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IBTK MUTATED                                                   0
  IBTK WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IBTK MUTATED                                                                   4
  IBTK WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IBTK MUTATED                                                    0
  IBTK WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IBTK MUTATED                                                  3
  IBTK WILD-TYPE                                               58
D924V9, multiclass
                                                                   clus
vv                                                                  IBTK MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  IBTK WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IBTK MUTATED    15   0   0   3
  IBTK WILD-TYPE 296  14  15  21
D924V10, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  R0           15            296
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D924V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  IBTK MUTATED       5                         1
  IBTK WILD-TYPE    82                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IBTK MUTATED                                           0     9
  IBTK WILD-TYPE                                         1   234
D924V12, multiclass
                                           clus
vv                                          IBTK MUTATED IBTK WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D924V13, binary
                cls
clus               0   1
  IBTK MUTATED     0  14
  IBTK WILD-TYPE   4 296
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED      0   14
  IBTK WILD-TYPE    4  296
                        clus
vv                       IBTK MUTATED IBTK WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           14            296
[1] 2 2
[1] FALSE

Clustering(925) Variable = SALL2 MUTATION ANALYSIS
D925V1, survival
                 sevent
clus2               0   1
  SALL2 MUTATED     8   6
  SALL2 WILD-TYPE 222 133
  SALL2 MUTATED SALL2 WILD-TYPE 
             14             355 
  SALL2 MUTATED SALL2 WILD-TYPE 
              6             133 
$`SALL2 MUTATED`
TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A4CS TCGA-BR-A4QL 
       31.10        31.27        31.96         8.22         1.48        16.14 
TCGA-CD-A4MI TCGA-D7-5578 TCGA-HF-7132 TCGA-HU-A4G9 TCGA-HU-A4GQ TCGA-IN-A6RL 
       11.77        12.66        77.29        24.20         0.10        13.35 
TCGA-VQ-A8P2 TCGA-VQ-AA6A 
       38.14        38.93 

$`SALL2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-D7-5579 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-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-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-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 

  SALL2 MUTATED SALL2 WILD-TYPE 
            0.1             0.0 
  SALL2 MUTATED SALL2 WILD-TYPE 
          77.29          122.30 
  SALL2 MUTATED SALL2 WILD-TYPE 
          20.17           14.17 
[1] "0.1 - 77.3 (20.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D925V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SALL2 MUTATED         0        1        0        1         0         0
  SALL2 WILD-TYPE       2       14       40       29        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SALL2 MUTATED           0          4          1          6        1
  SALL2 WILD-TYPE         3         66         52         26       37
D925V3, multiclass
            clus
vv           SALL2 MUTATED SALL2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             1              52
  STAGE IIIC             6              26
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SALL2 MUTATED     1   2   3   8
  SALL2 WILD-TYPE  21  90 170  89
D925V4, multiclass
    clus
vv   SALL2 MUTATED SALL2 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             3             170
  T4             8              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
  SALL2 MUTATED     1   4   5   4
  SALL2 WILD-TYPE 117 100  72  73
D925V5, multiclass
    clus
vv   SALL2 MUTATED SALL2 WILD-TYPE
  N0             1             117
  N1             4             100
  N2             5              72
  N3             4              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"
D925V6, binary
                 cls
clus                0   1
  SALL2 MUTATED    13   1
  SALL2 WILD-TYPE 333  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL2 MUTATED     13    1
  SALL2 WILD-TYPE  333   28
   clus
vv  SALL2 MUTATED SALL2 WILD-TYPE
  0            13             333
  1             1              28
[1] 2 2
[1] FALSE
D925V7, binary
                 cls
clus                0   1
  SALL2 MUTATED     4  10
  SALL2 WILD-TYPE 141 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL2 MUTATED      4   10
  SALL2 WILD-TYPE  141  238
        clus
vv       SALL2 MUTATED SALL2 WILD-TYPE
  FEMALE             4             141
  MALE              10             238
[1] 2 2
[1] FALSE
D925V8, binary
                 cls
clus                0   1
  SALL2 MUTATED    11   3
  SALL2 WILD-TYPE 281  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL2 MUTATED     11    3
  SALL2 WILD-TYPE  281   56
     clus
vv    SALL2 MUTATED SALL2 WILD-TYPE
  NO             11             281
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SALL2 MUTATED                                          0
  SALL2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SALL2 MUTATED                                       0
  SALL2 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SALL2 MUTATED                                                        7
  SALL2 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SALL2 MUTATED                                                   2
  SALL2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SALL2 MUTATED                                                                   1
  SALL2 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SALL2 MUTATED                                                    0
  SALL2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SALL2 MUTATED                                                  4
  SALL2 WILD-TYPE                                               57
D925V9, multiclass
                                                                   clus
vv                                                                  SALL2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  SALL2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SALL2 MUTATED    12   1   0   0
  SALL2 WILD-TYPE 299  13  15  24
D925V10, multiclass
    clus
vv   SALL2 MUTATED SALL2 WILD-TYPE
  R0            12             299
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D925V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SALL2 MUTATED       4                         0
  SALL2 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SALL2 MUTATED                                           0     9
  SALL2 WILD-TYPE                                         1   234
D925V12, multiclass
                                           clus
vv                                          SALL2 MUTATED SALL2 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D925V13, binary
                 cls
clus                0   1
  SALL2 MUTATED     0  11
  SALL2 WILD-TYPE   4 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL2 MUTATED      0   11
  SALL2 WILD-TYPE    4  299
                        clus
vv                       SALL2 MUTATED SALL2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(926) Variable = ELMO1 MUTATION ANALYSIS
D926V1, survival
                 sevent
clus2               0   1
  ELMO1 MUTATED    15   7
  ELMO1 WILD-TYPE 215 132
  ELMO1 MUTATED ELMO1 WILD-TYPE 
             22             347 
  ELMO1 MUTATED ELMO1 WILD-TYPE 
              7             132 
$`ELMO1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6852 TCGA-BR-7958 
        6.97        30.90        34.68        15.95        44.94        29.56 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8382 TCGA-BR-A4J8 TCGA-CD-5800 TCGA-CD-A48A 
       14.43        29.59        25.05        13.51        13.15        12.43 
TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5721 TCGA-HF-7132 TCGA-HU-A4GP 
        6.58         9.01         7.07         6.02        77.29         8.98 
TCGA-HU-A4GX TCGA-SW-A7EA TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       20.25        19.04        38.14        37.22 

$`ELMO1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        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-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        0.00        18.97        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-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-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-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-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-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-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 

  ELMO1 MUTATED ELMO1 WILD-TYPE 
           6.02            0.00 
  ELMO1 MUTATED ELMO1 WILD-TYPE 
          77.29          122.30 
  ELMO1 MUTATED ELMO1 WILD-TYPE 
         17.495          14.070 
[1] "6.0 - 77.3 (17.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D926V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ELMO1 MUTATED         0        0        1        2         6         1
  ELMO1 WILD-TYPE       2       15       39       28        31        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ELMO1 MUTATED           1          3          2          2        3
  ELMO1 WILD-TYPE         2         67         51         30       35
D926V3, multiclass
            clus
vv           ELMO1 MUTATED ELMO1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               2              28
  STAGE IIA              6              31
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ELMO1 MUTATED     0   5   8   9
  ELMO1 WILD-TYPE  22  87 165  88
D926V4, multiclass
    clus
vv   ELMO1 MUTATED ELMO1 WILD-TYPE
  T1             0              22
  T2             5              87
  T3             8             165
  T4             9              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
  ELMO1 MUTATED     8   9   1   4
  ELMO1 WILD-TYPE 110  95  76  73
D926V5, multiclass
    clus
vv   ELMO1 MUTATED ELMO1 WILD-TYPE
  N0             8             110
  N1             9              95
  N2             1              76
  N3             4              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"
D926V6, binary
                 cls
clus                0   1
  ELMO1 MUTATED    21   1
  ELMO1 WILD-TYPE 325  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELMO1 MUTATED     21    1
  ELMO1 WILD-TYPE  325   28
   clus
vv  ELMO1 MUTATED ELMO1 WILD-TYPE
  0            21             325
  1             1              28
[1] 2 2
[1] FALSE
D926V7, binary
                 cls
clus                0   1
  ELMO1 MUTATED    12  11
  ELMO1 WILD-TYPE 133 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELMO1 MUTATED     12   11
  ELMO1 WILD-TYPE  133  237
        clus
vv       ELMO1 MUTATED ELMO1 WILD-TYPE
  FEMALE            12             133
  MALE              11             237
[1] 2 2
[1] FALSE
D926V8, binary
                 cls
clus                0   1
  ELMO1 MUTATED    16   4
  ELMO1 WILD-TYPE 276  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELMO1 MUTATED     16    4
  ELMO1 WILD-TYPE  276   55
     clus
vv    ELMO1 MUTATED ELMO1 WILD-TYPE
  NO             16             276
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ELMO1 MUTATED                                          0
  ELMO1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ELMO1 MUTATED                                       5
  ELMO1 WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ELMO1 MUTATED                                                       11
  ELMO1 WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ELMO1 MUTATED                                                   2
  ELMO1 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ELMO1 MUTATED                                                                   3
  ELMO1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ELMO1 MUTATED                                                    1
  ELMO1 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ELMO1 MUTATED                                                  1
  ELMO1 WILD-TYPE                                               60
D926V9, multiclass
                                                                   clus
vv                                                                  ELMO1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  ELMO1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ELMO1 MUTATED    16   1   1   3
  ELMO1 WILD-TYPE 295  13  14  21
D926V10, multiclass
    clus
vv   ELMO1 MUTATED ELMO1 WILD-TYPE
  R0            16             295
  R1             1              13
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D926V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ELMO1 MUTATED       5                         0
  ELMO1 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ELMO1 MUTATED                                           0    14
  ELMO1 WILD-TYPE                                         1   229
D926V12, multiclass
                                           clus
vv                                          ELMO1 MUTATED ELMO1 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D926V13, binary
                 cls
clus                0   1
  ELMO1 MUTATED     0  17
  ELMO1 WILD-TYPE   4 293
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELMO1 MUTATED      0   17
  ELMO1 WILD-TYPE    4  293
                        clus
vv                       ELMO1 MUTATED ELMO1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            17             293
[1] 2 2
[1] FALSE

Clustering(927) Variable = BRAF MUTATION ANALYSIS
D927V1, survival
                sevent
clus2              0   1
  BRAF MUTATED    10   5
  BRAF WILD-TYPE 220 134
  BRAF MUTATED BRAF WILD-TYPE 
            15            354 
  BRAF MUTATED BRAF WILD-TYPE 
             5            134 
$`BRAF MUTATED`
TCGA-BR-4201 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8366 TCGA-BR-8591 
       30.90        14.43        29.59         6.18         0.95        28.14 
TCGA-CD-5801 TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 TCGA-HU-A4G9 
       13.18         9.01         6.02        28.96        65.10        24.20 
TCGA-MX-A5UJ TCGA-VQ-A8P2 TCGA-VQ-AA68 
       19.73        38.14        43.66 

$`BRAF WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  BRAF MUTATED BRAF WILD-TYPE 
          0.95           0.00 
  BRAF MUTATED BRAF WILD-TYPE 
          65.1          122.3 
  BRAF MUTATED BRAF WILD-TYPE 
         24.20          14.07 
[1] "0.9 - 65.1 (24.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D927V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRAF MUTATED         0        2        2        0         2         2
  BRAF WILD-TYPE       2       13       38       30        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BRAF MUTATED           1          3          0          2        2
  BRAF WILD-TYPE         2         67         53         30       36
D927V3, multiclass
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  STAGE I               0              2
  STAGE IA              2             13
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             1              2
  STAGE IIIA            3             67
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BRAF MUTATED     2   3   4   8
  BRAF WILD-TYPE  20  89 169  89
D927V4, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1            2             20
  T2            3             89
  T3            4            169
  T4            8             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
  BRAF MUTATED     8   5   1   3
  BRAF WILD-TYPE 110  99  76  74
D927V5, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  N0            8            110
  N1            5             99
  N2            1             76
  N3            3             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"
D927V6, binary
                cls
clus               0   1
  BRAF MUTATED    16   1
  BRAF WILD-TYPE 330  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     16    1
  BRAF WILD-TYPE  330   28
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0           16            330
  1            1             28
[1] 2 2
[1] FALSE
D927V7, binary
                cls
clus               0   1
  BRAF MUTATED    10   8
  BRAF WILD-TYPE 135 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     10    8
  BRAF WILD-TYPE  135  240
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE           10            135
  MALE              8            240
[1] 2 2
[1] FALSE
D927V8, binary
                cls
clus               0   1
  BRAF MUTATED    11   3
  BRAF WILD-TYPE 281  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     11    3
  BRAF WILD-TYPE  281   56
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            11            281
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BRAF MUTATED                                          0
  BRAF WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BRAF MUTATED                                       1
  BRAF WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BRAF MUTATED                                                        7
  BRAF WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BRAF MUTATED                                                   1
  BRAF WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BRAF MUTATED                                                                   6
  BRAF WILD-TYPE                                                                62
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BRAF MUTATED                                                    0
  BRAF WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BRAF MUTATED                                                  3
  BRAF WILD-TYPE                                               58
D927V9, multiclass
                                                                   clus
vv                                                                  BRAF MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  BRAF WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             62
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BRAF MUTATED    15   0   1   2
  BRAF WILD-TYPE 296  14  14  22
D927V10, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0           15            296
  R1            0             14
  R2            1             14
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D927V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  BRAF MUTATED       2                         0
  BRAF WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRAF MUTATED                                           0    11
  BRAF WILD-TYPE                                         1   232
D927V12, multiclass
                                           clus
vv                                          BRAF MUTATED BRAF WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D927V13, binary
                cls
clus               0   1
  BRAF MUTATED     0  11
  BRAF WILD-TYPE   4 299
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      0   11
  BRAF WILD-TYPE    4  299
                        clus
vv                       BRAF MUTATED BRAF WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           11            299
[1] 2 2
[1] FALSE

Clustering(928) Variable = NFAT5 MUTATION ANALYSIS
D928V1, survival
                 sevent
clus2               0   1
  NFAT5 MUTATED     4   5
  NFAT5 WILD-TYPE 226 134
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              9             360 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              5             134 
$`NFAT5 MUTATED`
TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-CD-A4MI TCGA-CG-4305 TCGA-CG-5728 
        6.97         9.67        34.68        11.77        15.95        65.10 
TCGA-CG-5733 TCGA-HJ-7597 TCGA-HU-A4GN 
       21.07        26.47        29.98 

$`NFAT5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  NFAT5 MUTATED NFAT5 WILD-TYPE 
           6.97            0.00 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
           65.1           122.3 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
          21.07           14.12 
[1] "7.0 - 65.1 (21.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D928V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NFAT5 MUTATED         0        0        3        1         2         0
  NFAT5 WILD-TYPE       2       15       37       29        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFAT5 MUTATED           0          4          0          0        0
  NFAT5 WILD-TYPE         3         66         53         32       38
D928V3, multiclass
            clus
vv           NFAT5 MUTATED NFAT5 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NFAT5 MUTATED     0   6   3   1
  NFAT5 WILD-TYPE  22  86 170  96
D928V4, multiclass
    clus
vv   NFAT5 MUTATED NFAT5 WILD-TYPE
  T1             0              22
  T2             6              86
  T3             3             170
  T4             1              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
  NFAT5 MUTATED     5   5   1   0
  NFAT5 WILD-TYPE 113  99  76  77
D928V5, multiclass
    clus
vv   NFAT5 MUTATED NFAT5 WILD-TYPE
  N0             5             113
  N1             5              99
  N2             1              76
  N3             0              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"
D928V6, binary
                 cls
clus                0   1
  NFAT5 MUTATED    10   0
  NFAT5 WILD-TYPE 336  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED     10    0
  NFAT5 WILD-TYPE  336   29
   clus
vv  NFAT5 MUTATED NFAT5 WILD-TYPE
  0            10             336
  1             0              29
[1] 2 2
[1] FALSE
D928V7, binary
                 cls
clus                0   1
  NFAT5 MUTATED     8   4
  NFAT5 WILD-TYPE 137 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      8    4
  NFAT5 WILD-TYPE  137  244
        clus
vv       NFAT5 MUTATED NFAT5 WILD-TYPE
  FEMALE             8             137
  MALE               4             244
[1] 2 2
[1] FALSE
D928V8, binary
                 cls
clus                0   1
  NFAT5 MUTATED     9   0
  NFAT5 WILD-TYPE 283  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      9    0
  NFAT5 WILD-TYPE  283   59
     clus
vv    NFAT5 MUTATED NFAT5 WILD-TYPE
  NO              9             283
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NFAT5 MUTATED                                          1
  NFAT5 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NFAT5 MUTATED                                       0
  NFAT5 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NFAT5 MUTATED                                                        8
  NFAT5 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NFAT5 MUTATED                                                   0
  NFAT5 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NFAT5 MUTATED                                                                   2
  NFAT5 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NFAT5 MUTATED                                                    0
  NFAT5 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NFAT5 MUTATED                                                  1
  NFAT5 WILD-TYPE                                               60
D928V9, multiclass
                                                                   clus
vv                                                                  NFAT5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  NFAT5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NFAT5 MUTATED     7   0   0   4
  NFAT5 WILD-TYPE 304  14  15  20
D928V10, multiclass
    clus
vv   NFAT5 MUTATED NFAT5 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D928V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NFAT5 MUTATED       2                         0
  NFAT5 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NFAT5 MUTATED                                           0     7
  NFAT5 WILD-TYPE                                         1   236
D928V12, multiclass
                                           clus
vv                                          NFAT5 MUTATED NFAT5 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D928V13, binary
                 cls
clus                0   1
  NFAT5 MUTATED     0   9
  NFAT5 WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      0    9
  NFAT5 WILD-TYPE    4  301
                        clus
vv                       NFAT5 MUTATED NFAT5 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(929) Variable = ESRP2 MUTATION ANALYSIS
D929V1, survival
                 sevent
clus2               0   1
  ESRP2 MUTATED     5   3
  ESRP2 WILD-TYPE 225 136
  ESRP2 MUTATED ESRP2 WILD-TYPE 
              8             361 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
              3             136 
$`ESRP2 MUTATED`
TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-A4QL TCGA-CG-5721 TCGA-HU-A4GQ 
       34.68        32.25         0.26        16.14         6.02         0.10 
TCGA-HU-A4GU TCGA-SW-A7EA 
        6.58        19.04 

$`ESRP2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  ESRP2 MUTATED ESRP2 WILD-TYPE 
            0.1             0.0 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
          34.68          122.30 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
          11.36           14.27 
[1] "0.1 - 34.7 (11.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D929V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ESRP2 MUTATED         0        0        2        0         1         2
  ESRP2 WILD-TYPE       2       15       38       30        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ESRP2 MUTATED           0          0          1          1        1
  ESRP2 WILD-TYPE         3         70         52         31       37
D929V3, multiclass
            clus
vv           ESRP2 MUTATED ESRP2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ESRP2 MUTATED     0   2   3   3
  ESRP2 WILD-TYPE  22  90 170  94
D929V4, multiclass
    clus
vv   ESRP2 MUTATED ESRP2 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             3             170
  T4             3              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
  ESRP2 MUTATED     4   2   1   1
  ESRP2 WILD-TYPE 114 102  76  76
D929V5, multiclass
    clus
vv   ESRP2 MUTATED ESRP2 WILD-TYPE
  N0             4             114
  N1             2             102
  N2             1              76
  N3             1              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"
D929V6, binary
                 cls
clus                0   1
  ESRP2 MUTATED     8   0
  ESRP2 WILD-TYPE 338  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP2 MUTATED      8    0
  ESRP2 WILD-TYPE  338   29
   clus
vv  ESRP2 MUTATED ESRP2 WILD-TYPE
  0             8             338
  1             0              29
[1] 2 2
[1] FALSE
D929V7, binary
                 cls
clus                0   1
  ESRP2 MUTATED     5   3
  ESRP2 WILD-TYPE 140 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP2 MUTATED      5    3
  ESRP2 WILD-TYPE  140  245
        clus
vv       ESRP2 MUTATED ESRP2 WILD-TYPE
  FEMALE             5             140
  MALE               3             245
[1] 2 2
[1] FALSE
D929V8, binary
                 cls
clus                0   1
  ESRP2 MUTATED     8   0
  ESRP2 WILD-TYPE 284  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP2 MUTATED      8    0
  ESRP2 WILD-TYPE  284   59
     clus
vv    ESRP2 MUTATED ESRP2 WILD-TYPE
  NO              8             284
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ESRP2 MUTATED                                          0
  ESRP2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ESRP2 MUTATED                                       2
  ESRP2 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ESRP2 MUTATED                                                        4
  ESRP2 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ESRP2 MUTATED                                                   0
  ESRP2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ESRP2 MUTATED                                                                   1
  ESRP2 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ESRP2 MUTATED                                                    0
  ESRP2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ESRP2 MUTATED                                                  1
  ESRP2 WILD-TYPE                                               60
D929V9, multiclass
                                                                   clus
vv                                                                  ESRP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  ESRP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ESRP2 MUTATED     8   0   0   0
  ESRP2 WILD-TYPE 303  14  15  24
D929V10, multiclass
    clus
vv   ESRP2 MUTATED ESRP2 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D929V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ESRP2 MUTATED       2                         0
  ESRP2 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ESRP2 MUTATED                                           0     5
  ESRP2 WILD-TYPE                                         1   238
D929V12, multiclass
                                           clus
vv                                          ESRP2 MUTATED ESRP2 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D929V13, binary
                 cls
clus                0   1
  ESRP2 MUTATED     0   7
  ESRP2 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP2 MUTATED      0    7
  ESRP2 WILD-TYPE    4  303
                        clus
vv                       ESRP2 MUTATED ESRP2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(930) Variable = DHX36 MUTATION ANALYSIS
D930V1, survival
                 sevent
clus2               0   1
  DHX36 MUTATED    10   7
  DHX36 WILD-TYPE 220 132
  DHX36 MUTATED DHX36 WILD-TYPE 
             17             352 
  DHX36 MUTATED DHX36 WILD-TYPE 
              7             132 
$`DHX36 MUTATED`
TCGA-EQ-A4SO TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6453 
       16.24         6.97         9.34         9.67        34.68        15.95 
TCGA-BR-7707 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-4305 
       35.84         3.72         1.12        31.96        16.14        15.95 
TCGA-CG-4306 TCGA-CG-5726 TCGA-CG-5728 TCGA-HU-A4GN TCGA-HU-A4GQ 
        1.02        28.96        65.10        29.98         0.10 

$`DHX36 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-6455 
        4.08         4.08         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-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-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-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-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-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-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-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 

  DHX36 MUTATED DHX36 WILD-TYPE 
            0.1             0.0 
  DHX36 MUTATED DHX36 WILD-TYPE 
           65.1           122.3 
  DHX36 MUTATED DHX36 WILD-TYPE 
          15.95           14.12 
[1] "0.1 - 65.1 (15.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D930V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DHX36 MUTATED         0        1        3        1         4         0
  DHX36 WILD-TYPE       2       14       37       29        33        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DHX36 MUTATED           0          2          2          2        2
  DHX36 WILD-TYPE         3         68         51         30       36
D930V3, multiclass
            clus
vv           DHX36 MUTATED DHX36 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               1              29
  STAGE IIA              4              33
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DHX36 MUTATED     2   6   5   5
  DHX36 WILD-TYPE  20  86 168  92
D930V4, multiclass
    clus
vv   DHX36 MUTATED DHX36 WILD-TYPE
  T1             2              20
  T2             6              86
  T3             5             168
  T4             5              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
  DHX36 MUTATED     7   6   4   1
  DHX36 WILD-TYPE 111  98  73  76
D930V5, multiclass
    clus
vv   DHX36 MUTATED DHX36 WILD-TYPE
  N0             7             111
  N1             6              98
  N2             4              73
  N3             1              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"
D930V6, binary
                 cls
clus                0   1
  DHX36 MUTATED    16   2
  DHX36 WILD-TYPE 330  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED     16    2
  DHX36 WILD-TYPE  330   27
   clus
vv  DHX36 MUTATED DHX36 WILD-TYPE
  0            16             330
  1             2              27
[1] 2 2
[1] FALSE
D930V7, binary
                 cls
clus                0   1
  DHX36 MUTATED     9  11
  DHX36 WILD-TYPE 136 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED      9   11
  DHX36 WILD-TYPE  136  237
        clus
vv       DHX36 MUTATED DHX36 WILD-TYPE
  FEMALE             9             136
  MALE              11             237
[1] 2 2
[1] FALSE
D930V8, binary
                 cls
clus                0   1
  DHX36 MUTATED    14   1
  DHX36 WILD-TYPE 278  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED     14    1
  DHX36 WILD-TYPE  278   58
     clus
vv    DHX36 MUTATED DHX36 WILD-TYPE
  NO             14             278
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DHX36 MUTATED                                          0
  DHX36 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DHX36 MUTATED                                       0
  DHX36 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DHX36 MUTATED                                                       14
  DHX36 WILD-TYPE                                                    144
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DHX36 MUTATED                                                   0
  DHX36 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DHX36 MUTATED                                                                   2
  DHX36 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DHX36 MUTATED                                                    0
  DHX36 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DHX36 MUTATED                                                  3
  DHX36 WILD-TYPE                                               58
D930V9, multiclass
                                                                   clus
vv                                                                  DHX36 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  DHX36 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DHX36 MUTATED    14   0   1   5
  DHX36 WILD-TYPE 297  14  14  19
D930V10, multiclass
    clus
vv   DHX36 MUTATED DHX36 WILD-TYPE
  R0            14             297
  R1             0              14
  R2             1              14
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D930V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DHX36 MUTATED       3                         0
  DHX36 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DHX36 MUTATED                                           0    13
  DHX36 WILD-TYPE                                         1   230
D930V12, multiclass
                                           clus
vv                                          DHX36 MUTATED DHX36 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D930V13, binary
                 cls
clus                0   1
  DHX36 MUTATED     0  16
  DHX36 WILD-TYPE   4 294
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED      0   16
  DHX36 WILD-TYPE    4  294
                        clus
vv                       DHX36 MUTATED DHX36 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            16             294
[1] 2 2
[1] FALSE

Clustering(931) Variable = ZCCHC6 MUTATION ANALYSIS
D931V1, survival
                  sevent
clus2                0   1
  ZCCHC6 MUTATED     8   2
  ZCCHC6 WILD-TYPE 222 137
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
              10              359 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
               2              137 
$`ZCCHC6 MUTATED`
TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-8360 TCGA-BR-8680 
       26.70         9.67        34.68        32.78         6.18        31.96 
TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-A4GN TCGA-HU-A4GX 
       77.29        26.47        29.98        20.25 

$`ZCCHC6 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
            6.18             0.00 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
           77.29           122.30 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
           28.34            14.07 
[1] "6.2 - 77.3 (28.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3"  
D931V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZCCHC6 MUTATED         0        0        1        1         4         1
  ZCCHC6 WILD-TYPE       2       15       39       29        33        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZCCHC6 MUTATED           0          1          0          1        2
  ZCCHC6 WILD-TYPE         3         69         53         31       36
D931V3, multiclass
            clus
vv           ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               4               33
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZCCHC6 MUTATED     0   3   3   5
  ZCCHC6 WILD-TYPE  22  89 170  92
D931V4, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              3              170
  T4              5               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
  ZCCHC6 MUTATED     6   2   3   0
  ZCCHC6 WILD-TYPE 112 102  74  77
D931V5, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  N0              6              112
  N1              2              102
  N2              3               74
  N3              0               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"
D931V6, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED    10   1
  ZCCHC6 WILD-TYPE 336  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED     10    1
  ZCCHC6 WILD-TYPE  336   28
   clus
vv  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  0             10              336
  1              1               28
[1] 2 2
[1] FALSE
D931V7, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED     8   4
  ZCCHC6 WILD-TYPE 137 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED      8    4
  ZCCHC6 WILD-TYPE  137  244
        clus
vv       ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  FEMALE              8              137
  MALE                4              244
[1] 2 2
[1] FALSE
D931V8, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED     9   1
  ZCCHC6 WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED      9    1
  ZCCHC6 WILD-TYPE  283   58
     clus
vv    ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZCCHC6 MUTATED                                          1
  ZCCHC6 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZCCHC6 MUTATED                                       2
  ZCCHC6 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZCCHC6 MUTATED                                                        5
  ZCCHC6 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZCCHC6 MUTATED                                                   1
  ZCCHC6 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZCCHC6 MUTATED                                                                   1
  ZCCHC6 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZCCHC6 MUTATED                                                    0
  ZCCHC6 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZCCHC6 MUTATED                                                  2
  ZCCHC6 WILD-TYPE                                               59
D931V9, multiclass
                                                                   clus
vv                                                                  ZCCHC6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  ZCCHC6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZCCHC6 MUTATED     9   0   0   3
  ZCCHC6 WILD-TYPE 302  14  15  21
D931V10, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D931V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZCCHC6 MUTATED       3                         0
  ZCCHC6 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZCCHC6 MUTATED                                           0     8
  ZCCHC6 WILD-TYPE                                         1   235
D931V12, multiclass
                                           clus
vv                                          ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D931V13, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED     0  11
  ZCCHC6 WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED      0   11
  ZCCHC6 WILD-TYPE    4  299
                        clus
vv                       ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(932) Variable = C8ORF38 MUTATION ANALYSIS
D932V1, survival
                   sevent
clus2                 0   1
  C8ORF38 MUTATED     6   1
  C8ORF38 WILD-TYPE 224 138
  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
                7               362 
  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
                1               138 
$`C8ORF38 MUTATED`
TCGA-BR-4201 TCGA-BR-8078 TCGA-F1-6874 TCGA-HU-A4GX TCGA-HU-A4HD TCGA-MX-A5UJ 
       30.90        29.59        14.47        20.25        33.40        19.73 
TCGA-SW-A7EA 
       19.04 

$`C8ORF38 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-F1-6875 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-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-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 

  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
            14.47              0.00 
  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
             33.4             122.3 
  C8ORF38 MUTATED C8ORF38 WILD-TYPE 
           20.250            14.055 
[1] "14.5 - 33.4 (20.2)" "0.0 - 122.3 (14.1)"
[1] "hr=" "3.8"
D932V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C8ORF38 MUTATED         0        0        2        0         0         1
  C8ORF38 WILD-TYPE       2       15       38       30        37        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C8ORF38 MUTATED           0          2          0          1        1
  C8ORF38 WILD-TYPE         3         68         53         31       37
D932V3, multiclass
            clus
vv           C8ORF38 MUTATED C8ORF38 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                0                37
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C8ORF38 MUTATED     0   3   2   3
  C8ORF38 WILD-TYPE  22  89 171  94
D932V4, multiclass
    clus
vv   C8ORF38 MUTATED C8ORF38 WILD-TYPE
  T1               0                22
  T2               3                89
  T3               2               171
  T4               3                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
  C8ORF38 MUTATED     3   0   4   0
  C8ORF38 WILD-TYPE 115 104  73  77
D932V5, multiclass
    clus
vv   C8ORF38 MUTATED C8ORF38 WILD-TYPE
  N0               3               115
  N1               0               104
  N2               4                73
  N3               0                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"
D932V6, binary
                   cls
clus                  0   1
  C8ORF38 MUTATED     8   0
  C8ORF38 WILD-TYPE 338  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF38 MUTATED      8    0
  C8ORF38 WILD-TYPE  338   29
   clus
vv  C8ORF38 MUTATED C8ORF38 WILD-TYPE
  0               8               338
  1               0                29
[1] 2 2
[1] FALSE
D932V7, binary
                   cls
clus                  0   1
  C8ORF38 MUTATED     6   2
  C8ORF38 WILD-TYPE 139 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF38 MUTATED      6    2
  C8ORF38 WILD-TYPE  139  246
        clus
vv       C8ORF38 MUTATED C8ORF38 WILD-TYPE
  FEMALE               6               139
  MALE                 2               246
[1] 2 2
[1] FALSE
D932V8, binary
                   cls
clus                  0   1
  C8ORF38 MUTATED     7   0
  C8ORF38 WILD-TYPE 285  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF38 MUTATED      7    0
  C8ORF38 WILD-TYPE  285   59
     clus
vv    C8ORF38 MUTATED C8ORF38 WILD-TYPE
  NO                7               285
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C8ORF38 MUTATED                                          0
  C8ORF38 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C8ORF38 MUTATED                                       2
  C8ORF38 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C8ORF38 MUTATED                                                        3
  C8ORF38 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C8ORF38 MUTATED                                                   0
  C8ORF38 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C8ORF38 MUTATED                                                                   1
  C8ORF38 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C8ORF38 MUTATED                                                    0
  C8ORF38 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C8ORF38 MUTATED                                                  2
  C8ORF38 WILD-TYPE                                               59
D932V9, multiclass
                                                                   clus
vv                                                                  C8ORF38 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  C8ORF38 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C8ORF38 MUTATED     6   0   0   2
  C8ORF38 WILD-TYPE 305  14  15  22
D932V10, multiclass
    clus
vv   C8ORF38 MUTATED C8ORF38 WILD-TYPE
  R0               6               305
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D932V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C8ORF38 MUTATED       2                         0
  C8ORF38 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C8ORF38 MUTATED                                           0     6
  C8ORF38 WILD-TYPE                                         1   237
D932V12, multiclass
                                           clus
vv                                          C8ORF38 MUTATED C8ORF38 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D932V13, binary
                   cls
clus                  0   1
  C8ORF38 MUTATED     0   8
  C8ORF38 WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C8ORF38 MUTATED      0    8
  C8ORF38 WILD-TYPE    4  302
                        clus
vv                       C8ORF38 MUTATED C8ORF38 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(933) Variable = NTAN1 MUTATION ANALYSIS
D933V1, survival
                 sevent
clus2               0   1
  NTAN1 MUTATED     4   1
  NTAN1 WILD-TYPE 226 138
  NTAN1 MUTATED NTAN1 WILD-TYPE 
              5             364 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
              1             138 
$`NTAN1 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-CG-5721 TCGA-HF-A5NB 
       30.90        34.68        35.84         6.02        30.51 

$`NTAN1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  NTAN1 MUTATED NTAN1 WILD-TYPE 
           6.02            0.00 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
          35.84          122.30 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
          30.90           14.12 
[1] "6.0 - 35.8 (30.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.8"
D933V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NTAN1 MUTATED         0        0        1        0         1         0
  NTAN1 WILD-TYPE       2       15       39       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NTAN1 MUTATED           0          0          0          1        1
  NTAN1 WILD-TYPE         3         70         53         31       37
D933V3, multiclass
            clus
vv           NTAN1 MUTATED NTAN1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NTAN1 MUTATED     0   2   1   2
  NTAN1 WILD-TYPE  22  90 172  95
D933V4, multiclass
    clus
vv   NTAN1 MUTATED NTAN1 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             1             172
  T4             2              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
  NTAN1 MUTATED     2   1   0   1
  NTAN1 WILD-TYPE 116 103  77  76
D933V5, multiclass
    clus
vv   NTAN1 MUTATED NTAN1 WILD-TYPE
  N0             2             116
  N1             1             103
  N2             0              77
  N3             1              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"
D933V6, binary
                 cls
clus                0   1
  NTAN1 MUTATED     5   0
  NTAN1 WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      5    0
  NTAN1 WILD-TYPE  341   29
   clus
vv  NTAN1 MUTATED NTAN1 WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D933V7, binary
                 cls
clus                0   1
  NTAN1 MUTATED     4   1
  NTAN1 WILD-TYPE 141 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      4    1
  NTAN1 WILD-TYPE  141  247
        clus
vv       NTAN1 MUTATED NTAN1 WILD-TYPE
  FEMALE             4             141
  MALE               1             247
[1] 2 2
[1] FALSE
D933V8, binary
                 cls
clus                0   1
  NTAN1 MUTATED     4   1
  NTAN1 WILD-TYPE 288  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      4    1
  NTAN1 WILD-TYPE  288   58
     clus
vv    NTAN1 MUTATED NTAN1 WILD-TYPE
  NO              4             288
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NTAN1 MUTATED                                          0
  NTAN1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NTAN1 MUTATED                                       0
  NTAN1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NTAN1 MUTATED                                                        3
  NTAN1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NTAN1 MUTATED                                                   1
  NTAN1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NTAN1 MUTATED                                                                   1
  NTAN1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NTAN1 MUTATED                                                    0
  NTAN1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NTAN1 MUTATED                                                  0
  NTAN1 WILD-TYPE                                               61
D933V9, multiclass
                                                                   clus
vv                                                                  NTAN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  NTAN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NTAN1 MUTATED     3   1   0   1
  NTAN1 WILD-TYPE 308  13  15  23
D933V10, multiclass
    clus
vv   NTAN1 MUTATED NTAN1 WILD-TYPE
  R0             3             308
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D933V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NTAN1 MUTATED       0                         0
  NTAN1 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NTAN1 MUTATED                                           0     3
  NTAN1 WILD-TYPE                                         1   240
D933V12, multiclass
                                           clus
vv                                          NTAN1 MUTATED NTAN1 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D933V13, binary
                 cls
clus                0   1
  NTAN1 MUTATED     0   3
  NTAN1 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      0    3
  NTAN1 WILD-TYPE    4  307
                        clus
vv                       NTAN1 MUTATED NTAN1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(934) Variable = MLXIPL MUTATION ANALYSIS
D934V1, survival
                  sevent
clus2                0   1
  MLXIPL MUTATED     9   3
  MLXIPL WILD-TYPE 221 136
  MLXIPL MUTATED MLXIPL WILD-TYPE 
              12              357 
  MLXIPL MUTATED MLXIPL WILD-TYPE 
               3              136 
$`MLXIPL MUTATED`
TCGA-BR-6452 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A453 TCGA-CD-8535 TCGA-CG-4305 
       34.68         1.12        31.96         6.08        12.82        15.95 
TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-MX-A5UJ 
        1.02         6.02       105.07         0.10         6.58        19.73 

$`MLXIPL WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         8.98         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-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 

  MLXIPL MUTATED MLXIPL WILD-TYPE 
             0.1              0.0 
  MLXIPL MUTATED MLXIPL WILD-TYPE 
          105.07           122.30 
  MLXIPL MUTATED MLXIPL WILD-TYPE 
            9.70            14.43 
[1] "0.1 - 105.1 (9.7)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.3"
D934V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MLXIPL MUTATED         0        0        0        2         2         1
  MLXIPL WILD-TYPE       2       15       40       28        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MLXIPL MUTATED           0          2          0          1        4
  MLXIPL WILD-TYPE         3         68         53         31       34
D934V3, multiclass
            clus
vv           MLXIPL MUTATED MLXIPL WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                2               28
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                4               34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MLXIPL MUTATED     1   2   6   4
  MLXIPL WILD-TYPE  21  90 167  93
D934V4, multiclass
    clus
vv   MLXIPL MUTATED MLXIPL WILD-TYPE
  T1              1               21
  T2              2               90
  T3              6              167
  T4              4               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
  MLXIPL MUTATED     2   5   4   1
  MLXIPL WILD-TYPE 116  99  73  76
D934V5, multiclass
    clus
vv   MLXIPL MUTATED MLXIPL WILD-TYPE
  N0              2              116
  N1              5               99
  N2              4               73
  N3              1               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"
D934V6, binary
                  cls
clus                 0   1
  MLXIPL MUTATED    10   3
  MLXIPL WILD-TYPE 336  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLXIPL MUTATED     10    3
  MLXIPL WILD-TYPE  336   26
   clus
vv  MLXIPL MUTATED MLXIPL WILD-TYPE
  0             10              336
  1              3               26
[1] 2 2
[1] FALSE
D934V7, binary
                  cls
clus                 0   1
  MLXIPL MUTATED     4   9
  MLXIPL WILD-TYPE 141 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLXIPL MUTATED      4    9
  MLXIPL WILD-TYPE  141  239
        clus
vv       MLXIPL MUTATED MLXIPL WILD-TYPE
  FEMALE              4              141
  MALE                9              239
[1] 2 2
[1] FALSE
D934V8, binary
                  cls
clus                 0   1
  MLXIPL MUTATED    11   0
  MLXIPL WILD-TYPE 281  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLXIPL MUTATED     11    0
  MLXIPL WILD-TYPE  281   59
     clus
vv    MLXIPL MUTATED MLXIPL WILD-TYPE
  NO              11              281
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MLXIPL MUTATED                                          1
  MLXIPL WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MLXIPL MUTATED                                       1
  MLXIPL WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MLXIPL MUTATED                                                        7
  MLXIPL WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MLXIPL MUTATED                                                   0
  MLXIPL WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MLXIPL MUTATED                                                                   1
  MLXIPL WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MLXIPL MUTATED                                                    0
  MLXIPL WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MLXIPL MUTATED                                                  3
  MLXIPL WILD-TYPE                                               58
D934V9, multiclass
                                                                   clus
vv                                                                  MLXIPL MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  MLXIPL WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MLXIPL MUTATED    11   0   1   1
  MLXIPL WILD-TYPE 300  14  14  23
D934V10, multiclass
    clus
vv   MLXIPL MUTATED MLXIPL WILD-TYPE
  R0             11              300
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D934V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MLXIPL MUTATED       5                         0
  MLXIPL WILD-TYPE    82                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MLXIPL MUTATED                                           0     4
  MLXIPL WILD-TYPE                                         1   239
D934V12, multiclass
                                           clus
vv                                          MLXIPL MUTATED MLXIPL WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D934V13, binary
                  cls
clus                 0   1
  MLXIPL MUTATED     0   9
  MLXIPL WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLXIPL MUTATED      0    9
  MLXIPL WILD-TYPE    4  301
                        clus
vv                       MLXIPL MUTATED MLXIPL WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(935) Variable = SFRS18 MUTATION ANALYSIS
D935V1, survival
                  sevent
clus2                0   1
  SFRS18 MUTATED    11   2
  SFRS18 WILD-TYPE 219 137
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              13              356 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
               2              137 
$`SFRS18 MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8368 
       11.70         6.97         6.61        34.68        32.25         4.31 
TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-8533 TCGA-HF-A5NB TCGA-HU-A4G9 
       31.27         1.12        31.96        15.39        30.51        24.20 
TCGA-HU-A4GT 
        6.51 

$`SFRS18 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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 
           15.39            14.22 
[1] "1.1 - 34.7 (15.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.5"
D935V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SFRS18 MUTATED         0        1        3        1         3         1
  SFRS18 WILD-TYPE       2       14       37       29        34        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFRS18 MUTATED           1          1          0          2        1
  SFRS18 WILD-TYPE         2         69         53         30       37
D935V3, multiclass
            clus
vv           SFRS18 MUTATED SFRS18 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                3               37
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               1               51
  STAGE III               1                2
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SFRS18 MUTATED     1   4   5   4
  SFRS18 WILD-TYPE  21  88 168  93
D935V4, multiclass
    clus
vv   SFRS18 MUTATED SFRS18 WILD-TYPE
  T1              1               21
  T2              4               88
  T3              5              168
  T4              4               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
  SFRS18 MUTATED     9   2   1   2
  SFRS18 WILD-TYPE 109 102  76  75
D935V5, multiclass
    clus
vv   SFRS18 MUTATED SFRS18 WILD-TYPE
  N0              9              109
  N1              2              102
  N2              1               76
  N3              2               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"
D935V6, binary
                  cls
clus                 0   1
  SFRS18 MUTATED    13   1
  SFRS18 WILD-TYPE 333  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED     13    1
  SFRS18 WILD-TYPE  333   28
   clus
vv  SFRS18 MUTATED SFRS18 WILD-TYPE
  0             13              333
  1              1               28
[1] 2 2
[1] FALSE
D935V7, binary
                  cls
clus                 0   1
  SFRS18 MUTATED     9   6
  SFRS18 WILD-TYPE 136 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED      9    6
  SFRS18 WILD-TYPE  136  242
        clus
vv       SFRS18 MUTATED SFRS18 WILD-TYPE
  FEMALE              9              136
  MALE                6              242
[1] 2 2
[1] FALSE
D935V8, binary
                  cls
clus                 0   1
  SFRS18 MUTATED    12   1
  SFRS18 WILD-TYPE 280  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED     12    1
  SFRS18 WILD-TYPE  280   58
     clus
vv    SFRS18 MUTATED SFRS18 WILD-TYPE
  NO              12              280
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SFRS18 MUTATED                                          0
  SFRS18 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SFRS18 MUTATED                                       1
  SFRS18 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SFRS18 MUTATED                                                        9
  SFRS18 WILD-TYPE                                                    149
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SFRS18 MUTATED                                                   1
  SFRS18 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SFRS18 MUTATED                                                                   1
  SFRS18 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SFRS18 MUTATED                                                    0
  SFRS18 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SFRS18 MUTATED                                                  3
  SFRS18 WILD-TYPE                                               58
D935V9, multiclass
                                                                   clus
vv                                                                  SFRS18 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  SFRS18 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SFRS18 MUTATED    11   1   0   3
  SFRS18 WILD-TYPE 300  13  15  21
D935V10, multiclass
    clus
vv   SFRS18 MUTATED SFRS18 WILD-TYPE
  R0             11              300
  R1              1               13
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D935V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SFRS18 MUTATED       4                         0
  SFRS18 WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SFRS18 MUTATED                                           0     9
  SFRS18 WILD-TYPE                                         1   234
D935V12, multiclass
                                           clus
vv                                          SFRS18 MUTATED SFRS18 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D935V13, binary
                  cls
clus                 0   1
  SFRS18 MUTATED     0  13
  SFRS18 WILD-TYPE   4 297
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED      0   13
  SFRS18 WILD-TYPE    4  297
                        clus
vv                       SFRS18 MUTATED SFRS18 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             13              297
[1] 2 2
[1] FALSE

Clustering(936) Variable = PADI3 MUTATION ANALYSIS
D936V1, survival
                 sevent
clus2               0   1
  PADI3 MUTATED     6   6
  PADI3 WILD-TYPE 224 133
  PADI3 MUTATED PADI3 WILD-TYPE 
             12             357 
  PADI3 MUTATED PADI3 WILD-TYPE 
              6             133 
$`PADI3 MUTATED`
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8361 
        9.67        34.68        36.16        32.25         6.18        31.10 
TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5726 TCGA-D7-5577 TCGA-D7-A6EY TCGA-HU-A4GU 
       11.77         1.02        28.96        25.71        11.44         6.58 

$`PADI3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-D7-5578 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-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-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 

  PADI3 MUTATED PADI3 WILD-TYPE 
           1.02            0.00 
  PADI3 MUTATED PADI3 WILD-TYPE 
          36.16          122.30 
  PADI3 MUTATED PADI3 WILD-TYPE 
          18.74           14.27 
[1] "1.0 - 36.2 (18.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D936V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PADI3 MUTATED         0        2        1        0         2         2
  PADI3 WILD-TYPE       2       13       39       30        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PADI3 MUTATED           0          2          1          1        1
  PADI3 WILD-TYPE         3         68         52         31       37
D936V3, multiclass
            clus
vv           PADI3 MUTATED PADI3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PADI3 MUTATED     2   2   6   2
  PADI3 WILD-TYPE  20  90 167  95
D936V4, multiclass
    clus
vv   PADI3 MUTATED PADI3 WILD-TYPE
  T1             2              20
  T2             2              90
  T3             6             167
  T4             2              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
  PADI3 MUTATED     6   2   2   2
  PADI3 WILD-TYPE 112 102  75  75
D936V5, multiclass
    clus
vv   PADI3 MUTATED PADI3 WILD-TYPE
  N0             6             112
  N1             2             102
  N2             2              75
  N3             2              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"
D936V6, binary
                 cls
clus                0   1
  PADI3 MUTATED    12   1
  PADI3 WILD-TYPE 334  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PADI3 MUTATED     12    1
  PADI3 WILD-TYPE  334   28
   clus
vv  PADI3 MUTATED PADI3 WILD-TYPE
  0            12             334
  1             1              28
[1] 2 2
[1] FALSE
D936V7, binary
                 cls
clus                0   1
  PADI3 MUTATED     6   7
  PADI3 WILD-TYPE 139 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PADI3 MUTATED      6    7
  PADI3 WILD-TYPE  139  241
        clus
vv       PADI3 MUTATED PADI3 WILD-TYPE
  FEMALE             6             139
  MALE               7             241
[1] 2 2
[1] FALSE
D936V8, binary
                 cls
clus                0   1
  PADI3 MUTATED    10   0
  PADI3 WILD-TYPE 282  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PADI3 MUTATED     10    0
  PADI3 WILD-TYPE  282   59
     clus
vv    PADI3 MUTATED PADI3 WILD-TYPE
  NO             10             282
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PADI3 MUTATED                                          0
  PADI3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PADI3 MUTATED                                       1
  PADI3 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PADI3 MUTATED                                                        6
  PADI3 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PADI3 MUTATED                                                   0
  PADI3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PADI3 MUTATED                                                                   3
  PADI3 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PADI3 MUTATED                                                    1
  PADI3 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PADI3 MUTATED                                                  2
  PADI3 WILD-TYPE                                               59
D936V9, multiclass
                                                                   clus
vv                                                                  PADI3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  PADI3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PADI3 MUTATED    10   0   1   1
  PADI3 WILD-TYPE 301  14  14  23
D936V10, multiclass
    clus
vv   PADI3 MUTATED PADI3 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D936V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PADI3 MUTATED       2                         0
  PADI3 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PADI3 MUTATED                                           0     8
  PADI3 WILD-TYPE                                         1   235
D936V12, multiclass
                                           clus
vv                                          PADI3 MUTATED PADI3 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D936V13, binary
                 cls
clus                0   1
  PADI3 MUTATED     0  10
  PADI3 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PADI3 MUTATED      0   10
  PADI3 WILD-TYPE    4  300
                        clus
vv                       PADI3 MUTATED PADI3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(937) Variable = SLC38A6 MUTATION ANALYSIS
D937V1, survival
                   sevent
clus2                 0   1
  SLC38A6 MUTATED     7   1
  SLC38A6 WILD-TYPE 223 138
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
                8               361 
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
                1               138 
$`SLC38A6 MUTATED`
TCGA-BR-8372 TCGA-BR-8487 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4437 TCGA-CG-5721 
       31.27         1.12        12.43         6.58         8.05         6.02 
TCGA-CG-5728 TCGA-FP-7829 
       65.10        19.53 

$`SLC38A6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
             1.12              0.00 
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
             65.1             122.3 
  SLC38A6 MUTATED SLC38A6 WILD-TYPE 
            10.24             14.43 
[1] "1.1 - 65.1 (10.2)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "2.7"
D937V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC38A6 MUTATED         0        0        1        2         2         1
  SLC38A6 WILD-TYPE       2       15       39       28        35        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC38A6 MUTATED           0          0          0          1        1
  SLC38A6 WILD-TYPE         3         70         53         31       37
D937V3, multiclass
            clus
vv           SLC38A6 MUTATED SLC38A6 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 2                28
  STAGE IIA                2                35
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC38A6 MUTATED     0   2   4   2
  SLC38A6 WILD-TYPE  22  90 169  95
D937V4, multiclass
    clus
vv   SLC38A6 MUTATED SLC38A6 WILD-TYPE
  T1               0                22
  T2               2                90
  T3               4               169
  T4               2                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
  SLC38A6 MUTATED     4   3   0   1
  SLC38A6 WILD-TYPE 114 101  77  76
D937V5, multiclass
    clus
vv   SLC38A6 MUTATED SLC38A6 WILD-TYPE
  N0               4               114
  N1               3               101
  N2               0                77
  N3               1                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"
D937V6, binary
                   cls
clus                  0   1
  SLC38A6 MUTATED     8   0
  SLC38A6 WILD-TYPE 338  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A6 MUTATED      8    0
  SLC38A6 WILD-TYPE  338   29
   clus
vv  SLC38A6 MUTATED SLC38A6 WILD-TYPE
  0               8               338
  1               0                29
[1] 2 2
[1] FALSE
D937V7, binary
                   cls
clus                  0   1
  SLC38A6 MUTATED     2   6
  SLC38A6 WILD-TYPE 143 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A6 MUTATED      2    6
  SLC38A6 WILD-TYPE  143  242
        clus
vv       SLC38A6 MUTATED SLC38A6 WILD-TYPE
  FEMALE               2               143
  MALE                 6               242
[1] 2 2
[1] FALSE
D937V8, binary
                   cls
clus                  0   1
  SLC38A6 MUTATED     6   1
  SLC38A6 WILD-TYPE 286  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A6 MUTATED      6    1
  SLC38A6 WILD-TYPE  286   58
     clus
vv    SLC38A6 MUTATED SLC38A6 WILD-TYPE
  NO                6               286
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC38A6 MUTATED                                          0
  SLC38A6 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC38A6 MUTATED                                       1
  SLC38A6 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC38A6 MUTATED                                                        3
  SLC38A6 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC38A6 MUTATED                                                   1
  SLC38A6 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC38A6 MUTATED                                                                   3
  SLC38A6 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC38A6 MUTATED                                                    0
  SLC38A6 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC38A6 MUTATED                                                  0
  SLC38A6 WILD-TYPE                                               61
D937V9, multiclass
                                                                   clus
vv                                                                  SLC38A6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  SLC38A6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC38A6 MUTATED     7   0   0   0
  SLC38A6 WILD-TYPE 304  14  15  24
D937V10, multiclass
    clus
vv   SLC38A6 MUTATED SLC38A6 WILD-TYPE
  R0               7               304
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D937V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC38A6 MUTATED       2                         0
  SLC38A6 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC38A6 MUTATED                                           0     3
  SLC38A6 WILD-TYPE                                         1   240
D937V12, multiclass
                                           clus
vv                                          SLC38A6 MUTATED SLC38A6 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D937V13, binary
                   cls
clus                  0   1
  SLC38A6 MUTATED     0   5
  SLC38A6 WILD-TYPE   4 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A6 MUTATED      0    5
  SLC38A6 WILD-TYPE    4  305
                        clus
vv                       SLC38A6 MUTATED SLC38A6 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(938) Variable = RGS22 MUTATION ANALYSIS
D938V1, survival
                 sevent
clus2               0   1
  RGS22 MUTATED    14   5
  RGS22 WILD-TYPE 216 134
  RGS22 MUTATED RGS22 WILD-TYPE 
             19             350 
  RGS22 MUTATED RGS22 WILD-TYPE 
              5             134 
$`RGS22 MUTATED`
TCGA-B7-5816 TCGA-BR-4191 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7707 
       26.70        18.35        34.68        30.90        44.94        35.84 
TCGA-BR-8059 TCGA-BR-8372 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-4437 TCGA-CG-5728 
       14.43        31.27        31.96        16.14         8.05        65.10 
TCGA-CG-5733 TCGA-HU-A4GH TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-MX-A5UJ 
       21.07        11.77         0.10         6.51         6.58        19.73 
TCGA-MX-A666 
       14.04 

$`RGS22 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-7196 
       19.89        12.16         8.98        40.21        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-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-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-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-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-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-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-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-R5-A7O7 
        2.53         5.56        63.62        36.95         3.72        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 

  RGS22 MUTATED RGS22 WILD-TYPE 
            0.1             0.0 
  RGS22 MUTATED RGS22 WILD-TYPE 
           65.1           122.3 
  RGS22 MUTATED RGS22 WILD-TYPE 
         19.730          14.055 
[1] "0.1 - 65.1 (19.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D938V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RGS22 MUTATED         0        1        3        1         5         2
  RGS22 WILD-TYPE       2       14       37       29        32        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RGS22 MUTATED           1          3          1          2        1
  RGS22 WILD-TYPE         2         67         52         30       37
D938V3, multiclass
            clus
vv           RGS22 MUTATED RGS22 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               1              29
  STAGE IIA              5              32
  STAGE IIB              2              50
  STAGE III              1               2
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RGS22 MUTATED     1   6   8   5
  RGS22 WILD-TYPE  21  86 165  92
D938V4, multiclass
    clus
vv   RGS22 MUTATED RGS22 WILD-TYPE
  T1             1              21
  T2             6              86
  T3             8             165
  T4             5              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
  RGS22 MUTATED     9   4   5   2
  RGS22 WILD-TYPE 109 100  72  75
D938V5, multiclass
    clus
vv   RGS22 MUTATED RGS22 WILD-TYPE
  N0             9             109
  N1             4             100
  N2             5              72
  N3             2              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"
D938V6, binary
                 cls
clus                0   1
  RGS22 MUTATED    19   1
  RGS22 WILD-TYPE 327  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED     19    1
  RGS22 WILD-TYPE  327   28
   clus
vv  RGS22 MUTATED RGS22 WILD-TYPE
  0            19             327
  1             1              28
[1] 2 2
[1] FALSE
D938V7, binary
                 cls
clus                0   1
  RGS22 MUTATED     9  12
  RGS22 WILD-TYPE 136 236
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED      9   12
  RGS22 WILD-TYPE  136  236
        clus
vv       RGS22 MUTATED RGS22 WILD-TYPE
  FEMALE             9             136
  MALE              12             236
[1] 2 2
[1] FALSE
D938V8, binary
                 cls
clus                0   1
  RGS22 MUTATED    18   0
  RGS22 WILD-TYPE 274  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED     18    0
  RGS22 WILD-TYPE  274   59
     clus
vv    RGS22 MUTATED RGS22 WILD-TYPE
  NO             18             274
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RGS22 MUTATED                                          0
  RGS22 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RGS22 MUTATED                                       2
  RGS22 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RGS22 MUTATED                                                        9
  RGS22 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RGS22 MUTATED                                                   0
  RGS22 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RGS22 MUTATED                                                                   5
  RGS22 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RGS22 MUTATED                                                    0
  RGS22 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RGS22 MUTATED                                                  5
  RGS22 WILD-TYPE                                               56
D938V9, multiclass
                                                                   clus
vv                                                                  RGS22 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              5
                                                                   clus
vv                                                                  RGS22 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RGS22 MUTATED    19   0   0   1
  RGS22 WILD-TYPE 292  14  15  23
D938V10, multiclass
    clus
vv   RGS22 MUTATED RGS22 WILD-TYPE
  R0            19             292
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D938V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RGS22 MUTATED       5                         0
  RGS22 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RGS22 MUTATED                                           0    12
  RGS22 WILD-TYPE                                         1   231
D938V12, multiclass
                                           clus
vv                                          RGS22 MUTATED RGS22 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D938V13, binary
                 cls
clus                0   1
  RGS22 MUTATED     0  17
  RGS22 WILD-TYPE   4 293
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED      0   17
  RGS22 WILD-TYPE    4  293
                        clus
vv                       RGS22 MUTATED RGS22 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            17             293
[1] 2 2
[1] FALSE

Clustering(939) Variable = EVI5 MUTATION ANALYSIS
D939V1, survival
                sevent
clus2              0   1
  EVI5 MUTATED     9   0
  EVI5 WILD-TYPE 221 139
  EVI5 MUTATED EVI5 WILD-TYPE 
             9            360 
  EVI5 MUTATED EVI5 WILD-TYPE 
             0            139 
$`EVI5 MUTATED`
TCGA-B7-5816 TCGA-BR-6852 TCGA-BR-7958 TCGA-BR-8360 TCGA-BR-8680 TCGA-CG-5721 
       26.70        44.94        29.56         6.18        31.96         6.02 
TCGA-CG-5728 TCGA-D7-8572 TCGA-HU-A4GH 
       65.10        16.80        11.77 

$`EVI5 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        3.45         9.07        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-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-D7-8573 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-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-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 

  EVI5 MUTATED EVI5 WILD-TYPE 
          6.02           0.00 
  EVI5 MUTATED EVI5 WILD-TYPE 
          65.1          122.3 
  EVI5 MUTATED EVI5 WILD-TYPE 
         26.70          14.12 
[1] "6.0 - 65.1 (26.7)"  "0.0 - 122.3 (14.1)"
[1] "hr="     "2.6e+07"
D939V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EVI5 MUTATED         0        1        1        0         2         2
  EVI5 WILD-TYPE       2       14       39       30        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EVI5 MUTATED           0          0          1          0        2
  EVI5 WILD-TYPE         3         70         52         32       36
D939V3, multiclass
            clus
vv           EVI5 MUTATED EVI5 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EVI5 MUTATED     1   2   2   4
  EVI5 WILD-TYPE  21  90 171  93
D939V4, multiclass
    clus
vv   EVI5 MUTATED EVI5 WILD-TYPE
  T1            1             21
  T2            2             90
  T3            2            171
  T4            4             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
  EVI5 MUTATED     6   2   2   0
  EVI5 WILD-TYPE 112 102  75  77
D939V5, multiclass
    clus
vv   EVI5 MUTATED EVI5 WILD-TYPE
  N0            6            112
  N1            2            102
  N2            2             75
  N3            0             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"
D939V6, binary
                cls
clus               0   1
  EVI5 MUTATED     9   1
  EVI5 WILD-TYPE 337  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  EVI5 MUTATED      9    1
  EVI5 WILD-TYPE  337   28
   clus
vv  EVI5 MUTATED EVI5 WILD-TYPE
  0            9            337
  1            1             28
[1] 2 2
[1] FALSE
D939V7, binary
                cls
clus               0   1
  EVI5 MUTATED     4   6
  EVI5 WILD-TYPE 141 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  EVI5 MUTATED      4    6
  EVI5 WILD-TYPE  141  242
        clus
vv       EVI5 MUTATED EVI5 WILD-TYPE
  FEMALE            4            141
  MALE              6            242
[1] 2 2
[1] FALSE
D939V8, binary
                cls
clus               0   1
  EVI5 MUTATED     8   0
  EVI5 WILD-TYPE 284  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  EVI5 MUTATED      8    0
  EVI5 WILD-TYPE  284   59
     clus
vv    EVI5 MUTATED EVI5 WILD-TYPE
  NO             8            284
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EVI5 MUTATED                                          0
  EVI5 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EVI5 MUTATED                                       1
  EVI5 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EVI5 MUTATED                                                        4
  EVI5 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EVI5 MUTATED                                                   0
  EVI5 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EVI5 MUTATED                                                                   3
  EVI5 WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EVI5 MUTATED                                                    0
  EVI5 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EVI5 MUTATED                                                  2
  EVI5 WILD-TYPE                                               59
D939V9, multiclass
                                                                   clus
vv                                                                  EVI5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  EVI5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EVI5 MUTATED     9   0   0   1
  EVI5 WILD-TYPE 302  14  15  23
D939V10, multiclass
    clus
vv   EVI5 MUTATED EVI5 WILD-TYPE
  R0            9            302
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D939V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  EVI5 MUTATED       2                         0
  EVI5 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EVI5 MUTATED                                           0     6
  EVI5 WILD-TYPE                                         1   237
D939V12, multiclass
                                           clus
vv                                          EVI5 MUTATED EVI5 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D939V13, binary
                cls
clus               0   1
  EVI5 MUTATED     0   8
  EVI5 WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  EVI5 MUTATED      0    8
  EVI5 WILD-TYPE    4  302
                        clus
vv                       EVI5 MUTATED EVI5 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(940) Variable = POU5F1B MUTATION ANALYSIS
D940V1, survival
                   sevent
clus2                 0   1
  POU5F1B MUTATED     4   4
  POU5F1B WILD-TYPE 226 135
  POU5F1B MUTATED POU5F1B WILD-TYPE 
                8               361 
  POU5F1B MUTATED POU5F1B WILD-TYPE 
                4               135 
$`POU5F1B MUTATED`
TCGA-BR-6452 TCGA-BR-7959 TCGA-BR-8382 TCGA-CD-A4MJ TCGA-CG-5725 TCGA-HJ-7597 
       34.68        33.21        25.05        12.62        15.02        26.47 
TCGA-HU-A4GT TCGA-VQ-A91Q 
        6.51        20.81 

$`POU5F1B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-5726 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        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-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-A91U TCGA-VQ-A91V 
       22.19        17.85         1.87        15.65         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 

  POU5F1B MUTATED POU5F1B WILD-TYPE 
             6.51              0.00 
  POU5F1B MUTATED POU5F1B WILD-TYPE 
            34.68            122.30 
  POU5F1B MUTATED POU5F1B WILD-TYPE 
            22.93             14.07 
[1] "6.5 - 34.7 (22.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D940V2, 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       2       15       37       30        35        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POU5F1B MUTATED           0          1          0          1        1
  POU5F1B WILD-TYPE         3         69         53         31       37
D940V3, multiclass
            clus
vv           POU5F1B MUTATED POU5F1B WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 3                37
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  POU5F1B MUTATED     0   3   3   2
  POU5F1B WILD-TYPE  22  89 170  95
D940V4, multiclass
    clus
vv   POU5F1B MUTATED POU5F1B WILD-TYPE
  T1               0                22
  T2               3                89
  T3               3               170
  T4               2                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
  POU5F1B MUTATED     5   1   0   2
  POU5F1B WILD-TYPE 113 103  77  75
D940V5, multiclass
    clus
vv   POU5F1B MUTATED POU5F1B WILD-TYPE
  N0               5               113
  N1               1               103
  N2               0                77
  N3               2                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"
D940V6, binary
                   cls
clus                  0   1
  POU5F1B MUTATED     7   0
  POU5F1B WILD-TYPE 339  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POU5F1B MUTATED      7    0
  POU5F1B WILD-TYPE  339   29
   clus
vv  POU5F1B MUTATED POU5F1B WILD-TYPE
  0               7               339
  1               0                29
[1] 2 2
[1] FALSE
D940V7, binary
                   cls
clus                  0   1
  POU5F1B MUTATED     4   4
  POU5F1B WILD-TYPE 141 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POU5F1B MUTATED      4    4
  POU5F1B WILD-TYPE  141  244
        clus
vv       POU5F1B MUTATED POU5F1B WILD-TYPE
  FEMALE               4               141
  MALE                 4               244
[1] 2 2
[1] FALSE
D940V8, binary
                   cls
clus                  0   1
  POU5F1B MUTATED     7   1
  POU5F1B WILD-TYPE 285  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POU5F1B MUTATED      7    1
  POU5F1B WILD-TYPE  285   58
     clus
vv    POU5F1B MUTATED POU5F1B WILD-TYPE
  NO                7               285
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  POU5F1B MUTATED                                          1
  POU5F1B WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  POU5F1B MUTATED                                       0
  POU5F1B WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  POU5F1B MUTATED                                                        4
  POU5F1B WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  POU5F1B MUTATED                                                   1
  POU5F1B WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  POU5F1B MUTATED                                                                   0
  POU5F1B WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  POU5F1B MUTATED                                                    0
  POU5F1B WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  POU5F1B MUTATED                                                  2
  POU5F1B WILD-TYPE                                               59
D940V9, multiclass
                                                                   clus
vv                                                                  POU5F1B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  POU5F1B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  POU5F1B MUTATED     7   0   0   0
  POU5F1B WILD-TYPE 304  14  15  24
D940V10, multiclass
    clus
vv   POU5F1B MUTATED POU5F1B WILD-TYPE
  R0               7               304
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D940V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  POU5F1B MUTATED       2                         0
  POU5F1B WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  POU5F1B MUTATED                                           0     4
  POU5F1B WILD-TYPE                                         1   239
D940V12, multiclass
                                           clus
vv                                          POU5F1B MUTATED POU5F1B WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D940V13, binary
                   cls
clus                  0   1
  POU5F1B MUTATED     0   6
  POU5F1B WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POU5F1B MUTATED      0    6
  POU5F1B WILD-TYPE    4  304
                        clus
vv                       POU5F1B MUTATED POU5F1B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(941) Variable = NEIL1 MUTATION ANALYSIS
D941V1, survival
                 sevent
clus2               0   1
  NEIL1 MUTATED     2   3
  NEIL1 WILD-TYPE 228 136
  NEIL1 MUTATED NEIL1 WILD-TYPE 
              5             364 
  NEIL1 MUTATED NEIL1 WILD-TYPE 
              3             136 
$`NEIL1 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8295 TCGA-CG-5726 
       21.99        34.68        32.25         2.20        28.96 

$`NEIL1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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 

  NEIL1 MUTATED NEIL1 WILD-TYPE 
            2.2             0.0 
  NEIL1 MUTATED NEIL1 WILD-TYPE 
          34.68          122.30 
  NEIL1 MUTATED NEIL1 WILD-TYPE 
          28.96           14.12 
[1] "2.2 - 34.7 (29.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D941V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NEIL1 MUTATED         0        1        0        0         1         3
  NEIL1 WILD-TYPE       2       14       40       30        36        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NEIL1 MUTATED           0          0          0          0        1
  NEIL1 WILD-TYPE         3         70         53         32       37
D941V3, multiclass
            clus
vv           NEIL1 MUTATED NEIL1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NEIL1 MUTATED     2   0   1   4
  NEIL1 WILD-TYPE  20  92 172  93
D941V4, multiclass
    clus
vv   NEIL1 MUTATED NEIL1 WILD-TYPE
  T1             2              20
  T2             0              92
  T3             1             172
  T4             4              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
  NEIL1 MUTATED     5   1   0   0
  NEIL1 WILD-TYPE 113 103  77  77
D941V5, multiclass
    clus
vv   NEIL1 MUTATED NEIL1 WILD-TYPE
  N0             5             113
  N1             1             103
  N2             0              77
  N3             0              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"
D941V6, binary
                 cls
clus                0   1
  NEIL1 MUTATED     6   1
  NEIL1 WILD-TYPE 340  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NEIL1 MUTATED      6    1
  NEIL1 WILD-TYPE  340   28
   clus
vv  NEIL1 MUTATED NEIL1 WILD-TYPE
  0             6             340
  1             1              28
[1] 2 2
[1] FALSE
D941V7, binary
                 cls
clus                0   1
  NEIL1 MUTATED     5   2
  NEIL1 WILD-TYPE 140 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NEIL1 MUTATED      5    2
  NEIL1 WILD-TYPE  140  246
        clus
vv       NEIL1 MUTATED NEIL1 WILD-TYPE
  FEMALE             5             140
  MALE               2             246
[1] 2 2
[1] FALSE
D941V8, binary
                 cls
clus                0   1
  NEIL1 MUTATED     5   0
  NEIL1 WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NEIL1 MUTATED      5    0
  NEIL1 WILD-TYPE  287   59
     clus
vv    NEIL1 MUTATED NEIL1 WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NEIL1 MUTATED                                          0
  NEIL1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NEIL1 MUTATED                                       0
  NEIL1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NEIL1 MUTATED                                                        4
  NEIL1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NEIL1 MUTATED                                                   0
  NEIL1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NEIL1 MUTATED                                                                   3
  NEIL1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NEIL1 MUTATED                                                    0
  NEIL1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NEIL1 MUTATED                                                  0
  NEIL1 WILD-TYPE                                               61
D941V9, multiclass
                                                                   clus
vv                                                                  NEIL1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  NEIL1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NEIL1 MUTATED     5   0   1   1
  NEIL1 WILD-TYPE 306  14  14  23
D941V10, multiclass
    clus
vv   NEIL1 MUTATED NEIL1 WILD-TYPE
  R0             5             306
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D941V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NEIL1 MUTATED       0                         0
  NEIL1 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NEIL1 MUTATED                                           0     5
  NEIL1 WILD-TYPE                                         1   238
D941V12, multiclass
                                           clus
vv                                          NEIL1 MUTATED NEIL1 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D941V13, binary
                 cls
clus                0   1
  NEIL1 MUTATED     0   5
  NEIL1 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NEIL1 MUTATED      0    5
  NEIL1 WILD-TYPE    4  305
                        clus
vv                       NEIL1 MUTATED NEIL1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(942) Variable = LRRFIP2 MUTATION ANALYSIS
D942V1, survival
                   sevent
clus2                 0   1
  LRRFIP2 MUTATED     7   0
  LRRFIP2 WILD-TYPE 223 139
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
                7               362 
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
                0               139 
$`LRRFIP2 MUTATED`
TCGA-BR-6452 TCGA-CG-4305 TCGA-CG-5728 TCGA-D7-8572 TCGA-HU-A4G9 TCGA-HU-A4GU 
       34.68        15.95        65.10        16.80        24.20         6.58 
TCGA-HU-A4H3 
       29.00 

$`LRRFIP2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
             6.58              0.00 
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
             65.1             122.3 
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
            24.20             14.07 
[1] "6.6 - 65.1 (24.2)"  "0.0 - 122.3 (14.1)"
[1] "hr="     "9300000"
D942V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRRFIP2 MUTATED         0        1        1        1         1         2
  LRRFIP2 WILD-TYPE       2       14       39       29        36        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRFIP2 MUTATED           0          0          0          1        0
  LRRFIP2 WILD-TYPE         3         70         53         31       38
D942V3, multiclass
            clus
vv           LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  LRRFIP2 MUTATED     2   3   2   1
  LRRFIP2 WILD-TYPE  20  89 171  96
D942V4, multiclass
    clus
vv   LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  T1               2                20
  T2               3                89
  T3               2               171
  T4               1                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
  LRRFIP2 MUTATED     3   2   1   1
  LRRFIP2 WILD-TYPE 115 102  76  76
D942V5, multiclass
    clus
vv   LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  N0               3               115
  N1               2               102
  N2               1                76
  N3               1                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"
D942V6, binary
                   cls
clus                  0   1
  LRRFIP2 MUTATED     8   0
  LRRFIP2 WILD-TYPE 338  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP2 MUTATED      8    0
  LRRFIP2 WILD-TYPE  338   29
   clus
vv  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  0               8               338
  1               0                29
[1] 2 2
[1] FALSE
D942V7, binary
                   cls
clus                  0   1
  LRRFIP2 MUTATED     5   3
  LRRFIP2 WILD-TYPE 140 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP2 MUTATED      5    3
  LRRFIP2 WILD-TYPE  140  245
        clus
vv       LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  FEMALE               5               140
  MALE                 3               245
[1] 2 2
[1] FALSE
D942V8, binary
                   cls
clus                  0   1
  LRRFIP2 MUTATED     5   0
  LRRFIP2 WILD-TYPE 287  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP2 MUTATED      5    0
  LRRFIP2 WILD-TYPE  287   59
     clus
vv    LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  NO                5               287
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LRRFIP2 MUTATED                                          0
  LRRFIP2 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LRRFIP2 MUTATED                                       2
  LRRFIP2 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LRRFIP2 MUTATED                                                        4
  LRRFIP2 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LRRFIP2 MUTATED                                                   0
  LRRFIP2 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LRRFIP2 MUTATED                                                                   1
  LRRFIP2 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LRRFIP2 MUTATED                                                    0
  LRRFIP2 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LRRFIP2 MUTATED                                                  1
  LRRFIP2 WILD-TYPE                                               60
D942V9, multiclass
                                                                   clus
vv                                                                  LRRFIP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  LRRFIP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  LRRFIP2 MUTATED     7   0   0   1
  LRRFIP2 WILD-TYPE 304  14  15  23
D942V10, multiclass
    clus
vv   LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  R0               7               304
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D942V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  LRRFIP2 MUTATED       3                         0
  LRRFIP2 WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LRRFIP2 MUTATED                                           0     3
  LRRFIP2 WILD-TYPE                                         1   240
D942V12, multiclass
                                           clus
vv                                          LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D942V13, binary
                   cls
clus                  0   1
  LRRFIP2 MUTATED     0   6
  LRRFIP2 WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP2 MUTATED      0    6
  LRRFIP2 WILD-TYPE    4  304
                        clus
vv                       LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(943) Variable = IGDCC4 MUTATION ANALYSIS
D943V1, survival
                  sevent
clus2                0   1
  IGDCC4 MUTATED     6   5
  IGDCC4 WILD-TYPE 224 134
  IGDCC4 MUTATED IGDCC4 WILD-TYPE 
              11              358 
  IGDCC4 MUTATED IGDCC4 WILD-TYPE 
               5              134 
$`IGDCC4 MUTATED`
TCGA-CG-4460 TCGA-BR-4257 TCGA-BR-7707 TCGA-CD-8533 TCGA-CD-A48C TCGA-CG-4304 
       21.99         9.67        35.84        15.39        11.61        27.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5723 TCGA-HJ-7597 TCGA-VQ-A8P2 
        1.02         0.99       105.07        26.47        38.14 

$`IGDCC4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-4305 TCGA-CG-4306 TCGA-CG-4436 
       12.62        20.02         3.02        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-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 
        6.97        36.00         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-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 

  IGDCC4 MUTATED IGDCC4 WILD-TYPE 
            0.99             0.00 
  IGDCC4 MUTATED IGDCC4 WILD-TYPE 
          105.07           122.30 
  IGDCC4 MUTATED IGDCC4 WILD-TYPE 
           21.99            14.12 
[1] "1.0 - 105.1 (22.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D943V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IGDCC4 MUTATED         0        0        4        2         0         1
  IGDCC4 WILD-TYPE       2       15       36       28        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGDCC4 MUTATED           0          1          0          0        2
  IGDCC4 WILD-TYPE         3         69         53         32       36
D943V3, multiclass
            clus
vv           IGDCC4 MUTATED IGDCC4 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                4               36
  STAGE II                2               28
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IGDCC4 MUTATED     1   5   2   3
  IGDCC4 WILD-TYPE  21  87 171  94
D943V4, multiclass
    clus
vv   IGDCC4 MUTATED IGDCC4 WILD-TYPE
  T1              1               21
  T2              5               87
  T3              2              171
  T4              3               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
  IGDCC4 MUTATED     6   5   0   0
  IGDCC4 WILD-TYPE 112  99  77  77
D943V5, multiclass
    clus
vv   IGDCC4 MUTATED IGDCC4 WILD-TYPE
  N0              6              112
  N1              5               99
  N2              0               77
  N3              0               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"
D943V6, binary
                  cls
clus                 0   1
  IGDCC4 MUTATED    10   2
  IGDCC4 WILD-TYPE 336  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGDCC4 MUTATED     10    2
  IGDCC4 WILD-TYPE  336   27
   clus
vv  IGDCC4 MUTATED IGDCC4 WILD-TYPE
  0             10              336
  1              2               27
[1] 2 2
[1] FALSE
D943V7, binary
                  cls
clus                 0   1
  IGDCC4 MUTATED     8   5
  IGDCC4 WILD-TYPE 137 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGDCC4 MUTATED      8    5
  IGDCC4 WILD-TYPE  137  243
        clus
vv       IGDCC4 MUTATED IGDCC4 WILD-TYPE
  FEMALE              8              137
  MALE                5              243
[1] 2 2
[1] FALSE
D943V8, binary
                  cls
clus                 0   1
  IGDCC4 MUTATED     7   1
  IGDCC4 WILD-TYPE 285  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGDCC4 MUTATED      7    1
  IGDCC4 WILD-TYPE  285   58
     clus
vv    IGDCC4 MUTATED IGDCC4 WILD-TYPE
  NO               7              285
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IGDCC4 MUTATED                                          1
  IGDCC4 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IGDCC4 MUTATED                                       0
  IGDCC4 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IGDCC4 MUTATED                                                        9
  IGDCC4 WILD-TYPE                                                    149
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IGDCC4 MUTATED                                                   1
  IGDCC4 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IGDCC4 MUTATED                                                                   2
  IGDCC4 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IGDCC4 MUTATED                                                    0
  IGDCC4 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IGDCC4 MUTATED                                                  0
  IGDCC4 WILD-TYPE                                               61
D943V9, multiclass
                                                                   clus
vv                                                                  IGDCC4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  IGDCC4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IGDCC4 MUTATED     8   0   1   3
  IGDCC4 WILD-TYPE 303  14  14  21
D943V10, multiclass
    clus
vv   IGDCC4 MUTATED IGDCC4 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              1               14
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D943V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  IGDCC4 MUTATED       2                         0
  IGDCC4 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IGDCC4 MUTATED                                           0     6
  IGDCC4 WILD-TYPE                                         1   237
D943V12, multiclass
                                           clus
vv                                          IGDCC4 MUTATED IGDCC4 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D943V13, binary
                  cls
clus                 0   1
  IGDCC4 MUTATED     0   7
  IGDCC4 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGDCC4 MUTATED      0    7
  IGDCC4 WILD-TYPE    4  303
                        clus
vv                       IGDCC4 MUTATED IGDCC4 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(944) Variable = TRPM6 MUTATION ANALYSIS
D944V1, survival
                 sevent
clus2               0   1
  TRPM6 MUTATED    14   7
  TRPM6 WILD-TYPE 216 132
  TRPM6 MUTATED TRPM6 WILD-TYPE 
             21             348 
  TRPM6 MUTATED TRPM6 WILD-TYPE 
              7             132 
$`TRPM6 MUTATED`
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-8059 
       34.68        32.78        44.94         9.21        39.78        14.43 
TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8680 TCGA-BR-A452 TCGA-BR-A4QL TCGA-CD-5813 
       31.10        31.27        31.96         7.53        16.14        12.39 
TCGA-CD-8535 TCGA-CD-A4MI TCGA-CG-5721 TCGA-D7-8576 TCGA-HU-8602 TCGA-HU-A4H2 
       12.82        11.77         6.02        14.66        22.32        12.95 
TCGA-IN-7808 TCGA-VQ-A8P2 TCGA-VQ-AA68 
        3.45        38.14        43.66 

$`TRPM6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-D7-8578 
       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-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-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-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 

  TRPM6 MUTATED TRPM6 WILD-TYPE 
           3.45            0.00 
  TRPM6 MUTATED TRPM6 WILD-TYPE 
          44.94          122.30 
  TRPM6 MUTATED TRPM6 WILD-TYPE 
          16.14           14.07 
[1] "3.5 - 44.9 (16.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D944V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRPM6 MUTATED         0        0        0        2         3         2
  TRPM6 WILD-TYPE       2       15       40       28        34        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRPM6 MUTATED           1          4          3          3        2
  TRPM6 WILD-TYPE         2         66         50         29       36
D944V3, multiclass
            clus
vv           TRPM6 MUTATED TRPM6 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               2              28
  STAGE IIA              3              34
  STAGE IIB              2              50
  STAGE III              1               2
  STAGE IIIA             4              66
  STAGE IIIB             3              50
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRPM6 MUTATED     0   0  12   9
  TRPM6 WILD-TYPE  22  92 161  88
D944V4, multiclass
    clus
vv   TRPM6 MUTATED TRPM6 WILD-TYPE
  T1             0              22
  T2             0              92
  T3            12             161
  T4             9              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
  TRPM6 MUTATED     6   7   2   6
  TRPM6 WILD-TYPE 112  97  75  71
D944V5, multiclass
    clus
vv   TRPM6 MUTATED TRPM6 WILD-TYPE
  N0             6             112
  N1             7              97
  N2             2              75
  N3             6              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"
D944V6, binary
                 cls
clus                0   1
  TRPM6 MUTATED    20   2
  TRPM6 WILD-TYPE 326  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM6 MUTATED     20    2
  TRPM6 WILD-TYPE  326   27
   clus
vv  TRPM6 MUTATED TRPM6 WILD-TYPE
  0            20             326
  1             2              27
[1] 2 2
[1] FALSE
D944V7, binary
                 cls
clus                0   1
  TRPM6 MUTATED    11  11
  TRPM6 WILD-TYPE 134 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM6 MUTATED     11   11
  TRPM6 WILD-TYPE  134  237
        clus
vv       TRPM6 MUTATED TRPM6 WILD-TYPE
  FEMALE            11             134
  MALE              11             237
[1] 2 2
[1] FALSE
D944V8, binary
                 cls
clus                0   1
  TRPM6 MUTATED    19   2
  TRPM6 WILD-TYPE 273  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM6 MUTATED     19    2
  TRPM6 WILD-TYPE  273   57
     clus
vv    TRPM6 MUTATED TRPM6 WILD-TYPE
  NO             19             273
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TRPM6 MUTATED                                          0
  TRPM6 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TRPM6 MUTATED                                       2
  TRPM6 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRPM6 MUTATED                                                       11
  TRPM6 WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TRPM6 MUTATED                                                   2
  TRPM6 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRPM6 MUTATED                                                                   2
  TRPM6 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TRPM6 MUTATED                                                    0
  TRPM6 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TRPM6 MUTATED                                                  5
  TRPM6 WILD-TYPE                                               56
D944V9, multiclass
                                                                   clus
vv                                                                  TRPM6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              5
                                                                   clus
vv                                                                  TRPM6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRPM6 MUTATED    18   0   0   1
  TRPM6 WILD-TYPE 293  14  15  23
D944V10, multiclass
    clus
vv   TRPM6 MUTATED TRPM6 WILD-TYPE
  R0            18             293
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D944V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TRPM6 MUTATED       7                         0
  TRPM6 WILD-TYPE    80                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRPM6 MUTATED                                           0    14
  TRPM6 WILD-TYPE                                         1   229
D944V12, multiclass
                                           clus
vv                                          TRPM6 MUTATED TRPM6 WILD-TYPE
  ASIAN                                                 7              80
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                14             229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D944V13, binary
                 cls
clus                0   1
  TRPM6 MUTATED     0  19
  TRPM6 WILD-TYPE   4 291
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM6 MUTATED      0   19
  TRPM6 WILD-TYPE    4  291
                        clus
vv                       TRPM6 MUTATED TRPM6 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            19             291
[1] 2 2
[1] FALSE

Clustering(945) Variable = IL1F7 MUTATION ANALYSIS
D945V1, survival
                 sevent
clus2               0   1
  IL1F7 MUTATED     2   1
  IL1F7 WILD-TYPE 228 138
  IL1F7 MUTATED IL1F7 WILD-TYPE 
              3             366 
  IL1F7 MUTATED IL1F7 WILD-TYPE 
              1             138 
$`IL1F7 MUTATED`
TCGA-BR-4280 TCGA-BR-8368 TCGA-MX-A5UJ 
        6.61         4.31        19.73 

$`IL1F7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  IL1F7 MUTATED IL1F7 WILD-TYPE 
           4.31            0.00 
  IL1F7 MUTATED IL1F7 WILD-TYPE 
          19.73          122.30 
  IL1F7 MUTATED IL1F7 WILD-TYPE 
           6.61           14.35 
[1] "4.3 - 19.7 (6.6)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "1.6"
D945V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IL1F7 MUTATED         0        0        1        0         0         0
  IL1F7 WILD-TYPE       2       15       39       30        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL1F7 MUTATED           1          1          0          0        0
  IL1F7 WILD-TYPE         2         69         53         32       38
D945V3, multiclass
            clus
vv           IL1F7 MUTATED IL1F7 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              1               2
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IL1F7 MUTATED     0   2   1   0
  IL1F7 WILD-TYPE  22  90 172  97
D945V4, multiclass
    clus
vv   IL1F7 MUTATED IL1F7 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             1             172
  T4             0              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
  IL1F7 MUTATED     1   1   1   0
  IL1F7 WILD-TYPE 117 103  76  77
D945V5, multiclass
    clus
vv   IL1F7 MUTATED IL1F7 WILD-TYPE
  N0             1             117
  N1             1             103
  N2             1              76
  N3             0              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"
D945V6, binary
                 cls
clus                0   1
  IL1F7 MUTATED     3   0
  IL1F7 WILD-TYPE 343  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1F7 MUTATED      3    0
  IL1F7 WILD-TYPE  343   29
   clus
vv  IL1F7 MUTATED IL1F7 WILD-TYPE
  0             3             343
  1             0              29
[1] 2 2
[1] FALSE
D945V7, binary
                 cls
clus                0   1
  IL1F7 MUTATED     3   0
  IL1F7 WILD-TYPE 142 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1F7 MUTATED      3    0
  IL1F7 WILD-TYPE  142  248
        clus
vv       IL1F7 MUTATED IL1F7 WILD-TYPE
  FEMALE             3             142
  MALE               0             248
[1] 2 2
[1] FALSE
D945V8, binary
                 cls
clus                0   1
  IL1F7 MUTATED     3   0
  IL1F7 WILD-TYPE 289  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1F7 MUTATED      3    0
  IL1F7 WILD-TYPE  289   59
     clus
vv    IL1F7 MUTATED IL1F7 WILD-TYPE
  NO              3             289
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IL1F7 MUTATED                                          0
  IL1F7 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IL1F7 MUTATED                                       0
  IL1F7 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IL1F7 MUTATED                                                        2
  IL1F7 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IL1F7 MUTATED                                                   0
  IL1F7 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IL1F7 MUTATED                                                                   0
  IL1F7 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IL1F7 MUTATED                                                    0
  IL1F7 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IL1F7 MUTATED                                                  1
  IL1F7 WILD-TYPE                                               60
D945V9, multiclass
                                                                   clus
vv                                                                  IL1F7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  IL1F7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IL1F7 MUTATED     2   0   0   1
  IL1F7 WILD-TYPE 309  14  15  23
D945V10, multiclass
    clus
vv   IL1F7 MUTATED IL1F7 WILD-TYPE
  R0             2             309
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D945V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IL1F7 MUTATED       0                         0
  IL1F7 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IL1F7 MUTATED                                           0     3
  IL1F7 WILD-TYPE                                         1   240
D945V12, multiclass
                                           clus
vv                                          IL1F7 MUTATED IL1F7 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D945V13, binary
                 cls
clus                0   1
  IL1F7 MUTATED     0   3
  IL1F7 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1F7 MUTATED      0    3
  IL1F7 WILD-TYPE    4  307
                        clus
vv                       IL1F7 MUTATED IL1F7 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(946) Variable = BRPF3 MUTATION ANALYSIS
D946V1, survival
                 sevent
clus2               0   1
  BRPF3 MUTATED     6   4
  BRPF3 WILD-TYPE 224 135
  BRPF3 MUTATED BRPF3 WILD-TYPE 
             10             359 
  BRPF3 MUTATED BRPF3 WILD-TYPE 
              4             135 
$`BRPF3 MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-8078 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-4437 
        6.97         9.34        29.59         6.58        11.77         8.05 
TCGA-CG-5728 TCGA-D7-A4YT TCGA-F1-6874 TCGA-HU-8602 
       65.10        14.27        14.47        22.32 

$`BRPF3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-F1-6875 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-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 

  BRPF3 MUTATED BRPF3 WILD-TYPE 
           6.58            0.00 
  BRPF3 MUTATED BRPF3 WILD-TYPE 
           65.1           122.3 
  BRPF3 MUTATED BRPF3 WILD-TYPE 
          13.02           14.43 
[1] "6.6 - 65.1 (13.0)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D946V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BRPF3 MUTATED         0        0        2        1         1         2
  BRPF3 WILD-TYPE       2       15       38       29        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BRPF3 MUTATED           0          3          0          0        0
  BRPF3 WILD-TYPE         3         67         53         32       38
D946V3, multiclass
            clus
vv           BRPF3 MUTATED BRPF3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BRPF3 MUTATED     0   4   3   2
  BRPF3 WILD-TYPE  22  88 170  95
D946V4, multiclass
    clus
vv   BRPF3 MUTATED BRPF3 WILD-TYPE
  T1             0              22
  T2             4              88
  T3             3             170
  T4             2              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
  BRPF3 MUTATED     5   4   0   1
  BRPF3 WILD-TYPE 113 100  77  76
D946V5, multiclass
    clus
vv   BRPF3 MUTATED BRPF3 WILD-TYPE
  N0             5             113
  N1             4             100
  N2             0              77
  N3             1              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"
D946V6, binary
                 cls
clus                0   1
  BRPF3 MUTATED    10   0
  BRPF3 WILD-TYPE 336  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRPF3 MUTATED     10    0
  BRPF3 WILD-TYPE  336   29
   clus
vv  BRPF3 MUTATED BRPF3 WILD-TYPE
  0            10             336
  1             0              29
[1] 2 2
[1] FALSE
D946V7, binary
                 cls
clus                0   1
  BRPF3 MUTATED     4   7
  BRPF3 WILD-TYPE 141 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRPF3 MUTATED      4    7
  BRPF3 WILD-TYPE  141  241
        clus
vv       BRPF3 MUTATED BRPF3 WILD-TYPE
  FEMALE             4             141
  MALE               7             241
[1] 2 2
[1] FALSE
D946V8, binary
                 cls
clus                0   1
  BRPF3 MUTATED     9   0
  BRPF3 WILD-TYPE 283  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRPF3 MUTATED      9    0
  BRPF3 WILD-TYPE  283   59
     clus
vv    BRPF3 MUTATED BRPF3 WILD-TYPE
  NO              9             283
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BRPF3 MUTATED                                          0
  BRPF3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BRPF3 MUTATED                                       2
  BRPF3 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BRPF3 MUTATED                                                        5
  BRPF3 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BRPF3 MUTATED                                                   0
  BRPF3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BRPF3 MUTATED                                                                   3
  BRPF3 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BRPF3 MUTATED                                                    0
  BRPF3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BRPF3 MUTATED                                                  1
  BRPF3 WILD-TYPE                                               60
D946V9, multiclass
                                                                   clus
vv                                                                  BRPF3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  BRPF3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BRPF3 MUTATED     6   0   0   3
  BRPF3 WILD-TYPE 305  14  15  21
D946V10, multiclass
    clus
vv   BRPF3 MUTATED BRPF3 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D946V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BRPF3 MUTATED       3                         0
  BRPF3 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BRPF3 MUTATED                                           0     6
  BRPF3 WILD-TYPE                                         1   237
D946V12, multiclass
                                           clus
vv                                          BRPF3 MUTATED BRPF3 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D946V13, binary
                 cls
clus                0   1
  BRPF3 MUTATED     0   9
  BRPF3 WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRPF3 MUTATED      0    9
  BRPF3 WILD-TYPE    4  301
                        clus
vv                       BRPF3 MUTATED BRPF3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(947) Variable = ACACB MUTATION ANALYSIS
D947V1, survival
                 sevent
clus2               0   1
  ACACB MUTATED    22   7
  ACACB WILD-TYPE 208 132
  ACACB MUTATED ACACB WILD-TYPE 
             29             340 
  ACACB MUTATED ACACB WILD-TYPE 
              7             132 
$`ACACB MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7703 
        6.97         9.34        34.68        32.78        44.94        36.16 
TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8589 
       32.25         0.26         4.31        14.04         5.39        27.12 
TCGA-BR-8680 TCGA-BR-A4IY TCGA-CD-5798 TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5725 
       31.96        12.89        13.41         6.58         6.02        15.02 
TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-8573 TCGA-D7-A4YV TCGA-HF-A5NB TCGA-HU-8602 
       17.85        15.22        19.50         5.92        30.51        22.32 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-IN-A6RJ TCGA-VQ-A8P2 
        0.10         6.58        14.07        12.46        38.14 

$`ACACB WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       26.33         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-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-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-5800 
        1.15        21.44        16.14         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-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-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-D7-6525 
       19.13        20.55        18.84        18.54        18.61        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-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        16.80        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-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-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-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-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 

  ACACB MUTATED ACACB WILD-TYPE 
            0.1             0.0 
  ACACB MUTATED ACACB WILD-TYPE 
          44.94          122.30 
  ACACB MUTATED ACACB WILD-TYPE 
          14.07           14.35 
[1] "0.1 - 44.9 (14.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.6"
D947V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACACB MUTATED         0        2        5        2         5         5
  ACACB WILD-TYPE       2       13       35       28        32        47
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACACB MUTATED           0          4          2          2        2
  ACACB WILD-TYPE         3         66         51         30       36
D947V3, multiclass
            clus
vv           ACACB MUTATED ACACB WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               5              35
  STAGE II               2              28
  STAGE IIA              5              32
  STAGE IIB              5              47
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACACB MUTATED     3   5  12  10
  ACACB WILD-TYPE  19  87 161  87
D947V4, multiclass
    clus
vv   ACACB MUTATED ACACB WILD-TYPE
  T1             3              19
  T2             5              87
  T3            12             161
  T4            10              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
  ACACB MUTATED    16  10   3   2
  ACACB WILD-TYPE 102  94  74  75
D947V5, multiclass
    clus
vv   ACACB MUTATED ACACB WILD-TYPE
  N0            16             102
  N1            10              94
  N2             3              74
  N3             2              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"
D947V6, binary
                 cls
clus                0   1
  ACACB MUTATED    29   1
  ACACB WILD-TYPE 317  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACACB MUTATED     29    1
  ACACB WILD-TYPE  317   28
   clus
vv  ACACB MUTATED ACACB WILD-TYPE
  0            29             317
  1             1              28
[1] 2 2
[1] FALSE
D947V7, binary
                 cls
clus                0   1
  ACACB MUTATED    14  18
  ACACB WILD-TYPE 131 230
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACACB MUTATED     14   18
  ACACB WILD-TYPE  131  230
        clus
vv       ACACB MUTATED ACACB WILD-TYPE
  FEMALE            14             131
  MALE              18             230
[1] 2 2
[1] FALSE
D947V8, binary
                 cls
clus                0   1
  ACACB MUTATED    27   2
  ACACB WILD-TYPE 265  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACACB MUTATED     27    2
  ACACB WILD-TYPE  265   57
     clus
vv    ACACB MUTATED ACACB WILD-TYPE
  NO             27             265
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ACACB MUTATED                                          0
  ACACB WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ACACB MUTATED                                       4
  ACACB WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ACACB MUTATED                                                       16
  ACACB WILD-TYPE                                                    142
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ACACB MUTATED                                                   3
  ACACB WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ACACB MUTATED                                                                   2
  ACACB WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ACACB MUTATED                                                    1
  ACACB WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ACACB MUTATED                                                  6
  ACACB WILD-TYPE                                               55
D947V9, multiclass
                                                                   clus
vv                                                                  ACACB MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              6
                                                                   clus
vv                                                                  ACACB WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ACACB MUTATED    23   2   0   5
  ACACB WILD-TYPE 288  12  15  19
D947V10, multiclass
    clus
vv   ACACB MUTATED ACACB WILD-TYPE
  R0            23             288
  R1             2              12
  R2             0              15
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D947V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ACACB MUTATED       8                         0
  ACACB WILD-TYPE    79                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ACACB MUTATED                                           0    21
  ACACB WILD-TYPE                                         1   222
D947V12, multiclass
                                           clus
vv                                          ACACB MUTATED ACACB WILD-TYPE
  ASIAN                                                 8              79
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                21             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D947V13, binary
                 cls
clus                0   1
  ACACB MUTATED     0  28
  ACACB WILD-TYPE   4 282
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACACB MUTATED      0   28
  ACACB WILD-TYPE    4  282
                        clus
vv                       ACACB MUTATED ACACB WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            28             282
[1] 2 2
[1] FALSE

Clustering(948) Variable = PIGZ MUTATION ANALYSIS
D948V1, survival
                sevent
clus2              0   1
  PIGZ MUTATED     5   3
  PIGZ WILD-TYPE 225 136
  PIGZ MUTATED PIGZ WILD-TYPE 
             8            361 
  PIGZ MUTATED PIGZ WILD-TYPE 
             3            136 
$`PIGZ MUTATED`
TCGA-BR-4184 TCGA-BR-4255 TCGA-BR-6452 TCGA-D7-A6EY TCGA-HU-8249 TCGA-HU-8602 
        6.97         4.08        34.68        11.44        28.96        22.32 
TCGA-HU-A4G8 TCGA-HU-A4GU 
       22.68         6.58 

$`PIGZ WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-4256 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       30.90         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-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-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
        5.92        24.39        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-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 

  PIGZ MUTATED PIGZ WILD-TYPE 
          4.08           0.00 
  PIGZ MUTATED PIGZ WILD-TYPE 
         34.68         122.30 
  PIGZ MUTATED PIGZ WILD-TYPE 
         16.88          14.27 
[1] "4.1 - 34.7 (16.9)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D948V2, 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       2       15       40       30        36        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIGZ MUTATED           0          3          1          0        0
  PIGZ WILD-TYPE         3         67         52         32       38
D948V3, multiclass
            clus
vv           PIGZ MUTATED PIGZ WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PIGZ MUTATED     0   0   7   1
  PIGZ WILD-TYPE  22  92 166  96
D948V4, multiclass
    clus
vv   PIGZ MUTATED PIGZ WILD-TYPE
  T1            0             22
  T2            0             92
  T3            7            166
  T4            1             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
  PIGZ MUTATED     2   4   1   1
  PIGZ WILD-TYPE 116 100  76  76
D948V5, multiclass
    clus
vv   PIGZ MUTATED PIGZ WILD-TYPE
  N0            2            116
  N1            4            100
  N2            1             76
  N3            1             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"
D948V6, binary
                cls
clus               0   1
  PIGZ MUTATED     8   0
  PIGZ WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGZ MUTATED      8    0
  PIGZ WILD-TYPE  338   29
   clus
vv  PIGZ MUTATED PIGZ WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D948V7, binary
                cls
clus               0   1
  PIGZ MUTATED     6   3
  PIGZ WILD-TYPE 139 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGZ MUTATED      6    3
  PIGZ WILD-TYPE  139  245
        clus
vv       PIGZ MUTATED PIGZ WILD-TYPE
  FEMALE            6            139
  MALE              3            245
[1] 2 2
[1] FALSE
D948V8, binary
                cls
clus               0   1
  PIGZ MUTATED     8   0
  PIGZ WILD-TYPE 284  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGZ MUTATED      8    0
  PIGZ WILD-TYPE  284   59
     clus
vv    PIGZ MUTATED PIGZ WILD-TYPE
  NO             8            284
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PIGZ MUTATED                                          0
  PIGZ WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PIGZ MUTATED                                       3
  PIGZ WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIGZ MUTATED                                                        4
  PIGZ WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PIGZ MUTATED                                                   0
  PIGZ WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIGZ MUTATED                                                                   0
  PIGZ WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PIGZ MUTATED                                                    0
  PIGZ WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PIGZ MUTATED                                                  2
  PIGZ WILD-TYPE                                               59
D948V9, multiclass
                                                                   clus
vv                                                                  PIGZ MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  PIGZ WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PIGZ MUTATED     5   0   0   3
  PIGZ WILD-TYPE 306  14  15  21
D948V10, multiclass
    clus
vv   PIGZ MUTATED PIGZ WILD-TYPE
  R0            5            306
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D948V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PIGZ MUTATED       4                         0
  PIGZ WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIGZ MUTATED                                           0     5
  PIGZ WILD-TYPE                                         1   238
D948V12, multiclass
                                           clus
vv                                          PIGZ MUTATED PIGZ WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D948V13, binary
                cls
clus               0   1
  PIGZ MUTATED     0   9
  PIGZ WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGZ MUTATED      0    9
  PIGZ WILD-TYPE    4  301
                        clus
vv                       PIGZ MUTATED PIGZ WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(949) Variable = SPATA2L MUTATION ANALYSIS
D949V1, survival
                   sevent
clus2                 0   1
  SPATA2L MUTATED     4   1
  SPATA2L WILD-TYPE 226 138
  SPATA2L MUTATED SPATA2L WILD-TYPE 
                5               364 
  SPATA2L MUTATED SPATA2L WILD-TYPE 
                1               138 
$`SPATA2L MUTATED`
TCGA-BR-6452 TCGA-BR-8360 TCGA-CD-A4MG TCGA-CG-5721 TCGA-MX-A5UJ 
       34.68         6.18         6.58         6.02        19.73 

$`SPATA2L WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  SPATA2L MUTATED SPATA2L WILD-TYPE 
             6.02              0.00 
  SPATA2L MUTATED SPATA2L WILD-TYPE 
            34.68            122.30 
  SPATA2L MUTATED SPATA2L WILD-TYPE 
             6.58             14.35 
[1] "6.0 - 34.7 (6.6)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D949V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPATA2L MUTATED         0        0        0        0         3         0
  SPATA2L WILD-TYPE       2       15       40       30        34        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPATA2L MUTATED           0          1          0          0        2
  SPATA2L WILD-TYPE         3         69         53         32       36
D949V3, multiclass
            clus
vv           SPATA2L MUTATED SPATA2L WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                3                34
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SPATA2L MUTATED     0   0   4   2
  SPATA2L WILD-TYPE  22  92 169  95
D949V4, multiclass
    clus
vv   SPATA2L MUTATED SPATA2L WILD-TYPE
  T1               0                22
  T2               0                92
  T3               4               169
  T4               2                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
  SPATA2L MUTATED     3   1   2   0
  SPATA2L WILD-TYPE 115 103  75  77
D949V5, multiclass
    clus
vv   SPATA2L MUTATED SPATA2L WILD-TYPE
  N0               3               115
  N1               1               103
  N2               2                75
  N3               0                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"
D949V6, binary
                   cls
clus                  0   1
  SPATA2L MUTATED     6   0
  SPATA2L WILD-TYPE 340  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA2L MUTATED      6    0
  SPATA2L WILD-TYPE  340   29
   clus
vv  SPATA2L MUTATED SPATA2L WILD-TYPE
  0               6               340
  1               0                29
[1] 2 2
[1] FALSE
D949V7, binary
                   cls
clus                  0   1
  SPATA2L MUTATED     3   3
  SPATA2L WILD-TYPE 142 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA2L MUTATED      3    3
  SPATA2L WILD-TYPE  142  245
        clus
vv       SPATA2L MUTATED SPATA2L WILD-TYPE
  FEMALE               3               142
  MALE                 3               245
[1] 2 2
[1] FALSE
D949V8, binary
                   cls
clus                  0   1
  SPATA2L MUTATED     5   0
  SPATA2L WILD-TYPE 287  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA2L MUTATED      5    0
  SPATA2L WILD-TYPE  287   59
     clus
vv    SPATA2L MUTATED SPATA2L WILD-TYPE
  NO                5               287
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SPATA2L MUTATED                                          0
  SPATA2L WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SPATA2L MUTATED                                       1
  SPATA2L WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPATA2L MUTATED                                                        2
  SPATA2L WILD-TYPE                                                    156
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SPATA2L MUTATED                                                   0
  SPATA2L WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPATA2L MUTATED                                                                   2
  SPATA2L WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SPATA2L MUTATED                                                    0
  SPATA2L WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SPATA2L MUTATED                                                  1
  SPATA2L WILD-TYPE                                               60
D949V9, multiclass
                                                                   clus
vv                                                                  SPATA2L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  SPATA2L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SPATA2L MUTATED     4   0   0   1
  SPATA2L WILD-TYPE 307  14  15  23
D949V10, multiclass
    clus
vv   SPATA2L MUTATED SPATA2L WILD-TYPE
  R0               4               307
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D949V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SPATA2L MUTATED       1                         0
  SPATA2L WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPATA2L MUTATED                                           0     4
  SPATA2L WILD-TYPE                                         1   239
D949V12, multiclass
                                           clus
vv                                          SPATA2L MUTATED SPATA2L WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D949V13, binary
                   cls
clus                  0   1
  SPATA2L MUTATED     0   5
  SPATA2L WILD-TYPE   4 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA2L MUTATED      0    5
  SPATA2L WILD-TYPE    4  305
                        clus
vv                       SPATA2L MUTATED SPATA2L WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(950) Variable = SLC9A1 MUTATION ANALYSIS
D950V1, survival
                  sevent
clus2                0   1
  SLC9A1 MUTATED     7   4
  SLC9A1 WILD-TYPE 223 135
  SLC9A1 MUTATED SLC9A1 WILD-TYPE 
              11              358 
  SLC9A1 MUTATED SLC9A1 WILD-TYPE 
               4              135 
$`SLC9A1 MUTATED`
TCGA-CG-4460 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-A4QL 
       21.99        30.90         9.34        34.68        44.94        16.14 
TCGA-CD-A4MJ TCGA-CG-5728 TCGA-D7-A4YY TCGA-FP-A4BE TCGA-HF-7132 
       12.62        65.10        13.78        11.08        77.29 

$`SLC9A1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-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 

  SLC9A1 MUTATED SLC9A1 WILD-TYPE 
            9.34             0.00 
  SLC9A1 MUTATED SLC9A1 WILD-TYPE 
           77.29           122.30 
  SLC9A1 MUTATED SLC9A1 WILD-TYPE 
           21.99            14.12 
[1] "9.3 - 77.3 (22.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D950V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC9A1 MUTATED         0        0        2        1         3         0
  SLC9A1 WILD-TYPE       2       15       38       29        34        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A1 MUTATED           0          0          2          0        1
  SLC9A1 WILD-TYPE         3         70         51         32       37
D950V3, multiclass
            clus
vv           SLC9A1 MUTATED SLC9A1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              2               51
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLC9A1 MUTATED     0   4   5   1
  SLC9A1 WILD-TYPE  22  88 168  96
D950V4, multiclass
    clus
vv   SLC9A1 MUTATED SLC9A1 WILD-TYPE
  T1              0               22
  T2              4               88
  T3              5              168
  T4              1               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
  SLC9A1 MUTATED     5   3   0   2
  SLC9A1 WILD-TYPE 113 101  77  75
D950V5, multiclass
    clus
vv   SLC9A1 MUTATED SLC9A1 WILD-TYPE
  N0              5              113
  N1              3              101
  N2              0               77
  N3              2               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"
D950V6, binary
                  cls
clus                 0   1
  SLC9A1 MUTATED    11   1
  SLC9A1 WILD-TYPE 335  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A1 MUTATED     11    1
  SLC9A1 WILD-TYPE  335   28
   clus
vv  SLC9A1 MUTATED SLC9A1 WILD-TYPE
  0             11              335
  1              1               28
[1] 2 2
[1] FALSE
D950V7, binary
                  cls
clus                 0   1
  SLC9A1 MUTATED     6   6
  SLC9A1 WILD-TYPE 139 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A1 MUTATED      6    6
  SLC9A1 WILD-TYPE  139  242
        clus
vv       SLC9A1 MUTATED SLC9A1 WILD-TYPE
  FEMALE              6              139
  MALE                6              242
[1] 2 2
[1] FALSE
D950V8, binary
                  cls
clus                 0   1
  SLC9A1 MUTATED     7   3
  SLC9A1 WILD-TYPE 285  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A1 MUTATED      7    3
  SLC9A1 WILD-TYPE  285   56
     clus
vv    SLC9A1 MUTATED SLC9A1 WILD-TYPE
  NO               7              285
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC9A1 MUTATED                                          0
  SLC9A1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC9A1 MUTATED                                       0
  SLC9A1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC9A1 MUTATED                                                        9
  SLC9A1 WILD-TYPE                                                    149
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC9A1 MUTATED                                                   1
  SLC9A1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC9A1 MUTATED                                                                   2
  SLC9A1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC9A1 MUTATED                                                    0
  SLC9A1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC9A1 MUTATED                                                  0
  SLC9A1 WILD-TYPE                                               61
D950V9, multiclass
                                                                   clus
vv                                                                  SLC9A1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  SLC9A1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SLC9A1 MUTATED     7   0   1   3
  SLC9A1 WILD-TYPE 304  14  14  21
D950V10, multiclass
    clus
vv   SLC9A1 MUTATED SLC9A1 WILD-TYPE
  R0              7              304
  R1              0               14
  R2              1               14
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D950V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SLC9A1 MUTATED       1                         1
  SLC9A1 WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC9A1 MUTATED                                           0     7
  SLC9A1 WILD-TYPE                                         1   236
D950V12, multiclass
                                           clus
vv                                          SLC9A1 MUTATED SLC9A1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D950V13, binary
                  cls
clus                 0   1
  SLC9A1 MUTATED     0   9
  SLC9A1 WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A1 MUTATED      0    9
  SLC9A1 WILD-TYPE    4  301
                        clus
vv                       SLC9A1 MUTATED SLC9A1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(951) Variable = PAQR9 MUTATION ANALYSIS
D951V1, survival
                 sevent
clus2               0   1
  PAQR9 MUTATED     8   6
  PAQR9 WILD-TYPE 222 133
  PAQR9 MUTATED PAQR9 WILD-TYPE 
             14             355 
  PAQR9 MUTATED PAQR9 WILD-TYPE 
              6             133 
$`PAQR9 MUTATED`
TCGA-BR-7723 TCGA-BR-8297 TCGA-BR-8361 TCGA-CD-A486 TCGA-CG-4305 TCGA-CG-5725 
       28.73         7.40        31.10         6.31        15.95        15.02 
TCGA-D7-A6EY TCGA-F1-6875 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-MX-A5UJ TCGA-R5-A7O7 
       11.44        72.23        24.20        29.98        19.73        45.67 
TCGA-VQ-A8PE TCGA-VQ-A92D 
       22.19        66.81 

$`PAQR9 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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-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-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 

  PAQR9 MUTATED PAQR9 WILD-TYPE 
           6.31            0.00 
  PAQR9 MUTATED PAQR9 WILD-TYPE 
          72.23          122.30 
  PAQR9 MUTATED PAQR9 WILD-TYPE 
         23.195          14.040 
[1] "6.3 - 72.2 (23.2)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.2"
D951V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PAQR9 MUTATED         0        2        2        1         2         0
  PAQR9 WILD-TYPE       2       13       38       29        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAQR9 MUTATED           0          2          3          2        1
  PAQR9 WILD-TYPE         3         68         50         30       37
D951V3, multiclass
            clus
vv           PAQR9 MUTATED PAQR9 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             3              50
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PAQR9 MUTATED     2   5   6   3
  PAQR9 WILD-TYPE  20  87 167  94
D951V4, multiclass
    clus
vv   PAQR9 MUTATED PAQR9 WILD-TYPE
  T1             2              20
  T2             5              87
  T3             6             167
  T4             3              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
  PAQR9 MUTATED     6   3   2   4
  PAQR9 WILD-TYPE 112 101  75  73
D951V5, multiclass
    clus
vv   PAQR9 MUTATED PAQR9 WILD-TYPE
  N0             6             112
  N1             3             101
  N2             2              75
  N3             4              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"
D951V6, binary
                 cls
clus                0   1
  PAQR9 MUTATED    15   1
  PAQR9 WILD-TYPE 331  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAQR9 MUTATED     15    1
  PAQR9 WILD-TYPE  331   28
   clus
vv  PAQR9 MUTATED PAQR9 WILD-TYPE
  0            15             331
  1             1              28
[1] 2 2
[1] FALSE
D951V7, binary
                 cls
clus                0   1
  PAQR9 MUTATED     6  10
  PAQR9 WILD-TYPE 139 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAQR9 MUTATED      6   10
  PAQR9 WILD-TYPE  139  238
        clus
vv       PAQR9 MUTATED PAQR9 WILD-TYPE
  FEMALE             6             139
  MALE              10             238
[1] 2 2
[1] FALSE
D951V8, binary
                 cls
clus                0   1
  PAQR9 MUTATED    14   0
  PAQR9 WILD-TYPE 278  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAQR9 MUTATED     14    0
  PAQR9 WILD-TYPE  278   59
     clus
vv    PAQR9 MUTATED PAQR9 WILD-TYPE
  NO             14             278
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PAQR9 MUTATED                                          0
  PAQR9 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PAQR9 MUTATED                                       1
  PAQR9 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAQR9 MUTATED                                                        8
  PAQR9 WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PAQR9 MUTATED                                                   0
  PAQR9 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PAQR9 MUTATED                                                                   0
  PAQR9 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PAQR9 MUTATED                                                    0
  PAQR9 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PAQR9 MUTATED                                                  7
  PAQR9 WILD-TYPE                                               54
D951V9, multiclass
                                                                   clus
vv                                                                  PAQR9 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              7
                                                                   clus
vv                                                                  PAQR9 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PAQR9 MUTATED    12   0   0   2
  PAQR9 WILD-TYPE 299  14  15  22
D951V10, multiclass
    clus
vv   PAQR9 MUTATED PAQR9 WILD-TYPE
  R0            12             299
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D951V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PAQR9 MUTATED       3                         1
  PAQR9 WILD-TYPE    84                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PAQR9 MUTATED                                           0    10
  PAQR9 WILD-TYPE                                         1   233
D951V12, multiclass
                                           clus
vv                                          PAQR9 MUTATED PAQR9 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D951V13, binary
                 cls
clus                0   1
  PAQR9 MUTATED     1  11
  PAQR9 WILD-TYPE   3 299
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAQR9 MUTATED      1   11
  PAQR9 WILD-TYPE    3  299
                        clus
vv                       PAQR9 MUTATED PAQR9 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            11             299
[1] 2 2
[1] FALSE

Clustering(952) Variable = BTBD10 MUTATION ANALYSIS
D952V1, survival
                  sevent
clus2                0   1
  BTBD10 MUTATED     1   4
  BTBD10 WILD-TYPE 229 135
  BTBD10 MUTATED BTBD10 WILD-TYPE 
               5              364 
  BTBD10 MUTATED BTBD10 WILD-TYPE 
               4              135 
$`BTBD10 MUTATED`
TCGA-CG-4460 TCGA-BR-4257 TCGA-BR-8080 TCGA-HJ-7597 TCGA-VQ-A8P2 
       21.99         9.67         9.60        26.47        38.14 

$`BTBD10 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  BTBD10 MUTATED BTBD10 WILD-TYPE 
             9.6              0.0 
  BTBD10 MUTATED BTBD10 WILD-TYPE 
           38.14           122.30 
  BTBD10 MUTATED BTBD10 WILD-TYPE 
           21.99            14.22 
[1] "9.6 - 38.1 (22.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.8"
D952V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BTBD10 MUTATED         0        0        1        0         0         0
  BTBD10 WILD-TYPE       2       15       39       30        37        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTBD10 MUTATED           0          1          0          1        1
  BTBD10 WILD-TYPE         3         69         53         31       37
D952V3, multiclass
            clus
vv           BTBD10 MUTATED BTBD10 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BTBD10 MUTATED     0   1   0   3
  BTBD10 WILD-TYPE  22  91 173  94
D952V4, multiclass
    clus
vv   BTBD10 MUTATED BTBD10 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              0              173
  T4              3               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
  BTBD10 MUTATED     1   2   0   1
  BTBD10 WILD-TYPE 117 102  77  76
D952V5, multiclass
    clus
vv   BTBD10 MUTATED BTBD10 WILD-TYPE
  N0              1              117
  N1              2              102
  N2              0               77
  N3              1               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"
D952V6, binary
                  cls
clus                 0   1
  BTBD10 MUTATED     3   1
  BTBD10 WILD-TYPE 343  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD10 MUTATED      3    1
  BTBD10 WILD-TYPE  343   28
   clus
vv  BTBD10 MUTATED BTBD10 WILD-TYPE
  0              3              343
  1              1               28
[1] 2 2
[1] FALSE
D952V7, binary
                  cls
clus                 0   1
  BTBD10 MUTATED     4   1
  BTBD10 WILD-TYPE 141 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD10 MUTATED      4    1
  BTBD10 WILD-TYPE  141  247
        clus
vv       BTBD10 MUTATED BTBD10 WILD-TYPE
  FEMALE              4              141
  MALE                1              247
[1] 2 2
[1] FALSE
D952V8, binary
                  cls
clus                 0   1
  BTBD10 MUTATED     4   1
  BTBD10 WILD-TYPE 288  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD10 MUTATED      4    1
  BTBD10 WILD-TYPE  288   58
     clus
vv    BTBD10 MUTATED BTBD10 WILD-TYPE
  NO               4              288
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BTBD10 MUTATED                                          1
  BTBD10 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BTBD10 MUTATED                                       0
  BTBD10 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BTBD10 MUTATED                                                        1
  BTBD10 WILD-TYPE                                                    157
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BTBD10 MUTATED                                                   2
  BTBD10 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BTBD10 MUTATED                                                                   1
  BTBD10 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BTBD10 MUTATED                                                    0
  BTBD10 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BTBD10 MUTATED                                                  0
  BTBD10 WILD-TYPE                                               61
D952V9, multiclass
                                                                   clus
vv                                                                  BTBD10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  BTBD10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BTBD10 MUTATED     3   0   1   1
  BTBD10 WILD-TYPE 308  14  14  23
D952V10, multiclass
    clus
vv   BTBD10 MUTATED BTBD10 WILD-TYPE
  R0              3              308
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D952V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  BTBD10 MUTATED       0                         0
  BTBD10 WILD-TYPE    87                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BTBD10 MUTATED                                           0     4
  BTBD10 WILD-TYPE                                         1   239
D952V12, multiclass
                                           clus
vv                                          BTBD10 MUTATED BTBD10 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D952V13, binary
                  cls
clus                 0   1
  BTBD10 MUTATED     0   3
  BTBD10 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD10 MUTATED      0    3
  BTBD10 WILD-TYPE    4  307
                        clus
vv                       BTBD10 MUTATED BTBD10 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(953) Variable = RAB40B MUTATION ANALYSIS
D953V1, survival
                  sevent
clus2                0   1
  RAB40B MUTATED     5   0
  RAB40B WILD-TYPE 225 139
  RAB40B MUTATED RAB40B WILD-TYPE 
               5              364 
  RAB40B MUTATED RAB40B WILD-TYPE 
               0              139 
$`RAB40B MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-HF-7132 TCGA-HF-A5NB TCGA-VQ-AA6J 
       34.68        29.59        77.29        30.51        27.55 

$`RAB40B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  RAB40B MUTATED RAB40B WILD-TYPE 
           27.55             0.00 
  RAB40B MUTATED RAB40B WILD-TYPE 
           77.29           122.30 
  RAB40B MUTATED RAB40B WILD-TYPE 
           30.51            14.07 
[1] "27.6 - 77.3 (30.5)" "0.0 - 122.3 (14.1)"
[1] "hr="     "9400000"
D953V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAB40B MUTATED         0        0        1        1         1         1
  RAB40B WILD-TYPE       2       15       39       29        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAB40B MUTATED           0          1          1          1        0
  RAB40B WILD-TYPE         3         69         52         31       38
D953V3, multiclass
            clus
vv           RAB40B MUTATED RAB40B WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RAB40B MUTATED     0   2   1   4
  RAB40B WILD-TYPE  22  90 172  93
D953V4, multiclass
    clus
vv   RAB40B MUTATED RAB40B WILD-TYPE
  T1              0               22
  T2              2               90
  T3              1              172
  T4              4               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
  RAB40B MUTATED     4   2   1   1
  RAB40B WILD-TYPE 114 102  76  76
D953V5, multiclass
    clus
vv   RAB40B MUTATED RAB40B WILD-TYPE
  N0              4              114
  N1              2              102
  N2              1               76
  N3              1               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"
D953V6, binary
                  cls
clus                 0   1
  RAB40B MUTATED     8   0
  RAB40B WILD-TYPE 338  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB40B MUTATED      8    0
  RAB40B WILD-TYPE  338   29
   clus
vv  RAB40B MUTATED RAB40B WILD-TYPE
  0              8              338
  1              0               29
[1] 2 2
[1] FALSE
D953V7, binary
                  cls
clus                 0   1
  RAB40B MUTATED     5   3
  RAB40B WILD-TYPE 140 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB40B MUTATED      5    3
  RAB40B WILD-TYPE  140  245
        clus
vv       RAB40B MUTATED RAB40B WILD-TYPE
  FEMALE              5              140
  MALE                3              245
[1] 2 2
[1] FALSE
D953V8, binary
                  cls
clus                 0   1
  RAB40B MUTATED     3   2
  RAB40B WILD-TYPE 289  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB40B MUTATED      3    2
  RAB40B WILD-TYPE  289   57
     clus
vv    RAB40B MUTATED RAB40B WILD-TYPE
  NO               3              289
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RAB40B MUTATED                                          0
  RAB40B WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RAB40B MUTATED                                       0
  RAB40B WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RAB40B MUTATED                                                        4
  RAB40B WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RAB40B MUTATED                                                   2
  RAB40B WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RAB40B MUTATED                                                                   2
  RAB40B WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RAB40B MUTATED                                                    0
  RAB40B WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RAB40B MUTATED                                                  0
  RAB40B WILD-TYPE                                               61
D953V9, multiclass
                                                                   clus
vv                                                                  RAB40B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  RAB40B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RAB40B MUTATED     5   1   0   2
  RAB40B WILD-TYPE 306  13  15  22
D953V10, multiclass
    clus
vv   RAB40B MUTATED RAB40B WILD-TYPE
  R0              5              306
  R1              1               13
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D953V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  RAB40B MUTATED       0                         1
  RAB40B WILD-TYPE    87                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAB40B MUTATED                                           0     4
  RAB40B WILD-TYPE                                         1   239
D953V12, multiclass
                                           clus
vv                                          RAB40B MUTATED RAB40B WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D953V13, binary
                  cls
clus                 0   1
  RAB40B MUTATED     0   4
  RAB40B WILD-TYPE   4 306
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB40B MUTATED      0    4
  RAB40B WILD-TYPE    4  306
                        clus
vv                       RAB40B MUTATED RAB40B WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              306
[1] 2 2
[1] FALSE

Clustering(954) Variable = CSNK1G3 MUTATION ANALYSIS
D954V1, survival
                   sevent
clus2                 0   1
  CSNK1G3 MUTATED     6   2
  CSNK1G3 WILD-TYPE 224 137
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                8               361 
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                2               137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  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            14.270 
[1] "0.1 - 77.3 (14.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.6"
D954V2, 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       1       15       40       29        35        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK1G3 MUTATED           0          1          0          1        1
  CSNK1G3 WILD-TYPE         3         69         53         31       37
D954V3, multiclass
            clus
vv           CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 1                29
  STAGE IIA                2                35
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CSNK1G3 MUTATED     1   1   3   4
  CSNK1G3 WILD-TYPE  21  91 170  93
D954V4, multiclass
    clus
vv   CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  T1               1                21
  T2               1                91
  T3               3               170
  T4               4                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
  CSNK1G3 MUTATED     4   4   1   0
  CSNK1G3 WILD-TYPE 114 100  76  77
D954V5, multiclass
    clus
vv   CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  N0               4               114
  N1               4               100
  N2               1                76
  N3               0                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"
D954V6, binary
                   cls
clus                  0   1
  CSNK1G3 MUTATED     7   0
  CSNK1G3 WILD-TYPE 339  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      7    0
  CSNK1G3 WILD-TYPE  339   29
   clus
vv  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  0               7               339
  1               0                29
[1] 2 2
[1] FALSE
D954V7, binary
                   cls
clus                  0   1
  CSNK1G3 MUTATED     4   5
  CSNK1G3 WILD-TYPE 141 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      4    5
  CSNK1G3 WILD-TYPE  141  243
        clus
vv       CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  FEMALE               4               141
  MALE                 5               243
[1] 2 2
[1] FALSE
D954V8, binary
                   cls
clus                  0   1
  CSNK1G3 MUTATED     8   1
  CSNK1G3 WILD-TYPE 284  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      8    1
  CSNK1G3 WILD-TYPE  284   58
     clus
vv    CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  NO                8               284
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CSNK1G3 MUTATED                                          0
  CSNK1G3 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CSNK1G3 MUTATED                                       1
  CSNK1G3 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CSNK1G3 MUTATED                                                        5
  CSNK1G3 WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CSNK1G3 MUTATED                                                   1
  CSNK1G3 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CSNK1G3 MUTATED                                                                   1
  CSNK1G3 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CSNK1G3 MUTATED                                                    0
  CSNK1G3 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CSNK1G3 MUTATED                                                  1
  CSNK1G3 WILD-TYPE                                               60
D954V9, multiclass
                                                                   clus
vv                                                                  CSNK1G3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  CSNK1G3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CSNK1G3 MUTATED     8   0   0   1
  CSNK1G3 WILD-TYPE 303  14  15  23
D954V10, multiclass
    clus
vv   CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  R0               8               303
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D954V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CSNK1G3 MUTATED       2                         1
  CSNK1G3 WILD-TYPE    85                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CSNK1G3 MUTATED                                           0     4
  CSNK1G3 WILD-TYPE                                         1   239
D954V12, multiclass
                                           clus
vv                                          CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D954V13, binary
                   cls
clus                  0   1
  CSNK1G3 MUTATED     0   7
  CSNK1G3 WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      0    7
  CSNK1G3 WILD-TYPE    4  303
                        clus
vv                       CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(955) Variable = ITGB8 MUTATION ANALYSIS
D955V1, survival
                 sevent
clus2               0   1
  ITGB8 MUTATED     8   6
  ITGB8 WILD-TYPE 222 133
  ITGB8 MUTATED ITGB8 WILD-TYPE 
             14             355 
  ITGB8 MUTATED ITGB8 WILD-TYPE 
              6             133 
$`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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         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-F1-6875 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-8244 
       77.29        63.06        52.21        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-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 

  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          14.070 
[1] "1.0 - 34.7 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D955V2, 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       2       15       37       29        35        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ITGB8 MUTATED           0          1          0          2        3
  ITGB8 WILD-TYPE         3         69         53         30       35
D955V3, multiclass
            clus
vv           ITGB8 MUTATED ITGB8 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGB8 MUTATED     0   4   4   7
  ITGB8 WILD-TYPE  22  88 169  90
D955V4, multiclass
    clus
vv   ITGB8 MUTATED ITGB8 WILD-TYPE
  T1             0              22
  T2             4              88
  T3             4             169
  T4             7              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
  ITGB8 MUTATED     8   3   2   2
  ITGB8 WILD-TYPE 110 101  75  75
D955V5, multiclass
    clus
vv   ITGB8 MUTATED ITGB8 WILD-TYPE
  N0             8             110
  N1             3             101
  N2             2              75
  N3             2              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"
D955V6, binary
                 cls
clus                0   1
  ITGB8 MUTATED    11   3
  ITGB8 WILD-TYPE 335  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB8 MUTATED     11    3
  ITGB8 WILD-TYPE  335   26
   clus
vv  ITGB8 MUTATED ITGB8 WILD-TYPE
  0            11             335
  1             3              26
[1] 2 2
[1] FALSE
D955V7, binary
                 cls
clus                0   1
  ITGB8 MUTATED     9   6
  ITGB8 WILD-TYPE 136 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB8 MUTATED      9    6
  ITGB8 WILD-TYPE  136  242
        clus
vv       ITGB8 MUTATED ITGB8 WILD-TYPE
  FEMALE             9             136
  MALE               6             242
[1] 2 2
[1] FALSE
D955V8, binary
                 cls
clus                0   1
  ITGB8 MUTATED    12   1
  ITGB8 WILD-TYPE 280  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB8 MUTATED     12    1
  ITGB8 WILD-TYPE  280   58
     clus
vv    ITGB8 MUTATED ITGB8 WILD-TYPE
  NO             12             280
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ITGB8 MUTATED                                          1
  ITGB8 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ITGB8 MUTATED                                       3
  ITGB8 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ITGB8 MUTATED                                                        3
  ITGB8 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ITGB8 MUTATED                                                   0
  ITGB8 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ITGB8 MUTATED                                                                   4
  ITGB8 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ITGB8 MUTATED                                                    1
  ITGB8 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ITGB8 MUTATED                                                  3
  ITGB8 WILD-TYPE                                               58
D955V9, multiclass
                                                                   clus
vv                                                                  ITGB8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  ITGB8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ITGB8 MUTATED    12   0   1   0
  ITGB8 WILD-TYPE 299  14  14  24
D955V10, multiclass
    clus
vv   ITGB8 MUTATED ITGB8 WILD-TYPE
  R0            12             299
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D955V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ITGB8 MUTATED       4                         0
  ITGB8 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ITGB8 MUTATED                                           0     8
  ITGB8 WILD-TYPE                                         1   235
D955V12, multiclass
                                           clus
vv                                          ITGB8 MUTATED ITGB8 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D955V13, binary
                 cls
clus                0   1
  ITGB8 MUTATED     0  12
  ITGB8 WILD-TYPE   4 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB8 MUTATED      0   12
  ITGB8 WILD-TYPE    4  298
                        clus
vv                       ITGB8 MUTATED ITGB8 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(956) Variable = ADAMTS18 MUTATION ANALYSIS
D956V1, survival
                    sevent
clus2                  0   1
  ADAMTS18 MUTATED    13  13
  ADAMTS18 WILD-TYPE 217 126
  ADAMTS18 MUTATED ADAMTS18 WILD-TYPE 
                26                343 
  ADAMTS18 MUTATED ADAMTS18 WILD-TYPE 
                13                126 
$`ADAMTS18 MUTATED`
TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7717 TCGA-BR-8059 
       30.90         9.57        34.68        36.16        18.15        14.43 
TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8591 
        0.26        31.27        25.05         9.21         1.12        28.14 
TCGA-BR-8680 TCGA-CD-A4MJ TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-6818 TCGA-D7-A6EY 
       31.96        12.62        28.96        21.07        12.36        11.44 
TCGA-FP-A4BE TCGA-HF-7134 TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4H4 TCGA-IN-8663 
       11.08        52.21        22.32        24.20        23.84         3.39 
TCGA-RD-A8MW TCGA-VQ-A8PK 
       37.91        17.85 

$`ADAMTS18 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-7704 TCGA-BR-7707 TCGA-BR-7715 
       44.94        21.90         9.21        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-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-8486 
       14.79         7.36         3.72         5.39        25.18        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-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-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       15.02        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-D7-6820 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-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB 
        0.56         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-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-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-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-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 

  ADAMTS18 MUTATED ADAMTS18 WILD-TYPE 
              0.26               0.00 
  ADAMTS18 MUTATED ADAMTS18 WILD-TYPE 
             52.21             122.30 
  ADAMTS18 MUTATED ADAMTS18 WILD-TYPE 
            21.695             14.040 
[1] "0.3 - 52.2 (21.7)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.1"
D956V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ADAMTS18 MUTATED         0        4        3        1         3         3
  ADAMTS18 WILD-TYPE       2       11       37       29        34        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAMTS18 MUTATED           1          3          3          4        2
  ADAMTS18 WILD-TYPE         2         67         50         28       36
D956V3, multiclass
            clus
vv           ADAMTS18 MUTATED ADAMTS18 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  4                 11
  STAGE IB                  3                 37
  STAGE II                  1                 29
  STAGE IIA                 3                 34
  STAGE IIB                 3                 49
  STAGE III                 1                  2
  STAGE IIIA                3                 67
  STAGE IIIB                3                 50
  STAGE IIIC                4                 28
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ADAMTS18 MUTATED     5   9   7   8
  ADAMTS18 WILD-TYPE  17  83 166  89
D956V4, multiclass
    clus
vv   ADAMTS18 MUTATED ADAMTS18 WILD-TYPE
  T1                5                 17
  T2                9                 83
  T3                7                166
  T4                8                 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
  ADAMTS18 MUTATED    11   4   5   7
  ADAMTS18 WILD-TYPE 107 100  72  70
D956V5, multiclass
    clus
vv   ADAMTS18 MUTATED ADAMTS18 WILD-TYPE
  N0               11                107
  N1                4                100
  N2                5                 72
  N3                7                 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"
D956V6, binary
                    cls
clus                   0   1
  ADAMTS18 MUTATED    28   1
  ADAMTS18 WILD-TYPE 318  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS18 MUTATED     28    1
  ADAMTS18 WILD-TYPE  318   28
   clus
vv  ADAMTS18 MUTATED ADAMTS18 WILD-TYPE
  0               28                318
  1                1                 28
[1] 2 2
[1] FALSE
D956V7, binary
                    cls
clus                   0   1
  ADAMTS18 MUTATED    12  17
  ADAMTS18 WILD-TYPE 133 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS18 MUTATED     12   17
  ADAMTS18 WILD-TYPE  133  231
        clus
vv       ADAMTS18 MUTATED ADAMTS18 WILD-TYPE
  FEMALE               12                133
  MALE                 17                231
[1] 2 2
[1] FALSE
D956V8, binary
                    cls
clus                   0   1
  ADAMTS18 MUTATED    22   4
  ADAMTS18 WILD-TYPE 270  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS18 MUTATED     22    4
  ADAMTS18 WILD-TYPE  270   55
     clus
vv    ADAMTS18 MUTATED ADAMTS18 WILD-TYPE
  NO                22                270
  YES                4                 55
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ADAMTS18 MUTATED                                          0
  ADAMTS18 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ADAMTS18 MUTATED                                       2
  ADAMTS18 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ADAMTS18 MUTATED                                                       15
  ADAMTS18 WILD-TYPE                                                    143
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ADAMTS18 MUTATED                                                   0
  ADAMTS18 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ADAMTS18 MUTATED                                                                   7
  ADAMTS18 WILD-TYPE                                                                61
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ADAMTS18 MUTATED                                                    1
  ADAMTS18 WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ADAMTS18 MUTATED                                                  4
  ADAMTS18 WILD-TYPE                                               57
D956V9, multiclass
                                                                   clus
vv                                                                  ADAMTS18 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          15
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                7
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 4
                                                                   clus
vv                                                                  ADAMTS18 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           143
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 61
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ADAMTS18 MUTATED    24   1   0   3
  ADAMTS18 WILD-TYPE 287  13  15  21
D956V10, multiclass
    clus
vv   ADAMTS18 MUTATED ADAMTS18 WILD-TYPE
  R0               24                287
  R1                1                 13
  R2                0                 15
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D956V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  ADAMTS18 MUTATED       5                         1
  ADAMTS18 WILD-TYPE    82                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ADAMTS18 MUTATED                                           0    18
  ADAMTS18 WILD-TYPE                                         1   225
D956V12, multiclass
                                           clus
vv                                          ADAMTS18 MUTATED ADAMTS18 WILD-TYPE
  ASIAN                                                    5                 82
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   18                225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D956V13, binary
                    cls
clus                   0   1
  ADAMTS18 MUTATED     0  23
  ADAMTS18 WILD-TYPE   4 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS18 MUTATED      0   23
  ADAMTS18 WILD-TYPE    4  287
                        clus
vv                       ADAMTS18 MUTATED ADAMTS18 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               23                287
[1] 2 2
[1] FALSE

Clustering(957) Variable = NPR3 MUTATION ANALYSIS
D957V1, survival
                sevent
clus2              0   1
  NPR3 MUTATED     7   1
  NPR3 WILD-TYPE 223 138
  NPR3 MUTATED NPR3 WILD-TYPE 
             8            361 
  NPR3 MUTATED NPR3 WILD-TYPE 
             1            138 
$`NPR3 MUTATED`
TCGA-BR-4184 TCGA-BR-8081 TCGA-BR-8680 TCGA-BR-A4J8 TCGA-CG-4305 TCGA-CG-5721 
        6.97        32.25        31.96        13.51        15.95         6.02 
TCGA-CG-5723 TCGA-HU-A4G8 
      105.07        22.68 

$`NPR3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  NPR3 MUTATED NPR3 WILD-TYPE 
          6.02           0.00 
  NPR3 MUTATED NPR3 WILD-TYPE 
        105.07         122.30 
  NPR3 MUTATED NPR3 WILD-TYPE 
        19.315         14.170 
[1] "6.0 - 105.1 (19.3)" "0.0 - 122.3 (14.2)"
[1] "hr=" "4"  
D957V2, 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       2       15       40       28        37        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NPR3 MUTATED           0          2          1          1        2
  NPR3 WILD-TYPE         3         68         52         31       36
D957V3, multiclass
            clus
vv           NPR3 MUTATED NPR3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              2             28
  STAGE IIA             0             37
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NPR3 MUTATED     0   2   3   5
  NPR3 WILD-TYPE  22  90 170  92
D957V4, multiclass
    clus
vv   NPR3 MUTATED NPR3 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            3            170
  T4            5             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
  NPR3 MUTATED     2   5   1   2
  NPR3 WILD-TYPE 116  99  76  75
D957V5, multiclass
    clus
vv   NPR3 MUTATED NPR3 WILD-TYPE
  N0            2            116
  N1            5             99
  N2            1             76
  N3            2             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"
D957V6, binary
                cls
clus               0   1
  NPR3 MUTATED     8   1
  NPR3 WILD-TYPE 338  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR3 MUTATED      8    1
  NPR3 WILD-TYPE  338   28
   clus
vv  NPR3 MUTATED NPR3 WILD-TYPE
  0            8            338
  1            1             28
[1] 2 2
[1] FALSE
D957V7, binary
                cls
clus               0   1
  NPR3 MUTATED     5   5
  NPR3 WILD-TYPE 140 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR3 MUTATED      5    5
  NPR3 WILD-TYPE  140  243
        clus
vv       NPR3 MUTATED NPR3 WILD-TYPE
  FEMALE            5            140
  MALE              5            243
[1] 2 2
[1] FALSE
D957V8, binary
                cls
clus               0   1
  NPR3 MUTATED     9   0
  NPR3 WILD-TYPE 283  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR3 MUTATED      9    0
  NPR3 WILD-TYPE  283   59
     clus
vv    NPR3 MUTATED NPR3 WILD-TYPE
  NO             9            283
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NPR3 MUTATED                                          0
  NPR3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NPR3 MUTATED                                       1
  NPR3 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NPR3 MUTATED                                                        7
  NPR3 WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NPR3 MUTATED                                                   0
  NPR3 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NPR3 MUTATED                                                                   1
  NPR3 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NPR3 MUTATED                                                    0
  NPR3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NPR3 MUTATED                                                  1
  NPR3 WILD-TYPE                                               60
D957V9, multiclass
                                                                   clus
vv                                                                  NPR3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  NPR3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NPR3 MUTATED     7   0   0   2
  NPR3 WILD-TYPE 304  14  15  22
D957V10, multiclass
    clus
vv   NPR3 MUTATED NPR3 WILD-TYPE
  R0            7            304
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D957V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NPR3 MUTATED       2                         0
  NPR3 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NPR3 MUTATED                                           0     5
  NPR3 WILD-TYPE                                         1   238
D957V12, multiclass
                                           clus
vv                                          NPR3 MUTATED NPR3 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D957V13, binary
                cls
clus               0   1
  NPR3 MUTATED     0   7
  NPR3 WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPR3 MUTATED      0    7
  NPR3 WILD-TYPE    4  303
                        clus
vv                       NPR3 MUTATED NPR3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(958) Variable = MTSS1L MUTATION ANALYSIS
D958V1, survival
                  sevent
clus2                0   1
  MTSS1L MUTATED     5   4
  MTSS1L WILD-TYPE 225 135
  MTSS1L MUTATED MTSS1L WILD-TYPE 
               9              360 
  MTSS1L MUTATED MTSS1L WILD-TYPE 
               4              135 
$`MTSS1L MUTATED`
TCGA-BR-6706 TCGA-BR-6802 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-A4QL TCGA-CD-A4MG 
       18.05        30.90        31.27         1.12        16.14         6.58 
TCGA-CG-4306 TCGA-HF-A5NB TCGA-HU-A4H3 
        1.02        30.51        29.00 

$`MTSS1L WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       32.78        25.61        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-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-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-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-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 

  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            14.12 
[1] "1.0 - 31.3 (18.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D958V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MTSS1L MUTATED         0        0        0        0         2         0
  MTSS1L WILD-TYPE       2       15       40       30        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MTSS1L MUTATED           0          2          1          3        1
  MTSS1L WILD-TYPE         3         68         52         29       37
D958V3, multiclass
            clus
vv           MTSS1L MUTATED MTSS1L WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              3               29
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MTSS1L MUTATED     0   0   7   3
  MTSS1L WILD-TYPE  22  92 166  94
D958V4, multiclass
    clus
vv   MTSS1L MUTATED MTSS1L WILD-TYPE
  T1              0               22
  T2              0               92
  T3              7              166
  T4              3               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
  MTSS1L MUTATED     2   1   2   4
  MTSS1L WILD-TYPE 116 103  75  73
D958V5, multiclass
    clus
vv   MTSS1L MUTATED MTSS1L WILD-TYPE
  N0              2              116
  N1              1              103
  N2              2               75
  N3              4               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"
D958V6, binary
                  cls
clus                 0   1
  MTSS1L MUTATED     8   1
  MTSS1L WILD-TYPE 338  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTSS1L MUTATED      8    1
  MTSS1L WILD-TYPE  338   28
   clus
vv  MTSS1L MUTATED MTSS1L WILD-TYPE
  0              8              338
  1              1               28
[1] 2 2
[1] FALSE
D958V7, binary
                  cls
clus                 0   1
  MTSS1L MUTATED     5   5
  MTSS1L WILD-TYPE 140 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTSS1L MUTATED      5    5
  MTSS1L WILD-TYPE  140  243
        clus
vv       MTSS1L MUTATED MTSS1L WILD-TYPE
  FEMALE              5              140
  MALE                5              243
[1] 2 2
[1] FALSE
D958V8, binary
                  cls
clus                 0   1
  MTSS1L MUTATED     6   1
  MTSS1L WILD-TYPE 286  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTSS1L MUTATED      6    1
  MTSS1L WILD-TYPE  286   58
     clus
vv    MTSS1L MUTATED MTSS1L WILD-TYPE
  NO               6              286
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MTSS1L MUTATED                                          0
  MTSS1L WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MTSS1L MUTATED                                       2
  MTSS1L WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MTSS1L MUTATED                                                        7
  MTSS1L WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MTSS1L MUTATED                                                   1
  MTSS1L WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MTSS1L MUTATED                                                                   0
  MTSS1L WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MTSS1L MUTATED                                                    0
  MTSS1L WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MTSS1L MUTATED                                                  0
  MTSS1L WILD-TYPE                                               61
D958V9, multiclass
                                                                   clus
vv                                                                  MTSS1L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  MTSS1L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MTSS1L MUTATED     6   1   1   1
  MTSS1L WILD-TYPE 305  13  14  23
D958V10, multiclass
    clus
vv   MTSS1L MUTATED MTSS1L WILD-TYPE
  R0              6              305
  R1              1               13
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D958V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MTSS1L MUTATED       2                         0
  MTSS1L WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MTSS1L MUTATED                                           0     6
  MTSS1L WILD-TYPE                                         1   237
D958V12, multiclass
                                           clus
vv                                          MTSS1L MUTATED MTSS1L WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D958V13, binary
                  cls
clus                 0   1
  MTSS1L MUTATED     0   8
  MTSS1L WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTSS1L MUTATED      0    8
  MTSS1L WILD-TYPE    4  302
                        clus
vv                       MTSS1L MUTATED MTSS1L WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(959) Variable = MINA MUTATION ANALYSIS
D959V1, survival
                sevent
clus2              0   1
  MINA MUTATED     4   4
  MINA WILD-TYPE 226 135
  MINA MUTATED MINA WILD-TYPE 
             8            361 
  MINA MUTATED MINA WILD-TYPE 
             4            135 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       32.94        54.12        26.04        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       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          14.17 
[1] "0.3 - 38.1 (20.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D959V2, 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       2       15       39       30        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MINA MUTATED           0          4          0          0        1
  MINA WILD-TYPE         3         66         53         32       37
D959V3, multiclass
            clus
vv           MINA MUTATED MINA WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            4             66
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MINA MUTATED     0   2   3   3
  MINA WILD-TYPE  22  90 170  94
D959V4, multiclass
    clus
vv   MINA MUTATED MINA WILD-TYPE
  T1            0             22
  T2            2             90
  T3            3            170
  T4            3             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
  MINA MUTATED     3   2   2   1
  MINA WILD-TYPE 115 102  75  76
D959V5, multiclass
    clus
vv   MINA MUTATED MINA WILD-TYPE
  N0            3            115
  N1            2            102
  N2            2             75
  N3            1             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"
D959V6, binary
                cls
clus               0   1
  MINA MUTATED     6   1
  MINA WILD-TYPE 340  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MINA MUTATED      6    1
  MINA WILD-TYPE  340   28
   clus
vv  MINA MUTATED MINA WILD-TYPE
  0            6            340
  1            1             28
[1] 2 2
[1] FALSE
D959V7, binary
                cls
clus               0   1
  MINA MUTATED     6   2
  MINA WILD-TYPE 139 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  MINA MUTATED      6    2
  MINA WILD-TYPE  139  246
        clus
vv       MINA MUTATED MINA WILD-TYPE
  FEMALE            6            139
  MALE              2            246
[1] 2 2
[1] FALSE
D959V8, binary
                cls
clus               0   1
  MINA MUTATED     6   1
  MINA WILD-TYPE 286  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  MINA MUTATED      6    1
  MINA WILD-TYPE  286   58
     clus
vv    MINA MUTATED MINA WILD-TYPE
  NO             6            286
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MINA MUTATED                                          0
  MINA WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MINA MUTATED                                       1
  MINA WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MINA MUTATED                                                        4
  MINA WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MINA MUTATED                                                   1
  MINA WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MINA MUTATED                                                                   1
  MINA WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MINA MUTATED                                                    0
  MINA WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MINA MUTATED                                                  1
  MINA WILD-TYPE                                               60
D959V9, multiclass
                                                                   clus
vv                                                                  MINA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  MINA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MINA MUTATED     6   0   1   1
  MINA WILD-TYPE 305  14  14  23
D959V10, multiclass
    clus
vv   MINA MUTATED MINA WILD-TYPE
  R0            6            305
  R1            0             14
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D959V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MINA MUTATED       0                         0
  MINA WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MINA MUTATED                                           0     6
  MINA WILD-TYPE                                         1   237
D959V12, multiclass
                                           clus
vv                                          MINA MUTATED MINA WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D959V13, binary
                cls
clus               0   1
  MINA MUTATED     0   5
  MINA WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  MINA MUTATED      0    5
  MINA WILD-TYPE    4  305
                        clus
vv                       MINA MUTATED MINA WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(960) Variable = CYTH3 MUTATION ANALYSIS
D960V1, survival
                 sevent
clus2               0   1
  CYTH3 MUTATED     2   3
  CYTH3 WILD-TYPE 228 136
  CYTH3 MUTATED CYTH3 WILD-TYPE 
              5             364 
  CYTH3 MUTATED CYTH3 WILD-TYPE 
              3             136 
$`CYTH3 MUTATED`
TCGA-CG-4460 TCGA-BR-4201 TCGA-CG-4306 TCGA-HU-A4GX TCGA-MX-A5UJ 
       21.99        30.90         1.02        20.25        19.73 

$`CYTH3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  CYTH3 MUTATED CYTH3 WILD-TYPE 
           1.02            0.00 
  CYTH3 MUTATED CYTH3 WILD-TYPE 
           30.9           122.3 
  CYTH3 MUTATED CYTH3 WILD-TYPE 
          20.25           14.12 
[1] "1.0 - 30.9 (20.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D960V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CYTH3 MUTATED         0        0        0        0         0         0
  CYTH3 WILD-TYPE       2       15       40       30        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYTH3 MUTATED           0          1          0          1        3
  CYTH3 WILD-TYPE         3         69         53         31       35
D960V3, multiclass
            clus
vv           CYTH3 MUTATED CYTH3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CYTH3 MUTATED     0   1   2   3
  CYTH3 WILD-TYPE  22  91 171  94
D960V4, multiclass
    clus
vv   CYTH3 MUTATED CYTH3 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             2             171
  T4             3              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
  CYTH3 MUTATED     0   1   4   0
  CYTH3 WILD-TYPE 118 103  73  77
D960V5, multiclass
    clus
vv   CYTH3 MUTATED CYTH3 WILD-TYPE
  N0             0             118
  N1             1             103
  N2             4              73
  N3             0              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"
D960V6, binary
                 cls
clus                0   1
  CYTH3 MUTATED     4   2
  CYTH3 WILD-TYPE 342  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH3 MUTATED      4    2
  CYTH3 WILD-TYPE  342   27
   clus
vv  CYTH3 MUTATED CYTH3 WILD-TYPE
  0             4             342
  1             2              27
[1] 2 2
[1] FALSE
D960V7, binary
                 cls
clus                0   1
  CYTH3 MUTATED     5   1
  CYTH3 WILD-TYPE 140 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH3 MUTATED      5    1
  CYTH3 WILD-TYPE  140  247
        clus
vv       CYTH3 MUTATED CYTH3 WILD-TYPE
  FEMALE             5             140
  MALE               1             247
[1] 2 2
[1] FALSE
D960V8, binary
                 cls
clus                0   1
  CYTH3 MUTATED     4   0
  CYTH3 WILD-TYPE 288  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH3 MUTATED      4    0
  CYTH3 WILD-TYPE  288   59
     clus
vv    CYTH3 MUTATED CYTH3 WILD-TYPE
  NO              4             288
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CYTH3 MUTATED                                          0
  CYTH3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CYTH3 MUTATED                                       1
  CYTH3 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CYTH3 MUTATED                                                        3
  CYTH3 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CYTH3 MUTATED                                                   0
  CYTH3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CYTH3 MUTATED                                                                   1
  CYTH3 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CYTH3 MUTATED                                                    0
  CYTH3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CYTH3 MUTATED                                                  1
  CYTH3 WILD-TYPE                                               60
D960V9, multiclass
                                                                   clus
vv                                                                  CYTH3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  CYTH3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CYTH3 MUTATED     2   0   2   2
  CYTH3 WILD-TYPE 309  14  13  22
D960V10, multiclass
    clus
vv   CYTH3 MUTATED CYTH3 WILD-TYPE
  R0             2             309
  R1             0              14
  R2             2              13
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D960V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CYTH3 MUTATED       1                         0
  CYTH3 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CYTH3 MUTATED                                           0     3
  CYTH3 WILD-TYPE                                         1   240
D960V12, multiclass
                                           clus
vv                                          CYTH3 MUTATED CYTH3 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D960V13, binary
                 cls
clus                0   1
  CYTH3 MUTATED     0   4
  CYTH3 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH3 MUTATED      0    4
  CYTH3 WILD-TYPE    4  306
                        clus
vv                       CYTH3 MUTATED CYTH3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(961) Variable = PCDH19 MUTATION ANALYSIS
D961V1, survival
                  sevent
clus2                0   1
  PCDH19 MUTATED    17   6
  PCDH19 WILD-TYPE 213 133
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              23              346 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
               6              133 
$`PCDH19 MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7957 
       26.70        34.68        19.33        44.94        35.84         9.07 
TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8372 TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-4306 
       31.10        14.04        31.27        31.96        15.95         1.02 
TCGA-CG-4465 TCGA-D7-8574 TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-F1-6874 TCGA-HF-7132 
        9.01        17.19        14.76        11.44        14.47        77.29 
TCGA-HF-A5NB TCGA-HU-A4G9 TCGA-HU-A4H4 TCGA-RD-A7BS TCGA-VQ-A8P3 
       30.51        24.20        23.84        11.05        37.22 

$`PCDH19 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-8370 TCGA-BR-8371 TCGA-BR-8373 
        0.95        26.33         4.31         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-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-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-D7-8575 
       11.31        12.33        24.72        16.80        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-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       36.43        13.78        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-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-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-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-A7BT TCGA-RD-A7BW 
       74.53         6.08         4.60         9.24         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-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 

  PCDH19 MUTATED PCDH19 WILD-TYPE 
            1.02             0.00 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
           77.29           122.30 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
           23.84            13.94 
[1] "1.0 - 77.3 (23.8)"  "0.0 - 122.3 (13.9)"
[1] "hr=" "2"  
D961V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PCDH19 MUTATED         0        1        3        2         2         4
  PCDH19 WILD-TYPE       2       14       37       28        35        48
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDH19 MUTATED           0          3          2          3        4
  PCDH19 WILD-TYPE         3         67         51         29       34
D961V3, multiclass
            clus
vv           PCDH19 MUTATED PCDH19 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                3               37
  STAGE II                2               28
  STAGE IIA               2               35
  STAGE IIB               4               48
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              2               51
  STAGE IIIC              3               29
  STAGE IV                4               34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PCDH19 MUTATED     1   8   9   7
  PCDH19 WILD-TYPE  21  84 164  90
D961V4, multiclass
    clus
vv   PCDH19 MUTATED PCDH19 WILD-TYPE
  T1              1               21
  T2              8               84
  T3              9              164
  T4              7               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
  PCDH19 MUTATED     7   6   5   7
  PCDH19 WILD-TYPE 111  98  72  70
D961V5, multiclass
    clus
vv   PCDH19 MUTATED PCDH19 WILD-TYPE
  N0              7              111
  N1              6               98
  N2              5               72
  N3              7               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
  PCDH19 MUTATED    21   4
  PCDH19 WILD-TYPE 325  25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     21    4
  PCDH19 WILD-TYPE  325   25
   clus
vv  PCDH19 MUTATED PCDH19 WILD-TYPE
  0             21              325
  1              4               25
[1] 2 2
[1] FALSE
D961V7, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    16  10
  PCDH19 WILD-TYPE 129 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     16   10
  PCDH19 WILD-TYPE  129  238
        clus
vv       PCDH19 MUTATED PCDH19 WILD-TYPE
  FEMALE             16              129
  MALE               10              238
[1] 2 2
[1] FALSE
D961V8, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    16   5
  PCDH19 WILD-TYPE 276  54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     16    5
  PCDH19 WILD-TYPE  276   54
     clus
vv    PCDH19 MUTATED PCDH19 WILD-TYPE
  NO              16              276
  YES              5               54
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PCDH19 MUTATED                                          0
  PCDH19 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PCDH19 MUTATED                                       3
  PCDH19 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PCDH19 MUTATED                                                       12
  PCDH19 WILD-TYPE                                                    146
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PCDH19 MUTATED                                                   3
  PCDH19 WILD-TYPE                                                18
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PCDH19 MUTATED                                                                   3
  PCDH19 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PCDH19 MUTATED                                                    0
  PCDH19 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PCDH19 MUTATED                                                  5
  PCDH19 WILD-TYPE                                               56
D961V9, multiclass
                                                                   clus
vv                                                                  PCDH19 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               5
                                                                   clus
vv                                                                  PCDH19 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PCDH19 MUTATED    21   1   2   2
  PCDH19 WILD-TYPE 290  13  13  22
D961V10, multiclass
    clus
vv   PCDH19 MUTATED PCDH19 WILD-TYPE
  R0             21              290
  R1              1               13
  R2              2               13
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D961V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PCDH19 MUTATED       3                         0
  PCDH19 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PCDH19 MUTATED                                           0    17
  PCDH19 WILD-TYPE                                         1   226
D961V12, multiclass
                                           clus
vv                                          PCDH19 MUTATED PCDH19 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 17              226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D961V13, binary
                  cls
clus                 0   1
  PCDH19 MUTATED     0  19
  PCDH19 WILD-TYPE   4 291
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED      0   19
  PCDH19 WILD-TYPE    4  291
                        clus
vv                       PCDH19 MUTATED PCDH19 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             19              291
[1] 2 2
[1] FALSE

Clustering(962) Variable = C11ORF88 MUTATION ANALYSIS
D962V1, survival
                    sevent
clus2                  0   1
  C11ORF88 MUTATED     6   0
  C11ORF88 WILD-TYPE 224 139
  C11ORF88 MUTATED C11ORF88 WILD-TYPE 
                 6                363 
  C11ORF88 MUTATED C11ORF88 WILD-TYPE 
                 0                139 
$`C11ORF88 MUTATED`
TCGA-BR-7703 TCGA-BR-8589 TCGA-BR-8680 TCGA-CG-5721 TCGA-HF-7132 TCGA-KB-A6F5 
       36.16        27.12        31.96         6.02        77.29         5.56 

$`C11ORF88 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  C11ORF88 MUTATED C11ORF88 WILD-TYPE 
              5.56               0.00 
  C11ORF88 MUTATED C11ORF88 WILD-TYPE 
             77.29             122.30 
  C11ORF88 MUTATED C11ORF88 WILD-TYPE 
             29.54              14.17 
[1] "5.6 - 77.3 (29.5)"  "0.0 - 122.3 (14.2)"
[1] "hr="     "9400000"
D962V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C11ORF88 MUTATED         0        1        0        1         0         0
  C11ORF88 WILD-TYPE       2       14       40       29        37        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C11ORF88 MUTATED           0          2          1          0        2
  C11ORF88 WILD-TYPE         3         68         52         32       36
D962V3, multiclass
            clus
vv           C11ORF88 MUTATED C11ORF88 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  0                 40
  STAGE II                  1                 29
  STAGE IIA                 0                 37
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                1                 52
  STAGE IIIC                0                 32
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C11ORF88 MUTATED     1   1   1   4
  C11ORF88 WILD-TYPE  21  91 172  93
D962V4, multiclass
    clus
vv   C11ORF88 MUTATED C11ORF88 WILD-TYPE
  T1                1                 21
  T2                1                 91
  T3                1                172
  T4                4                 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
  C11ORF88 MUTATED     2   3   2   0
  C11ORF88 WILD-TYPE 116 101  75  77
D962V5, multiclass
    clus
vv   C11ORF88 MUTATED C11ORF88 WILD-TYPE
  N0                2                116
  N1                3                101
  N2                2                 75
  N3                0                 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"
D962V6, binary
                    cls
clus                   0   1
  C11ORF88 MUTATED     6   1
  C11ORF88 WILD-TYPE 340  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF88 MUTATED      6    1
  C11ORF88 WILD-TYPE  340   28
   clus
vv  C11ORF88 MUTATED C11ORF88 WILD-TYPE
  0                6                340
  1                1                 28
[1] 2 2
[1] FALSE
D962V7, binary
                    cls
clus                   0   1
  C11ORF88 MUTATED     1   6
  C11ORF88 WILD-TYPE 144 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF88 MUTATED      1    6
  C11ORF88 WILD-TYPE  144  242
        clus
vv       C11ORF88 MUTATED C11ORF88 WILD-TYPE
  FEMALE                1                144
  MALE                  6                242
[1] 2 2
[1] FALSE
D962V8, binary
                    cls
clus                   0   1
  C11ORF88 MUTATED     5   1
  C11ORF88 WILD-TYPE 287  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF88 MUTATED      5    1
  C11ORF88 WILD-TYPE  287   58
     clus
vv    C11ORF88 MUTATED C11ORF88 WILD-TYPE
  NO                 5                287
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C11ORF88 MUTATED                                          0
  C11ORF88 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C11ORF88 MUTATED                                       0
  C11ORF88 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C11ORF88 MUTATED                                                        2
  C11ORF88 WILD-TYPE                                                    156
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C11ORF88 MUTATED                                                   1
  C11ORF88 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C11ORF88 MUTATED                                                                   2
  C11ORF88 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C11ORF88 MUTATED                                                    1
  C11ORF88 WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C11ORF88 MUTATED                                                  1
  C11ORF88 WILD-TYPE                                               60
D962V9, multiclass
                                                                   clus
vv                                                                  C11ORF88 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  C11ORF88 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C11ORF88 MUTATED     6   0   0   1
  C11ORF88 WILD-TYPE 305  14  15  23
D962V10, multiclass
    clus
vv   C11ORF88 MUTATED C11ORF88 WILD-TYPE
  R0                6                305
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D962V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C11ORF88 MUTATED       1                         0
  C11ORF88 WILD-TYPE    86                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C11ORF88 MUTATED                                           0     3
  C11ORF88 WILD-TYPE                                         1   240
D962V12, multiclass
                                           clus
vv                                          C11ORF88 MUTATED C11ORF88 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D962V13, binary
                    cls
clus                   0   1
  C11ORF88 MUTATED     0   4
  C11ORF88 WILD-TYPE   4 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF88 MUTATED      0    4
  C11ORF88 WILD-TYPE    4  306
                        clus
vv                       C11ORF88 MUTATED C11ORF88 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                4                306
[1] 2 2
[1] FALSE

Clustering(963) Variable = MON2 MUTATION ANALYSIS
D963V1, survival
                sevent
clus2              0   1
  MON2 MUTATED    11   3
  MON2 WILD-TYPE 219 136
  MON2 MUTATED MON2 WILD-TYPE 
            14            355 
  MON2 MUTATED MON2 WILD-TYPE 
             3            136 
$`MON2 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-6452 TCGA-BR-6852 
       26.70         6.97         9.34         9.57        34.68        44.94 
TCGA-BR-7196 TCGA-BR-8370 TCGA-BR-8680 TCGA-CG-5723 TCGA-HF-A5NB TCGA-HU-A4G8 
       21.90         3.32        31.96       105.07        30.51        22.68 
TCGA-HU-A4GT TCGA-VQ-A8P2 
        6.51        38.14 

$`MON2 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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 
         24.69          14.07 
[1] "3.3 - 105.1 (24.7)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.4"
D963V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MON2 MUTATED         0        0        1        2         3         2
  MON2 WILD-TYPE       2       15       39       28        34        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MON2 MUTATED           0          2          1          1        2
  MON2 WILD-TYPE         3         68         52         31       36
D963V3, multiclass
            clus
vv           MON2 MUTATED MON2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              2             28
  STAGE IIA             3             34
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MON2 MUTATED     1   3   7   4
  MON2 WILD-TYPE  21  89 166  93
D963V4, multiclass
    clus
vv   MON2 MUTATED MON2 WILD-TYPE
  T1            1             21
  T2            3             89
  T3            7            166
  T4            4             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
  MON2 MUTATED     5   6   1   3
  MON2 WILD-TYPE 113  98  76  74
D963V5, multiclass
    clus
vv   MON2 MUTATED MON2 WILD-TYPE
  N0            5            113
  N1            6             98
  N2            1             76
  N3            3             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"
D963V6, binary
                cls
clus               0   1
  MON2 MUTATED    13   2
  MON2 WILD-TYPE 333  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  MON2 MUTATED     13    2
  MON2 WILD-TYPE  333   27
   clus
vv  MON2 MUTATED MON2 WILD-TYPE
  0           13            333
  1            2             27
[1] 2 2
[1] FALSE
D963V7, binary
                cls
clus               0   1
  MON2 MUTATED     7   9
  MON2 WILD-TYPE 138 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  MON2 MUTATED      7    9
  MON2 WILD-TYPE  138  239
        clus
vv       MON2 MUTATED MON2 WILD-TYPE
  FEMALE            7            138
  MALE              9            239
[1] 2 2
[1] FALSE
D963V8, binary
                cls
clus               0   1
  MON2 MUTATED    12   2
  MON2 WILD-TYPE 280  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  MON2 MUTATED     12    2
  MON2 WILD-TYPE  280   57
     clus
vv    MON2 MUTATED MON2 WILD-TYPE
  NO            12            280
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MON2 MUTATED                                          0
  MON2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MON2 MUTATED                                       3
  MON2 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MON2 MUTATED                                                        8
  MON2 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MON2 MUTATED                                                   2
  MON2 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MON2 MUTATED                                                                   1
  MON2 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MON2 MUTATED                                                    0
  MON2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MON2 MUTATED                                                  2
  MON2 WILD-TYPE                                               59
D963V9, multiclass
                                                                   clus
vv                                                                  MON2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  MON2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MON2 MUTATED    10   1   0   4
  MON2 WILD-TYPE 301  13  15  20
D963V10, multiclass
    clus
vv   MON2 MUTATED MON2 WILD-TYPE
  R0           10            301
  R1            1             13
  R2            0             15
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D963V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MON2 MUTATED       3                         0
  MON2 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MON2 MUTATED                                           0    10
  MON2 WILD-TYPE                                         1   233
D963V12, multiclass
                                           clus
vv                                          MON2 MUTATED MON2 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               10            233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D963V13, binary
                cls
clus               0   1
  MON2 MUTATED     0  12
  MON2 WILD-TYPE   4 298
[1] "tbl2"
                cls
clus             [,1] [,2]
  MON2 MUTATED      0   12
  MON2 WILD-TYPE    4  298
                        clus
vv                       MON2 MUTATED MON2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           12            298
[1] 2 2
[1] FALSE

Clustering(964) Variable = AKD1 MUTATION ANALYSIS
D964V1, survival
                sevent
clus2              0   1
  AKD1 MUTATED    11   4
  AKD1 WILD-TYPE 219 135
  AKD1 MUTATED AKD1 WILD-TYPE 
            15            354 
  AKD1 MUTATED AKD1 WILD-TYPE 
             4            135 
$`AKD1 MUTATED`
TCGA-BR-6452 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4QL 
       34.68        31.27         1.12        28.14        31.96        16.14 
TCGA-CD-5801 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5721 TCGA-HF-A5NB TCGA-HU-A4GQ 
       13.18        15.95         1.02         6.02        30.51         0.10 
TCGA-HU-A4GY TCGA-R5-A7ZI TCGA-VQ-A8P2 
        0.26        74.53        38.14 

$`AKD1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  AKD1 MUTATED AKD1 WILD-TYPE 
           0.1            0.0 
  AKD1 MUTATED AKD1 WILD-TYPE 
         74.53         122.30 
  AKD1 MUTATED AKD1 WILD-TYPE 
         16.14          14.12 
[1] "0.1 - 74.5 (16.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D964V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AKD1 MUTATED         0        0        0        1         2         0
  AKD1 WILD-TYPE       2       15       40       29        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKD1 MUTATED           0          3          1          4        4
  AKD1 WILD-TYPE         3         67         52         28       34
D964V3, multiclass
            clus
vv           AKD1 MUTATED AKD1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            1             52
  STAGE IIIC            4             28
  STAGE IV              4             34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AKD1 MUTATED     0   1   5   9
  AKD1 WILD-TYPE  22  91 168  88
D964V4, multiclass
    clus
vv   AKD1 MUTATED AKD1 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            5            168
  T4            9             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
  AKD1 MUTATED     2   6   3   4
  AKD1 WILD-TYPE 116  98  74  73
D964V5, multiclass
    clus
vv   AKD1 MUTATED AKD1 WILD-TYPE
  N0            2            116
  N1            6             98
  N2            3             74
  N3            4             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"
D964V6, binary
                cls
clus               0   1
  AKD1 MUTATED    12   3
  AKD1 WILD-TYPE 334  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKD1 MUTATED     12    3
  AKD1 WILD-TYPE  334   26
   clus
vv  AKD1 MUTATED AKD1 WILD-TYPE
  0           12            334
  1            3             26
[1] 2 2
[1] FALSE
D964V7, binary
                cls
clus               0   1
  AKD1 MUTATED     6   9
  AKD1 WILD-TYPE 139 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKD1 MUTATED      6    9
  AKD1 WILD-TYPE  139  239
        clus
vv       AKD1 MUTATED AKD1 WILD-TYPE
  FEMALE            6            139
  MALE              9            239
[1] 2 2
[1] FALSE
D964V8, binary
                cls
clus               0   1
  AKD1 MUTATED    12   2
  AKD1 WILD-TYPE 280  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKD1 MUTATED     12    2
  AKD1 WILD-TYPE  280   57
     clus
vv    AKD1 MUTATED AKD1 WILD-TYPE
  NO            12            280
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AKD1 MUTATED                                          0
  AKD1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AKD1 MUTATED                                       2
  AKD1 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AKD1 MUTATED                                                        8
  AKD1 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AKD1 MUTATED                                                   2
  AKD1 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AKD1 MUTATED                                                                   1
  AKD1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AKD1 MUTATED                                                    0
  AKD1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AKD1 MUTATED                                                  2
  AKD1 WILD-TYPE                                               59
D964V9, multiclass
                                                                   clus
vv                                                                  AKD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  AKD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AKD1 MUTATED    13   1   1   0
  AKD1 WILD-TYPE 298  13  14  24
D964V10, multiclass
    clus
vv   AKD1 MUTATED AKD1 WILD-TYPE
  R0           13            298
  R1            1             13
  R2            1             14
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D964V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  AKD1 MUTATED       4                         0
  AKD1 WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AKD1 MUTATED                                           0     7
  AKD1 WILD-TYPE                                         1   236
D964V12, multiclass
                                           clus
vv                                          AKD1 MUTATED AKD1 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D964V13, binary
                cls
clus               0   1
  AKD1 MUTATED     1   9
  AKD1 WILD-TYPE   3 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKD1 MUTATED      1    9
  AKD1 WILD-TYPE    3  301
                        clus
vv                       AKD1 MUTATED AKD1 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(965) Variable = EXOSC8 MUTATION ANALYSIS
D965V1, survival
                  sevent
clus2                0   1
  EXOSC8 MUTATED     3   1
  EXOSC8 WILD-TYPE 227 138
  EXOSC8 MUTATED EXOSC8 WILD-TYPE 
               4              365 
  EXOSC8 MUTATED EXOSC8 WILD-TYPE 
               1              138 
$`EXOSC8 MUTATED`
TCGA-BR-4201 TCGA-BR-8078 TCGA-BR-8372 TCGA-HU-A4H4 
       30.90        29.59        31.27        23.84 

$`EXOSC8 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-5578 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-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-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 

  EXOSC8 MUTATED EXOSC8 WILD-TYPE 
           23.84             0.00 
  EXOSC8 MUTATED EXOSC8 WILD-TYPE 
           31.27           122.30 
  EXOSC8 MUTATED EXOSC8 WILD-TYPE 
          30.245           14.070 
[1] "23.8 - 31.3 (30.2)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.6"
D965V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EXOSC8 MUTATED         0        0        1        0         0         2
  EXOSC8 WILD-TYPE       2       15       39       30        37        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EXOSC8 MUTATED           0          1          0          1        0
  EXOSC8 WILD-TYPE         3         69         53         31       38
D965V3, multiclass
            clus
vv           EXOSC8 MUTATED EXOSC8 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EXOSC8 MUTATED     0   3   0   3
  EXOSC8 WILD-TYPE  22  89 173  94
D965V4, multiclass
    clus
vv   EXOSC8 MUTATED EXOSC8 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              0              173
  T4              3               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
  EXOSC8 MUTATED     3   0   1   1
  EXOSC8 WILD-TYPE 115 104  76  76
D965V5, multiclass
    clus
vv   EXOSC8 MUTATED EXOSC8 WILD-TYPE
  N0              3              115
  N1              0              104
  N2              1               76
  N3              1               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"
D965V6, binary
                  cls
clus                 0   1
  EXOSC8 MUTATED     6   0
  EXOSC8 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC8 MUTATED      6    0
  EXOSC8 WILD-TYPE  340   29
   clus
vv  EXOSC8 MUTATED EXOSC8 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D965V7, binary
                  cls
clus                 0   1
  EXOSC8 MUTATED     4   2
  EXOSC8 WILD-TYPE 141 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC8 MUTATED      4    2
  EXOSC8 WILD-TYPE  141  246
        clus
vv       EXOSC8 MUTATED EXOSC8 WILD-TYPE
  FEMALE              4              141
  MALE                2              246
[1] 2 2
[1] FALSE
D965V8, binary
                  cls
clus                 0   1
  EXOSC8 MUTATED     4   0
  EXOSC8 WILD-TYPE 288  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC8 MUTATED      4    0
  EXOSC8 WILD-TYPE  288   59
     clus
vv    EXOSC8 MUTATED EXOSC8 WILD-TYPE
  NO               4              288
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EXOSC8 MUTATED                                          0
  EXOSC8 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EXOSC8 MUTATED                                       0
  EXOSC8 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EXOSC8 MUTATED                                                        4
  EXOSC8 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EXOSC8 MUTATED                                                   0
  EXOSC8 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EXOSC8 MUTATED                                                                   1
  EXOSC8 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EXOSC8 MUTATED                                                    0
  EXOSC8 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EXOSC8 MUTATED                                                  1
  EXOSC8 WILD-TYPE                                               60
D965V9, multiclass
                                                                   clus
vv                                                                  EXOSC8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  EXOSC8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EXOSC8 MUTATED     4   0   0   2
  EXOSC8 WILD-TYPE 307  14  15  22
D965V10, multiclass
    clus
vv   EXOSC8 MUTATED EXOSC8 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D965V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  EXOSC8 MUTATED       1                         0
  EXOSC8 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EXOSC8 MUTATED                                           0     4
  EXOSC8 WILD-TYPE                                         1   239
D965V12, multiclass
                                           clus
vv                                          EXOSC8 MUTATED EXOSC8 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D965V13, binary
                  cls
clus                 0   1
  EXOSC8 MUTATED     0   5
  EXOSC8 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC8 MUTATED      0    5
  EXOSC8 WILD-TYPE    4  305
                        clus
vv                       EXOSC8 MUTATED EXOSC8 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(966) Variable = CDH11 MUTATION ANALYSIS
D966V1, survival
                 sevent
clus2               0   1
  CDH11 MUTATED    21   9
  CDH11 WILD-TYPE 209 130
  CDH11 MUTATED CDH11 WILD-TYPE 
             30             339 
  CDH11 MUTATED CDH11 WILD-TYPE 
              9             130 
$`CDH11 MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7197 
       26.70        19.56        30.90        34.68        44.94         9.21 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-8059 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8382 
       35.84        18.15        14.43        31.10        14.04        25.05 
TCGA-BR-A4IY TCGA-CD-8527 TCGA-CG-4306 TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-6527 
       12.89         7.17         1.02        12.03        12.66        10.26 
TCGA-D7-6822 TCGA-FP-A4BE TCGA-HF-7132 TCGA-HU-8244 TCGA-HU-A4GH TCGA-HU-A4GN 
       12.33        11.08        77.29        24.39        11.77        29.98 
TCGA-HU-A4GU TCGA-IN-A6RI TCGA-IN-A7NU TCGA-R5-A7ZE TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        6.58        18.38        11.70        18.21        37.41        38.14 

$`CDH11 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        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-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-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-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-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-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-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-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-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-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        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-D7-6528 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-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-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-A4GJ TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        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-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-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-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 

  CDH11 MUTATED CDH11 WILD-TYPE 
           1.02            0.00 
  CDH11 MUTATED CDH11 WILD-TYPE 
          77.29          122.30 
  CDH11 MUTATED CDH11 WILD-TYPE 
          18.18           14.07 
[1] "1.0 - 77.3 (18.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D966V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDH11 MUTATED         1        2        2        4         4         3
  CDH11 WILD-TYPE       1       13       38       26        33        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDH11 MUTATED           1          3          2          3        4
  CDH11 WILD-TYPE         2         67         51         29       34
D966V3, multiclass
            clus
vv           CDH11 MUTATED CDH11 WILD-TYPE
  STAGE I                1               1
  STAGE IA               2              13
  STAGE IB               2              38
  STAGE II               4              26
  STAGE IIA              4              33
  STAGE IIB              3              49
  STAGE III              1               2
  STAGE IIIA             3              67
  STAGE IIIB             2              51
  STAGE IIIC             3              29
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDH11 MUTATED     3   7  13   8
  CDH11 WILD-TYPE  19  85 160  89
D966V4, multiclass
    clus
vv   CDH11 MUTATED CDH11 WILD-TYPE
  T1             3              19
  T2             7              85
  T3            13             160
  T4             8              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
  CDH11 MUTATED    11  10   4   5
  CDH11 WILD-TYPE 107  94  73  72
D966V5, multiclass
    clus
vv   CDH11 MUTATED CDH11 WILD-TYPE
  N0            11             107
  N1            10              94
  N2             4              73
  N3             5              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"
D966V6, binary
                 cls
clus                0   1
  CDH11 MUTATED    28   3
  CDH11 WILD-TYPE 318  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH11 MUTATED     28    3
  CDH11 WILD-TYPE  318   26
   clus
vv  CDH11 MUTATED CDH11 WILD-TYPE
  0            28             318
  1             3              26
[1] 2 2
[1] FALSE
D966V7, binary
                 cls
clus                0   1
  CDH11 MUTATED    13  19
  CDH11 WILD-TYPE 132 229
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH11 MUTATED     13   19
  CDH11 WILD-TYPE  132  229
        clus
vv       CDH11 MUTATED CDH11 WILD-TYPE
  FEMALE            13             132
  MALE              19             229
[1] 2 2
[1] FALSE
D966V8, binary
                 cls
clus                0   1
  CDH11 MUTATED    25   4
  CDH11 WILD-TYPE 267  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH11 MUTATED     25    4
  CDH11 WILD-TYPE  267   55
     clus
vv    CDH11 MUTATED CDH11 WILD-TYPE
  NO             25             267
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CDH11 MUTATED                                          0
  CDH11 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CDH11 MUTATED                                       4
  CDH11 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDH11 MUTATED                                                       16
  CDH11 WILD-TYPE                                                    142
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CDH11 MUTATED                                                   2
  CDH11 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDH11 MUTATED                                                                   2
  CDH11 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CDH11 MUTATED                                                    1
  CDH11 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CDH11 MUTATED                                                  7
  CDH11 WILD-TYPE                                               54
D966V9, multiclass
                                                                   clus
vv                                                                  CDH11 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              7
                                                                   clus
vv                                                                  CDH11 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               54
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDH11 MUTATED    25   0   2   3
  CDH11 WILD-TYPE 286  14  13  21
D966V10, multiclass
    clus
vv   CDH11 MUTATED CDH11 WILD-TYPE
  R0            25             286
  R1             0              14
  R2             2              13
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D966V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CDH11 MUTATED       6                         1
  CDH11 WILD-TYPE    81                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDH11 MUTATED                                           0    22
  CDH11 WILD-TYPE                                         1   221
D966V12, multiclass
                                           clus
vv                                          CDH11 MUTATED CDH11 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                22             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D966V13, binary
                 cls
clus                0   1
  CDH11 MUTATED     0  27
  CDH11 WILD-TYPE   4 283
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH11 MUTATED      0   27
  CDH11 WILD-TYPE    4  283
                        clus
vv                       CDH11 MUTATED CDH11 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            27             283
[1] 2 2
[1] FALSE

Clustering(967) Variable = HCRTR1 MUTATION ANALYSIS
D967V1, survival
                  sevent
clus2                0   1
  HCRTR1 MUTATED     4   1
  HCRTR1 WILD-TYPE 226 138
  HCRTR1 MUTATED HCRTR1 WILD-TYPE 
               5              364 
  HCRTR1 MUTATED HCRTR1 WILD-TYPE 
               1              138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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            14.12 
[1] "7.4 - 105.1 (30.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "3.1"
D967V2, 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       2       15       40       29        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HCRTR1 MUTATED           0          2          0          1        0
  HCRTR1 WILD-TYPE         3         68         53         31       38
D967V3, multiclass
            clus
vv           HCRTR1 MUTATED HCRTR1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HCRTR1 MUTATED     0   3   1   2
  HCRTR1 WILD-TYPE  22  89 172  95
D967V4, multiclass
    clus
vv   HCRTR1 MUTATED HCRTR1 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              1              172
  T4              2               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
  HCRTR1 MUTATED     1   2   1   1
  HCRTR1 WILD-TYPE 117 102  76  76
D967V5, multiclass
    clus
vv   HCRTR1 MUTATED HCRTR1 WILD-TYPE
  N0              1              117
  N1              2              102
  N2              1               76
  N3              1               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"
D967V6, binary
                  cls
clus                 0   1
  HCRTR1 MUTATED     6   0
  HCRTR1 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR1 MUTATED      6    0
  HCRTR1 WILD-TYPE  340   29
   clus
vv  HCRTR1 MUTATED HCRTR1 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D967V7, binary
                  cls
clus                 0   1
  HCRTR1 MUTATED     3   3
  HCRTR1 WILD-TYPE 142 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR1 MUTATED      3    3
  HCRTR1 WILD-TYPE  142  245
        clus
vv       HCRTR1 MUTATED HCRTR1 WILD-TYPE
  FEMALE              3              142
  MALE                3              245
[1] 2 2
[1] FALSE
D967V8, binary
                  cls
clus                 0   1
  HCRTR1 MUTATED     5   0
  HCRTR1 WILD-TYPE 287  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR1 MUTATED      5    0
  HCRTR1 WILD-TYPE  287   59
     clus
vv    HCRTR1 MUTATED HCRTR1 WILD-TYPE
  NO               5              287
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HCRTR1 MUTATED                                          0
  HCRTR1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HCRTR1 MUTATED                                       1
  HCRTR1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HCRTR1 MUTATED                                                        3
  HCRTR1 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HCRTR1 MUTATED                                                   0
  HCRTR1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HCRTR1 MUTATED                                                                   0
  HCRTR1 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HCRTR1 MUTATED                                                    0
  HCRTR1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HCRTR1 MUTATED                                                  2
  HCRTR1 WILD-TYPE                                               59
D967V9, multiclass
                                                                   clus
vv                                                                  HCRTR1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  HCRTR1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HCRTR1 MUTATED     4   0   0   2
  HCRTR1 WILD-TYPE 307  14  15  22
D967V10, multiclass
    clus
vv   HCRTR1 MUTATED HCRTR1 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D967V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  HCRTR1 MUTATED       1                         0
  HCRTR1 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HCRTR1 MUTATED                                           0     4
  HCRTR1 WILD-TYPE                                         1   239
D967V12, multiclass
                                           clus
vv                                          HCRTR1 MUTATED HCRTR1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D967V13, binary
                  cls
clus                 0   1
  HCRTR1 MUTATED     0   5
  HCRTR1 WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR1 MUTATED      0    5
  HCRTR1 WILD-TYPE    4  305
                        clus
vv                       HCRTR1 MUTATED HCRTR1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(968) Variable = ANKRD12 MUTATION ANALYSIS
D968V1, survival
                   sevent
clus2                 0   1
  ANKRD12 MUTATED    12   6
  ANKRD12 WILD-TYPE 218 133
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
               18               351 
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
                6               133 
$`ANKRD12 MUTATED`
TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8361 TCGA-BR-8680 TCGA-BR-A4J8 TCGA-BR-A4QL 
       44.94        29.59        31.10        31.96        13.51        16.14 
TCGA-CD-A4MG TCGA-CG-5726 TCGA-CG-5733 TCGA-D7-6528 TCGA-HF-A5NB TCGA-HU-8243 
        6.58        28.96        21.07        15.22        30.51         5.92 
TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-MX-A5UG TCGA-R5-A7ZI TCGA-SW-A7EA TCGA-VQ-A8P2 
       24.20         6.51         3.72        74.53        19.04        38.14 

$`ANKRD12 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM 
       32.52        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-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-D7-6815 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-8244 
       77.29        63.06        52.21        26.47         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-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-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       36.95        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 

  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
             3.72              0.00 
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
            74.53            122.30 
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
           22.635            14.040 
[1] "3.7 - 74.5 (22.6)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.5"
D968V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKRD12 MUTATED         0        2        2        0         3         2
  ANKRD12 WILD-TYPE       2       13       38       30        34        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD12 MUTATED           0          4          2          3        2
  ANKRD12 WILD-TYPE         3         66         51         29       36
D968V3, multiclass
            clus
vv           ANKRD12 MUTATED ANKRD12 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                13
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                3                34
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               4                66
  STAGE IIIB               2                51
  STAGE IIIC               3                29
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD12 MUTATED     2   3   6   9
  ANKRD12 WILD-TYPE  20  89 167  88
D968V4, multiclass
    clus
vv   ANKRD12 MUTATED ANKRD12 WILD-TYPE
  T1               2                20
  T2               3                89
  T3               6               167
  T4               9                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
  ANKRD12 MUTATED    10   3   3   4
  ANKRD12 WILD-TYPE 108 101  74  73
D968V5, multiclass
    clus
vv   ANKRD12 MUTATED ANKRD12 WILD-TYPE
  N0              10               108
  N1               3               101
  N2               3                74
  N3               4                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"
D968V6, binary
                   cls
clus                  0   1
  ANKRD12 MUTATED    18   2
  ANKRD12 WILD-TYPE 328  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD12 MUTATED     18    2
  ANKRD12 WILD-TYPE  328   27
   clus
vv  ANKRD12 MUTATED ANKRD12 WILD-TYPE
  0              18               328
  1               2                27
[1] 2 2
[1] FALSE
D968V7, binary
                   cls
clus                  0   1
  ANKRD12 MUTATED    13   7
  ANKRD12 WILD-TYPE 132 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD12 MUTATED     13    7
  ANKRD12 WILD-TYPE  132  241
        clus
vv       ANKRD12 MUTATED ANKRD12 WILD-TYPE
  FEMALE              13               132
  MALE                 7               241
[1] 2 2
[1] FALSE
D968V8, binary
                   cls
clus                  0   1
  ANKRD12 MUTATED    16   2
  ANKRD12 WILD-TYPE 276  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD12 MUTATED     16    2
  ANKRD12 WILD-TYPE  276   57
     clus
vv    ANKRD12 MUTATED ANKRD12 WILD-TYPE
  NO               16               276
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ANKRD12 MUTATED                                          0
  ANKRD12 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ANKRD12 MUTATED                                       4
  ANKRD12 WILD-TYPE                                    66
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANKRD12 MUTATED                                                        6
  ANKRD12 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ANKRD12 MUTATED                                                   2
  ANKRD12 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANKRD12 MUTATED                                                                   3
  ANKRD12 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ANKRD12 MUTATED                                                    0
  ANKRD12 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ANKRD12 MUTATED                                                  5
  ANKRD12 WILD-TYPE                                               56
D968V9, multiclass
                                                                   clus
vv                                                                  ANKRD12 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                5
                                                                   clus
vv                                                                  ANKRD12 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ANKRD12 MUTATED    17   1   0   1
  ANKRD12 WILD-TYPE 294  13  15  23
D968V10, multiclass
    clus
vv   ANKRD12 MUTATED ANKRD12 WILD-TYPE
  R0              17               294
  R1               1                13
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D968V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ANKRD12 MUTATED       6                         0
  ANKRD12 WILD-TYPE    81                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANKRD12 MUTATED                                           0    11
  ANKRD12 WILD-TYPE                                         1   232
D968V12, multiclass
                                           clus
vv                                          ANKRD12 MUTATED ANKRD12 WILD-TYPE
  ASIAN                                                   6                81
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D968V13, binary
                   cls
clus                  0   1
  ANKRD12 MUTATED     1  15
  ANKRD12 WILD-TYPE   3 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD12 MUTATED      1   15
  ANKRD12 WILD-TYPE    3  295
                        clus
vv                       ANKRD12 MUTATED ANKRD12 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              15               295
[1] 2 2
[1] FALSE

Clustering(969) Variable = BMPR1B MUTATION ANALYSIS
D969V1, survival
                  sevent
clus2                0   1
  BMPR1B MUTATED     6   1
  BMPR1B WILD-TYPE 224 138
  BMPR1B MUTATED BMPR1B WILD-TYPE 
               7              362 
  BMPR1B MUTATED BMPR1B WILD-TYPE 
               1              138 
$`BMPR1B MUTATED`
TCGA-BR-7958 TCGA-BR-8078 TCGA-CG-4465 TCGA-HU-A4G9 TCGA-HU-A4H3 TCGA-VQ-A8DT 
       29.56        29.59         9.01        24.20        29.00        48.79 
TCGA-VQ-A8P2 
       38.14 

$`BMPR1B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  BMPR1B MUTATED BMPR1B WILD-TYPE 
            9.01             0.00 
  BMPR1B MUTATED BMPR1B WILD-TYPE 
           48.79           122.30 
  BMPR1B MUTATED BMPR1B WILD-TYPE 
           29.56            14.07 
[1] "9.0 - 48.8 (29.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "4.3"
D969V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BMPR1B MUTATED         1        1        0        0         0         1
  BMPR1B WILD-TYPE       1       14       40       30        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BMPR1B MUTATED           0          1          2          1        2
  BMPR1B WILD-TYPE         3         69         51         31       36
D969V3, multiclass
            clus
vv           BMPR1B MUTATED BMPR1B WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              2               51
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BMPR1B MUTATED     2   0   1   6
  BMPR1B WILD-TYPE  20  92 172  91
D969V4, multiclass
    clus
vv   BMPR1B MUTATED BMPR1B WILD-TYPE
  T1              2               20
  T2              0               92
  T3              1              172
  T4              6               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
  BMPR1B MUTATED     3   2   1   3
  BMPR1B WILD-TYPE 115 102  76  74
D969V5, multiclass
    clus
vv   BMPR1B MUTATED BMPR1B WILD-TYPE
  N0              3              115
  N1              2              102
  N2              1               76
  N3              3               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"
D969V6, binary
                  cls
clus                 0   1
  BMPR1B MUTATED     7   1
  BMPR1B WILD-TYPE 339  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1B MUTATED      7    1
  BMPR1B WILD-TYPE  339   28
   clus
vv  BMPR1B MUTATED BMPR1B WILD-TYPE
  0              7              339
  1              1               28
[1] 2 2
[1] FALSE
D969V7, binary
                  cls
clus                 0   1
  BMPR1B MUTATED     5   4
  BMPR1B WILD-TYPE 140 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1B MUTATED      5    4
  BMPR1B WILD-TYPE  140  244
        clus
vv       BMPR1B MUTATED BMPR1B WILD-TYPE
  FEMALE              5              140
  MALE                4              244
[1] 2 2
[1] FALSE
D969V8, binary
                  cls
clus                 0   1
  BMPR1B MUTATED     4   2
  BMPR1B WILD-TYPE 288  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1B MUTATED      4    2
  BMPR1B WILD-TYPE  288   57
     clus
vv    BMPR1B MUTATED BMPR1B WILD-TYPE
  NO               4              288
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BMPR1B MUTATED                                          0
  BMPR1B WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BMPR1B MUTATED                                       2
  BMPR1B WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BMPR1B MUTATED                                                        4
  BMPR1B WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BMPR1B MUTATED                                                   1
  BMPR1B WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BMPR1B MUTATED                                                                   1
  BMPR1B WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BMPR1B MUTATED                                                    0
  BMPR1B WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BMPR1B MUTATED                                                  1
  BMPR1B WILD-TYPE                                               60
D969V9, multiclass
                                                                   clus
vv                                                                  BMPR1B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  BMPR1B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BMPR1B MUTATED     7   0   1   1
  BMPR1B WILD-TYPE 304  14  14  23
D969V10, multiclass
    clus
vv   BMPR1B MUTATED BMPR1B WILD-TYPE
  R0              7              304
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D969V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  BMPR1B MUTATED       2                         1
  BMPR1B WILD-TYPE    85                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BMPR1B MUTATED                                           0     4
  BMPR1B WILD-TYPE                                         1   239
D969V12, multiclass
                                           clus
vv                                          BMPR1B MUTATED BMPR1B WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D969V13, binary
                  cls
clus                 0   1
  BMPR1B MUTATED     0   6
  BMPR1B WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1B MUTATED      0    6
  BMPR1B WILD-TYPE    4  304
                        clus
vv                       BMPR1B MUTATED BMPR1B WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(970) Variable = CRYBG3 MUTATION ANALYSIS
D970V1, survival
                  sevent
clus2                0   1
  CRYBG3 MUTATED    11   3
  CRYBG3 WILD-TYPE 219 136
  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
              14              355 
  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
               3              136 
$`CRYBG3 MUTATED`
TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-CD-5813 
       34.68         4.31        27.12        28.14        31.96        12.39 
TCGA-CD-A4MJ TCGA-D7-A4YV TCGA-D7-A4YX TCGA-HU-8604 TCGA-HU-A4G8 TCGA-HU-A4GT 
       12.62         5.92        36.43        22.82        22.68         6.51 
TCGA-R5-A7ZI TCGA-VQ-AA6G 
       74.53        26.04 

$`CRYBG3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       38.93        32.94        54.12        16.14        27.55        12.43 
TCGA-ZA-A8F6 
       17.26 

  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
            4.31             0.00 
  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
           74.53           122.30 
  CRYBG3 MUTATED CRYBG3 WILD-TYPE 
           24.43            14.07 
[1] "4.3 - 74.5 (24.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.4"
D970V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CRYBG3 MUTATED         0        0        2        1         4         3
  CRYBG3 WILD-TYPE       2       15       38       29        33        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CRYBG3 MUTATED           0          0          1          1        2
  CRYBG3 WILD-TYPE         3         70         52         31       36
D970V3, multiclass
            clus
vv           CRYBG3 MUTATED CRYBG3 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               4               33
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CRYBG3 MUTATED     0   2   8   4
  CRYBG3 WILD-TYPE  22  90 165  93
D970V4, multiclass
    clus
vv   CRYBG3 MUTATED CRYBG3 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              8              165
  T4              4               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
  CRYBG3 MUTATED     7   5   1   1
  CRYBG3 WILD-TYPE 111  99  76  76
D970V5, multiclass
    clus
vv   CRYBG3 MUTATED CRYBG3 WILD-TYPE
  N0              7              111
  N1              5               99
  N2              1               76
  N3              1               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"
D970V6, binary
                  cls
clus                 0   1
  CRYBG3 MUTATED    12   2
  CRYBG3 WILD-TYPE 334  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBG3 MUTATED     12    2
  CRYBG3 WILD-TYPE  334   27
   clus
vv  CRYBG3 MUTATED CRYBG3 WILD-TYPE
  0             12              334
  1              2               27
[1] 2 2
[1] FALSE
D970V7, binary
                  cls
clus                 0   1
  CRYBG3 MUTATED     7   7
  CRYBG3 WILD-TYPE 138 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBG3 MUTATED      7    7
  CRYBG3 WILD-TYPE  138  241
        clus
vv       CRYBG3 MUTATED CRYBG3 WILD-TYPE
  FEMALE              7              138
  MALE                7              241
[1] 2 2
[1] FALSE
D970V8, binary
                  cls
clus                 0   1
  CRYBG3 MUTATED    14   0
  CRYBG3 WILD-TYPE 278  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBG3 MUTATED     14    0
  CRYBG3 WILD-TYPE  278   59
     clus
vv    CRYBG3 MUTATED CRYBG3 WILD-TYPE
  NO              14              278
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CRYBG3 MUTATED                                          0
  CRYBG3 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CRYBG3 MUTATED                                       2
  CRYBG3 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CRYBG3 MUTATED                                                        6
  CRYBG3 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CRYBG3 MUTATED                                                   1
  CRYBG3 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CRYBG3 MUTATED                                                                   1
  CRYBG3 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CRYBG3 MUTATED                                                    0
  CRYBG3 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CRYBG3 MUTATED                                                  4
  CRYBG3 WILD-TYPE                                               57
D970V9, multiclass
                                                                   clus
vv                                                                  CRYBG3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  CRYBG3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CRYBG3 MUTATED    11   0   0   0
  CRYBG3 WILD-TYPE 300  14  15  24
D970V10, multiclass
    clus
vv   CRYBG3 MUTATED CRYBG3 WILD-TYPE
  R0             11              300
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D970V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CRYBG3 MUTATED       6                         0
  CRYBG3 WILD-TYPE    81                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CRYBG3 MUTATED                                           0     8
  CRYBG3 WILD-TYPE                                         1   235
D970V12, multiclass
                                           clus
vv                                          CRYBG3 MUTATED CRYBG3 WILD-TYPE
  ASIAN                                                  6               81
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D970V13, binary
                  cls
clus                 0   1
  CRYBG3 MUTATED     1  12
  CRYBG3 WILD-TYPE   3 298
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBG3 MUTATED      1   12
  CRYBG3 WILD-TYPE    3  298
                        clus
vv                       CRYBG3 MUTATED CRYBG3 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             12              298
[1] 2 2
[1] FALSE

Clustering(971) Variable = KIDINS220 MUTATION ANALYSIS
D971V1, survival
                     sevent
clus2                   0   1
  KIDINS220 MUTATED    12   4
  KIDINS220 WILD-TYPE 218 135
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
                 16                 353 
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
                  4                 135 
$`KIDINS220 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 
       21.99         6.97        18.35        34.68        35.84         1.12 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-D7-6815 TCGA-F1-A448 TCGA-HF-7133 TCGA-HU-A4G8 
        6.58         6.02        15.98        21.27        63.06        22.68 
TCGA-HU-A4GH TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-VQ-A8P2 
       11.77        20.25        29.00        38.14 

$`KIDINS220 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-D7-6817 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-F1-6874 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-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-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-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-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 

  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
               1.12                0.00 
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
              63.06              122.30 
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
              20.76               14.07 
[1] "1.1 - 63.1 (20.8)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D971V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIDINS220 MUTATED         0        1        1        0         3         2
  KIDINS220 WILD-TYPE       2       14       39       30        34        50
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIDINS220 MUTATED           0          3          1          2        3
  KIDINS220 WILD-TYPE         3         67         52         30       35
D971V3, multiclass
            clus
vv           KIDINS220 MUTATED KIDINS220 WILD-TYPE
  STAGE I                    0                   2
  STAGE IA                   1                  14
  STAGE IB                   1                  39
  STAGE II                   0                  30
  STAGE IIA                  3                  34
  STAGE IIB                  2                  50
  STAGE III                  0                   3
  STAGE IIIA                 3                  67
  STAGE IIIB                 1                  52
  STAGE IIIC                 2                  30
  STAGE IV                   3                  35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  KIDINS220 MUTATED     1   3   6   6
  KIDINS220 WILD-TYPE  21  89 167  91
D971V4, multiclass
    clus
vv   KIDINS220 MUTATED KIDINS220 WILD-TYPE
  T1                 1                  21
  T2                 3                  89
  T3                 6                 167
  T4                 6                  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
  KIDINS220 MUTATED     6   6   2   3
  KIDINS220 WILD-TYPE 112  98  75  74
D971V5, multiclass
    clus
vv   KIDINS220 MUTATED KIDINS220 WILD-TYPE
  N0                 6                 112
  N1                 6                  98
  N2                 2                  75
  N3                 3                  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"
D971V6, binary
                     cls
clus                    0   1
  KIDINS220 MUTATED    16   1
  KIDINS220 WILD-TYPE 330  28
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIDINS220 MUTATED     16    1
  KIDINS220 WILD-TYPE  330   28
   clus
vv  KIDINS220 MUTATED KIDINS220 WILD-TYPE
  0                16                 330
  1                 1                  28
[1] 2 2
[1] FALSE
D971V7, binary
                     cls
clus                    0   1
  KIDINS220 MUTATED    11   7
  KIDINS220 WILD-TYPE 134 241
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIDINS220 MUTATED     11    7
  KIDINS220 WILD-TYPE  134  241
        clus
vv       KIDINS220 MUTATED KIDINS220 WILD-TYPE
  FEMALE                11                 134
  MALE                   7                 241
[1] 2 2
[1] FALSE
D971V8, binary
                     cls
clus                    0   1
  KIDINS220 MUTATED    12   3
  KIDINS220 WILD-TYPE 280  56
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIDINS220 MUTATED     12    3
  KIDINS220 WILD-TYPE  280   56
     clus
vv    KIDINS220 MUTATED KIDINS220 WILD-TYPE
  NO                 12                 280
  YES                 3                  56
[1] 2 2
[1] FALSE
                     vv
clus                  STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIDINS220 MUTATED                                          0
  KIDINS220 WILD-TYPE                                        8
                     vv
clus                  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIDINS220 MUTATED                                       4
  KIDINS220 WILD-TYPE                                    66
                     vv
clus                  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIDINS220 MUTATED                                                        7
  KIDINS220 WILD-TYPE                                                    151
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIDINS220 MUTATED                                                   3
  KIDINS220 WILD-TYPE                                                18
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIDINS220 MUTATED                                                                   2
  KIDINS220 WILD-TYPE                                                                66
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIDINS220 MUTATED                                                    0
  KIDINS220 WILD-TYPE                                                  5
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIDINS220 MUTATED                                                  2
  KIDINS220 WILD-TYPE                                               59
D971V9, multiclass
                                                                   clus
vv                                                                  KIDINS220 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  2
                                                                   clus
vv                                                                  KIDINS220 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                            8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                              66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                  18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                  5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                   59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  KIDINS220 MUTATED    10   1   1   4
  KIDINS220 WILD-TYPE 301  13  14  20
D971V10, multiclass
    clus
vv   KIDINS220 MUTATED KIDINS220 WILD-TYPE
  R0                10                 301
  R1                 1                  13
  R2                 1                  14
  RX                 4                  20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D971V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN
  KIDINS220 MUTATED       5                         0
  KIDINS220 WILD-TYPE    82                         9
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIDINS220 MUTATED                                           0    10
  KIDINS220 WILD-TYPE                                         1   233
D971V12, multiclass
                                           clus
vv                                          KIDINS220 MUTATED
  ASIAN                                                     5
  BLACK OR AFRICAN AMERICAN                                 0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                    10
                                           clus
vv                                          KIDINS220 WILD-TYPE
  ASIAN                                                      82
  BLACK OR AFRICAN AMERICAN                                   9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   1
  WHITE                                                     233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D971V13, binary
                     cls
clus                    0   1
  KIDINS220 MUTATED     1  13
  KIDINS220 WILD-TYPE   3 297
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIDINS220 MUTATED      1   13
  KIDINS220 WILD-TYPE    3  297
                        clus
vv                       KIDINS220 MUTATED KIDINS220 WILD-TYPE
  HISPANIC OR LATINO                     1                   3
  NOT HISPANIC OR LATINO                13                 297
[1] 2 2
[1] FALSE

Clustering(972) Variable = INSM2 MUTATION ANALYSIS
D972V1, survival
                 sevent
clus2               0   1
  INSM2 MUTATED     7   4
  INSM2 WILD-TYPE 223 135
  INSM2 MUTATED INSM2 WILD-TYPE 
             11             358 
  INSM2 MUTATED INSM2 WILD-TYPE 
              4             135 
$`INSM2 MUTATED`
TCGA-B7-5816 TCGA-BR-4280 TCGA-BR-8059 TCGA-BR-8368 TCGA-BR-8382 TCGA-CG-5721 
       26.70         6.61        14.43         4.31        25.05         6.02 
TCGA-CG-5728 TCGA-D7-A4YV TCGA-HF-A5NB TCGA-MX-A5UJ TCGA-VQ-A8P2 
       65.10         5.92        30.51        19.73        38.14 

$`INSM2 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  INSM2 MUTATED INSM2 WILD-TYPE 
           4.31            0.00 
  INSM2 MUTATED INSM2 WILD-TYPE 
           65.1           122.3 
  INSM2 MUTATED INSM2 WILD-TYPE 
          19.73           14.12 
[1] "4.3 - 65.1 (19.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D972V2, 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       1       15       38       30        37        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INSM2 MUTATED           2          2          0          2        1
  INSM2 WILD-TYPE         1         68         53         30       37
D972V3, multiclass
            clus
vv           INSM2 MUTATED INSM2 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              2              50
  STAGE III              2               1
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  INSM2 MUTATED     1   3   2   6
  INSM2 WILD-TYPE  21  89 171  91
D972V4, multiclass
    clus
vv   INSM2 MUTATED INSM2 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             2             171
  T4             6              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
  INSM2 MUTATED     3   6   1   2
  INSM2 WILD-TYPE 115  98  76  75
D972V5, multiclass
    clus
vv   INSM2 MUTATED INSM2 WILD-TYPE
  N0             3             115
  N1             6              98
  N2             1              76
  N3             2              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"
D972V6, binary
                 cls
clus                0   1
  INSM2 MUTATED    11   0
  INSM2 WILD-TYPE 335  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED     11    0
  INSM2 WILD-TYPE  335   29
   clus
vv  INSM2 MUTATED INSM2 WILD-TYPE
  0            11             335
  1             0              29
[1] 2 2
[1] FALSE
D972V7, binary
                 cls
clus                0   1
  INSM2 MUTATED     8   4
  INSM2 WILD-TYPE 137 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED      8    4
  INSM2 WILD-TYPE  137  244
        clus
vv       INSM2 MUTATED INSM2 WILD-TYPE
  FEMALE             8             137
  MALE               4             244
[1] 2 2
[1] FALSE
D972V8, binary
                 cls
clus                0   1
  INSM2 MUTATED     9   2
  INSM2 WILD-TYPE 283  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED      9    2
  INSM2 WILD-TYPE  283   57
     clus
vv    INSM2 MUTATED INSM2 WILD-TYPE
  NO              9             283
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  INSM2 MUTATED                                          0
  INSM2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  INSM2 MUTATED                                       1
  INSM2 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  INSM2 MUTATED                                                        4
  INSM2 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  INSM2 MUTATED                                                   2
  INSM2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  INSM2 MUTATED                                                                   3
  INSM2 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  INSM2 MUTATED                                                    0
  INSM2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  INSM2 MUTATED                                                  2
  INSM2 WILD-TYPE                                               59
D972V9, multiclass
                                                                   clus
vv                                                                  INSM2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  INSM2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  INSM2 MUTATED    10   1   0   1
  INSM2 WILD-TYPE 301  13  15  23
D972V10, multiclass
    clus
vv   INSM2 MUTATED INSM2 WILD-TYPE
  R0            10             301
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D972V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  INSM2 MUTATED       0                         1
  INSM2 WILD-TYPE    87                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  INSM2 MUTATED                                           0     8
  INSM2 WILD-TYPE                                         1   235
D972V12, multiclass
                                           clus
vv                                          INSM2 MUTATED INSM2 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D972V13, binary
                 cls
clus                0   1
  INSM2 MUTATED     0   8
  INSM2 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED      0    8
  INSM2 WILD-TYPE    4  302
                        clus
vv                       INSM2 MUTATED INSM2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(973) Variable = ELOVL2 MUTATION ANALYSIS
D973V1, survival
                  sevent
clus2                0   1
  ELOVL2 MUTATED     4   2
  ELOVL2 WILD-TYPE 226 137
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
               6              363 
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
               2              137 
$`ELOVL2 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8363 TCGA-CD-8535 TCGA-D7-A4YY TCGA-HU-A4G2 
        6.97        34.68         0.26        12.82        13.78        24.30 

$`ELOVL2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
            0.26             0.00 
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
           34.68           122.30 
  ELOVL2 MUTATED ELOVL2 WILD-TYPE 
           13.30            14.43 
[1] "0.3 - 34.7 (13.3)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1"  
D973V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ELOVL2 MUTATED         0        0        1        0         1         1
  ELOVL2 WILD-TYPE       2       15       39       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ELOVL2 MUTATED           0          3          1          0        0
  ELOVL2 WILD-TYPE         3         67         52         32       38
D973V3, multiclass
            clus
vv           ELOVL2 MUTATED ELOVL2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ELOVL2 MUTATED     0   1   6   0
  ELOVL2 WILD-TYPE  22  91 167  97
D973V4, multiclass
    clus
vv   ELOVL2 MUTATED ELOVL2 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              6              167
  T4              0               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
  ELOVL2 MUTATED     2   4   0   1
  ELOVL2 WILD-TYPE 116 100  77  76
D973V5, multiclass
    clus
vv   ELOVL2 MUTATED ELOVL2 WILD-TYPE
  N0              2              116
  N1              4              100
  N2              0               77
  N3              1               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"
D973V6, binary
                  cls
clus                 0   1
  ELOVL2 MUTATED     6   0
  ELOVL2 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL2 MUTATED      6    0
  ELOVL2 WILD-TYPE  340   29
   clus
vv  ELOVL2 MUTATED ELOVL2 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D973V7, binary
                  cls
clus                 0   1
  ELOVL2 MUTATED     2   5
  ELOVL2 WILD-TYPE 143 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL2 MUTATED      2    5
  ELOVL2 WILD-TYPE  143  243
        clus
vv       ELOVL2 MUTATED ELOVL2 WILD-TYPE
  FEMALE              2              143
  MALE                5              243
[1] 2 2
[1] FALSE
D973V8, binary
                  cls
clus                 0   1
  ELOVL2 MUTATED     5   2
  ELOVL2 WILD-TYPE 287  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL2 MUTATED      5    2
  ELOVL2 WILD-TYPE  287   57
     clus
vv    ELOVL2 MUTATED ELOVL2 WILD-TYPE
  NO               5              287
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ELOVL2 MUTATED                                          0
  ELOVL2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ELOVL2 MUTATED                                       1
  ELOVL2 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ELOVL2 MUTATED                                                        6
  ELOVL2 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ELOVL2 MUTATED                                                   0
  ELOVL2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ELOVL2 MUTATED                                                                   0
  ELOVL2 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ELOVL2 MUTATED                                                    0
  ELOVL2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ELOVL2 MUTATED                                                  0
  ELOVL2 WILD-TYPE                                               61
D973V9, multiclass
                                                                   clus
vv                                                                  ELOVL2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  ELOVL2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ELOVL2 MUTATED     5   1   0   1
  ELOVL2 WILD-TYPE 306  13  15  23
D973V10, multiclass
    clus
vv   ELOVL2 MUTATED ELOVL2 WILD-TYPE
  R0              5              306
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D973V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ELOVL2 MUTATED       2                         0
  ELOVL2 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ELOVL2 MUTATED                                           0     4
  ELOVL2 WILD-TYPE                                         1   239
D973V12, multiclass
                                           clus
vv                                          ELOVL2 MUTATED ELOVL2 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D973V13, binary
                  cls
clus                 0   1
  ELOVL2 MUTATED     0   6
  ELOVL2 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ELOVL2 MUTATED      0    6
  ELOVL2 WILD-TYPE    4  304
                        clus
vv                       ELOVL2 MUTATED ELOVL2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(974) Variable = GON4L MUTATION ANALYSIS
D974V1, survival
                 sevent
clus2               0   1
  GON4L MUTATED     7   4
  GON4L WILD-TYPE 223 135
  GON4L MUTATED GON4L WILD-TYPE 
             11             358 
  GON4L MUTATED GON4L WILD-TYPE 
              4             135 
$`GON4L MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8372 TCGA-CD-A4MI 
       26.70        30.90        34.68        29.59        31.27        11.77 
TCGA-CD-A4MJ TCGA-CG-5733 TCGA-D7-A6EY TCGA-HU-A4H3 TCGA-VQ-A8P2 
       12.62        21.07        11.44        29.00        38.14 

$`GON4L WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  GON4L MUTATED GON4L WILD-TYPE 
          11.44            0.00 
  GON4L MUTATED GON4L WILD-TYPE 
          38.14          122.30 
  GON4L MUTATED GON4L WILD-TYPE 
          29.00           14.07 
[1] "11.4 - 38.1 (29.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D974V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GON4L MUTATED         1        0        1        0         1         2
  GON4L WILD-TYPE       1       15       39       30        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GON4L MUTATED           0          3          1          2        0
  GON4L WILD-TYPE         3         67         52         30       38
D974V3, multiclass
            clus
vv           GON4L MUTATED GON4L WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GON4L MUTATED     1   3   3   5
  GON4L WILD-TYPE  21  89 170  92
D974V4, multiclass
    clus
vv   GON4L MUTATED GON4L WILD-TYPE
  T1             1              21
  T2             3              89
  T3             3             170
  T4             5              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
  GON4L MUTATED     4   3   1   3
  GON4L WILD-TYPE 114 101  76  74
D974V5, multiclass
    clus
vv   GON4L MUTATED GON4L WILD-TYPE
  N0             4             114
  N1             3             101
  N2             1              76
  N3             3              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"
D974V6, binary
                 cls
clus                0   1
  GON4L MUTATED    11   0
  GON4L WILD-TYPE 335  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED     11    0
  GON4L WILD-TYPE  335   29
   clus
vv  GON4L MUTATED GON4L WILD-TYPE
  0            11             335
  1             0              29
[1] 2 2
[1] FALSE
D974V7, binary
                 cls
clus                0   1
  GON4L MUTATED     7   5
  GON4L WILD-TYPE 138 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED      7    5
  GON4L WILD-TYPE  138  243
        clus
vv       GON4L MUTATED GON4L WILD-TYPE
  FEMALE             7             138
  MALE               5             243
[1] 2 2
[1] FALSE
D974V8, binary
                 cls
clus                0   1
  GON4L MUTATED    10   1
  GON4L WILD-TYPE 282  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED     10    1
  GON4L WILD-TYPE  282   58
     clus
vv    GON4L MUTATED GON4L WILD-TYPE
  NO             10             282
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GON4L MUTATED                                          0
  GON4L WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GON4L MUTATED                                       2
  GON4L WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GON4L MUTATED                                                        7
  GON4L WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GON4L MUTATED                                                   1
  GON4L WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GON4L MUTATED                                                                   1
  GON4L WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GON4L MUTATED                                                    0
  GON4L WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GON4L MUTATED                                                  1
  GON4L WILD-TYPE                                               60
D974V9, multiclass
                                                                   clus
vv                                                                  GON4L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  GON4L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GON4L MUTATED     9   0   0   1
  GON4L WILD-TYPE 302  14  15  23
D974V10, multiclass
    clus
vv   GON4L MUTATED GON4L WILD-TYPE
  R0             9             302
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D974V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GON4L MUTATED       3                         1
  GON4L WILD-TYPE    84                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GON4L MUTATED                                           0     7
  GON4L WILD-TYPE                                         1   236
D974V12, multiclass
                                           clus
vv                                          GON4L MUTATED GON4L WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D974V13, binary
                 cls
clus                0   1
  GON4L MUTATED     0  10
  GON4L WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED      0   10
  GON4L WILD-TYPE    4  300
                        clus
vv                       GON4L MUTATED GON4L WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(975) Variable = MSL3 MUTATION ANALYSIS
D975V1, survival
                sevent
clus2              0   1
  MSL3 MUTATED     6   3
  MSL3 WILD-TYPE 224 136
  MSL3 MUTATED MSL3 WILD-TYPE 
             9            360 
  MSL3 MUTATED MSL3 WILD-TYPE 
             3            136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-7722 
       36.16        35.24        35.84        33.63        39.78        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-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-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-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.84        18.54        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-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 

  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          14.12 
[1] "1.1 - 32.2 (18.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D975V2, 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       2       15       37       30        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MSL3 MUTATED           0          1          0          0        3
  MSL3 WILD-TYPE         3         69         53         32       35
D975V3, multiclass
            clus
vv           MSL3 MUTATED MSL3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              3             37
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MSL3 MUTATED     0   3   2   4
  MSL3 WILD-TYPE  22  89 171  93
D975V4, multiclass
    clus
vv   MSL3 MUTATED MSL3 WILD-TYPE
  T1            0             22
  T2            3             89
  T3            2            171
  T4            4             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
  MSL3 MUTATED     5   3   1   0
  MSL3 WILD-TYPE 113 101  76  77
D975V5, multiclass
    clus
vv   MSL3 MUTATED MSL3 WILD-TYPE
  N0            5            113
  N1            3            101
  N2            1             76
  N3            0             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"
D975V6, binary
                cls
clus               0   1
  MSL3 MUTATED     7   1
  MSL3 WILD-TYPE 339  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL3 MUTATED      7    1
  MSL3 WILD-TYPE  339   28
   clus
vv  MSL3 MUTATED MSL3 WILD-TYPE
  0            7            339
  1            1             28
[1] 2 2
[1] FALSE
D975V7, binary
                cls
clus               0   1
  MSL3 MUTATED     3   6
  MSL3 WILD-TYPE 142 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL3 MUTATED      3    6
  MSL3 WILD-TYPE  142  242
        clus
vv       MSL3 MUTATED MSL3 WILD-TYPE
  FEMALE            3            142
  MALE              6            242
[1] 2 2
[1] FALSE
D975V8, binary
                cls
clus               0   1
  MSL3 MUTATED     9   0
  MSL3 WILD-TYPE 283  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL3 MUTATED      9    0
  MSL3 WILD-TYPE  283   59
     clus
vv    MSL3 MUTATED MSL3 WILD-TYPE
  NO             9            283
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MSL3 MUTATED                                          1
  MSL3 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MSL3 MUTATED                                       1
  MSL3 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MSL3 MUTATED                                                        4
  MSL3 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MSL3 MUTATED                                                   0
  MSL3 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MSL3 MUTATED                                                                   2
  MSL3 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MSL3 MUTATED                                                    0
  MSL3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MSL3 MUTATED                                                  1
  MSL3 WILD-TYPE                                               60
D975V9, multiclass
                                                                   clus
vv                                                                  MSL3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  MSL3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MSL3 MUTATED     9   0   0   0
  MSL3 WILD-TYPE 302  14  15  24
D975V10, multiclass
    clus
vv   MSL3 MUTATED MSL3 WILD-TYPE
  R0            9            302
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D975V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  MSL3 MUTATED       2                         0
  MSL3 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MSL3 MUTATED                                           0     6
  MSL3 WILD-TYPE                                         1   237
D975V12, multiclass
                                           clus
vv                                          MSL3 MUTATED MSL3 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D975V13, binary
                cls
clus               0   1
  MSL3 MUTATED     0   8
  MSL3 WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSL3 MUTATED      0    8
  MSL3 WILD-TYPE    4  302
                        clus
vv                       MSL3 MUTATED MSL3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(976) Variable = FANCA MUTATION ANALYSIS
D976V1, survival
                 sevent
clus2               0   1
  FANCA MUTATED     7   4
  FANCA WILD-TYPE 223 135
  FANCA MUTATED FANCA WILD-TYPE 
             11             358 
  FANCA MUTATED FANCA WILD-TYPE 
              4             135 
$`FANCA MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8372 
       21.99        26.70         6.97        34.68        31.10        31.27 
TCGA-BR-A453 TCGA-D7-A6EZ TCGA-FP-A9TM TCGA-HU-A4GX TCGA-VQ-A8P2 
        6.08        20.32         6.21        20.25        38.14 

$`FANCA WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-A4CQ TCGA-BR-A4CS 
       10.68        34.13        13.87         7.53        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-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-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 

  FANCA MUTATED FANCA WILD-TYPE 
           6.08            0.00 
  FANCA MUTATED FANCA WILD-TYPE 
          38.14          122.30 
  FANCA MUTATED FANCA WILD-TYPE 
          21.99           14.07 
[1] "6.1 - 38.1 (22.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D976V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FANCA MUTATED         0        0        1        0         1         1
  FANCA WILD-TYPE       2       15       39       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FANCA MUTATED           0          3          0          3        2
  FANCA WILD-TYPE         3         67         53         29       36
D976V3, multiclass
            clus
vv           FANCA MUTATED FANCA WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FANCA MUTATED     1   1   3   7
  FANCA WILD-TYPE  21  91 170  90
D976V4, multiclass
    clus
vv   FANCA MUTATED FANCA WILD-TYPE
  T1             1              21
  T2             1              91
  T3             3             170
  T4             7              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
  FANCA MUTATED     3   4   3   2
  FANCA WILD-TYPE 115 100  74  75
D976V5, multiclass
    clus
vv   FANCA MUTATED FANCA WILD-TYPE
  N0             3             115
  N1             4             100
  N2             3              74
  N3             2              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"
D976V6, binary
                 cls
clus                0   1
  FANCA MUTATED     9   2
  FANCA WILD-TYPE 337  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANCA MUTATED      9    2
  FANCA WILD-TYPE  337   27
   clus
vv  FANCA MUTATED FANCA WILD-TYPE
  0             9             337
  1             2              27
[1] 2 2
[1] FALSE
D976V7, binary
                 cls
clus                0   1
  FANCA MUTATED     5   7
  FANCA WILD-TYPE 140 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANCA MUTATED      5    7
  FANCA WILD-TYPE  140  241
        clus
vv       FANCA MUTATED FANCA WILD-TYPE
  FEMALE             5             140
  MALE               7             241
[1] 2 2
[1] FALSE
D976V8, binary
                 cls
clus                0   1
  FANCA MUTATED     9   2
  FANCA WILD-TYPE 283  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANCA MUTATED      9    2
  FANCA WILD-TYPE  283   57
     clus
vv    FANCA MUTATED FANCA WILD-TYPE
  NO              9             283
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FANCA MUTATED                                          1
  FANCA WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FANCA MUTATED                                       2
  FANCA WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FANCA MUTATED                                                        5
  FANCA WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FANCA MUTATED                                                   1
  FANCA WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FANCA MUTATED                                                                   3
  FANCA WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FANCA MUTATED                                                    0
  FANCA WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FANCA MUTATED                                                  0
  FANCA WILD-TYPE                                               61
D976V9, multiclass
                                                                   clus
vv                                                                  FANCA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  FANCA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FANCA MUTATED    10   0   1   1
  FANCA WILD-TYPE 301  14  14  23
D976V10, multiclass
    clus
vv   FANCA MUTATED FANCA WILD-TYPE
  R0            10             301
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D976V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FANCA MUTATED       2                         0
  FANCA WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FANCA MUTATED                                           0     8
  FANCA WILD-TYPE                                         1   235
D976V12, multiclass
                                           clus
vv                                          FANCA MUTATED FANCA WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D976V13, binary
                 cls
clus                0   1
  FANCA MUTATED     0   9
  FANCA WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FANCA MUTATED      0    9
  FANCA WILD-TYPE    4  301
                        clus
vv                       FANCA MUTATED FANCA WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(977) Variable = SMPD1 MUTATION ANALYSIS
D977V1, survival
                 sevent
clus2               0   1
  SMPD1 MUTATED     4   0
  SMPD1 WILD-TYPE 226 139
  SMPD1 MUTATED SMPD1 WILD-TYPE 
              4             365 
  SMPD1 MUTATED SMPD1 WILD-TYPE 
              0             139 
$`SMPD1 MUTATED`
TCGA-B7-A5TI TCGA-BR-8591 TCGA-BR-8680 TCGA-VQ-A8P2 
       19.56        28.14        31.96        38.14 

$`SMPD1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  SMPD1 MUTATED SMPD1 WILD-TYPE 
          19.56            0.00 
  SMPD1 MUTATED SMPD1 WILD-TYPE 
          38.14          122.30 
  SMPD1 MUTATED SMPD1 WILD-TYPE 
          30.05           14.07 
[1] "19.6 - 38.1 (30.1)" "0.0 - 122.3 (14.1)"
[1] "hr="     "9200000"
D977V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SMPD1 MUTATED         0        0        0        0         0         0
  SMPD1 WILD-TYPE       2       15       40       30        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMPD1 MUTATED           0          2          0          2        1
  SMPD1 WILD-TYPE         3         68         53         30       37
D977V3, multiclass
            clus
vv           SMPD1 MUTATED SMPD1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMPD1 MUTATED     1   0   0   5
  SMPD1 WILD-TYPE  21  92 173  92
D977V4, multiclass
    clus
vv   SMPD1 MUTATED SMPD1 WILD-TYPE
  T1             1              21
  T2             0              92
  T3             0             173
  T4             5              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
  SMPD1 MUTATED     1   1   1   2
  SMPD1 WILD-TYPE 117 103  76  75
D977V5, multiclass
    clus
vv   SMPD1 MUTATED SMPD1 WILD-TYPE
  N0             1             117
  N1             1             103
  N2             1              76
  N3             2              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"
D977V6, binary
                 cls
clus                0   1
  SMPD1 MUTATED     5   1
  SMPD1 WILD-TYPE 341  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMPD1 MUTATED      5    1
  SMPD1 WILD-TYPE  341   28
   clus
vv  SMPD1 MUTATED SMPD1 WILD-TYPE
  0             5             341
  1             1              28
[1] 2 2
[1] FALSE
D977V7, binary
                 cls
clus                0   1
  SMPD1 MUTATED     2   4
  SMPD1 WILD-TYPE 143 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMPD1 MUTATED      2    4
  SMPD1 WILD-TYPE  143  244
        clus
vv       SMPD1 MUTATED SMPD1 WILD-TYPE
  FEMALE             2             143
  MALE               4             244
[1] 2 2
[1] FALSE
D977V8, binary
                 cls
clus                0   1
  SMPD1 MUTATED     3   1
  SMPD1 WILD-TYPE 289  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMPD1 MUTATED      3    1
  SMPD1 WILD-TYPE  289   58
     clus
vv    SMPD1 MUTATED SMPD1 WILD-TYPE
  NO              3             289
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SMPD1 MUTATED                                          0
  SMPD1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SMPD1 MUTATED                                       1
  SMPD1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMPD1 MUTATED                                                        3
  SMPD1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SMPD1 MUTATED                                                   1
  SMPD1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMPD1 MUTATED                                                                   0
  SMPD1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SMPD1 MUTATED                                                    0
  SMPD1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SMPD1 MUTATED                                                  1
  SMPD1 WILD-TYPE                                               60
D977V9, multiclass
                                                                   clus
vv                                                                  SMPD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  SMPD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SMPD1 MUTATED     3   0   0   2
  SMPD1 WILD-TYPE 308  14  15  22
D977V10, multiclass
    clus
vv   SMPD1 MUTATED SMPD1 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D977V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SMPD1 MUTATED       1                         0
  SMPD1 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMPD1 MUTATED                                           0     5
  SMPD1 WILD-TYPE                                         1   238
D977V12, multiclass
                                           clus
vv                                          SMPD1 MUTATED SMPD1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D977V13, binary
                 cls
clus                0   1
  SMPD1 MUTATED     0   5
  SMPD1 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMPD1 MUTATED      0    5
  SMPD1 WILD-TYPE    4  305
                        clus
vv                       SMPD1 MUTATED SMPD1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(978) Variable = IKBIP MUTATION ANALYSIS
D978V1, survival
                 sevent
clus2               0   1
  IKBIP MUTATED     2   1
  IKBIP WILD-TYPE 228 138
  IKBIP MUTATED IKBIP WILD-TYPE 
              3             366 
  IKBIP MUTATED IKBIP WILD-TYPE 
              1             138 
$`IKBIP MUTATED`
TCGA-D7-6525 TCGA-HF-7132 TCGA-VQ-A8P2 
       13.35        77.29        38.14 

$`IKBIP WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-D7-6526 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-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 

  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           14.22 
[1] "13.3 - 77.3 (38.1)" "0.0 - 122.3 (14.2)"
[1] "hr=" "2.2"
D978V2, continuous
[1] "Remove cluster labels:" "IKBIP MUTATED"         
clus
  IKBIP MUTATED IKBIP WILD-TYPE 
              2             384 
     TCGA-CG-4444      TCGA-CG-4460      TCGA-CG-4475      TCGA-CG-4476 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-5716      TCGA-CG-5727      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-B7-5816 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-B7-5818      TCGA-B7-A5TI      TCGA-B7-A5TJ      TCGA-B7-A5TK 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-B7-A5TN      TCGA-BR-4183      TCGA-BR-4184      TCGA-BR-4187 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4188      TCGA-BR-4191      TCGA-BR-4201      TCGA-BR-4253 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257      TCGA-BR-4267 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292      TCGA-BR-4294 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4357      TCGA-BR-4361      TCGA-BR-4362      TCGA-BR-4363 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4366      TCGA-BR-4368      TCGA-BR-4369      TCGA-BR-4370 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4371      TCGA-BR-6452      TCGA-BR-6453      TCGA-BR-6454 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457      TCGA-BR-6458 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565      TCGA-BR-6566 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707      TCGA-BR-6709 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7704      TCGA-BR-7707      TCGA-BR-7715      TCGA-BR-7716 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7717      TCGA-BR-7722      TCGA-BR-7723      TCGA-BR-7851 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7901      TCGA-BR-7957      TCGA-BR-7958      TCGA-BR-7959 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8058      TCGA-BR-8059      TCGA-BR-8060      TCGA-BR-8077 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8078      TCGA-BR-8080      TCGA-BR-8081      TCGA-BR-8284 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8285      TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8295      TCGA-BR-8297      TCGA-BR-8360      TCGA-BR-8361 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373      TCGA-BR-8380 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4J4      TCGA-BR-A4J5      TCGA-BR-A4J6      TCGA-BR-A4J7 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4QI      TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5798 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-5799      TCGA-CD-5802      TCGA-CD-5803      TCGA-CD-5804 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-5813      TCGA-CD-8524      TCGA-CD-8525      TCGA-CD-8526 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-8527      TCGA-CD-8528      TCGA-CD-8529      TCGA-CD-8530 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-8531      TCGA-CD-8532      TCGA-CD-8533      TCGA-CD-8534 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A486      TCGA-CD-A487 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-A489      TCGA-CD-A48A      TCGA-CD-A48C      TCGA-CD-A4MG 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-A4MH      TCGA-CD-A4MI      TCGA-CD-A4MJ      TCGA-CG-4300 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4306 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-4436      TCGA-CG-4437      TCGA-CG-4438      TCGA-CG-4440 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-4441      TCGA-CG-4442      TCGA-CG-4443      TCGA-CG-4449 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-4455      TCGA-CG-4462      TCGA-CG-4465      TCGA-CG-4466 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-4469      TCGA-CG-4474      TCGA-CG-4477      TCGA-CG-5717 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-5718      TCGA-CG-5719      TCGA-CG-5720      TCGA-CG-5721 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-5722      TCGA-CG-5723      TCGA-CG-5724      TCGA-CG-5725 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-5726      TCGA-CG-5728      TCGA-CG-5730      TCGA-CG-5732 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CG-5733      TCGA-CG-5734      TCGA-D7-5577      TCGA-D7-5578 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-5579      TCGA-D7-6518      TCGA-D7-6519      TCGA-D7-6520 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-6521      TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6526 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-8572      TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-8576      TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-A4YU      TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-A4Z0      TCGA-D7-A6ET      TCGA-D7-A6EV      TCGA-D7-A6EX 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-A6EY      TCGA-D7-A6EZ      TCGA-D7-A6F0      TCGA-D7-A6F2 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-D7-A747      TCGA-D7-A748      TCGA-D7-A74A      TCGA-D7-A74B 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-EQ-5647      TCGA-EQ-8122      TCGA-F1-6874      TCGA-F1-6875 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-F1-A448      TCGA-F1-A72C      TCGA-FP-7735      TCGA-FP-7829 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BE 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-FP-A4BF      TCGA-FP-A9TM      TCGA-HF-A5NB      TCGA-HJ-7597 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-8238      TCGA-HU-8243      TCGA-HU-8244      TCGA-HU-8249 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4GH      TCGA-HU-A4GJ      TCGA-HU-A4GN      TCGA-HU-A4GP 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4HB      TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-8462      TCGA-IN-8663      TCGA-IN-A6RI      TCGA-IN-A6RJ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-A6RL      TCGA-IN-A6RN      TCGA-IN-A6RO      TCGA-IN-A6RP 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-A6RR      TCGA-IN-A6RS      TCGA-IN-A7NR      TCGA-IN-A7NT 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-A7NU      TCGA-IN-AB1V      TCGA-IN-AB1X      TCGA-IP-7968 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-KB-A6F5      TCGA-KB-A6F7      TCGA-KB-A93J      TCGA-MX-A5UG 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-MX-A5UJ      TCGA-MX-A666      TCGA-R5-A7O7      TCGA-R5-A7ZE 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-R5-A7ZF      TCGA-R5-A7ZI      TCGA-R5-A7ZR      TCGA-R5-A804 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-R5-A805      TCGA-RD-A7BS      TCGA-RD-A7BT      TCGA-RD-A7BW 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-RD-A7C1      TCGA-RD-A8MV      TCGA-RD-A8MW      TCGA-RD-A8N0 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-RD-A8N1      TCGA-RD-A8N2      TCGA-RD-A8N4      TCGA-RD-A8N5 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-RD-A8N6      TCGA-RD-A8N9      TCGA-SW-A7EA      TCGA-SW-A7EB 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-A8DL      TCGA-VQ-A8DT      TCGA-VQ-A8DU      TCGA-VQ-A8DV 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-A8DZ      TCGA-VQ-A8E2      TCGA-VQ-A8E7      TCGA-VQ-A8P3 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-A8PE      TCGA-VQ-A8PK      TCGA-VQ-A8PM      TCGA-VQ-A8PQ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-A91Q      TCGA-VQ-A91U      TCGA-VQ-A91V      TCGA-VQ-A92D 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-A94T      TCGA-VQ-AA64      TCGA-VQ-AA68      TCGA-VQ-AA69 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-AA6A      TCGA-VQ-AA6B      TCGA-VQ-AA6F      TCGA-VQ-AA6G 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-AA6I      TCGA-VQ-AA6J      TCGA-VQ-AA6K      TCGA-ZA-A8F6 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "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       2       15       40       29        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IKBIP MUTATED           0          2          0          0        0
  IKBIP WILD-TYPE         3         68         53         32       38
D978V3, multiclass
            clus
vv           IKBIP MUTATED IKBIP WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IKBIP MUTATED     0   2   0   1
  IKBIP WILD-TYPE  22  90 173  96
D978V4, multiclass
    clus
vv   IKBIP MUTATED IKBIP WILD-TYPE
  T1             0              22
  T2             2              90
  T3             0             173
  T4             1              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
  IKBIP MUTATED     0   2   1   0
  IKBIP WILD-TYPE 118 102  76  77
D978V5, multiclass
    clus
vv   IKBIP MUTATED IKBIP WILD-TYPE
  N0             0             118
  N1             2             102
  N2             1              76
  N3             0              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"
D978V6, binary
                 cls
clus                0   1
  IKBIP MUTATED     3   0
  IKBIP WILD-TYPE 343  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBIP MUTATED      3    0
  IKBIP WILD-TYPE  343   29
   clus
vv  IKBIP MUTATED IKBIP WILD-TYPE
  0             3             343
  1             0              29
[1] 2 2
[1] FALSE
D978V7, binary
                 cls
clus                0   1
  IKBIP MUTATED     0   3
  IKBIP WILD-TYPE 145 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBIP MUTATED      0    3
  IKBIP WILD-TYPE  145  245
        clus
vv       IKBIP MUTATED IKBIP WILD-TYPE
  FEMALE             0             145
  MALE               3             245
[1] 2 2
[1] FALSE
D978V8, binary
                 cls
clus                0   1
  IKBIP MUTATED     1   2
  IKBIP WILD-TYPE 291  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBIP MUTATED      1    2
  IKBIP WILD-TYPE  291   57
     clus
vv    IKBIP MUTATED IKBIP WILD-TYPE
  NO              1             291
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IKBIP MUTATED                                          0
  IKBIP WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IKBIP MUTATED                                       1
  IKBIP WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IKBIP MUTATED                                                        0
  IKBIP WILD-TYPE                                                    158
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IKBIP MUTATED                                                   2
  IKBIP WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IKBIP MUTATED                                                                   0
  IKBIP WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IKBIP MUTATED                                                    0
  IKBIP WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IKBIP MUTATED                                                  0
  IKBIP WILD-TYPE                                               61
D978V9, multiclass
                                                                   clus
vv                                                                  IKBIP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        0
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  IKBIP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        158
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IKBIP MUTATED     3   0   0   0
  IKBIP WILD-TYPE 308  14  15  24
D978V10, multiclass
    clus
vv   IKBIP MUTATED IKBIP WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D978V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IKBIP MUTATED       0                         0
  IKBIP WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IKBIP MUTATED                                           0     2
  IKBIP WILD-TYPE                                         1   241
D978V12, multiclass
[1] "Remove cluster labels:" "IKBIP MUTATED"         
clus
  IKBIP MUTATED IKBIP WILD-TYPE 
              2             338 
     TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-FP-A8CX      TCGA-KB-A93G 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-MX-A663      TCGA-B7-5816      TCGA-B7-5818      TCGA-B7-A5TI 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-B7-A5TJ      TCGA-B7-A5TK      TCGA-B7-A5TN      TCGA-BR-4183 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4184      TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4201      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4257      TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4292      TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4362      TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-4369      TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6452 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6453      TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6457      TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6565      TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6707      TCGA-BR-6709      TCGA-BR-6710      TCGA-BR-6801 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-6802      TCGA-BR-6803      TCGA-BR-6852      TCGA-BR-7196 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7704      TCGA-BR-7707 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8060      TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8081      TCGA-BR-8284      TCGA-BR-8285      TCGA-BR-8286 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8289      TCGA-BR-8291      TCGA-BR-8295      TCGA-BR-8297 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8360      TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8365      TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8369      TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8373      TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8384      TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8485 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8486      TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8590      TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8677      TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8682      TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-8690      TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A453      TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4IU      TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4J1      TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J5 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4J6      TCGA-BR-A4J7      TCGA-BR-A4J8      TCGA-BR-A4PD 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QL 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-BR-A4QM      TCGA-CD-5798      TCGA-CD-5799      TCGA-CD-5800 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-5801      TCGA-CD-5802      TCGA-CD-5803      TCGA-CD-5804 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-5813      TCGA-CD-8524      TCGA-CD-8525      TCGA-CD-8526 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-8527      TCGA-CD-8528      TCGA-CD-8529      TCGA-CD-8530 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-8531      TCGA-CD-8532      TCGA-CD-8533      TCGA-CD-8534 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-8535      TCGA-CD-8536      TCGA-CD-A486      TCGA-CD-A487 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-A489      TCGA-CD-A48A      TCGA-CD-A48C      TCGA-CD-A4MG 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-CD-A4MH      TCGA-CD-A4MI      TCGA-CD-A4MJ      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-HJ-7597 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-8238      TCGA-HU-8243      TCGA-HU-8244      TCGA-HU-8249 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4GH      TCGA-HU-A4GJ      TCGA-HU-A4GN      TCGA-HU-A4GP 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-HU-A4HB      TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-8462      TCGA-IN-8663      TCGA-IN-A6RI      TCGA-IN-A6RJ 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-A6RL      TCGA-IN-A6RN      TCGA-IN-A6RO      TCGA-IN-A6RP 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-A6RR      TCGA-IN-A6RS      TCGA-IN-A7NR      TCGA-IN-A7NT 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-IN-A7NU      TCGA-IN-AB1V      TCGA-IN-AB1X      TCGA-IP-7968 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-KB-A93J      TCGA-MX-A5UG      TCGA-MX-A5UJ      TCGA-MX-A666 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-R5-A7O7      TCGA-R5-A7ZE      TCGA-R5-A7ZF      TCGA-R5-A7ZI 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-R5-A7ZR      TCGA-R5-A804      TCGA-R5-A805      TCGA-RD-A7BS 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-RD-A7BT      TCGA-RD-A7BW      TCGA-RD-A7C1      TCGA-RD-A8MV 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-RD-A8MW      TCGA-RD-A8N0      TCGA-RD-A8N1      TCGA-RD-A8N2 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-RD-A8N4      TCGA-RD-A8N5      TCGA-RD-A8N6      TCGA-RD-A8N9 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-SW-A7EA      TCGA-SW-A7EB      TCGA-VQ-A8DL      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-A91U      TCGA-VQ-A92D      TCGA-VQ-AA64 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-AA68      TCGA-VQ-AA69      TCGA-VQ-AA6A      TCGA-VQ-AA6B 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-AA6F      TCGA-VQ-AA6G      TCGA-VQ-AA6I      TCGA-VQ-AA6J 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
     TCGA-VQ-AA6K      TCGA-ZA-A8F6 
"IKBIP WILD-TYPE" "IKBIP WILD-TYPE" 
D978V13, binary
                 cls
clus                0   1
  IKBIP MUTATED     0   1
  IKBIP WILD-TYPE   4 309
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBIP MUTATED      0    1
  IKBIP WILD-TYPE    4  309
                        clus
vv                       IKBIP MUTATED IKBIP WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             1             309
[1] 2 2
[1] FALSE

Clustering(979) Variable = LEFTY1 MUTATION ANALYSIS
D979V1, survival
                  sevent
clus2                0   1
  LEFTY1 MUTATED     2   1
  LEFTY1 WILD-TYPE 228 138
  LEFTY1 MUTATED LEFTY1 WILD-TYPE 
               3              366 
  LEFTY1 MUTATED LEFTY1 WILD-TYPE 
               1              138 
$`LEFTY1 MUTATED`
TCGA-CD-A48A TCGA-IN-8663 TCGA-VQ-A8P2 
       12.43         3.39        38.14 

$`LEFTY1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  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            14.35 
[1] "3.4 - 38.1 (12.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D979V2, 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       2       15       40       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LEFTY1 MUTATED           0          1          0          0        0
  LEFTY1 WILD-TYPE         3         69         53         32       38
D979V3, multiclass
            clus
vv           LEFTY1 MUTATED LEFTY1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LEFTY1 MUTATED     0   1   1   1
  LEFTY1 WILD-TYPE  22  91 172  96
D979V4, multiclass
    clus
vv   LEFTY1 MUTATED LEFTY1 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              1              172
  T4              1               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
  LEFTY1 MUTATED     1   1   1   0
  LEFTY1 WILD-TYPE 117 103  76  77
D979V5, multiclass
    clus
vv   LEFTY1 MUTATED LEFTY1 WILD-TYPE
  N0              1              117
  N1              1              103
  N2              1               76
  N3              0               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"
D979V6, binary
                  cls
clus                 0   1
  LEFTY1 MUTATED     3   0
  LEFTY1 WILD-TYPE 343  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEFTY1 MUTATED      3    0
  LEFTY1 WILD-TYPE  343   29
   clus
vv  LEFTY1 MUTATED LEFTY1 WILD-TYPE
  0              3              343
  1              0               29
[1] 2 2
[1] FALSE
D979V7, binary
                  cls
clus                 0   1
  LEFTY1 MUTATED     0   3
  LEFTY1 WILD-TYPE 145 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEFTY1 MUTATED      0    3
  LEFTY1 WILD-TYPE  145  245
        clus
vv       LEFTY1 MUTATED LEFTY1 WILD-TYPE
  FEMALE              0              145
  MALE                3              245
[1] 2 2
[1] FALSE
D979V8, binary
                  cls
clus                 0   1
  LEFTY1 MUTATED     1   2
  LEFTY1 WILD-TYPE 291  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEFTY1 MUTATED      1    2
  LEFTY1 WILD-TYPE  291   57
     clus
vv    LEFTY1 MUTATED LEFTY1 WILD-TYPE
  NO               1              291
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LEFTY1 MUTATED                                          0
  LEFTY1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LEFTY1 MUTATED                                       0
  LEFTY1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LEFTY1 MUTATED                                                        2
  LEFTY1 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LEFTY1 MUTATED                                                   1
  LEFTY1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LEFTY1 MUTATED                                                                   0
  LEFTY1 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LEFTY1 MUTATED                                                    0
  LEFTY1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LEFTY1 MUTATED                                                  0
  LEFTY1 WILD-TYPE                                               61
D979V9, multiclass
                                                                   clus
vv                                                                  LEFTY1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  LEFTY1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LEFTY1 MUTATED     2   0   0   0
  LEFTY1 WILD-TYPE 309  14  15  24
D979V10, multiclass
[1] "Remove cluster labels:" "LEFTY1 MUTATED"        
clus
  LEFTY1 MUTATED LEFTY1 WILD-TYPE 
               2              362 
      TCGA-CG-4444       TCGA-CG-4460       TCGA-CG-4475       TCGA-CG-4476 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-5716       TCGA-CG-5727       TCGA-EQ-A4SO       TCGA-F1-6177 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-FP-A8CX       TCGA-HF-7131       TCGA-KB-A93G       TCGA-MX-A663 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-BR-4183       TCGA-BR-4184 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-4187       TCGA-BR-4188       TCGA-BR-4191       TCGA-BR-4201 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256       TCGA-BR-4257 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4292 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-4294       TCGA-BR-4357       TCGA-BR-4361       TCGA-BR-4362 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-4363       TCGA-BR-4366       TCGA-BR-4368       TCGA-BR-4369 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-4370       TCGA-BR-4371       TCGA-BR-6452       TCGA-BR-6453 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-6709       TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-6803       TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-7703       TCGA-BR-7704       TCGA-BR-7707       TCGA-BR-7715 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-7716       TCGA-BR-7717       TCGA-BR-7722       TCGA-BR-7723 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-7851       TCGA-BR-7901       TCGA-BR-7957       TCGA-BR-7958 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-7959       TCGA-BR-8058       TCGA-BR-8059       TCGA-BR-8060 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080       TCGA-BR-8081 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8284       TCGA-BR-8285       TCGA-BR-8286       TCGA-BR-8289 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8297       TCGA-BR-8360 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364       TCGA-BR-8365 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368       TCGA-BR-8369 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372       TCGA-BR-8373 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382       TCGA-BR-8384 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485       TCGA-BR-8486 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589       TCGA-BR-8590 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676       TCGA-BR-8677 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680       TCGA-BR-8682 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J5       TCGA-BR-A4J6 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-A4J7       TCGA-BR-A4J8       TCGA-BR-A4PD       TCGA-BR-A4PE 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-A4PF       TCGA-BR-A4QI       TCGA-BR-A4QL       TCGA-BR-A4QM 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CD-5800       TCGA-CD-5801       TCGA-CD-5804       TCGA-CD-8524 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8527       TCGA-CD-8528 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CD-8529       TCGA-CD-8530       TCGA-CD-8531       TCGA-CD-8532 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CD-8533       TCGA-CD-8534       TCGA-CD-8535       TCGA-CD-8536 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CD-A487       TCGA-CG-4300       TCGA-CG-4301       TCGA-CG-4304 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-4305       TCGA-CG-4306       TCGA-CG-4436       TCGA-CG-4437 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-4438       TCGA-CG-4440       TCGA-CG-4441       TCGA-CG-4442 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-4443       TCGA-CG-4449       TCGA-CG-4455       TCGA-CG-4462 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-4465       TCGA-CG-4466       TCGA-CG-4469       TCGA-CG-4474 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-4477       TCGA-CG-5717       TCGA-CG-5718       TCGA-CG-5719 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-5720       TCGA-CG-5721       TCGA-CG-5722       TCGA-CG-5723 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-5724       TCGA-CG-5725       TCGA-CG-5726       TCGA-CG-5728 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-5730       TCGA-CG-5732       TCGA-CG-5733       TCGA-CG-5734 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-5577       TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-6519       TCGA-D7-6520       TCGA-D7-6521       TCGA-D7-6522 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-6524       TCGA-D7-6525       TCGA-D7-6526       TCGA-D7-6527 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-6528       TCGA-D7-6815       TCGA-D7-6817       TCGA-D7-6818 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-6820       TCGA-D7-6822       TCGA-D7-8570       TCGA-D7-8572 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-8573       TCGA-D7-8574       TCGA-D7-8575       TCGA-D7-8576 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-8578       TCGA-D7-8579       TCGA-D7-A4YT       TCGA-D7-A4YU 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-A4YV       TCGA-D7-A4YX       TCGA-D7-A4YY       TCGA-D7-A4Z0 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-A6ET       TCGA-D7-A6EV       TCGA-D7-A6EX       TCGA-D7-A6EY 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-A6EZ       TCGA-D7-A6F0       TCGA-D7-A6F2       TCGA-D7-A747 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-A748       TCGA-D7-A74A       TCGA-D7-A74B       TCGA-EQ-5647 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-F1-6874       TCGA-F1-6875       TCGA-F1-A448       TCGA-F1-A72C 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-FP-7735       TCGA-FP-7829       TCGA-FP-7998       TCGA-FP-8099 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-FP-8209       TCGA-FP-8211       TCGA-FP-8631       TCGA-FP-A4BE 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-FP-A4BF       TCGA-FP-A9TM       TCGA-HF-7132       TCGA-HF-7133 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HF-7134       TCGA-HF-7136       TCGA-HF-A5NB       TCGA-HJ-7597 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-8238       TCGA-HU-8243       TCGA-HU-8244       TCGA-HU-8249 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-8602       TCGA-HU-8604       TCGA-HU-8608       TCGA-HU-8610 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6       TCGA-HU-A4G9 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-A4GC       TCGA-HU-A4GD       TCGA-HU-A4GF       TCGA-HU-A4GH 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-A4GJ       TCGA-HU-A4GN       TCGA-HU-A4GP       TCGA-HU-A4GQ 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX       TCGA-HU-A4GY 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3       TCGA-HU-A4H4 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8       TCGA-HU-A4HB 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-8462       TCGA-IN-A6RI 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-IN-A6RJ       TCGA-IN-A6RL       TCGA-IN-A6RN       TCGA-IN-A6RO 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-IN-A6RP       TCGA-IN-A6RR       TCGA-IN-A6RS       TCGA-IN-A7NR 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-IN-A7NT       TCGA-IN-A7NU       TCGA-IN-AB1V       TCGA-IN-AB1X 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-IP-7968       TCGA-KB-A6F5       TCGA-KB-A6F7       TCGA-KB-A93J 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-MX-A5UG       TCGA-MX-A5UJ       TCGA-R5-A7ZI       TCGA-RD-A7BS 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-RD-A7BT       TCGA-RD-A7BW       TCGA-RD-A7C1       TCGA-RD-A8MV 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-RD-A8MW       TCGA-RD-A8N0       TCGA-RD-A8N1       TCGA-RD-A8N2 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-RD-A8N4       TCGA-RD-A8N5       TCGA-RD-A8N6       TCGA-RD-A8N9 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-SW-A7EA       TCGA-SW-A7EB       TCGA-VQ-A8DL       TCGA-VQ-A8DT 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-VQ-A8DU       TCGA-VQ-A8DV       TCGA-VQ-A8DZ       TCGA-VQ-A8E2 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-VQ-A8E7       TCGA-VQ-A8P3       TCGA-VQ-A8PE       TCGA-VQ-A8PK 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-VQ-A8PM       TCGA-VQ-A8PQ       TCGA-VQ-A91Q       TCGA-VQ-A91U 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-VQ-A91V       TCGA-VQ-A92D       TCGA-VQ-A94T       TCGA-VQ-AA64 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-VQ-AA68       TCGA-VQ-AA69       TCGA-VQ-AA6A       TCGA-VQ-AA6B 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-VQ-AA6F       TCGA-VQ-AA6G       TCGA-VQ-AA6I       TCGA-VQ-AA6J 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-VQ-AA6K       TCGA-ZA-A8F6 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
D979V11, continuous
[1] "Remove cluster labels:" "LEFTY1 MUTATED"        
clus
  LEFTY1 MUTATED LEFTY1 WILD-TYPE 
               2              341 
      TCGA-CG-4444       TCGA-CG-4460       TCGA-CG-4475       TCGA-CG-4476 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-5727       TCGA-EQ-A4SO       TCGA-F1-6177       TCGA-FP-A8CX 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HF-7131       TCGA-KB-A93G       TCGA-MX-A663       TCGA-B7-5816 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-B7-A5TI       TCGA-BR-4183       TCGA-BR-4184       TCGA-BR-4188 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-4191       TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4361 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-4362       TCGA-BR-4368       TCGA-BR-6452       TCGA-BR-6453 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564       TCGA-BR-6565 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-6709       TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-6803       TCGA-BR-6852       TCGA-BR-7196       TCGA-BR-7197 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-7703       TCGA-BR-7704       TCGA-BR-7707       TCGA-BR-7715 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-7716       TCGA-BR-7717       TCGA-BR-7722       TCGA-BR-7723 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-7851       TCGA-BR-7901       TCGA-BR-7957       TCGA-BR-7958 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-7959       TCGA-BR-8058       TCGA-BR-8059       TCGA-BR-8060 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080       TCGA-BR-8081 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8284       TCGA-BR-8285       TCGA-BR-8286       TCGA-BR-8289 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8297       TCGA-BR-8360 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364       TCGA-BR-8365 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368       TCGA-BR-8369 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372       TCGA-BR-8373 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382       TCGA-BR-8384 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485       TCGA-BR-8486 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589       TCGA-BR-8590 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676       TCGA-BR-8677 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680       TCGA-BR-8682 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687       TCGA-BR-8690 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452       TCGA-BR-A453 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS       TCGA-BR-A4IU 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ       TCGA-BR-A4J1 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J5       TCGA-BR-A4J6 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-A4J8       TCGA-BR-A4PD       TCGA-BR-A4PE       TCGA-BR-A4PF 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-BR-A4QI       TCGA-BR-A4QL       TCGA-BR-A4QM       TCGA-CD-5804 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CD-8525       TCGA-CD-8526       TCGA-CD-8531       TCGA-CD-8535 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CD-A487       TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-4436       TCGA-CG-4437       TCGA-CG-4438       TCGA-CG-4440 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-4441       TCGA-CG-4442       TCGA-CG-4443       TCGA-CG-4449 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-4455       TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-4469       TCGA-CG-4474       TCGA-CG-4477       TCGA-CG-5717 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-5718       TCGA-CG-5719       TCGA-CG-5720       TCGA-CG-5721 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-5722       TCGA-CG-5723       TCGA-CG-5724       TCGA-CG-5725 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-5726       TCGA-CG-5728       TCGA-CG-5730       TCGA-CG-5732 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-CG-5733       TCGA-CG-5734       TCGA-D7-5577       TCGA-D7-5578 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-5579       TCGA-D7-6518       TCGA-D7-6519       TCGA-D7-6520 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-6521       TCGA-D7-6522       TCGA-D7-6524       TCGA-D7-6525 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-6526       TCGA-D7-6527       TCGA-D7-6528       TCGA-D7-6815 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-6817       TCGA-D7-6818       TCGA-D7-6820       TCGA-D7-6822 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-8570       TCGA-D7-8572       TCGA-D7-8573       TCGA-D7-8574 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-8575       TCGA-D7-8576       TCGA-D7-8578       TCGA-D7-8579 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-A4YT       TCGA-D7-A4YU       TCGA-D7-A4YV       TCGA-D7-A4YX 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-A4YY       TCGA-D7-A4Z0       TCGA-D7-A6ET       TCGA-D7-A6EV 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-A6EX       TCGA-D7-A6EY       TCGA-D7-A6EZ       TCGA-D7-A6F0 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-A6F2       TCGA-D7-A747       TCGA-D7-A748       TCGA-D7-A74A 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-D7-A74B       TCGA-EQ-5647       TCGA-EQ-8122       TCGA-F1-6874 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-F1-6875       TCGA-F1-A448       TCGA-F1-A72C       TCGA-FP-7735 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-FP-7829       TCGA-FP-7916       TCGA-FP-7998       TCGA-FP-8099 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-FP-8209       TCGA-FP-8210       TCGA-FP-8211       TCGA-FP-8631 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-FP-A4BE       TCGA-FP-A4BF       TCGA-FP-A9TM       TCGA-HF-7132 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HF-7133       TCGA-HF-7134       TCGA-HF-7136       TCGA-HF-A5NB 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HJ-7597       TCGA-HU-8238       TCGA-HU-8243       TCGA-HU-8244 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-8249       TCGA-HU-8602       TCGA-HU-8604       TCGA-HU-8608 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-8610       TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-A4G8       TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-A4GF       TCGA-HU-A4GH       TCGA-HU-A4GJ       TCGA-HU-A4GN 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-A4GP       TCGA-HU-A4GQ       TCGA-HU-A4GT       TCGA-HU-A4GU 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-A4GX       TCGA-HU-A4GY       TCGA-HU-A4H0       TCGA-HU-A4H2 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-A4H3       TCGA-HU-A4H4       TCGA-HU-A4H5       TCGA-HU-A4H6 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-HU-A4H8       TCGA-HU-A4HB       TCGA-HU-A4HD       TCGA-IN-7806 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-IN-7808       TCGA-IN-8462       TCGA-IN-A6RI       TCGA-IN-A6RJ 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-IN-A6RL       TCGA-IN-A6RN       TCGA-IN-A6RO       TCGA-IN-A6RP 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-IN-A6RR       TCGA-IN-A6RS       TCGA-IN-A7NR       TCGA-IN-A7NT 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-IN-A7NU       TCGA-IN-AB1V       TCGA-IN-AB1X       TCGA-IP-7968 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-KB-A6F5       TCGA-KB-A6F7       TCGA-KB-A93J       TCGA-MX-A5UG 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-MX-A5UJ       TCGA-R5-A7ZI       TCGA-RD-A7BS       TCGA-RD-A7BT 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-RD-A7BW       TCGA-RD-A7C1       TCGA-RD-A8MV       TCGA-RD-A8MW 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-RD-A8N0       TCGA-RD-A8N1       TCGA-RD-A8N2       TCGA-RD-A8N4 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-RD-A8N5       TCGA-RD-A8N6       TCGA-RD-A8N9       TCGA-SW-A7EA 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-SW-A7EB       TCGA-VQ-A8DL       TCGA-VQ-A8DT       TCGA-VQ-A8DU 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-VQ-A8DV       TCGA-VQ-A8DZ       TCGA-VQ-A8E2       TCGA-VQ-A8E7 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-VQ-A8P3       TCGA-VQ-A8PE       TCGA-VQ-A8PK       TCGA-VQ-A8PM 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-VQ-A8PQ       TCGA-VQ-A91Q       TCGA-VQ-A91U       TCGA-VQ-A91V 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-VQ-A92D       TCGA-VQ-A94T       TCGA-VQ-AA64       TCGA-VQ-AA68 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-VQ-AA69       TCGA-VQ-AA6A       TCGA-VQ-AA6B       TCGA-VQ-AA6F 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-VQ-AA6G       TCGA-VQ-AA6I       TCGA-VQ-AA6J       TCGA-VQ-AA6K 
"LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" "LEFTY1 WILD-TYPE" 
      TCGA-ZA-A8F6 
"LEFTY1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  LEFTY1 MUTATED       1                         0
  LEFTY1 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LEFTY1 MUTATED                                           0     2
  LEFTY1 WILD-TYPE                                         1   241
D979V12, multiclass
                                           clus
vv                                          LEFTY1 MUTATED LEFTY1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D979V13, binary
                  cls
clus                 0   1
  LEFTY1 MUTATED     0   2
  LEFTY1 WILD-TYPE   4 308
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEFTY1 MUTATED      0    2
  LEFTY1 WILD-TYPE    4  308
                        clus
vv                       LEFTY1 MUTATED LEFTY1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              2              308
[1] 2 2
[1] FALSE

Clustering(980) Variable = PIWIL2 MUTATION ANALYSIS
D980V1, survival
                  sevent
clus2                0   1
  PIWIL2 MUTATED     6   3
  PIWIL2 WILD-TYPE 224 136
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
               9              360 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
               3              136 
$`PIWIL2 MUTATED`
TCGA-BR-4201 TCGA-BR-8368 TCGA-BR-A4QL TCGA-CG-5721 TCGA-D7-A6EY TCGA-HU-A4GT 
       30.90         4.31        16.14         6.02        11.44         6.51 
TCGA-R5-A7ZI TCGA-SW-A7EA TCGA-VQ-A8P2 
       74.53        19.04        38.14 

$`PIWIL2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
            4.31             0.00 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
           74.53           122.30 
  PIWIL2 MUTATED PIWIL2 WILD-TYPE 
           16.14            14.22 
[1] "4.3 - 74.5 (16.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D980V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIWIL2 MUTATED         0        0        2        0         1         0
  PIWIL2 WILD-TYPE       2       15       38       30        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIWIL2 MUTATED           0          1          2          0        2
  PIWIL2 WILD-TYPE         3         69         51         32       36
D980V3, multiclass
            clus
vv           PIWIL2 MUTATED PIWIL2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              2               51
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIWIL2 MUTATED     0   3   3   3
  PIWIL2 WILD-TYPE  22  89 170  94
D980V4, multiclass
    clus
vv   PIWIL2 MUTATED PIWIL2 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              3              170
  T4              3               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
  PIWIL2 MUTATED     3   3   0   2
  PIWIL2 WILD-TYPE 115 101  77  75
D980V5, multiclass
    clus
vv   PIWIL2 MUTATED PIWIL2 WILD-TYPE
  N0              3              115
  N1              3              101
  N2              0               77
  N3              2               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"
D980V6, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED     8   1
  PIWIL2 WILD-TYPE 338  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED      8    1
  PIWIL2 WILD-TYPE  338   28
   clus
vv  PIWIL2 MUTATED PIWIL2 WILD-TYPE
  0              8              338
  1              1               28
[1] 2 2
[1] FALSE
D980V7, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED     7   2
  PIWIL2 WILD-TYPE 138 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED      7    2
  PIWIL2 WILD-TYPE  138  246
        clus
vv       PIWIL2 MUTATED PIWIL2 WILD-TYPE
  FEMALE              7              138
  MALE                2              246
[1] 2 2
[1] FALSE
D980V8, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED     8   1
  PIWIL2 WILD-TYPE 284  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED      8    1
  PIWIL2 WILD-TYPE  284   58
     clus
vv    PIWIL2 MUTATED PIWIL2 WILD-TYPE
  NO               8              284
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PIWIL2 MUTATED                                          0
  PIWIL2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PIWIL2 MUTATED                                       2
  PIWIL2 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIWIL2 MUTATED                                                        3
  PIWIL2 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PIWIL2 MUTATED                                                   1
  PIWIL2 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIWIL2 MUTATED                                                                   1
  PIWIL2 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PIWIL2 MUTATED                                                    0
  PIWIL2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PIWIL2 MUTATED                                                  2
  PIWIL2 WILD-TYPE                                               59
D980V9, multiclass
                                                                   clus
vv                                                                  PIWIL2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  PIWIL2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PIWIL2 MUTATED     8   0   0   1
  PIWIL2 WILD-TYPE 303  14  15  23
D980V10, multiclass
    clus
vv   PIWIL2 MUTATED PIWIL2 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D980V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PIWIL2 MUTATED       1                         0
  PIWIL2 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIWIL2 MUTATED                                           0     7
  PIWIL2 WILD-TYPE                                         1   236
D980V12, multiclass
                                           clus
vv                                          PIWIL2 MUTATED PIWIL2 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D980V13, binary
                  cls
clus                 0   1
  PIWIL2 MUTATED     1   6
  PIWIL2 WILD-TYPE   3 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIWIL2 MUTATED      1    6
  PIWIL2 WILD-TYPE    3  304
                        clus
vv                       PIWIL2 MUTATED PIWIL2 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(981) Variable = ZNF7 MUTATION ANALYSIS
D981V1, survival
                sevent
clus2              0   1
  ZNF7 MUTATED     7   1
  ZNF7 WILD-TYPE 223 138
  ZNF7 MUTATED ZNF7 WILD-TYPE 
             8            361 
  ZNF7 MUTATED ZNF7 WILD-TYPE 
             1            138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-5579 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-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-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-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 

  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         14.070 
[1] "6.0 - 38.1 (22.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.9"
D981V2, 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       1       14       39       29        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF7 MUTATED           0          1          0          1        1
  ZNF7 WILD-TYPE         3         69         53         31       37
D981V3, multiclass
            clus
vv           ZNF7 MUTATED ZNF7 WILD-TYPE
  STAGE I               1              1
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZNF7 MUTATED     2   3   1   3
  ZNF7 WILD-TYPE  20  89 172  94
D981V4, multiclass
    clus
vv   ZNF7 MUTATED ZNF7 WILD-TYPE
  T1            2             20
  T2            3             89
  T3            1            172
  T4            3             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
  ZNF7 MUTATED     3   4   1   0
  ZNF7 WILD-TYPE 115 100  76  77
D981V5, multiclass
    clus
vv   ZNF7 MUTATED ZNF7 WILD-TYPE
  N0            3            115
  N1            4            100
  N2            1             76
  N3            0             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"
D981V6, binary
                cls
clus               0   1
  ZNF7 MUTATED     8   0
  ZNF7 WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF7 MUTATED      8    0
  ZNF7 WILD-TYPE  338   29
   clus
vv  ZNF7 MUTATED ZNF7 WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D981V7, binary
                cls
clus               0   1
  ZNF7 MUTATED     4   5
  ZNF7 WILD-TYPE 141 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF7 MUTATED      4    5
  ZNF7 WILD-TYPE  141  243
        clus
vv       ZNF7 MUTATED ZNF7 WILD-TYPE
  FEMALE            4            141
  MALE              5            243
[1] 2 2
[1] FALSE
D981V8, binary
                cls
clus               0   1
  ZNF7 MUTATED     7   2
  ZNF7 WILD-TYPE 285  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF7 MUTATED      7    2
  ZNF7 WILD-TYPE  285   57
     clus
vv    ZNF7 MUTATED ZNF7 WILD-TYPE
  NO             7            285
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF7 MUTATED                                          0
  ZNF7 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF7 MUTATED                                       1
  ZNF7 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF7 MUTATED                                                        5
  ZNF7 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF7 MUTATED                                                   1
  ZNF7 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF7 MUTATED                                                                   1
  ZNF7 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF7 MUTATED                                                    0
  ZNF7 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF7 MUTATED                                                  1
  ZNF7 WILD-TYPE                                               60
D981V9, multiclass
                                                                   clus
vv                                                                  ZNF7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  ZNF7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ZNF7 MUTATED     8   0   0   1
  ZNF7 WILD-TYPE 303  14  15  23
D981V10, multiclass
    clus
vv   ZNF7 MUTATED ZNF7 WILD-TYPE
  R0            8            303
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D981V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ZNF7 MUTATED       2                         2
  ZNF7 WILD-TYPE    85                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF7 MUTATED                                           0     3
  ZNF7 WILD-TYPE                                         1   240
D981V12, multiclass
                                           clus
vv                                          ZNF7 MUTATED ZNF7 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D981V13, binary
                cls
clus               0   1
  ZNF7 MUTATED     0   6
  ZNF7 WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF7 MUTATED      0    6
  ZNF7 WILD-TYPE    4  304
                        clus
vv                       ZNF7 MUTATED ZNF7 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(982) Variable = CHST4 MUTATION ANALYSIS
D982V1, survival
                 sevent
clus2               0   1
  CHST4 MUTATED     4   3
  CHST4 WILD-TYPE 226 136
  CHST4 MUTATED CHST4 WILD-TYPE 
              7             362 
  CHST4 MUTATED CHST4 WILD-TYPE 
              3             136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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           14.12 
[1] "0.1 - 38.1 (22.7)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D982V2, 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       2       14       40       30        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHST4 MUTATED           0          1          1          1        0
  CHST4 WILD-TYPE         3         69         52         31       38
D982V3, multiclass
            clus
vv           CHST4 MUTATED CHST4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CHST4 MUTATED     1   1   3   2
  CHST4 WILD-TYPE  21  91 170  95
D982V4, multiclass
    clus
vv   CHST4 MUTATED CHST4 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             3             170
  T4             2              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
  CHST4 MUTATED     2   2   2   1
  CHST4 WILD-TYPE 116 102  75  76
D982V5, multiclass
    clus
vv   CHST4 MUTATED CHST4 WILD-TYPE
  N0             2             116
  N1             2             102
  N2             2              75
  N3             1              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"
D982V6, binary
                 cls
clus                0   1
  CHST4 MUTATED     7   0
  CHST4 WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHST4 MUTATED      7    0
  CHST4 WILD-TYPE  339   29
   clus
vv  CHST4 MUTATED CHST4 WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D982V7, binary
                 cls
clus                0   1
  CHST4 MUTATED     4   3
  CHST4 WILD-TYPE 141 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHST4 MUTATED      4    3
  CHST4 WILD-TYPE  141  245
        clus
vv       CHST4 MUTATED CHST4 WILD-TYPE
  FEMALE             4             141
  MALE               3             245
[1] 2 2
[1] FALSE
D982V8, binary
                 cls
clus                0   1
  CHST4 MUTATED     6   1
  CHST4 WILD-TYPE 286  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHST4 MUTATED      6    1
  CHST4 WILD-TYPE  286   58
     clus
vv    CHST4 MUTATED CHST4 WILD-TYPE
  NO              6             286
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CHST4 MUTATED                                          0
  CHST4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CHST4 MUTATED                                       2
  CHST4 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CHST4 MUTATED                                                        1
  CHST4 WILD-TYPE                                                    157
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CHST4 MUTATED                                                   1
  CHST4 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CHST4 MUTATED                                                                   0
  CHST4 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CHST4 MUTATED                                                    0
  CHST4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CHST4 MUTATED                                                  3
  CHST4 WILD-TYPE                                               58
D982V9, multiclass
                                                                   clus
vv                                                                  CHST4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  CHST4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CHST4 MUTATED     5   0   0   0
  CHST4 WILD-TYPE 306  14  15  24
D982V10, multiclass
    clus
vv   CHST4 MUTATED CHST4 WILD-TYPE
  R0             5             306
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D982V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CHST4 MUTATED       5                         0
  CHST4 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CHST4 MUTATED                                           0     2
  CHST4 WILD-TYPE                                         1   241
D982V12, multiclass
                                           clus
vv                                          CHST4 MUTATED CHST4 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D982V13, binary
                 cls
clus                0   1
  CHST4 MUTATED     0   6
  CHST4 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHST4 MUTATED      0    6
  CHST4 WILD-TYPE    4  304
                        clus
vv                       CHST4 MUTATED CHST4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(983) Variable = SCGB1A1 MUTATION ANALYSIS
D983V1, survival
                   sevent
clus2                 0   1
  SCGB1A1 MUTATED     3   0
  SCGB1A1 WILD-TYPE 227 139
  SCGB1A1 MUTATED SCGB1A1 WILD-TYPE 
                3               366 
  SCGB1A1 MUTATED SCGB1A1 WILD-TYPE 
                0               139 
$`SCGB1A1 MUTATED`
TCGA-BR-8361 TCGA-HU-A4GT TCGA-VQ-A8P2 
       31.10         6.51        38.14 

$`SCGB1A1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  SCGB1A1 MUTATED SCGB1A1 WILD-TYPE 
             6.51              0.00 
  SCGB1A1 MUTATED SCGB1A1 WILD-TYPE 
            38.14            122.30 
  SCGB1A1 MUTATED SCGB1A1 WILD-TYPE 
            31.10             14.22 
[1] "6.5 - 38.1 (31.1)"  "0.0 - 122.3 (14.2)"
[1] "hr="     "9100000"
D983V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCGB1A1 MUTATED         0        0        0        0         1         0
  SCGB1A1 WILD-TYPE       2       15       40       30        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SCGB1A1 MUTATED           0          1          0          1        0
  SCGB1A1 WILD-TYPE         3         69         53         31       38
D983V3, multiclass
            clus
vv           SCGB1A1 MUTATED SCGB1A1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SCGB1A1 MUTATED     0   0   1   2
  SCGB1A1 WILD-TYPE  22  92 172  95
D983V4, multiclass
    clus
vv   SCGB1A1 MUTATED SCGB1A1 WILD-TYPE
  T1               0                22
  T2               0                92
  T3               1               172
  T4               2                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
  SCGB1A1 MUTATED     1   1   1   0
  SCGB1A1 WILD-TYPE 117 103  76  77
D983V5, multiclass
    clus
vv   SCGB1A1 MUTATED SCGB1A1 WILD-TYPE
  N0               1               117
  N1               1               103
  N2               1                76
  N3               0                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"
D983V6, binary
                   cls
clus                  0   1
  SCGB1A1 MUTATED     3   0
  SCGB1A1 WILD-TYPE 343  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SCGB1A1 MUTATED      3    0
  SCGB1A1 WILD-TYPE  343   29
   clus
vv  SCGB1A1 MUTATED SCGB1A1 WILD-TYPE
  0               3               343
  1               0                29
[1] 2 2
[1] FALSE
D983V7, binary
                   cls
clus                  0   1
  SCGB1A1 MUTATED     2   1
  SCGB1A1 WILD-TYPE 143 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SCGB1A1 MUTATED      2    1
  SCGB1A1 WILD-TYPE  143  247
        clus
vv       SCGB1A1 MUTATED SCGB1A1 WILD-TYPE
  FEMALE               2               143
  MALE                 1               247
[1] 2 2
[1] FALSE
D983V8, binary
                   cls
clus                  0   1
  SCGB1A1 MUTATED     2   1
  SCGB1A1 WILD-TYPE 290  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SCGB1A1 MUTATED      2    1
  SCGB1A1 WILD-TYPE  290   58
     clus
vv    SCGB1A1 MUTATED SCGB1A1 WILD-TYPE
  NO                2               290
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SCGB1A1 MUTATED                                          0
  SCGB1A1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SCGB1A1 MUTATED                                       0
  SCGB1A1 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SCGB1A1 MUTATED                                                        1
  SCGB1A1 WILD-TYPE                                                    157
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SCGB1A1 MUTATED                                                   1
  SCGB1A1 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SCGB1A1 MUTATED                                                                   0
  SCGB1A1 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SCGB1A1 MUTATED                                                    0
  SCGB1A1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SCGB1A1 MUTATED                                                  1
  SCGB1A1 WILD-TYPE                                               60
D983V9, multiclass
                                                                   clus
vv                                                                  SCGB1A1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  SCGB1A1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SCGB1A1 MUTATED     3   0   0   0
  SCGB1A1 WILD-TYPE 308  14  15  24
D983V10, multiclass
    clus
vv   SCGB1A1 MUTATED SCGB1A1 WILD-TYPE
  R0               3               308
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D983V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SCGB1A1 MUTATED       1                         0
  SCGB1A1 WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SCGB1A1 MUTATED                                           0     2
  SCGB1A1 WILD-TYPE                                         1   241
D983V12, multiclass
                                           clus
vv                                          SCGB1A1 MUTATED SCGB1A1 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   2               241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D983V13, binary
                   cls
clus                  0   1
  SCGB1A1 MUTATED     0   2
  SCGB1A1 WILD-TYPE   4 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SCGB1A1 MUTATED      0    2
  SCGB1A1 WILD-TYPE    4  308
                        clus
vv                       SCGB1A1 MUTATED SCGB1A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               2               308
[1] 2 2
[1] FALSE

Clustering(984) Variable = ZIM3 MUTATION ANALYSIS
D984V1, survival
                sevent
clus2              0   1
  ZIM3 MUTATED     2   8
  ZIM3 WILD-TYPE 228 131
  ZIM3 MUTATED ZIM3 WILD-TYPE 
            10            359 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
             8            131 
$`ZIM3 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6802 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8284 
        6.97         6.61        30.90        14.43         9.60         8.05 
TCGA-CG-5726 TCGA-D7-A6EY TCGA-HU-A4GH TCGA-RD-A8N6 
       28.96        11.44        11.77         8.94 

$`ZIM3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8060 TCGA-BR-8077 
        9.07        29.56        33.21        37.25        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       29.59        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-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-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-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-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-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 

  ZIM3 MUTATED ZIM3 WILD-TYPE 
          6.61           0.00 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
          30.9          122.3 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
         10.52          14.66 
[1] "6.6 - 30.9 (10.5)"  "0.0 - 122.3 (14.7)"
[1] "hr=" "2.8"
D984V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZIM3 MUTATED         0        2        0        0         0         0
  ZIM3 WILD-TYPE       2       13       40       30        37        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZIM3 MUTATED           2          3          1          2        1
  ZIM3 WILD-TYPE         1         67         52         30       37
D984V3, multiclass
            clus
vv           ZIM3 MUTATED ZIM3 WILD-TYPE
  STAGE I               0              2
  STAGE IA              2             13
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             0             52
  STAGE III             2              1
  STAGE IIIA            3             67
  STAGE IIIB            1             52
  STAGE IIIC            2             30
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZIM3 MUTATED     2   2   3   4
  ZIM3 WILD-TYPE  20  90 170  93
D984V4, multiclass
    clus
vv   ZIM3 MUTATED ZIM3 WILD-TYPE
  T1            2             20
  T2            2             90
  T3            3            170
  T4            4             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
  ZIM3 MUTATED     2   3   3   3
  ZIM3 WILD-TYPE 116 101  74  74
D984V5, multiclass
    clus
vv   ZIM3 MUTATED ZIM3 WILD-TYPE
  N0            2            116
  N1            3            101
  N2            3             74
  N3            3             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"
D984V6, binary
                cls
clus               0   1
  ZIM3 MUTATED    10   0
  ZIM3 WILD-TYPE 336  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZIM3 MUTATED     10    0
  ZIM3 WILD-TYPE  336   29
   clus
vv  ZIM3 MUTATED ZIM3 WILD-TYPE
  0           10            336
  1            0             29
[1] 2 2
[1] FALSE
D984V7, binary
                cls
clus               0   1
  ZIM3 MUTATED     6   5
  ZIM3 WILD-TYPE 139 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZIM3 MUTATED      6    5
  ZIM3 WILD-TYPE  139  243
        clus
vv       ZIM3 MUTATED ZIM3 WILD-TYPE
  FEMALE            6            139
  MALE              5            243
[1] 2 2
[1] FALSE
D984V8, binary
                cls
clus               0   1
  ZIM3 MUTATED     9   0
  ZIM3 WILD-TYPE 283  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZIM3 MUTATED      9    0
  ZIM3 WILD-TYPE  283   59
     clus
vv    ZIM3 MUTATED ZIM3 WILD-TYPE
  NO             9            283
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZIM3 MUTATED                                          0
  ZIM3 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZIM3 MUTATED                                       0
  ZIM3 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZIM3 MUTATED                                                        4
  ZIM3 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZIM3 MUTATED                                                   1
  ZIM3 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZIM3 MUTATED                                                                   4
  ZIM3 WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZIM3 MUTATED                                                    0
  ZIM3 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZIM3 MUTATED                                                  2
  ZIM3 WILD-TYPE                                               59
D984V9, multiclass
                                                                   clus
vv                                                                  ZIM3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  ZIM3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ZIM3 MUTATED     8   0   0   3
  ZIM3 WILD-TYPE 303  14  15  21
D984V10, multiclass
    clus
vv   ZIM3 MUTATED ZIM3 WILD-TYPE
  R0            8            303
  R1            0             14
  R2            0             15
  RX            3             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D984V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ZIM3 MUTATED       1                         0
  ZIM3 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZIM3 MUTATED                                           0     9
  ZIM3 WILD-TYPE                                         1   234
D984V12, multiclass
                                           clus
vv                                          ZIM3 MUTATED ZIM3 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D984V13, binary
                cls
clus               0   1
  ZIM3 MUTATED     0  10
  ZIM3 WILD-TYPE   4 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZIM3 MUTATED      0   10
  ZIM3 WILD-TYPE    4  300
                        clus
vv                       ZIM3 MUTATED ZIM3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           10            300
[1] 2 2
[1] FALSE

Clustering(985) Variable = ACTG2 MUTATION ANALYSIS
D985V1, survival
                 sevent
clus2               0   1
  ACTG2 MUTATED     5   3
  ACTG2 WILD-TYPE 225 136
  ACTG2 MUTATED ACTG2 WILD-TYPE 
              8             361 
  ACTG2 MUTATED ACTG2 WILD-TYPE 
              3             136 
$`ACTG2 MUTATED`
TCGA-BR-4184 TCGA-BR-6455 TCGA-BR-8690 TCGA-CG-4306 TCGA-CG-4437 TCGA-HU-A4G8 
        6.97        13.87        10.68         1.02         8.05        22.68 
TCGA-MX-A5UJ TCGA-R5-A7O7 
       19.73        45.67 

$`ACTG2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-6456 TCGA-BR-6457 
        9.57         6.61        34.68        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-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-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-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-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       15.95         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-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-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 

  ACTG2 MUTATED ACTG2 WILD-TYPE 
           1.02            0.00 
  ACTG2 MUTATED ACTG2 WILD-TYPE 
          45.67          122.30 
  ACTG2 MUTATED ACTG2 WILD-TYPE 
         12.275          14.430 
[1] "1.0 - 45.7 (12.3)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.2"
D985V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACTG2 MUTATED         0        0        0        1         0         2
  ACTG2 WILD-TYPE       2       15       40       29        37        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACTG2 MUTATED           0          3          1          0        2
  ACTG2 WILD-TYPE         3         67         52         32       36
D985V3, multiclass
            clus
vv           ACTG2 MUTATED ACTG2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACTG2 MUTATED     0   1   7   1
  ACTG2 WILD-TYPE  22  91 166  96
D985V4, multiclass
    clus
vv   ACTG2 MUTATED ACTG2 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             7             166
  T4             1              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
  ACTG2 MUTATED     1   6   2   1
  ACTG2 WILD-TYPE 117  98  75  76
D985V5, multiclass
    clus
vv   ACTG2 MUTATED ACTG2 WILD-TYPE
  N0             1             117
  N1             6              98
  N2             2              75
  N3             1              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"
D985V6, binary
                 cls
clus                0   1
  ACTG2 MUTATED     7   2
  ACTG2 WILD-TYPE 339  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTG2 MUTATED      7    2
  ACTG2 WILD-TYPE  339   27
   clus
vv  ACTG2 MUTATED ACTG2 WILD-TYPE
  0             7             339
  1             2              27
[1] 2 2
[1] FALSE
D985V7, binary
                 cls
clus                0   1
  ACTG2 MUTATED     5   5
  ACTG2 WILD-TYPE 140 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTG2 MUTATED      5    5
  ACTG2 WILD-TYPE  140  243
        clus
vv       ACTG2 MUTATED ACTG2 WILD-TYPE
  FEMALE             5             140
  MALE               5             243
[1] 2 2
[1] FALSE
D985V8, binary
                 cls
clus                0   1
  ACTG2 MUTATED     7   0
  ACTG2 WILD-TYPE 285  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTG2 MUTATED      7    0
  ACTG2 WILD-TYPE  285   59
     clus
vv    ACTG2 MUTATED ACTG2 WILD-TYPE
  NO              7             285
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ACTG2 MUTATED                                          0
  ACTG2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ACTG2 MUTATED                                       1
  ACTG2 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ACTG2 MUTATED                                                        6
  ACTG2 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ACTG2 MUTATED                                                   0
  ACTG2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ACTG2 MUTATED                                                                   1
  ACTG2 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ACTG2 MUTATED                                                    0
  ACTG2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ACTG2 MUTATED                                                  2
  ACTG2 WILD-TYPE                                               59
D985V9, multiclass
                                                                   clus
vv                                                                  ACTG2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  ACTG2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ACTG2 MUTATED     4   0   1   3
  ACTG2 WILD-TYPE 307  14  14  21
D985V10, multiclass
    clus
vv   ACTG2 MUTATED ACTG2 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D985V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ACTG2 MUTATED       1                         0
  ACTG2 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ACTG2 MUTATED                                           0     7
  ACTG2 WILD-TYPE                                         1   236
D985V12, multiclass
                                           clus
vv                                          ACTG2 MUTATED ACTG2 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D985V13, binary
                 cls
clus                0   1
  ACTG2 MUTATED     1   7
  ACTG2 WILD-TYPE   3 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTG2 MUTATED      1    7
  ACTG2 WILD-TYPE    3  303
                        clus
vv                       ACTG2 MUTATED ACTG2 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(986) Variable = PIK3CB MUTATION ANALYSIS
D986V1, survival
                  sevent
clus2                0   1
  PIK3CB MUTATED     8   3
  PIK3CB WILD-TYPE 222 136
  PIK3CB MUTATED PIK3CB WILD-TYPE 
              11              358 
  PIK3CB MUTATED PIK3CB WILD-TYPE 
               3              136 
$`PIK3CB MUTATED`
TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8285 TCGA-BR-8364 
        6.97         9.67        34.68        29.59         0.56        22.19 
TCGA-BR-8680 TCGA-BR-A4PD TCGA-CD-8525 TCGA-CG-5728 TCGA-HU-A4GU 
       31.96        20.65        12.59        65.10         6.58 

$`PIK3CB WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-8286 TCGA-BR-8289 
        0.69         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-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-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-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-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-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 

  PIK3CB MUTATED PIK3CB WILD-TYPE 
            0.56             0.00 
  PIK3CB MUTATED PIK3CB WILD-TYPE 
            65.1            122.3 
  PIK3CB MUTATED PIK3CB WILD-TYPE 
           20.65            14.22 
[1] "0.6 - 65.1 (20.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D986V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIK3CB MUTATED         0        0        1        0         1         3
  PIK3CB WILD-TYPE       2       15       39       30        36        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3CB MUTATED           0          2          0          2        1
  PIK3CB WILD-TYPE         3         68         53         30       37
D986V3, multiclass
            clus
vv           PIK3CB MUTATED PIK3CB WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3CB MUTATED     0   1   4   5
  PIK3CB WILD-TYPE  22  91 169  92
D986V4, multiclass
    clus
vv   PIK3CB MUTATED PIK3CB WILD-TYPE
  T1              0               22
  T2              1               91
  T3              4              169
  T4              5               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
  PIK3CB MUTATED     4   3   2   1
  PIK3CB WILD-TYPE 114 101  75  76
D986V5, multiclass
    clus
vv   PIK3CB MUTATED PIK3CB WILD-TYPE
  N0              4              114
  N1              3              101
  N2              2               75
  N3              1               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"
D986V6, binary
                  cls
clus                 0   1
  PIK3CB MUTATED     9   1
  PIK3CB WILD-TYPE 337  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CB MUTATED      9    1
  PIK3CB WILD-TYPE  337   28
   clus
vv  PIK3CB MUTATED PIK3CB WILD-TYPE
  0              9              337
  1              1               28
[1] 2 2
[1] FALSE
D986V7, binary
                  cls
clus                 0   1
  PIK3CB MUTATED     8   3
  PIK3CB WILD-TYPE 137 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CB MUTATED      8    3
  PIK3CB WILD-TYPE  137  245
        clus
vv       PIK3CB MUTATED PIK3CB WILD-TYPE
  FEMALE              8              137
  MALE                3              245
[1] 2 2
[1] FALSE
D986V8, binary
                  cls
clus                 0   1
  PIK3CB MUTATED     9   1
  PIK3CB WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CB MUTATED      9    1
  PIK3CB WILD-TYPE  283   58
     clus
vv    PIK3CB MUTATED PIK3CB WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PIK3CB MUTATED                                          0
  PIK3CB WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PIK3CB MUTATED                                       2
  PIK3CB WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIK3CB MUTATED                                                        5
  PIK3CB WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PIK3CB MUTATED                                                   1
  PIK3CB WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIK3CB MUTATED                                                                   2
  PIK3CB WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PIK3CB MUTATED                                                    0
  PIK3CB WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PIK3CB MUTATED                                                  1
  PIK3CB WILD-TYPE                                               60
D986V9, multiclass
                                                                   clus
vv                                                                  PIK3CB MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  PIK3CB WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PIK3CB MUTATED     9   0   0   2
  PIK3CB WILD-TYPE 302  14  15  22
D986V10, multiclass
    clus
vv   PIK3CB MUTATED PIK3CB WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D986V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PIK3CB MUTATED       3                         0
  PIK3CB WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIK3CB MUTATED                                           0     7
  PIK3CB WILD-TYPE                                         1   236
D986V12, multiclass
                                           clus
vv                                          PIK3CB MUTATED PIK3CB WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D986V13, binary
                  cls
clus                 0   1
  PIK3CB MUTATED     0  10
  PIK3CB WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CB MUTATED      0   10
  PIK3CB WILD-TYPE    4  300
                        clus
vv                       PIK3CB MUTATED PIK3CB WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(987) Variable = LAT2 MUTATION ANALYSIS
D987V1, survival
                sevent
clus2              0   1
  LAT2 MUTATED     4   4
  LAT2 WILD-TYPE 226 135
  LAT2 MUTATED LAT2 WILD-TYPE 
             8            361 
  LAT2 MUTATED LAT2 WILD-TYPE 
             4            135 
$`LAT2 MUTATED`
TCGA-BR-4184 TCGA-CD-A4MI TCGA-CG-5728 TCGA-CG-5730 TCGA-D7-A6EY TCGA-IN-A6RI 
        6.97        11.77        65.10         4.01        11.44        18.38 
TCGA-IN-A6RR TCGA-VQ-A8P2 
        6.74        38.14 

$`LAT2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       15.02        28.96        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-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-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 

  LAT2 MUTATED LAT2 WILD-TYPE 
          4.01           0.00 
  LAT2 MUTATED LAT2 WILD-TYPE 
          65.1          122.3 
  LAT2 MUTATED LAT2 WILD-TYPE 
        11.605         14.430 
[1] "4.0 - 65.1 (11.6)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.4"
D987V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LAT2 MUTATED         1        0        1        0         0         0
  LAT2 WILD-TYPE       1       15       39       30        37        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LAT2 MUTATED           0          4          1          0        1
  LAT2 WILD-TYPE         3         66         52         32       37
D987V3, multiclass
            clus
vv           LAT2 MUTATED LAT2 WILD-TYPE
  STAGE I               1              1
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            4             66
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LAT2 MUTATED     1   2   4   1
  LAT2 WILD-TYPE  21  90 169  96
D987V4, multiclass
    clus
vv   LAT2 MUTATED LAT2 WILD-TYPE
  T1            1             21
  T2            2             90
  T3            4            169
  T4            1             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
  LAT2 MUTATED     2   5   0   1
  LAT2 WILD-TYPE 116  99  77  76
D987V5, multiclass
    clus
vv   LAT2 MUTATED LAT2 WILD-TYPE
  N0            2            116
  N1            5             99
  N2            0             77
  N3            1             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"
D987V6, binary
                cls
clus               0   1
  LAT2 MUTATED     6   1
  LAT2 WILD-TYPE 340  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  LAT2 MUTATED      6    1
  LAT2 WILD-TYPE  340   28
   clus
vv  LAT2 MUTATED LAT2 WILD-TYPE
  0            6            340
  1            1             28
[1] 2 2
[1] FALSE
D987V7, binary
                cls
clus               0   1
  LAT2 MUTATED     3   5
  LAT2 WILD-TYPE 142 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  LAT2 MUTATED      3    5
  LAT2 WILD-TYPE  142  243
        clus
vv       LAT2 MUTATED LAT2 WILD-TYPE
  FEMALE            3            142
  MALE              5            243
[1] 2 2
[1] FALSE
D987V8, binary
                cls
clus               0   1
  LAT2 MUTATED     5   1
  LAT2 WILD-TYPE 287  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  LAT2 MUTATED      5    1
  LAT2 WILD-TYPE  287   58
     clus
vv    LAT2 MUTATED LAT2 WILD-TYPE
  NO             5            287
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LAT2 MUTATED                                          0
  LAT2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LAT2 MUTATED                                       0
  LAT2 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LAT2 MUTATED                                                        4
  LAT2 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LAT2 MUTATED                                                   1
  LAT2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LAT2 MUTATED                                                                   2
  LAT2 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LAT2 MUTATED                                                    0
  LAT2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LAT2 MUTATED                                                  1
  LAT2 WILD-TYPE                                               60
D987V9, multiclass
                                                                   clus
vv                                                                  LAT2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  LAT2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LAT2 MUTATED     5   0   1   1
  LAT2 WILD-TYPE 306  14  14  23
D987V10, multiclass
    clus
vv   LAT2 MUTATED LAT2 WILD-TYPE
  R0            5            306
  R1            0             14
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D987V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  LAT2 MUTATED       1                         0
  LAT2 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LAT2 MUTATED                                           0     5
  LAT2 WILD-TYPE                                         1   238
D987V12, multiclass
                                           clus
vv                                          LAT2 MUTATED LAT2 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D987V13, binary
                cls
clus               0   1
  LAT2 MUTATED     0   5
  LAT2 WILD-TYPE   4 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  LAT2 MUTATED      0    5
  LAT2 WILD-TYPE    4  305
                        clus
vv                       LAT2 MUTATED LAT2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(988) Variable = ZBTB40 MUTATION ANALYSIS
D988V1, survival
                  sevent
clus2                0   1
  ZBTB40 MUTATED     8   3
  ZBTB40 WILD-TYPE 222 136
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
              11              358 
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
               3              136 
$`ZBTB40 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8370 TCGA-BR-8676 TCGA-CD-A48C TCGA-CG-5733 
       30.90        34.68         3.32         7.53        11.61        21.07 
TCGA-F1-A448 TCGA-HF-7132 TCGA-HU-A4GU TCGA-IN-A6RJ TCGA-VQ-A8P2 
       21.27        77.29         6.58        12.46        38.14 

$`ZBTB40 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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 

  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
            3.32             0.00 
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
           77.29           122.30 
  ZBTB40 MUTATED ZBTB40 WILD-TYPE 
           21.07            14.22 
[1] "3.3 - 77.3 (21.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.7"
D988V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZBTB40 MUTATED         0        1        0        1         1         2
  ZBTB40 WILD-TYPE       2       14       40       29        36        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB40 MUTATED           0          2          3          0        0
  ZBTB40 WILD-TYPE         3         68         50         32       38
D988V3, multiclass
            clus
vv           ZBTB40 MUTATED ZBTB40 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              3               50
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB40 MUTATED     1   3   6   1
  ZBTB40 WILD-TYPE  21  89 167  96
D988V4, multiclass
    clus
vv   ZBTB40 MUTATED ZBTB40 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              6              167
  T4              1               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
  ZBTB40 MUTATED     2   4   1   3
  ZBTB40 WILD-TYPE 116 100  76  74
D988V5, multiclass
    clus
vv   ZBTB40 MUTATED ZBTB40 WILD-TYPE
  N0              2              116
  N1              4              100
  N2              1               76
  N3              3               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"
D988V6, binary
                  cls
clus                 0   1
  ZBTB40 MUTATED    11   0
  ZBTB40 WILD-TYPE 335  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB40 MUTATED     11    0
  ZBTB40 WILD-TYPE  335   29
   clus
vv  ZBTB40 MUTATED ZBTB40 WILD-TYPE
  0             11              335
  1              0               29
[1] 2 2
[1] FALSE
D988V7, binary
                  cls
clus                 0   1
  ZBTB40 MUTATED     4   7
  ZBTB40 WILD-TYPE 141 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB40 MUTATED      4    7
  ZBTB40 WILD-TYPE  141  241
        clus
vv       ZBTB40 MUTATED ZBTB40 WILD-TYPE
  FEMALE              4              141
  MALE                7              241
[1] 2 2
[1] FALSE
D988V8, binary
                  cls
clus                 0   1
  ZBTB40 MUTATED     8   3
  ZBTB40 WILD-TYPE 284  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB40 MUTATED      8    3
  ZBTB40 WILD-TYPE  284   56
     clus
vv    ZBTB40 MUTATED ZBTB40 WILD-TYPE
  NO               8              284
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZBTB40 MUTATED                                          0
  ZBTB40 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZBTB40 MUTATED                                       2
  ZBTB40 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZBTB40 MUTATED                                                        4
  ZBTB40 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZBTB40 MUTATED                                                   3
  ZBTB40 WILD-TYPE                                                18
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZBTB40 MUTATED                                                                   2
  ZBTB40 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZBTB40 MUTATED                                                    0
  ZBTB40 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZBTB40 MUTATED                                                  0
  ZBTB40 WILD-TYPE                                               61
D988V9, multiclass
                                                                   clus
vv                                                                  ZBTB40 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  ZBTB40 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZBTB40 MUTATED     9   0   0   1
  ZBTB40 WILD-TYPE 302  14  15  23
D988V10, multiclass
    clus
vv   ZBTB40 MUTATED ZBTB40 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D988V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZBTB40 MUTATED       2                         0
  ZBTB40 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZBTB40 MUTATED                                           0     7
  ZBTB40 WILD-TYPE                                         1   236
D988V12, multiclass
                                           clus
vv                                          ZBTB40 MUTATED ZBTB40 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D988V13, binary
                  cls
clus                 0   1
  ZBTB40 MUTATED     1   7
  ZBTB40 WILD-TYPE   3 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB40 MUTATED      1    7
  ZBTB40 WILD-TYPE    3  303
                        clus
vv                       ZBTB40 MUTATED ZBTB40 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(989) Variable = PIGO MUTATION ANALYSIS
D989V1, survival
                sevent
clus2              0   1
  PIGO MUTATED     8   1
  PIGO WILD-TYPE 222 138
  PIGO MUTATED PIGO WILD-TYPE 
             9            360 
  PIGO MUTATED PIGO WILD-TYPE 
             1            138 
$`PIGO MUTATED`
TCGA-BR-6452 TCGA-BR-8366 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-8529 TCGA-CD-8536 
       34.68         0.95         1.12        31.96        12.30        12.43 
TCGA-CD-A4MI TCGA-HF-7132 TCGA-HU-A4H3 
       11.77        77.29        29.00 

$`PIGO WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  PIGO MUTATED PIGO WILD-TYPE 
          0.95           0.00 
  PIGO MUTATED PIGO WILD-TYPE 
         77.29         122.30 
  PIGO MUTATED PIGO WILD-TYPE 
         12.43          14.35 
[1] "0.9 - 77.3 (12.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "4.1"
D989V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIGO MUTATED         0        0        0        2         3         0
  PIGO WILD-TYPE       2       15       40       28        34        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIGO MUTATED           0          1          0          1        2
  PIGO WILD-TYPE         3         69         53         31       36
D989V3, multiclass
            clus
vv           PIGO MUTATED PIGO WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              2             28
  STAGE IIA             3             34
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PIGO MUTATED     0   1   5   3
  PIGO WILD-TYPE  22  91 168  94
D989V4, multiclass
    clus
vv   PIGO MUTATED PIGO WILD-TYPE
  T1            0             22
  T2            1             91
  T3            5            168
  T4            3             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
  PIGO MUTATED     5   2   1   1
  PIGO WILD-TYPE 113 102  76  76
D989V5, multiclass
    clus
vv   PIGO MUTATED PIGO WILD-TYPE
  N0            5            113
  N1            2            102
  N2            1             76
  N3            1             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"
D989V6, binary
                cls
clus               0   1
  PIGO MUTATED     7   2
  PIGO WILD-TYPE 339  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGO MUTATED      7    2
  PIGO WILD-TYPE  339   27
   clus
vv  PIGO MUTATED PIGO WILD-TYPE
  0            7            339
  1            2             27
[1] 2 2
[1] FALSE
D989V7, binary
                cls
clus               0   1
  PIGO MUTATED     4   5
  PIGO WILD-TYPE 141 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGO MUTATED      4    5
  PIGO WILD-TYPE  141  243
        clus
vv       PIGO MUTATED PIGO WILD-TYPE
  FEMALE            4            141
  MALE              5            243
[1] 2 2
[1] FALSE
D989V8, binary
                cls
clus               0   1
  PIGO MUTATED     6   2
  PIGO WILD-TYPE 286  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGO MUTATED      6    2
  PIGO WILD-TYPE  286   57
     clus
vv    PIGO MUTATED PIGO WILD-TYPE
  NO             6            286
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PIGO MUTATED                                          0
  PIGO WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PIGO MUTATED                                       1
  PIGO WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIGO MUTATED                                                        5
  PIGO WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PIGO MUTATED                                                   2
  PIGO WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIGO MUTATED                                                                   0
  PIGO WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PIGO MUTATED                                                    0
  PIGO WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PIGO MUTATED                                                  1
  PIGO WILD-TYPE                                               60
D989V9, multiclass
                                                                   clus
vv                                                                  PIGO MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  PIGO WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PIGO MUTATED     8   0   0   0
  PIGO WILD-TYPE 303  14  15  24
D989V10, multiclass
    clus
vv   PIGO MUTATED PIGO WILD-TYPE
  R0            8            303
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D989V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PIGO MUTATED       5                         0
  PIGO WILD-TYPE    82                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIGO MUTATED                                           0     3
  PIGO WILD-TYPE                                         1   240
D989V12, multiclass
                                           clus
vv                                          PIGO MUTATED PIGO WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D989V13, binary
                cls
clus               0   1
  PIGO MUTATED     0   8
  PIGO WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGO MUTATED      0    8
  PIGO WILD-TYPE    4  302
                        clus
vv                       PIGO MUTATED PIGO WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(990) Variable = NAA16 MUTATION ANALYSIS
D990V1, survival
                 sevent
clus2               0   1
  NAA16 MUTATED     6   3
  NAA16 WILD-TYPE 224 136
  NAA16 MUTATED NAA16 WILD-TYPE 
              9             360 
  NAA16 MUTATED NAA16 WILD-TYPE 
              3             136 
$`NAA16 MUTATED`
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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  NAA16 MUTATED NAA16 WILD-TYPE 
           1.02            0.00 
  NAA16 MUTATED NAA16 WILD-TYPE 
         105.07          122.30 
  NAA16 MUTATED NAA16 WILD-TYPE 
          26.70           14.07 
[1] "1.0 - 105.1 (26.7)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D990V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NAA16 MUTATED         0        0        0        2         1         1
  NAA16 WILD-TYPE       2       15       40       28        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NAA16 MUTATED           0          1          1          0        2
  NAA16 WILD-TYPE         3         69         52         32       36
D990V3, multiclass
            clus
vv           NAA16 MUTATED NAA16 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               2              28
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NAA16 MUTATED     0   2   3   3
  NAA16 WILD-TYPE  22  90 170  94
D990V4, multiclass
    clus
vv   NAA16 MUTATED NAA16 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             3             170
  T4             3              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
  NAA16 MUTATED     2   3   2   1
  NAA16 WILD-TYPE 116 101  75  76
D990V5, multiclass
    clus
vv   NAA16 MUTATED NAA16 WILD-TYPE
  N0             2             116
  N1             3             101
  N2             2              75
  N3             1              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"
D990V6, binary
                 cls
clus                0   1
  NAA16 MUTATED     7   2
  NAA16 WILD-TYPE 339  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED      7    2
  NAA16 WILD-TYPE  339   27
   clus
vv  NAA16 MUTATED NAA16 WILD-TYPE
  0             7             339
  1             2              27
[1] 2 2
[1] FALSE
D990V7, binary
                 cls
clus                0   1
  NAA16 MUTATED     4   5
  NAA16 WILD-TYPE 141 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED      4    5
  NAA16 WILD-TYPE  141  243
        clus
vv       NAA16 MUTATED NAA16 WILD-TYPE
  FEMALE             4             141
  MALE               5             243
[1] 2 2
[1] FALSE
D990V8, binary
                 cls
clus                0   1
  NAA16 MUTATED     7   1
  NAA16 WILD-TYPE 285  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED      7    1
  NAA16 WILD-TYPE  285   58
     clus
vv    NAA16 MUTATED NAA16 WILD-TYPE
  NO              7             285
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NAA16 MUTATED                                          0
  NAA16 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NAA16 MUTATED                                       1
  NAA16 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NAA16 MUTATED                                                        5
  NAA16 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NAA16 MUTATED                                                   2
  NAA16 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NAA16 MUTATED                                                                   0
  NAA16 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NAA16 MUTATED                                                    0
  NAA16 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NAA16 MUTATED                                                  1
  NAA16 WILD-TYPE                                               60
D990V9, multiclass
                                                                   clus
vv                                                                  NAA16 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  NAA16 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NAA16 MUTATED     7   0   1   1
  NAA16 WILD-TYPE 304  14  14  23
D990V10, multiclass
    clus
vv   NAA16 MUTATED NAA16 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D990V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NAA16 MUTATED       1                         0
  NAA16 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NAA16 MUTATED                                           0     5
  NAA16 WILD-TYPE                                         1   238
D990V12, multiclass
                                           clus
vv                                          NAA16 MUTATED NAA16 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D990V13, binary
                 cls
clus                0   1
  NAA16 MUTATED     0   5
  NAA16 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA16 MUTATED      0    5
  NAA16 WILD-TYPE    4  305
                        clus
vv                       NAA16 MUTATED NAA16 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(991) Variable = NRN1 MUTATION ANALYSIS
D991V1, survival
                sevent
clus2              0   1
  NRN1 MUTATED     2   0
  NRN1 WILD-TYPE 228 139
  NRN1 MUTATED NRN1 WILD-TYPE 
             2            367 
  NRN1 MUTATED NRN1 WILD-TYPE 
             0            139 
$`NRN1 MUTATED`
TCGA-BR-8286 TCGA-VQ-A8P2 
       29.42        38.14 

$`NRN1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  NRN1 MUTATED NRN1 WILD-TYPE 
         29.42           0.00 
  NRN1 MUTATED NRN1 WILD-TYPE 
         38.14         122.30 
  NRN1 MUTATED NRN1 WILD-TYPE 
         33.78          14.17 
[1] "29.4 - 38.1 (33.8)" "0.0 - 122.3 (14.2)"
[1] "Remove cluster labels:" "NRN1 MUTATED"          
D991V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NRN1 MUTATED         1        0        0        1         0         0
  NRN1 WILD-TYPE       1       15       40       29        37        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NRN1 MUTATED           0          1          0          0        0
  NRN1 WILD-TYPE         3         69         53         32       38
D991V3, multiclass
            clus
vv           NRN1 MUTATED NRN1 WILD-TYPE
  STAGE I               1              1
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             0             37
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NRN1 MUTATED     1   0   1   1
  NRN1 WILD-TYPE  21  92 172  96
D991V4, multiclass
    clus
vv   NRN1 MUTATED NRN1 WILD-TYPE
  T1            1             21
  T2            0             92
  T3            1            172
  T4            1             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
  NRN1 MUTATED     1   2   0   0
  NRN1 WILD-TYPE 117 102  77  77
D991V5, multiclass
    clus
vv   NRN1 MUTATED NRN1 WILD-TYPE
  N0            1            117
  N1            2            102
  N2            0             77
  N3            0             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"
D991V6, binary
                cls
clus               0   1
  NRN1 MUTATED     2   0
  NRN1 WILD-TYPE 344  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRN1 MUTATED      2    0
  NRN1 WILD-TYPE  344   29
   clus
vv  NRN1 MUTATED NRN1 WILD-TYPE
  0            2            344
  1            0             29
[1] 2 2
[1] FALSE
D991V7, binary
                cls
clus               0   1
  NRN1 MUTATED     0   3
  NRN1 WILD-TYPE 145 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRN1 MUTATED      0    3
  NRN1 WILD-TYPE  145  245
        clus
vv       NRN1 MUTATED NRN1 WILD-TYPE
  FEMALE            0            145
  MALE              3            245
[1] 2 2
[1] FALSE
D991V8, binary
                cls
clus               0   1
  NRN1 MUTATED     2   1
  NRN1 WILD-TYPE 290  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRN1 MUTATED      2    1
  NRN1 WILD-TYPE  290   58
     clus
vv    NRN1 MUTATED NRN1 WILD-TYPE
  NO             2            290
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NRN1 MUTATED                                          0
  NRN1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NRN1 MUTATED                                       0
  NRN1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NRN1 MUTATED                                                        2
  NRN1 WILD-TYPE                                                    156
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NRN1 MUTATED                                                   1
  NRN1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NRN1 MUTATED                                                                   0
  NRN1 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NRN1 MUTATED                                                    0
  NRN1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NRN1 MUTATED                                                  0
  NRN1 WILD-TYPE                                               61
D991V9, multiclass
                                                                   clus
vv                                                                  NRN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  NRN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NRN1 MUTATED     3   0   0   0
  NRN1 WILD-TYPE 308  14  15  24
D991V10, multiclass
    clus
vv   NRN1 MUTATED NRN1 WILD-TYPE
  R0            3            308
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D991V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NRN1 MUTATED       0                         1
  NRN1 WILD-TYPE    87                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NRN1 MUTATED                                           0     2
  NRN1 WILD-TYPE                                         1   241
D991V12, multiclass
                                           clus
vv                                          NRN1 MUTATED NRN1 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D991V13, binary
                cls
clus               0   1
  NRN1 MUTATED     0   2
  NRN1 WILD-TYPE   4 308
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRN1 MUTATED      0    2
  NRN1 WILD-TYPE    4  308
                        clus
vv                       NRN1 MUTATED NRN1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            2            308
[1] 2 2
[1] FALSE

Clustering(992) Variable = EPN1 MUTATION ANALYSIS
D992V1, survival
                sevent
clus2              0   1
  EPN1 MUTATED     5   3
  EPN1 WILD-TYPE 225 136
  EPN1 MUTATED EPN1 WILD-TYPE 
             8            361 
  EPN1 MUTATED EPN1 WILD-TYPE 
             3            136 
$`EPN1 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8382 TCGA-BR-8487 
       21.99        34.68        44.94        36.16        25.05         1.12 
TCGA-CG-5733 TCGA-HU-A4H8 
       21.07        14.07 

$`EPN1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-7704 TCGA-BR-7707 TCGA-BR-7715 
       31.20        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-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-D7-6525 
       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-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 

  EPN1 MUTATED EPN1 WILD-TYPE 
          1.12           0.00 
  EPN1 MUTATED EPN1 WILD-TYPE 
         44.94         122.30 
  EPN1 MUTATED EPN1 WILD-TYPE 
         23.52          14.07 
[1] "1.1 - 44.9 (23.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.4"
D992V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPN1 MUTATED         0        1        1        0         3         0
  EPN1 WILD-TYPE       2       14       39       30        34        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPN1 MUTATED           0          1          0          1        1
  EPN1 WILD-TYPE         3         69         53         31       37
D992V3, multiclass
            clus
vv           EPN1 MUTATED EPN1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             3             34
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EPN1 MUTATED     2   1   3   2
  EPN1 WILD-TYPE  20  91 170  95
D992V4, multiclass
    clus
vv   EPN1 MUTATED EPN1 WILD-TYPE
  T1            2             20
  T2            1             91
  T3            3            170
  T4            2             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
  EPN1 MUTATED     4   2   1   1
  EPN1 WILD-TYPE 114 102  76  76
D992V5, multiclass
    clus
vv   EPN1 MUTATED EPN1 WILD-TYPE
  N0            4            114
  N1            2            102
  N2            1             76
  N3            1             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"
D992V6, binary
                cls
clus               0   1
  EPN1 MUTATED     7   1
  EPN1 WILD-TYPE 339  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPN1 MUTATED      7    1
  EPN1 WILD-TYPE  339   28
   clus
vv  EPN1 MUTATED EPN1 WILD-TYPE
  0            7            339
  1            1             28
[1] 2 2
[1] FALSE
D992V7, binary
                cls
clus               0   1
  EPN1 MUTATED     6   2
  EPN1 WILD-TYPE 139 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPN1 MUTATED      6    2
  EPN1 WILD-TYPE  139  246
        clus
vv       EPN1 MUTATED EPN1 WILD-TYPE
  FEMALE            6            139
  MALE              2            246
[1] 2 2
[1] FALSE
D992V8, binary
                cls
clus               0   1
  EPN1 MUTATED     8   0
  EPN1 WILD-TYPE 284  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPN1 MUTATED      8    0
  EPN1 WILD-TYPE  284   59
     clus
vv    EPN1 MUTATED EPN1 WILD-TYPE
  NO             8            284
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EPN1 MUTATED                                          0
  EPN1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EPN1 MUTATED                                       0
  EPN1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPN1 MUTATED                                                        4
  EPN1 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EPN1 MUTATED                                                   0
  EPN1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPN1 MUTATED                                                                   2
  EPN1 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EPN1 MUTATED                                                    1
  EPN1 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EPN1 MUTATED                                                  1
  EPN1 WILD-TYPE                                               60
D992V9, multiclass
                                                                   clus
vv                                                                  EPN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  EPN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EPN1 MUTATED     7   0   1   0
  EPN1 WILD-TYPE 304  14  14  24
D992V10, multiclass
    clus
vv   EPN1 MUTATED EPN1 WILD-TYPE
  R0            7            304
  R1            0             14
  R2            1             14
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D992V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  EPN1 MUTATED       1                         0
  EPN1 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPN1 MUTATED                                           0     5
  EPN1 WILD-TYPE                                         1   238
D992V12, multiclass
                                           clus
vv                                          EPN1 MUTATED EPN1 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D992V13, binary
                cls
clus               0   1
  EPN1 MUTATED     0   6
  EPN1 WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPN1 MUTATED      0    6
  EPN1 WILD-TYPE    4  304
                        clus
vv                       EPN1 MUTATED EPN1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(993) Variable = PPARG MUTATION ANALYSIS
D993V1, survival
                 sevent
clus2               0   1
  PPARG MUTATED     3   0
  PPARG WILD-TYPE 227 139
  PPARG MUTATED PPARG WILD-TYPE 
              3             366 
  PPARG MUTATED PPARG WILD-TYPE 
              0             139 
$`PPARG MUTATED`
TCGA-BR-6852 TCGA-CG-4305 TCGA-HU-A4H8 
       44.94        15.95        14.07 

$`PPARG WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  PPARG MUTATED PPARG WILD-TYPE 
          14.07            0.00 
  PPARG MUTATED PPARG WILD-TYPE 
          44.94          122.30 
  PPARG MUTATED PPARG WILD-TYPE 
          15.95           14.22 
[1] "14.1 - 44.9 (15.9)" "0.0 - 122.3 (14.2)"
[1] "hr="     "9100000"
D993V2, 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       2       15       39       29        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPARG MUTATED           0          0          0          0        0
  PPARG WILD-TYPE         3         70         53         32       38
D993V3, multiclass
            clus
vv           PPARG MUTATED PPARG WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PPARG MUTATED     1   1   2   0
  PPARG WILD-TYPE  21  91 171  97
D993V4, multiclass
    clus
vv   PPARG MUTATED PPARG WILD-TYPE
  T1             1              21
  T2             1              91
  T3             2             171
  T4             0              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
  PPARG MUTATED     1   2   0   0
  PPARG WILD-TYPE 117 102  77  77
D993V5, multiclass
    clus
vv   PPARG MUTATED PPARG WILD-TYPE
  N0             1             117
  N1             2             102
  N2             0              77
  N3             0              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"
D993V6, binary
                 cls
clus                0   1
  PPARG MUTATED     3   0
  PPARG WILD-TYPE 343  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPARG MUTATED      3    0
  PPARG WILD-TYPE  343   29
   clus
vv  PPARG MUTATED PPARG WILD-TYPE
  0             3             343
  1             0              29
[1] 2 2
[1] FALSE
D993V7, binary
                 cls
clus                0   1
  PPARG MUTATED     2   2
  PPARG WILD-TYPE 143 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPARG MUTATED      2    2
  PPARG WILD-TYPE  143  246
        clus
vv       PPARG MUTATED PPARG WILD-TYPE
  FEMALE             2             143
  MALE               2             246
[1] 2 2
[1] FALSE
D993V8, binary
                 cls
clus                0   1
  PPARG MUTATED     3   0
  PPARG WILD-TYPE 289  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPARG MUTATED      3    0
  PPARG WILD-TYPE  289   59
     clus
vv    PPARG MUTATED PPARG WILD-TYPE
  NO              3             289
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PPARG MUTATED                                          0
  PPARG WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PPARG MUTATED                                       0
  PPARG WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPARG MUTATED                                                        3
  PPARG WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PPARG MUTATED                                                   0
  PPARG WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPARG MUTATED                                                                   0
  PPARG WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PPARG MUTATED                                                    0
  PPARG WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PPARG MUTATED                                                  1
  PPARG WILD-TYPE                                               60
D993V9, multiclass
                                                                   clus
vv                                                                  PPARG MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  PPARG WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PPARG MUTATED     3   0   0   1
  PPARG WILD-TYPE 308  14  15  23
D993V10, multiclass
    clus
vv   PPARG MUTATED PPARG WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D993V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PPARG MUTATED       1                         0
  PPARG WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPARG MUTATED                                           0     2
  PPARG WILD-TYPE                                         1   241
D993V12, multiclass
                                           clus
vv                                          PPARG MUTATED PPARG WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D993V13, binary
                 cls
clus                0   1
  PPARG MUTATED     0   3
  PPARG WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPARG MUTATED      0    3
  PPARG WILD-TYPE    4  307
                        clus
vv                       PPARG MUTATED PPARG WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(994) Variable = C1ORF141 MUTATION ANALYSIS
D994V1, survival
                    sevent
clus2                  0   1
  C1ORF141 MUTATED     8   2
  C1ORF141 WILD-TYPE 222 137
  C1ORF141 MUTATED C1ORF141 WILD-TYPE 
                10                359 
  C1ORF141 MUTATED C1ORF141 WILD-TYPE 
                 2                137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  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             14.070 
[1] "3.5 - 115.7 (30.8)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.7"
D994V2, 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       2       15       38       29        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF141 MUTATED           0          0          1          3        1
  C1ORF141 WILD-TYPE         3         70         52         29       37
D994V3, multiclass
            clus
vv           C1ORF141 MUTATED C1ORF141 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  2                 38
  STAGE II                  1                 29
  STAGE IIA                 1                 36
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                1                 52
  STAGE IIIC                3                 29
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C1ORF141 MUTATED     0   3   4   5
  C1ORF141 WILD-TYPE  22  89 169  92
D994V4, multiclass
    clus
vv   C1ORF141 MUTATED C1ORF141 WILD-TYPE
  T1                0                 22
  T2                3                 89
  T3                4                169
  T4                5                 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
  C1ORF141 MUTATED     5   0   3   3
  C1ORF141 WILD-TYPE 113 104  74  74
D994V5, multiclass
    clus
vv   C1ORF141 MUTATED C1ORF141 WILD-TYPE
  N0                5                113
  N1                0                104
  N2                3                 74
  N3                3                 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"
D994V6, binary
                    cls
clus                   0   1
  C1ORF141 MUTATED    10   2
  C1ORF141 WILD-TYPE 336  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF141 MUTATED     10    2
  C1ORF141 WILD-TYPE  336   27
   clus
vv  C1ORF141 MUTATED C1ORF141 WILD-TYPE
  0               10                336
  1                2                 27
[1] 2 2
[1] FALSE
D994V7, binary
                    cls
clus                   0   1
  C1ORF141 MUTATED     5   7
  C1ORF141 WILD-TYPE 140 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF141 MUTATED      5    7
  C1ORF141 WILD-TYPE  140  241
        clus
vv       C1ORF141 MUTATED C1ORF141 WILD-TYPE
  FEMALE                5                140
  MALE                  7                241
[1] 2 2
[1] FALSE
D994V8, binary
                    cls
clus                   0   1
  C1ORF141 MUTATED     8   2
  C1ORF141 WILD-TYPE 284  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF141 MUTATED      8    2
  C1ORF141 WILD-TYPE  284   57
     clus
vv    C1ORF141 MUTATED C1ORF141 WILD-TYPE
  NO                 8                284
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C1ORF141 MUTATED                                          0
  C1ORF141 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C1ORF141 MUTATED                                       3
  C1ORF141 WILD-TYPE                                    67
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C1ORF141 MUTATED                                                        5
  C1ORF141 WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C1ORF141 MUTATED                                                   1
  C1ORF141 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C1ORF141 MUTATED                                                                   2
  C1ORF141 WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C1ORF141 MUTATED                                                    0
  C1ORF141 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C1ORF141 MUTATED                                                  1
  C1ORF141 WILD-TYPE                                               60
D994V9, multiclass
                                                                   clus
vv                                                                  C1ORF141 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  C1ORF141 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C1ORF141 MUTATED     7   2   0   1
  C1ORF141 WILD-TYPE 304  12  15  23
D994V10, multiclass
    clus
vv   C1ORF141 MUTATED C1ORF141 WILD-TYPE
  R0                7                304
  R1                2                 12
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D994V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C1ORF141 MUTATED       3                         0
  C1ORF141 WILD-TYPE    84                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C1ORF141 MUTATED                                           0     7
  C1ORF141 WILD-TYPE                                         1   236
D994V12, multiclass
                                           clus
vv                                          C1ORF141 MUTATED C1ORF141 WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D994V13, binary
                    cls
clus                   0   1
  C1ORF141 MUTATED     0  10
  C1ORF141 WILD-TYPE   4 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF141 MUTATED      0   10
  C1ORF141 WILD-TYPE    4  300
                        clus
vv                       C1ORF141 MUTATED C1ORF141 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               10                300
[1] 2 2
[1] FALSE

Clustering(995) Variable = EXOSC10 MUTATION ANALYSIS
D995V1, survival
                   sevent
clus2                 0   1
  EXOSC10 MUTATED     6   4
  EXOSC10 WILD-TYPE 224 135
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
               10               359 
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
                4               135 
$`EXOSC10 MUTATED`
TCGA-BR-4201 TCGA-BR-8059 TCGA-BR-8078 TCGA-CG-5721 TCGA-D7-A4YY TCGA-D7-A6EY 
       30.90        14.43        29.59         6.02        13.78        11.44 
TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-A4H8 TCGA-VQ-A8P2 
       11.08        26.47        14.07        38.14 

$`EXOSC10 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
             6.02              0.00 
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
            38.14            122.30 
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
            14.25             14.27 
[1] "6.0 - 38.1 (14.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D995V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EXOSC10 MUTATED         0        0        3        0         1         1
  EXOSC10 WILD-TYPE       2       15       37       30        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EXOSC10 MUTATED           1          1          2          0        1
  EXOSC10 WILD-TYPE         2         69         51         32       37
D995V3, multiclass
            clus
vv           EXOSC10 MUTATED EXOSC10 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 3                37
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                1                 2
  STAGE IIIA               1                69
  STAGE IIIB               2                51
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  EXOSC10 MUTATED     1   3   3   4
  EXOSC10 WILD-TYPE  21  89 170  93
D995V4, multiclass
    clus
vv   EXOSC10 MUTATED EXOSC10 WILD-TYPE
  T1               1                21
  T2               3                89
  T3               3               170
  T4               4                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
  EXOSC10 MUTATED     4   4   0   2
  EXOSC10 WILD-TYPE 114 100  77  75
D995V5, multiclass
    clus
vv   EXOSC10 MUTATED EXOSC10 WILD-TYPE
  N0               4               114
  N1               4               100
  N2               0                77
  N3               2                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"
D995V6, binary
                   cls
clus                  0   1
  EXOSC10 MUTATED    11   0
  EXOSC10 WILD-TYPE 335  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOSC10 MUTATED     11    0
  EXOSC10 WILD-TYPE  335   29
   clus
vv  EXOSC10 MUTATED EXOSC10 WILD-TYPE
  0              11               335
  1               0                29
[1] 2 2
[1] FALSE
D995V7, binary
                   cls
clus                  0   1
  EXOSC10 MUTATED     6   6
  EXOSC10 WILD-TYPE 139 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOSC10 MUTATED      6    6
  EXOSC10 WILD-TYPE  139  242
        clus
vv       EXOSC10 MUTATED EXOSC10 WILD-TYPE
  FEMALE               6               139
  MALE                 6               242
[1] 2 2
[1] FALSE
D995V8, binary
                   cls
clus                  0   1
  EXOSC10 MUTATED     8   3
  EXOSC10 WILD-TYPE 284  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOSC10 MUTATED      8    3
  EXOSC10 WILD-TYPE  284   56
     clus
vv    EXOSC10 MUTATED EXOSC10 WILD-TYPE
  NO                8               284
  YES               3                56
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EXOSC10 MUTATED                                          1
  EXOSC10 WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EXOSC10 MUTATED                                       0
  EXOSC10 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EXOSC10 MUTATED                                                        6
  EXOSC10 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EXOSC10 MUTATED                                                   1
  EXOSC10 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EXOSC10 MUTATED                                                                   2
  EXOSC10 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EXOSC10 MUTATED                                                    0
  EXOSC10 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EXOSC10 MUTATED                                                  2
  EXOSC10 WILD-TYPE                                               59
D995V9, multiclass
                                                                   clus
vv                                                                  EXOSC10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  EXOSC10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  EXOSC10 MUTATED    10   0   0   2
  EXOSC10 WILD-TYPE 301  14  15  22
D995V10, multiclass
    clus
vv   EXOSC10 MUTATED EXOSC10 WILD-TYPE
  R0              10               301
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D995V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  EXOSC10 MUTATED       1                         1
  EXOSC10 WILD-TYPE    86                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EXOSC10 MUTATED                                           0     9
  EXOSC10 WILD-TYPE                                         1   234
D995V12, multiclass
                                           clus
vv                                          EXOSC10 MUTATED EXOSC10 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D995V13, binary
                   cls
clus                  0   1
  EXOSC10 MUTATED     0  10
  EXOSC10 WILD-TYPE   4 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOSC10 MUTATED      0   10
  EXOSC10 WILD-TYPE    4  300
                        clus
vv                       EXOSC10 MUTATED EXOSC10 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              10               300
[1] 2 2
[1] FALSE

Clustering(996) Variable = ARID3A MUTATION ANALYSIS
D996V1, survival
                  sevent
clus2                0   1
  ARID3A MUTATED     6   0
  ARID3A WILD-TYPE 224 139
  ARID3A MUTATED ARID3A WILD-TYPE 
               6              363 
  ARID3A MUTATED ARID3A WILD-TYPE 
               0              139 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-D7-6528 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-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-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 

  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           14.170 
[1] "6.0 - 34.7 (21.5)"  "0.0 - 122.3 (14.2)"
[1] "hr="     "9200000"
D996V2, 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       2       14       40       30        34        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID3A MUTATED           0          0          0          0        1
  ARID3A WILD-TYPE         3         70         53         32       37
D996V3, multiclass
            clus
vv           ARID3A MUTATED ARID3A WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID3A MUTATED     1   2   2   1
  ARID3A WILD-TYPE  21  90 171  96
D996V4, multiclass
    clus
vv   ARID3A MUTATED ARID3A WILD-TYPE
  T1              1               21
  T2              2               90
  T3              2              171
  T4              1               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
  ARID3A MUTATED     3   3   0   0
  ARID3A WILD-TYPE 115 101  77  77
D996V5, multiclass
    clus
vv   ARID3A MUTATED ARID3A WILD-TYPE
  N0              3              115
  N1              3              101
  N2              0               77
  N3              0               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"
D996V6, binary
                  cls
clus                 0   1
  ARID3A MUTATED     6   0
  ARID3A WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID3A MUTATED      6    0
  ARID3A WILD-TYPE  340   29
   clus
vv  ARID3A MUTATED ARID3A WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D996V7, binary
                  cls
clus                 0   1
  ARID3A MUTATED     3   3
  ARID3A WILD-TYPE 142 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID3A MUTATED      3    3
  ARID3A WILD-TYPE  142  245
        clus
vv       ARID3A MUTATED ARID3A WILD-TYPE
  FEMALE              3              142
  MALE                3              245
[1] 2 2
[1] FALSE
D996V8, binary
                  cls
clus                 0   1
  ARID3A MUTATED     6   0
  ARID3A WILD-TYPE 286  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID3A MUTATED      6    0
  ARID3A WILD-TYPE  286   59
     clus
vv    ARID3A MUTATED ARID3A WILD-TYPE
  NO               6              286
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARID3A MUTATED                                          0
  ARID3A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARID3A MUTATED                                       0
  ARID3A WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARID3A MUTATED                                                        2
  ARID3A WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARID3A MUTATED                                                   0
  ARID3A WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARID3A MUTATED                                                                   1
  ARID3A WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARID3A MUTATED                                                    0
  ARID3A WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARID3A MUTATED                                                  3
  ARID3A WILD-TYPE                                               58
D996V9, multiclass
                                                                   clus
vv                                                                  ARID3A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  ARID3A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARID3A MUTATED     6   0   0   0
  ARID3A WILD-TYPE 305  14  15  24
D996V10, multiclass
    clus
vv   ARID3A MUTATED ARID3A WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D996V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ARID3A MUTATED       3                         0
  ARID3A WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID3A MUTATED                                           0     2
  ARID3A WILD-TYPE                                         1   241
D996V12, multiclass
                                           clus
vv                                          ARID3A MUTATED ARID3A WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D996V13, binary
                  cls
clus                 0   1
  ARID3A MUTATED     0   5
  ARID3A WILD-TYPE   4 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID3A MUTATED      0    5
  ARID3A WILD-TYPE    4  305
                        clus
vv                       ARID3A MUTATED ARID3A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(997) Variable = RAB14 MUTATION ANALYSIS
D997V1, survival
                 sevent
clus2               0   1
  RAB14 MUTATED     2   3
  RAB14 WILD-TYPE 228 136
  RAB14 MUTATED RAB14 WILD-TYPE 
              5             364 
  RAB14 MUTATED RAB14 WILD-TYPE 
              3             136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  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           14.35 
[1] "0.1 - 31.1 (12.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.1"
D997V2, 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       2       15       40       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAB14 MUTATED           0          1          1          2        0
  RAB14 WILD-TYPE         3         69         52         30       38
D997V3, multiclass
            clus
vv           RAB14 MUTATED RAB14 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAB14 MUTATED     0   0   3   2
  RAB14 WILD-TYPE  22  92 170  95
D997V4, multiclass
    clus
vv   RAB14 MUTATED RAB14 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             3             170
  T4             2              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
  RAB14 MUTATED     1   2   2   1
  RAB14 WILD-TYPE 117 102  75  76
D997V5, multiclass
    clus
vv   RAB14 MUTATED RAB14 WILD-TYPE
  N0             1             117
  N1             2             102
  N2             2              75
  N3             1              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"
D997V6, binary
                 cls
clus                0   1
  RAB14 MUTATED     5   0
  RAB14 WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB14 MUTATED      5    0
  RAB14 WILD-TYPE  341   29
   clus
vv  RAB14 MUTATED RAB14 WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D997V7, binary
                 cls
clus                0   1
  RAB14 MUTATED     4   2
  RAB14 WILD-TYPE 141 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB14 MUTATED      4    2
  RAB14 WILD-TYPE  141  246
        clus
vv       RAB14 MUTATED RAB14 WILD-TYPE
  FEMALE             4             141
  MALE               2             246
[1] 2 2
[1] FALSE
D997V8, binary
                 cls
clus                0   1
  RAB14 MUTATED     4   1
  RAB14 WILD-TYPE 288  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB14 MUTATED      4    1
  RAB14 WILD-TYPE  288   58
     clus
vv    RAB14 MUTATED RAB14 WILD-TYPE
  NO              4             288
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RAB14 MUTATED                                          0
  RAB14 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RAB14 MUTATED                                       0
  RAB14 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RAB14 MUTATED                                                        5
  RAB14 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RAB14 MUTATED                                                   0
  RAB14 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RAB14 MUTATED                                                                   0
  RAB14 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RAB14 MUTATED                                                    0
  RAB14 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RAB14 MUTATED                                                  1
  RAB14 WILD-TYPE                                               60
D997V9, multiclass
                                                                   clus
vv                                                                  RAB14 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  RAB14 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RAB14 MUTATED     3   0   0   2
  RAB14 WILD-TYPE 308  14  15  22
D997V10, multiclass
    clus
vv   RAB14 MUTATED RAB14 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D997V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RAB14 MUTATED       2                         0
  RAB14 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAB14 MUTATED                                           0     4
  RAB14 WILD-TYPE                                         1   239
D997V12, multiclass
                                           clus
vv                                          RAB14 MUTATED RAB14 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D997V13, binary
                 cls
clus                0   1
  RAB14 MUTATED     0   6
  RAB14 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB14 MUTATED      0    6
  RAB14 WILD-TYPE    4  304
                        clus
vv                       RAB14 MUTATED RAB14 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(998) Variable = IGSF9B MUTATION ANALYSIS
D998V1, survival
                  sevent
clus2                0   1
  IGSF9B MUTATED    12   4
  IGSF9B WILD-TYPE 218 135
  IGSF9B MUTATED IGSF9B WILD-TYPE 
              16              353 
  IGSF9B MUTATED IGSF9B WILD-TYPE 
               4              135 
$`IGSF9B MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8372 
       21.99        34.68        36.16        35.84        31.10        31.27 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5723 TCGA-HU-8602 TCGA-HU-A4GF TCGA-HU-A4H8 
        6.58         6.02       105.07        22.32        25.81        14.07 
TCGA-IN-7808 TCGA-MX-A5UJ TCGA-VQ-A8DZ TCGA-VQ-A8P2 
        3.45        19.73        13.02        38.14 

$`IGSF9B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        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-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-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-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 

  IGSF9B MUTATED IGSF9B WILD-TYPE 
            3.45             0.00 
  IGSF9B MUTATED IGSF9B WILD-TYPE 
          105.07           122.30 
  IGSF9B MUTATED IGSF9B WILD-TYPE 
          24.065           14.040 
[1] "3.5 - 105.1 (24.1)" "0.0 - 122.3 (14.0)"
[1] "hr=" "2.1"
D998V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IGSF9B MUTATED         0        1        2        1         3         2
  IGSF9B WILD-TYPE       2       14       38       29        34        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGSF9B MUTATED           0          3          0          2        4
  IGSF9B WILD-TYPE         3         67         53         30       34
D998V3, multiclass
            clus
vv           IGSF9B MUTATED IGSF9B WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                4               34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IGSF9B MUTATED     2   2   5  10
  IGSF9B WILD-TYPE  20  90 168  87
D998V4, multiclass
    clus
vv   IGSF9B MUTATED IGSF9B WILD-TYPE
  T1              2               20
  T2              2               90
  T3              5              168
  T4             10               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
  IGSF9B MUTATED     8   5   3   3
  IGSF9B WILD-TYPE 110  99  74  74
D998V5, multiclass
    clus
vv   IGSF9B MUTATED IGSF9B WILD-TYPE
  N0              8              110
  N1              5               99
  N2              3               74
  N3              3               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"
D998V6, binary
                  cls
clus                 0   1
  IGSF9B MUTATED    17   3
  IGSF9B WILD-TYPE 329  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGSF9B MUTATED     17    3
  IGSF9B WILD-TYPE  329   26
   clus
vv  IGSF9B MUTATED IGSF9B WILD-TYPE
  0             17              329
  1              3               26
[1] 2 2
[1] FALSE
D998V7, binary
                  cls
clus                 0   1
  IGSF9B MUTATED     9  11
  IGSF9B WILD-TYPE 136 237
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGSF9B MUTATED      9   11
  IGSF9B WILD-TYPE  136  237
        clus
vv       IGSF9B MUTATED IGSF9B WILD-TYPE
  FEMALE              9              136
  MALE               11              237
[1] 2 2
[1] FALSE
D998V8, binary
                  cls
clus                 0   1
  IGSF9B MUTATED    16   1
  IGSF9B WILD-TYPE 276  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGSF9B MUTATED     16    1
  IGSF9B WILD-TYPE  276   58
     clus
vv    IGSF9B MUTATED IGSF9B WILD-TYPE
  NO              16              276
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IGSF9B MUTATED                                          1
  IGSF9B WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IGSF9B MUTATED                                       3
  IGSF9B WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IGSF9B MUTATED                                                        8
  IGSF9B WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IGSF9B MUTATED                                                   1
  IGSF9B WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IGSF9B MUTATED                                                                   3
  IGSF9B WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IGSF9B MUTATED                                                    1
  IGSF9B WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IGSF9B MUTATED                                                  3
  IGSF9B WILD-TYPE                                               58
D998V9, multiclass
                                                                   clus
vv                                                                  IGSF9B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  IGSF9B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IGSF9B MUTATED    13   0   2   3
  IGSF9B WILD-TYPE 298  14  13  21
D998V10, multiclass
    clus
vv   IGSF9B MUTATED IGSF9B WILD-TYPE
  R0             13              298
  R1              0               14
  R2              2               13
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D998V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  IGSF9B MUTATED       4                         1
  IGSF9B WILD-TYPE    83                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IGSF9B MUTATED                                           0    12
  IGSF9B WILD-TYPE                                         1   231
D998V12, multiclass
                                           clus
vv                                          IGSF9B MUTATED IGSF9B WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 12              231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D998V13, binary
                  cls
clus                 0   1
  IGSF9B MUTATED     0  15
  IGSF9B WILD-TYPE   4 295
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGSF9B MUTATED      0   15
  IGSF9B WILD-TYPE    4  295
                        clus
vv                       IGSF9B MUTATED IGSF9B WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             15              295
[1] 2 2
[1] FALSE

Clustering(999) Variable = ARNT MUTATION ANALYSIS
D999V1, survival
                sevent
clus2              0   1
  ARNT MUTATED     5   2
  ARNT WILD-TYPE 225 137
  ARNT MUTATED ARNT WILD-TYPE 
             7            362 
  ARNT MUTATED ARNT WILD-TYPE 
             2            137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4MH 
       12.43         6.31        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-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-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 

  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          14.22 
[1] "5.9 - 74.5 (31.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.9"
D999V2, 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       2       15       39       30        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARNT MUTATED           0          1          0          1        2
  ARNT WILD-TYPE         3         69         53         31       36
D999V3, multiclass
            clus
vv           ARNT MUTATED ARNT WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ARNT MUTATED     0   1   3   4
  ARNT WILD-TYPE  22  91 170  93
D999V4, multiclass
    clus
vv   ARNT MUTATED ARNT WILD-TYPE
  T1            0             22
  T2            1             91
  T3            3            170
  T4            4             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
  ARNT MUTATED     2   4   1   1
  ARNT WILD-TYPE 116 100  76  76
D999V5, multiclass
    clus
vv   ARNT MUTATED ARNT WILD-TYPE
  N0            2            116
  N1            4            100
  N2            1             76
  N3            1             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"
D999V6, binary
                cls
clus               0   1
  ARNT MUTATED     6   2
  ARNT WILD-TYPE 340  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARNT MUTATED      6    2
  ARNT WILD-TYPE  340   27
   clus
vv  ARNT MUTATED ARNT WILD-TYPE
  0            6            340
  1            2             27
[1] 2 2
[1] FALSE
D999V7, binary
                cls
clus               0   1
  ARNT MUTATED     2   6
  ARNT WILD-TYPE 143 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARNT MUTATED      2    6
  ARNT WILD-TYPE  143  242
        clus
vv       ARNT MUTATED ARNT WILD-TYPE
  FEMALE            2            143
  MALE              6            242
[1] 2 2
[1] FALSE
D999V8, binary
                cls
clus               0   1
  ARNT MUTATED     6   1
  ARNT WILD-TYPE 286  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARNT MUTATED      6    1
  ARNT WILD-TYPE  286   58
     clus
vv    ARNT MUTATED ARNT WILD-TYPE
  NO             6            286
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARNT MUTATED                                          0
  ARNT WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARNT MUTATED                                       3
  ARNT WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARNT MUTATED                                                        1
  ARNT WILD-TYPE                                                    157
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARNT MUTATED                                                   1
  ARNT WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARNT MUTATED                                                                   1
  ARNT WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARNT MUTATED                                                    0
  ARNT WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARNT MUTATED                                                  2
  ARNT WILD-TYPE                                               59
D999V9, multiclass
                                                                   clus
vv                                                                  ARNT MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  ARNT WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ARNT MUTATED     7   0   0   0
  ARNT WILD-TYPE 304  14  15  24
D999V10, multiclass
    clus
vv   ARNT MUTATED ARNT WILD-TYPE
  R0            7            304
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D999V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ARNT MUTATED       3                         0
  ARNT WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARNT MUTATED                                           0     4
  ARNT WILD-TYPE                                         1   239
D999V12, multiclass
                                           clus
vv                                          ARNT MUTATED ARNT WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D999V13, binary
                cls
clus               0   1
  ARNT MUTATED     1   5
  ARNT WILD-TYPE   3 305
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARNT MUTATED      1    5
  ARNT WILD-TYPE    3  305
                        clus
vv                       ARNT MUTATED ARNT WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            5            305
[1] 2 2
[1] FALSE

Clustering(1000) Variable = CSNK2A2 MUTATION ANALYSIS
D1000V1, survival
                   sevent
clus2                 0   1
  CSNK2A2 MUTATED     7   1
  CSNK2A2 WILD-TYPE 223 138
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                8               361 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                1               138 
$`CSNK2A2 MUTATED`
TCGA-BR-7707 TCGA-BR-8372 TCGA-BR-8589 TCGA-BR-8680 TCGA-CD-8536 TCGA-KB-A93J 
       35.84        31.27        27.12        31.96        12.43        36.95 
TCGA-VQ-A8P2 TCGA-VQ-A8PE 
       38.14        22.19 

$`CSNK2A2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
            12.43              0.00 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
            38.14            122.30 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
           31.615            14.070 
[1] "12.4 - 38.1 (31.6)" "0.0 - 122.3 (14.1)"
[1] "hr=" "5.1"
D1000V2, 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       2       15       39       28        37        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK2A2 MUTATED           0          1          2          1        1
  CSNK2A2 WILD-TYPE         3         69         51         31       37
D1000V3, multiclass
            clus
vv           CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 2                28
  STAGE IIA                0                37
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               2                51
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CSNK2A2 MUTATED     0   2   2   4
  CSNK2A2 WILD-TYPE  22  90 171  93
D1000V4, multiclass
    clus
vv   CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  T1               0                22
  T2               2                90
  T3               2               171
  T4               4                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
  CSNK2A2 MUTATED     2   3   1   2
  CSNK2A2 WILD-TYPE 116 101  76  75
D1000V5, multiclass
    clus
vv   CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  N0               2               116
  N1               3               101
  N2               1                76
  N3               2                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"
D1000V6, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     7   1
  CSNK2A2 WILD-TYPE 339  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      7    1
  CSNK2A2 WILD-TYPE  339   28
   clus
vv  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  0               7               339
  1               1                28
[1] 2 2
[1] FALSE
D1000V7, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     1   7
  CSNK2A2 WILD-TYPE 144 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      1    7
  CSNK2A2 WILD-TYPE  144  241
        clus
vv       CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  FEMALE               1               144
  MALE                 7               241
[1] 2 2
[1] FALSE
D1000V8, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     6   2
  CSNK2A2 WILD-TYPE 286  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      6    2
  CSNK2A2 WILD-TYPE  286   57
     clus
vv    CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  NO                6               286
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CSNK2A2 MUTATED                                          0
  CSNK2A2 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CSNK2A2 MUTATED                                       1
  CSNK2A2 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CSNK2A2 MUTATED                                                        4
  CSNK2A2 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CSNK2A2 MUTATED                                                   1
  CSNK2A2 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CSNK2A2 MUTATED                                                                   0
  CSNK2A2 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CSNK2A2 MUTATED                                                    0
  CSNK2A2 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CSNK2A2 MUTATED                                                  2
  CSNK2A2 WILD-TYPE                                               59
D1000V9, multiclass
                                                                   clus
vv                                                                  CSNK2A2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  CSNK2A2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CSNK2A2 MUTATED     8   0   0   0
  CSNK2A2 WILD-TYPE 303  14  15  24
D1000V10, multiclass
    clus
vv   CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  R0               8               303
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1000V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CSNK2A2 MUTATED       2                         0
  CSNK2A2 WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CSNK2A2 MUTATED                                           0     6
  CSNK2A2 WILD-TYPE                                         1   237
D1000V12, multiclass
                                           clus
vv                                          CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1000V13, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     0   5
  CSNK2A2 WILD-TYPE   4 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      0    5
  CSNK2A2 WILD-TYPE    4  305
                        clus
vv                       CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(1001) Variable = HOXA1 MUTATION ANALYSIS
D1001V1, survival
                 sevent
clus2               0   1
  HOXA1 MUTATED     6   3
  HOXA1 WILD-TYPE 224 136
  HOXA1 MUTATED HOXA1 WILD-TYPE 
              9             360 
  HOXA1 MUTATED HOXA1 WILD-TYPE 
              3             136 
$`HOXA1 MUTATED`
TCGA-BR-4184 TCGA-BR-6852 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-5721 TCGA-CG-5723 
        6.97        44.94         6.58         1.02         6.02       105.07 
TCGA-F1-6874 TCGA-HF-A5NB TCGA-HU-A4GU 
       14.47        30.51         6.58 

$`HOXA1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-F1-6875 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-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 

  HOXA1 MUTATED HOXA1 WILD-TYPE 
           1.02            0.00 
  HOXA1 MUTATED HOXA1 WILD-TYPE 
         105.07          122.30 
  HOXA1 MUTATED HOXA1 WILD-TYPE 
           6.97           14.35 
[1] "1.0 - 105.1 (7.0)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D1001V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HOXA1 MUTATED         0        0        1        1         2         1
  HOXA1 WILD-TYPE       2       15       39       29        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HOXA1 MUTATED           0          1          0          2        2
  HOXA1 WILD-TYPE         3         69         53         30       36
D1001V3, multiclass
            clus
vv           HOXA1 MUTATED HOXA1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HOXA1 MUTATED     0   2   5   3
  HOXA1 WILD-TYPE  22  90 168  94
D1001V4, multiclass
    clus
vv   HOXA1 MUTATED HOXA1 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             5             168
  T4             3              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
  HOXA1 MUTATED     3   4   1   2
  HOXA1 WILD-TYPE 115 100  76  75
D1001V5, multiclass
    clus
vv   HOXA1 MUTATED HOXA1 WILD-TYPE
  N0             3             115
  N1             4             100
  N2             1              76
  N3             2              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"
D1001V6, binary
                 cls
clus                0   1
  HOXA1 MUTATED     8   1
  HOXA1 WILD-TYPE 338  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA1 MUTATED      8    1
  HOXA1 WILD-TYPE  338   28
   clus
vv  HOXA1 MUTATED HOXA1 WILD-TYPE
  0             8             338
  1             1              28
[1] 2 2
[1] FALSE
D1001V7, binary
                 cls
clus                0   1
  HOXA1 MUTATED     2   8
  HOXA1 WILD-TYPE 143 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA1 MUTATED      2    8
  HOXA1 WILD-TYPE  143  240
        clus
vv       HOXA1 MUTATED HOXA1 WILD-TYPE
  FEMALE             2             143
  MALE               8             240
[1] 2 2
[1] FALSE
D1001V8, binary
                 cls
clus                0   1
  HOXA1 MUTATED     8   1
  HOXA1 WILD-TYPE 284  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA1 MUTATED      8    1
  HOXA1 WILD-TYPE  284   58
     clus
vv    HOXA1 MUTATED HOXA1 WILD-TYPE
  NO              8             284
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HOXA1 MUTATED                                          0
  HOXA1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HOXA1 MUTATED                                       2
  HOXA1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HOXA1 MUTATED                                                        5
  HOXA1 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HOXA1 MUTATED                                                   1
  HOXA1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HOXA1 MUTATED                                                                   2
  HOXA1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HOXA1 MUTATED                                                    0
  HOXA1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HOXA1 MUTATED                                                  0
  HOXA1 WILD-TYPE                                               61
D1001V9, multiclass
                                                                   clus
vv                                                                  HOXA1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  HOXA1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HOXA1 MUTATED     5   2   1   1
  HOXA1 WILD-TYPE 306  12  14  23
D1001V10, multiclass
    clus
vv   HOXA1 MUTATED HOXA1 WILD-TYPE
  R0             5             306
  R1             2              12
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1001V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  HOXA1 MUTATED       2                         0
  HOXA1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HOXA1 MUTATED                                           0     4
  HOXA1 WILD-TYPE                                         1   239
D1001V12, multiclass
                                           clus
vv                                          HOXA1 MUTATED HOXA1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1001V13, binary
                 cls
clus                0   1
  HOXA1 MUTATED     0   6
  HOXA1 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA1 MUTATED      0    6
  HOXA1 WILD-TYPE    4  304
                        clus
vv                       HOXA1 MUTATED HOXA1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(1002) Variable = SYNJ1 MUTATION ANALYSIS
D1002V1, survival
                 sevent
clus2               0   1
  SYNJ1 MUTATED     5   3
  SYNJ1 WILD-TYPE 225 136
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
              8             361 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
              3             136 
$`SYNJ1 MUTATED`
TCGA-BR-8360 TCGA-BR-8680 TCGA-BR-A4CS TCGA-BR-A4QL TCGA-CG-5718 TCGA-HF-A5NB 
        6.18        31.96         1.48        16.14        36.00        30.51 
TCGA-HU-A4GH TCGA-HU-A4GT 
       11.77         6.51 

$`SYNJ1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
           1.48            0.00 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
           36.0           122.3 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
         13.955          14.270 
[1] "1.5 - 36.0 (14.0)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D1002V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SYNJ1 MUTATED         0        1        1        1         2         1
  SYNJ1 WILD-TYPE       2       14       39       29        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYNJ1 MUTATED           0          0          1          2        1
  SYNJ1 WILD-TYPE         3         70         52         30       37
D1002V3, multiclass
            clus
vv           SYNJ1 MUTATED SYNJ1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SYNJ1 MUTATED     1   2   3   4
  SYNJ1 WILD-TYPE  21  90 170  93
D1002V4, multiclass
    clus
vv   SYNJ1 MUTATED SYNJ1 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             3             170
  T4             4              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
  SYNJ1 MUTATED     5   1   1   3
  SYNJ1 WILD-TYPE 113 103  76  74
D1002V5, multiclass
    clus
vv   SYNJ1 MUTATED SYNJ1 WILD-TYPE
  N0             5             113
  N1             1             103
  N2             1              76
  N3             3              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"
D1002V6, binary
                 cls
clus                0   1
  SYNJ1 MUTATED    10   1
  SYNJ1 WILD-TYPE 336  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED     10    1
  SYNJ1 WILD-TYPE  336   28
   clus
vv  SYNJ1 MUTATED SYNJ1 WILD-TYPE
  0            10             336
  1             1              28
[1] 2 2
[1] FALSE
D1002V7, binary
                 cls
clus                0   1
  SYNJ1 MUTATED     5   6
  SYNJ1 WILD-TYPE 140 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED      5    6
  SYNJ1 WILD-TYPE  140  242
        clus
vv       SYNJ1 MUTATED SYNJ1 WILD-TYPE
  FEMALE             5             140
  MALE               6             242
[1] 2 2
[1] FALSE
D1002V8, binary
                 cls
clus                0   1
  SYNJ1 MUTATED     8   1
  SYNJ1 WILD-TYPE 284  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED      8    1
  SYNJ1 WILD-TYPE  284   58
     clus
vv    SYNJ1 MUTATED SYNJ1 WILD-TYPE
  NO              8             284
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SYNJ1 MUTATED                                          0
  SYNJ1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SYNJ1 MUTATED                                       0
  SYNJ1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SYNJ1 MUTATED                                                        3
  SYNJ1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SYNJ1 MUTATED                                                   1
  SYNJ1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SYNJ1 MUTATED                                                                   4
  SYNJ1 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SYNJ1 MUTATED                                                    0
  SYNJ1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SYNJ1 MUTATED                                                  3
  SYNJ1 WILD-TYPE                                               58
D1002V9, multiclass
                                                                   clus
vv                                                                  SYNJ1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  SYNJ1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SYNJ1 MUTATED     9   1   0   1
  SYNJ1 WILD-TYPE 302  13  15  23
D1002V10, multiclass
    clus
vv   SYNJ1 MUTATED SYNJ1 WILD-TYPE
  R0             9             302
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1002V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SYNJ1 MUTATED       3                         0
  SYNJ1 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SYNJ1 MUTATED                                           0     5
  SYNJ1 WILD-TYPE                                         1   238
D1002V12, multiclass
                                           clus
vv                                          SYNJ1 MUTATED SYNJ1 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1002V13, binary
                 cls
clus                0   1
  SYNJ1 MUTATED     0   8
  SYNJ1 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED      0    8
  SYNJ1 WILD-TYPE    4  302
                        clus
vv                       SYNJ1 MUTATED SYNJ1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(1003) Variable = ABCC2 MUTATION ANALYSIS
D1003V1, survival
                 sevent
clus2               0   1
  ABCC2 MUTATED    10   5
  ABCC2 WILD-TYPE 220 134
  ABCC2 MUTATED ABCC2 WILD-TYPE 
             15             354 
  ABCC2 MUTATED ABCC2 WILD-TYPE 
              5             134 
$`ABCC2 MUTATED`
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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-D7-6815 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-D7-8572 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-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-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-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
       24.30         5.59        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-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 

  ABCC2 MUTATED ABCC2 WILD-TYPE 
           6.02            0.00 
  ABCC2 MUTATED ABCC2 WILD-TYPE 
          45.67          122.30 
  ABCC2 MUTATED ABCC2 WILD-TYPE 
          22.32           14.07 
[1] "6.0 - 45.7 (22.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D1003V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCC2 MUTATED         0        1        2        1         2         2
  ABCC2 WILD-TYPE       2       14       38       29        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABCC2 MUTATED           0          2          1          0        4
  ABCC2 WILD-TYPE         3         68         52         32       34
D1003V3, multiclass
            clus
vv           ABCC2 MUTATED ABCC2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCC2 MUTATED     1   2   6   6
  ABCC2 WILD-TYPE  21  90 167  91
D1003V4, multiclass
    clus
vv   ABCC2 MUTATED ABCC2 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             6             167
  T4             6              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
  ABCC2 MUTATED     8   5   1   1
  ABCC2 WILD-TYPE 110  99  76  76
D1003V5, multiclass
    clus
vv   ABCC2 MUTATED ABCC2 WILD-TYPE
  N0             8             110
  N1             5              99
  N2             1              76
  N3             1              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"
D1003V6, binary
                 cls
clus                0   1
  ABCC2 MUTATED    14   1
  ABCC2 WILD-TYPE 332  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC2 MUTATED     14    1
  ABCC2 WILD-TYPE  332   28
   clus
vv  ABCC2 MUTATED ABCC2 WILD-TYPE
  0            14             332
  1             1              28
[1] 2 2
[1] FALSE
D1003V7, binary
                 cls
clus                0   1
  ABCC2 MUTATED     6  10
  ABCC2 WILD-TYPE 139 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC2 MUTATED      6   10
  ABCC2 WILD-TYPE  139  238
        clus
vv       ABCC2 MUTATED ABCC2 WILD-TYPE
  FEMALE             6             139
  MALE              10             238
[1] 2 2
[1] FALSE
D1003V8, binary
                 cls
clus                0   1
  ABCC2 MUTATED    13   2
  ABCC2 WILD-TYPE 279  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC2 MUTATED     13    2
  ABCC2 WILD-TYPE  279   57
     clus
vv    ABCC2 MUTATED ABCC2 WILD-TYPE
  NO             13             279
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ABCC2 MUTATED                                          0
  ABCC2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ABCC2 MUTATED                                       2
  ABCC2 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCC2 MUTATED                                                        6
  ABCC2 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ABCC2 MUTATED                                                   2
  ABCC2 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCC2 MUTATED                                                                   2
  ABCC2 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ABCC2 MUTATED                                                    1
  ABCC2 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ABCC2 MUTATED                                                  3
  ABCC2 WILD-TYPE                                               58
D1003V9, multiclass
                                                                   clus
vv                                                                  ABCC2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  ABCC2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCC2 MUTATED    11   0   0   3
  ABCC2 WILD-TYPE 300  14  15  21
D1003V10, multiclass
    clus
vv   ABCC2 MUTATED ABCC2 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1003V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCC2 MUTATED       3                         1
  ABCC2 WILD-TYPE    84                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCC2 MUTATED                                           0    11
  ABCC2 WILD-TYPE                                         1   232
D1003V12, multiclass
                                           clus
vv                                          ABCC2 MUTATED ABCC2 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1003V13, binary
                 cls
clus                0   1
  ABCC2 MUTATED     1  12
  ABCC2 WILD-TYPE   3 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC2 MUTATED      1   12
  ABCC2 WILD-TYPE    3  298
                        clus
vv                       ABCC2 MUTATED ABCC2 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(1004) Variable = HEPACAM2 MUTATION ANALYSIS
D1004V1, survival
                    sevent
clus2                  0   1
  HEPACAM2 MUTATED     2   3
  HEPACAM2 WILD-TYPE 228 136
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                 5                364 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                 3                136 
$`HEPACAM2 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8368 TCGA-CD-A4MG TCGA-D7-5578 
        6.97        30.90         4.31         6.58        12.66 

$`HEPACAM2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-5579 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 

  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
              4.31               0.00 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
              30.9              122.3 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
              6.97              14.45 
[1] "4.3 - 30.9 (7.0)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "2.4"
D1004V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HEPACAM2 MUTATED         0        0        1        0         1         1
  HEPACAM2 WILD-TYPE       2       15       39       30        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HEPACAM2 MUTATED           0          2          0          1        0
  HEPACAM2 WILD-TYPE         3         68         53         31       38
D1004V3, multiclass
            clus
vv           HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                0                 53
  STAGE IIIC                1                 31
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HEPACAM2 MUTATED     0   2   3   2
  HEPACAM2 WILD-TYPE  22  90 170  95
D1004V4, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  T1                0                 22
  T2                2                 90
  T3                3                170
  T4                2                 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
  HEPACAM2 MUTATED     3   2   1   1
  HEPACAM2 WILD-TYPE 115 102  76  76
D1004V5, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  N0                3                115
  N1                2                102
  N2                1                 76
  N3                1                 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"
D1004V6, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED     7   0
  HEPACAM2 WILD-TYPE 339  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED      7    0
  HEPACAM2 WILD-TYPE  339   29
   clus
vv  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  0                7                339
  1                0                 29
[1] 2 2
[1] FALSE
D1004V7, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED     3   5
  HEPACAM2 WILD-TYPE 142 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED      3    5
  HEPACAM2 WILD-TYPE  142  243
        clus
vv       HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  FEMALE                3                142
  MALE                  5                243
[1] 2 2
[1] FALSE
D1004V8, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED     7   0
  HEPACAM2 WILD-TYPE 285  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED      7    0
  HEPACAM2 WILD-TYPE  285   59
     clus
vv    HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  NO                 7                285
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HEPACAM2 MUTATED                                          0
  HEPACAM2 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HEPACAM2 MUTATED                                       1
  HEPACAM2 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HEPACAM2 MUTATED                                                        5
  HEPACAM2 WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HEPACAM2 MUTATED                                                   0
  HEPACAM2 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HEPACAM2 MUTATED                                                                   1
  HEPACAM2 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HEPACAM2 MUTATED                                                    0
  HEPACAM2 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HEPACAM2 MUTATED                                                  1
  HEPACAM2 WILD-TYPE                                               60
D1004V9, multiclass
                                                                   clus
vv                                                                  HEPACAM2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  HEPACAM2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HEPACAM2 MUTATED     3   1   0   3
  HEPACAM2 WILD-TYPE 308  13  15  21
D1004V10, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  R0                3                308
  R1                1                 13
  R2                0                 15
  RX                3                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1004V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  HEPACAM2 MUTATED       1                         0
  HEPACAM2 WILD-TYPE    86                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HEPACAM2 MUTATED                                           0     7
  HEPACAM2 WILD-TYPE                                         1   236
D1004V12, multiclass
                                           clus
vv                                          HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1004V13, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED     0   8
  HEPACAM2 WILD-TYPE   4 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED      0    8
  HEPACAM2 WILD-TYPE    4  302
                        clus
vv                       HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                8                302
[1] 2 2
[1] FALSE

Clustering(1005) Variable = MAP4K4 MUTATION ANALYSIS
D1005V1, survival
                  sevent
clus2                0   1
  MAP4K4 MUTATED     8   3
  MAP4K4 WILD-TYPE 222 136
  MAP4K4 MUTATED MAP4K4 WILD-TYPE 
              11              358 
  MAP4K4 MUTATED MAP4K4 WILD-TYPE 
               3              136 
$`MAP4K4 MUTATED`
TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-8680 TCGA-BR-A4CQ TCGA-CG-4305 TCGA-CG-5721 
       11.70        34.68        31.96        34.98        15.95         6.02 
TCGA-CG-5728 TCGA-HU-A4GQ TCGA-IN-A6RL TCGA-VQ-A8P2 TCGA-VQ-AA64 
       65.10         0.10        13.35        38.14        18.41 

$`MAP4K4 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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 

  MAP4K4 MUTATED MAP4K4 WILD-TYPE 
             0.1              0.0 
  MAP4K4 MUTATED MAP4K4 WILD-TYPE 
            65.1            122.3 
  MAP4K4 MUTATED MAP4K4 WILD-TYPE 
           18.41            14.12 
[1] "0.1 - 65.1 (18.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D1005V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP4K4 MUTATED         0        0        2        1         1         1
  MAP4K4 WILD-TYPE       2       15       38       29        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP4K4 MUTATED           0          3          1          1        2
  MAP4K4 WILD-TYPE         3         67         52         31       36
D1005V3, multiclass
            clus
vv           MAP4K4 MUTATED MAP4K4 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP4K4 MUTATED     0   4   2   6
  MAP4K4 WILD-TYPE  22  88 171  91
D1005V4, multiclass
    clus
vv   MAP4K4 MUTATED MAP4K4 WILD-TYPE
  T1              0               22
  T2              4               88
  T3              2              171
  T4              6               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
  MAP4K4 MUTATED     4   6   3   0
  MAP4K4 WILD-TYPE 114  98  74  77
D1005V5, multiclass
    clus
vv   MAP4K4 MUTATED MAP4K4 WILD-TYPE
  N0              4              114
  N1              6               98
  N2              3               74
  N3              0               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"
D1005V6, binary
                  cls
clus                 0   1
  MAP4K4 MUTATED    12   1
  MAP4K4 WILD-TYPE 334  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K4 MUTATED     12    1
  MAP4K4 WILD-TYPE  334   28
   clus
vv  MAP4K4 MUTATED MAP4K4 WILD-TYPE
  0             12              334
  1              1               28
[1] 2 2
[1] FALSE
D1005V7, binary
                  cls
clus                 0   1
  MAP4K4 MUTATED     3  10
  MAP4K4 WILD-TYPE 142 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K4 MUTATED      3   10
  MAP4K4 WILD-TYPE  142  238
        clus
vv       MAP4K4 MUTATED MAP4K4 WILD-TYPE
  FEMALE              3              142
  MALE               10              238
[1] 2 2
[1] FALSE
D1005V8, binary
                  cls
clus                 0   1
  MAP4K4 MUTATED     9   2
  MAP4K4 WILD-TYPE 283  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K4 MUTATED      9    2
  MAP4K4 WILD-TYPE  283   57
     clus
vv    MAP4K4 MUTATED MAP4K4 WILD-TYPE
  NO               9              283
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MAP4K4 MUTATED                                          0
  MAP4K4 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MAP4K4 MUTATED                                       1
  MAP4K4 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP4K4 MUTATED                                                        5
  MAP4K4 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MAP4K4 MUTATED                                                   1
  MAP4K4 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP4K4 MUTATED                                                                   4
  MAP4K4 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MAP4K4 MUTATED                                                    0
  MAP4K4 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MAP4K4 MUTATED                                                  2
  MAP4K4 WILD-TYPE                                               59
D1005V9, multiclass
                                                                   clus
vv                                                                  MAP4K4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  MAP4K4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP4K4 MUTATED    12   0   0   1
  MAP4K4 WILD-TYPE 299  14  15  23
D1005V10, multiclass
    clus
vv   MAP4K4 MUTATED MAP4K4 WILD-TYPE
  R0             12              299
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1005V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAP4K4 MUTATED       2                         0
  MAP4K4 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP4K4 MUTATED                                           0     8
  MAP4K4 WILD-TYPE                                         1   235
D1005V12, multiclass
                                           clus
vv                                          MAP4K4 MUTATED MAP4K4 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1005V13, binary
                  cls
clus                 0   1
  MAP4K4 MUTATED     0   8
  MAP4K4 WILD-TYPE   4 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K4 MUTATED      0    8
  MAP4K4 WILD-TYPE    4  302
                        clus
vv                       MAP4K4 MUTATED MAP4K4 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(1006) Variable = B4GALT6 MUTATION ANALYSIS
D1006V1, survival
                   sevent
clus2                 0   1
  B4GALT6 MUTATED     2   1
  B4GALT6 WILD-TYPE 228 138
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
                3               366 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
                1               138 
$`B4GALT6 MUTATED`
TCGA-BR-8485 TCGA-CD-A4MG TCGA-HF-A5NB 
        9.21         6.58        30.51 

$`B4GALT6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
             6.58              0.00 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
            30.51            122.30 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
             9.21             14.35 
[1] "6.6 - 30.5 (9.2)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D1006V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  B4GALT6 MUTATED         1        1        1        0         1         0
  B4GALT6 WILD-TYPE       1       14       39       30        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B4GALT6 MUTATED           0          0          0          2        0
  B4GALT6 WILD-TYPE         3         70         53         30       38
D1006V3, multiclass
            clus
vv           B4GALT6 MUTATED B4GALT6 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               2                30
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  B4GALT6 MUTATED     2   1   1   2
  B4GALT6 WILD-TYPE  20  91 172  95
D1006V4, multiclass
    clus
vv   B4GALT6 MUTATED B4GALT6 WILD-TYPE
  T1               2                20
  T2               1                91
  T3               1               172
  T4               2                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
  B4GALT6 MUTATED     3   1   0   2
  B4GALT6 WILD-TYPE 115 103  77  75
D1006V5, multiclass
    clus
vv   B4GALT6 MUTATED B4GALT6 WILD-TYPE
  N0               3               115
  N1               1               103
  N2               0                77
  N3               2                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"
D1006V6, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     5   0
  B4GALT6 WILD-TYPE 341  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      5    0
  B4GALT6 WILD-TYPE  341   29
   clus
vv  B4GALT6 MUTATED B4GALT6 WILD-TYPE
  0               5               341
  1               0                29
[1] 2 2
[1] FALSE
D1006V7, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     2   4
  B4GALT6 WILD-TYPE 143 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      2    4
  B4GALT6 WILD-TYPE  143  244
        clus
vv       B4GALT6 MUTATED B4GALT6 WILD-TYPE
  FEMALE               2               143
  MALE                 4               244
[1] 2 2
[1] FALSE
D1006V8, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     3   2
  B4GALT6 WILD-TYPE 289  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      3    2
  B4GALT6 WILD-TYPE  289   57
     clus
vv    B4GALT6 MUTATED B4GALT6 WILD-TYPE
  NO                3               289
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  B4GALT6 MUTATED                                          0
  B4GALT6 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  B4GALT6 MUTATED                                       1
  B4GALT6 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  B4GALT6 MUTATED                                                        3
  B4GALT6 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  B4GALT6 MUTATED                                                   1
  B4GALT6 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  B4GALT6 MUTATED                                                                   1
  B4GALT6 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  B4GALT6 MUTATED                                                    0
  B4GALT6 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  B4GALT6 MUTATED                                                  0
  B4GALT6 WILD-TYPE                                               61
D1006V9, multiclass
                                                                   clus
vv                                                                  B4GALT6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  B4GALT6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  B4GALT6 MUTATED     4   1   0   0
  B4GALT6 WILD-TYPE 307  13  15  24
D1006V10, multiclass
    clus
vv   B4GALT6 MUTATED B4GALT6 WILD-TYPE
  R0               4               307
  R1               1                13
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1006V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  B4GALT6 MUTATED       2                         1
  B4GALT6 WILD-TYPE    85                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  B4GALT6 MUTATED                                           0     1
  B4GALT6 WILD-TYPE                                         1   242
D1006V12, multiclass
                                           clus
vv                                          B4GALT6 MUTATED B4GALT6 WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   1               242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1006V13, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     0   4
  B4GALT6 WILD-TYPE   4 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      0    4
  B4GALT6 WILD-TYPE    4  306
                        clus
vv                       B4GALT6 MUTATED B4GALT6 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4               306
[1] 2 2
[1] FALSE

Clustering(1007) Variable = NAA25 MUTATION ANALYSIS
D1007V1, survival
                 sevent
clus2               0   1
  NAA25 MUTATED     8   5
  NAA25 WILD-TYPE 222 134
  NAA25 MUTATED NAA25 WILD-TYPE 
             13             356 
  NAA25 MUTATED NAA25 WILD-TYPE 
              5             134 
$`NAA25 MUTATED`
TCGA-CG-4460 TCGA-BR-6458 TCGA-BR-7716 TCGA-BR-8081 TCGA-BR-8363 TCGA-BR-8372 
       21.99        19.33        39.78        32.25         0.26        31.27 
TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A4MI TCGA-CG-5728 TCGA-D7-A6EV TCGA-HU-A4GX 
       12.07         6.31        11.77        65.10        11.24        20.25 
TCGA-HU-A4H3 
       29.00 

$`NAA25 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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 
          20.25           14.12 
[1] "0.3 - 65.1 (20.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D1007V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NAA25 MUTATED         1        0        2        1         1         5
  NAA25 WILD-TYPE       1       15       38       29        36        47
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NAA25 MUTATED           0          1          0          3        1
  NAA25 WILD-TYPE         3         69         53         29       37
D1007V3, multiclass
            clus
vv           NAA25 MUTATED NAA25 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              5              47
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NAA25 MUTATED     1   3   5   6
  NAA25 WILD-TYPE  21  89 168  91
D1007V4, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             5             168
  T4             6              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
  NAA25 MUTATED     6   5   2   2
  NAA25 WILD-TYPE 112  99  75  75
D1007V5, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  N0             6             112
  N1             5              99
  N2             2              75
  N3             2              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"
D1007V6, binary
                 cls
clus                0   1
  NAA25 MUTATED    13   1
  NAA25 WILD-TYPE 333  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED     13    1
  NAA25 WILD-TYPE  333   28
   clus
vv  NAA25 MUTATED NAA25 WILD-TYPE
  0            13             333
  1             1              28
[1] 2 2
[1] FALSE
D1007V7, binary
                 cls
clus                0   1
  NAA25 MUTATED     9   6
  NAA25 WILD-TYPE 136 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED      9    6
  NAA25 WILD-TYPE  136  242
        clus
vv       NAA25 MUTATED NAA25 WILD-TYPE
  FEMALE             9             136
  MALE               6             242
[1] 2 2
[1] FALSE
D1007V8, binary
                 cls
clus                0   1
  NAA25 MUTATED    13   0
  NAA25 WILD-TYPE 279  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED     13    0
  NAA25 WILD-TYPE  279   59
     clus
vv    NAA25 MUTATED NAA25 WILD-TYPE
  NO             13             279
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NAA25 MUTATED                                          0
  NAA25 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NAA25 MUTATED                                       3
  NAA25 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NAA25 MUTATED                                                        9
  NAA25 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NAA25 MUTATED                                                   0
  NAA25 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NAA25 MUTATED                                                                   3
  NAA25 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NAA25 MUTATED                                                    0
  NAA25 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NAA25 MUTATED                                                  0
  NAA25 WILD-TYPE                                               61
D1007V9, multiclass
                                                                   clus
vv                                                                  NAA25 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  NAA25 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NAA25 MUTATED    12   0   1   0
  NAA25 WILD-TYPE 299  14  14  24
D1007V10, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  R0            12             299
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1007V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  NAA25 MUTATED       5                         1
  NAA25 WILD-TYPE    82                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NAA25 MUTATED                                           0     7
  NAA25 WILD-TYPE                                         1   236
D1007V12, multiclass
                                           clus
vv                                          NAA25 MUTATED NAA25 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1007V13, binary
                 cls
clus                0   1
  NAA25 MUTATED     0  13
  NAA25 WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED      0   13
  NAA25 WILD-TYPE    4  297
                        clus
vv                       NAA25 MUTATED NAA25 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(1008) Variable = SAFB MUTATION ANALYSIS
D1008V1, survival
                sevent
clus2              0   1
  SAFB MUTATED     4   2
  SAFB WILD-TYPE 226 137
  SAFB MUTATED SAFB WILD-TYPE 
             6            363 
  SAFB MUTATED SAFB WILD-TYPE 
             2            137 
$`SAFB MUTATED`
TCGA-CG-4460 TCGA-BR-8360 TCGA-BR-A4J2 TCGA-D7-A4YY TCGA-HU-8602 TCGA-HU-A4GQ 
       21.99         6.18        14.17        13.78        22.32         0.10 

$`SAFB WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98         0.72         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-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-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 

  SAFB MUTATED SAFB WILD-TYPE 
           0.1            0.0 
  SAFB MUTATED SAFB WILD-TYPE 
         22.32         122.30 
  SAFB MUTATED SAFB WILD-TYPE 
        13.975         14.430 
[1] "0.1 - 22.3 (14.0)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D1008V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SAFB MUTATED         0        0        1        0         1         2
  SAFB WILD-TYPE       2       15       39       30        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SAFB MUTATED           0          0          1          1        1
  SAFB WILD-TYPE         3         70         52         31       37
D1008V3, multiclass
            clus
vv           SAFB MUTATED SAFB WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SAFB MUTATED     0   1   2   4
  SAFB WILD-TYPE  22  91 171  93
D1008V4, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  T1            0             22
  T2            1             91
  T3            2            171
  T4            4             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
  SAFB MUTATED     4   1   1   1
  SAFB WILD-TYPE 114 103  76  76
D1008V5, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  N0            4            114
  N1            1            103
  N2            1             76
  N3            1             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"
D1008V6, binary
                cls
clus               0   1
  SAFB MUTATED     7   1
  SAFB WILD-TYPE 339  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED      7    1
  SAFB WILD-TYPE  339   28
   clus
vv  SAFB MUTATED SAFB WILD-TYPE
  0            7            339
  1            1             28
[1] 2 2
[1] FALSE
D1008V7, binary
                cls
clus               0   1
  SAFB MUTATED     3   5
  SAFB WILD-TYPE 142 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED      3    5
  SAFB WILD-TYPE  142  243
        clus
vv       SAFB MUTATED SAFB WILD-TYPE
  FEMALE            3            142
  MALE              5            243
[1] 2 2
[1] FALSE
D1008V8, binary
                cls
clus               0   1
  SAFB MUTATED     5   1
  SAFB WILD-TYPE 287  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED      5    1
  SAFB WILD-TYPE  287   58
     clus
vv    SAFB MUTATED SAFB WILD-TYPE
  NO             5            287
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SAFB MUTATED                                          0
  SAFB WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SAFB MUTATED                                       2
  SAFB WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SAFB MUTATED                                                        2
  SAFB WILD-TYPE                                                    156
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SAFB MUTATED                                                   0
  SAFB WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SAFB MUTATED                                                                   3
  SAFB WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SAFB MUTATED                                                    0
  SAFB WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SAFB MUTATED                                                  1
  SAFB WILD-TYPE                                               60
D1008V9, multiclass
                                                                   clus
vv                                                                  SAFB MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  SAFB WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SAFB MUTATED     6   0   1   1
  SAFB WILD-TYPE 305  14  14  23
D1008V10, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  R0            6            305
  R1            0             14
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1008V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SAFB MUTATED       3                         0
  SAFB WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SAFB MUTATED                                           0     3
  SAFB WILD-TYPE                                         1   240
D1008V12, multiclass
                                           clus
vv                                          SAFB MUTATED SAFB WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1008V13, binary
                cls
clus               0   1
  SAFB MUTATED     0   6
  SAFB WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED      0    6
  SAFB WILD-TYPE    4  304
                        clus
vv                       SAFB MUTATED SAFB WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(1009) Variable = ABLIM2 MUTATION ANALYSIS
D1009V1, survival
                  sevent
clus2                0   1
  ABLIM2 MUTATED     8   4
  ABLIM2 WILD-TYPE 222 135
  ABLIM2 MUTATED ABLIM2 WILD-TYPE 
              12              357 
  ABLIM2 MUTATED ABLIM2 WILD-TYPE 
               4              135 
$`ABLIM2 MUTATED`
TCGA-BR-4184 TCGA-BR-8372 TCGA-BR-8382 TCGA-CG-4306 TCGA-CG-5723 TCGA-CG-5728 
        6.97        31.27        25.05         1.02       105.07        65.10 
TCGA-FP-A4BE TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-IN-A6RS TCGA-RD-A7C1 
       11.08        20.25         0.26        23.84        12.59        16.67 

$`ABLIM2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        6.58         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-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-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 

  ABLIM2 MUTATED ABLIM2 WILD-TYPE 
            0.26             0.00 
  ABLIM2 MUTATED ABLIM2 WILD-TYPE 
          105.07           122.30 
  ABLIM2 MUTATED ABLIM2 WILD-TYPE 
           18.46            14.17 
[1] "0.3 - 105.1 (18.5)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D1009V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABLIM2 MUTATED         1        1        2        1         1         2
  ABLIM2 WILD-TYPE       1       14       38       29        36        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABLIM2 MUTATED           0          2          0          3        1
  ABLIM2 WILD-TYPE         3         68         53         29       37
D1009V3, multiclass
            clus
vv           ABLIM2 MUTATED ABLIM2 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              3               29
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ABLIM2 MUTATED     2   4   3   5
  ABLIM2 WILD-TYPE  20  88 170  92
D1009V4, multiclass
    clus
vv   ABLIM2 MUTATED ABLIM2 WILD-TYPE
  T1              2               20
  T2              4               88
  T3              3              170
  T4              5               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
  ABLIM2 MUTATED     5   4   3   2
  ABLIM2 WILD-TYPE 113 100  74  75
D1009V5, multiclass
    clus
vv   ABLIM2 MUTATED ABLIM2 WILD-TYPE
  N0              5              113
  N1              4              100
  N2              3               74
  N3              2               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"
D1009V6, binary
                  cls
clus                 0   1
  ABLIM2 MUTATED    11   1
  ABLIM2 WILD-TYPE 335  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM2 MUTATED     11    1
  ABLIM2 WILD-TYPE  335   28
   clus
vv  ABLIM2 MUTATED ABLIM2 WILD-TYPE
  0             11              335
  1              1               28
[1] 2 2
[1] FALSE
D1009V7, binary
                  cls
clus                 0   1
  ABLIM2 MUTATED     5   9
  ABLIM2 WILD-TYPE 140 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM2 MUTATED      5    9
  ABLIM2 WILD-TYPE  140  239
        clus
vv       ABLIM2 MUTATED ABLIM2 WILD-TYPE
  FEMALE              5              140
  MALE                9              239
[1] 2 2
[1] FALSE
D1009V8, binary
                  cls
clus                 0   1
  ABLIM2 MUTATED    11   1
  ABLIM2 WILD-TYPE 281  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM2 MUTATED     11    1
  ABLIM2 WILD-TYPE  281   58
     clus
vv    ABLIM2 MUTATED ABLIM2 WILD-TYPE
  NO              11              281
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ABLIM2 MUTATED                                          0
  ABLIM2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ABLIM2 MUTATED                                       3
  ABLIM2 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABLIM2 MUTATED                                                        8
  ABLIM2 WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ABLIM2 MUTATED                                                   0
  ABLIM2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABLIM2 MUTATED                                                                   2
  ABLIM2 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ABLIM2 MUTATED                                                    0
  ABLIM2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ABLIM2 MUTATED                                                  1
  ABLIM2 WILD-TYPE                                               60
D1009V9, multiclass
                                                                   clus
vv                                                                  ABLIM2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ABLIM2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ABLIM2 MUTATED    12   0   1   1
  ABLIM2 WILD-TYPE 299  14  14  23
D1009V10, multiclass
    clus
vv   ABLIM2 MUTATED ABLIM2 WILD-TYPE
  R0             12              299
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1009V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ABLIM2 MUTATED       3                         2
  ABLIM2 WILD-TYPE    84                         7
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABLIM2 MUTATED                                           0     6
  ABLIM2 WILD-TYPE                                         1   237
D1009V12, multiclass
                                           clus
vv                                          ABLIM2 MUTATED ABLIM2 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              2                7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1009V13, binary
                  cls
clus                 0   1
  ABLIM2 MUTATED     0  11
  ABLIM2 WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM2 MUTATED      0   11
  ABLIM2 WILD-TYPE    4  299
                        clus
vv                       ABLIM2 MUTATED ABLIM2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(1010) Variable = CEL MUTATION ANALYSIS
D1010V1, survival
               sevent
clus2             0   1
  CEL MUTATED    10   3
  CEL WILD-TYPE 220 136
  CEL MUTATED CEL WILD-TYPE 
           13           356 
  CEL MUTATED CEL WILD-TYPE 
            3           136 
$`CEL MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8487 TCGA-CD-8527 TCGA-CD-A4MI TCGA-CG-5721 
       34.68        29.59         1.12         7.17        11.77         6.02 
TCGA-CG-5728 TCGA-D7-6526 TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-A4GT TCGA-HU-A4GX 
       65.10        17.19        77.29        26.47         6.51        20.25 
TCGA-R5-A7ZI 
       74.53 

$`CEL WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-6527 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-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-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-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         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-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 

  CEL MUTATED CEL WILD-TYPE 
         1.12          0.00 
  CEL MUTATED CEL WILD-TYPE 
        77.29        122.30 
  CEL MUTATED CEL WILD-TYPE 
        20.25         14.12 
[1] "1.1 - 77.3 (20.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.2"
D1010V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CEL MUTATED         0        0        3        2         3         2
  CEL WILD-TYPE       2       15       37       28        34        50
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEL MUTATED           0          2          0          1        2
  CEL WILD-TYPE         3         68         53         31       36
D1010V3, multiclass
            clus
vv           CEL MUTATED CEL WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             3            37
  STAGE II             2            28
  STAGE IIA            3            34
  STAGE IIB            2            50
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           0            53
  STAGE IIIC           1            31
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CEL MUTATED     0   5   5   5
  CEL WILD-TYPE  22  87 168  92
D1010V4, multiclass
    clus
vv   CEL MUTATED CEL WILD-TYPE
  T1           0            22
  T2           5            87
  T3           5           168
  T4           5            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
  CEL MUTATED     8   5   2   0
  CEL WILD-TYPE 110  99  75  77
D1010V5, multiclass
    clus
vv   CEL MUTATED CEL WILD-TYPE
  N0           8           110
  N1           5            99
  N2           2            75
  N3           0            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"
D1010V6, binary
               cls
clus              0   1
  CEL MUTATED    13   1
  CEL WILD-TYPE 333  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED     13    1
  CEL WILD-TYPE  333   28
   clus
vv  CEL MUTATED CEL WILD-TYPE
  0          13           333
  1           1            28
[1] 2 2
[1] FALSE
D1010V7, binary
               cls
clus              0   1
  CEL MUTATED    10   5
  CEL WILD-TYPE 135 243
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED     10    5
  CEL WILD-TYPE  135  243
        clus
vv       CEL MUTATED CEL WILD-TYPE
  FEMALE          10           135
  MALE             5           243
[1] 2 2
[1] FALSE
D1010V8, binary
               cls
clus              0   1
  CEL MUTATED    12   1
  CEL WILD-TYPE 280  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED     12    1
  CEL WILD-TYPE  280   58
     clus
vv    CEL MUTATED CEL WILD-TYPE
  NO           12           280
  YES           1            58
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CEL MUTATED                                          1
  CEL WILD-TYPE                                        7
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CEL MUTATED                                       2
  CEL WILD-TYPE                                    68
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CEL MUTATED                                                        4
  CEL WILD-TYPE                                                    154
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CEL MUTATED                                                   1
  CEL WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CEL MUTATED                                                                   5
  CEL WILD-TYPE                                                                63
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CEL MUTATED                                                    0
  CEL WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CEL MUTATED                                                  2
  CEL WILD-TYPE                                               59
D1010V9, multiclass
                                                                   clus
vv                                                                  CEL MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            2
                                                                   clus
vv                                                                  CEL WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  CEL MUTATED    14   0   0   0
  CEL WILD-TYPE 297  14  15  24
D1010V10, multiclass
    clus
vv   CEL MUTATED CEL WILD-TYPE
  R0          14           297
  R1           0            14
  R2           0            15
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1010V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CEL MUTATED       4                         0
  CEL WILD-TYPE    83                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CEL MUTATED                                           0     7
  CEL WILD-TYPE                                         1   236
D1010V12, multiclass
                                           clus
vv                                          CEL MUTATED CEL WILD-TYPE
  ASIAN                                               4            83
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               7           236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1010V13, binary
               cls
clus              0   1
  CEL MUTATED     1  10
  CEL WILD-TYPE   3 300
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      1   10
  CEL WILD-TYPE    3  300
                        clus
vv                       CEL MUTATED CEL WILD-TYPE
  HISPANIC OR LATINO               1             3
  NOT HISPANIC OR LATINO          10           300
[1] 2 2
[1] FALSE

Clustering(1011) Variable = FAM178A MUTATION ANALYSIS
D1011V1, survival
                   sevent
clus2                 0   1
  FAM178A MUTATED     7   4
  FAM178A WILD-TYPE 223 135
  FAM178A MUTATED FAM178A WILD-TYPE 
               11               358 
  FAM178A MUTATED FAM178A WILD-TYPE 
                4               135 
$`FAM178A MUTATED`
TCGA-BR-4257 TCGA-BR-7707 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-8527 
        9.67        35.84        31.27         1.12        31.96         7.17 
TCGA-CG-5721 TCGA-CG-5726 TCGA-HU-A4G8 TCGA-HU-A4GQ TCGA-VQ-A8P2 
        6.02        28.96        22.68         0.10        38.14 

$`FAM178A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  FAM178A MUTATED FAM178A WILD-TYPE 
              0.1               0.0 
  FAM178A MUTATED FAM178A WILD-TYPE 
            38.14            122.30 
  FAM178A MUTATED FAM178A WILD-TYPE 
            22.68             14.22 
[1] "0.1 - 38.1 (22.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D1011V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM178A MUTATED         0        1        1        1         1         1
  FAM178A WILD-TYPE       2       14       39       29        36        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM178A MUTATED           0          1          0          2        2
  FAM178A WILD-TYPE         3         69         53         30       36
D1011V3, multiclass
            clus
vv           FAM178A MUTATED FAM178A WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               2                30
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM178A MUTATED     1   2   2   5
  FAM178A WILD-TYPE  21  90 171  92
D1011V4, multiclass
    clus
vv   FAM178A MUTATED FAM178A WILD-TYPE
  T1               1                21
  T2               2                90
  T3               2               171
  T4               5                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
  FAM178A MUTATED     3   4   2   1
  FAM178A WILD-TYPE 115 100  75  76
D1011V5, multiclass
    clus
vv   FAM178A MUTATED FAM178A WILD-TYPE
  N0               3               115
  N1               4               100
  N2               2                75
  N3               1                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"
D1011V6, binary
                   cls
clus                  0   1
  FAM178A MUTATED    10   1
  FAM178A WILD-TYPE 336  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM178A MUTATED     10    1
  FAM178A WILD-TYPE  336   28
   clus
vv  FAM178A MUTATED FAM178A WILD-TYPE
  0              10               336
  1               1                28
[1] 2 2
[1] FALSE
D1011V7, binary
                   cls
clus                  0   1
  FAM178A MUTATED     5   6
  FAM178A WILD-TYPE 140 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM178A MUTATED      5    6
  FAM178A WILD-TYPE  140  242
        clus
vv       FAM178A MUTATED FAM178A WILD-TYPE
  FEMALE               5               140
  MALE                 6               242
[1] 2 2
[1] FALSE
D1011V8, binary
                   cls
clus                  0   1
  FAM178A MUTATED     9   1
  FAM178A WILD-TYPE 283  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM178A MUTATED      9    1
  FAM178A WILD-TYPE  283   58
     clus
vv    FAM178A MUTATED FAM178A WILD-TYPE
  NO                9               283
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM178A MUTATED                                          0
  FAM178A WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM178A MUTATED                                       1
  FAM178A WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM178A MUTATED                                                        4
  FAM178A WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM178A MUTATED                                                   1
  FAM178A WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM178A MUTATED                                                                   3
  FAM178A WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM178A MUTATED                                                    0
  FAM178A WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM178A MUTATED                                                  2
  FAM178A WILD-TYPE                                               59
D1011V9, multiclass
                                                                   clus
vv                                                                  FAM178A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  FAM178A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM178A MUTATED     9   0   0   1
  FAM178A WILD-TYPE 302  14  15  23
D1011V10, multiclass
    clus
vv   FAM178A MUTATED FAM178A WILD-TYPE
  R0               9               302
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1011V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM178A MUTATED       4                         0
  FAM178A WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM178A MUTATED                                           0     5
  FAM178A WILD-TYPE                                         1   238
D1011V12, multiclass
                                           clus
vv                                          FAM178A MUTATED FAM178A WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1011V13, binary
                   cls
clus                  0   1
  FAM178A MUTATED     0   8
  FAM178A WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM178A MUTATED      0    8
  FAM178A WILD-TYPE    4  302
                        clus
vv                       FAM178A MUTATED FAM178A WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(1012) Variable = BUB1B MUTATION ANALYSIS
D1012V1, survival
                 sevent
clus2               0   1
  BUB1B MUTATED     9   2
  BUB1B WILD-TYPE 221 137
  BUB1B MUTATED BUB1B WILD-TYPE 
             11             358 
  BUB1B MUTATED BUB1B WILD-TYPE 
              2             137 
$`BUB1B MUTATED`
TCGA-BR-4280 TCGA-BR-8078 TCGA-BR-8360 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8589 
        6.61        29.59         6.18         4.31         1.12        27.12 
TCGA-BR-8680 TCGA-D7-5577 TCGA-HF-7132 TCGA-HU-A4GN TCGA-KB-A6F5 
       31.96        25.71        77.29        29.98         5.56 

$`BUB1B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-5578 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-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-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-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 

  BUB1B MUTATED BUB1B WILD-TYPE 
           1.12            0.00 
  BUB1B MUTATED BUB1B WILD-TYPE 
          77.29          122.30 
  BUB1B MUTATED BUB1B WILD-TYPE 
          25.71           14.22 
[1] "1.1 - 77.3 (25.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.4"
D1012V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BUB1B MUTATED         0        0        1        1         3         2
  BUB1B WILD-TYPE       2       15       39       29        34        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BUB1B MUTATED           1          2          1          0        1
  BUB1B WILD-TYPE         2         68         52         32       37
D1012V3, multiclass
            clus
vv           BUB1B MUTATED BUB1B WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              2              50
  STAGE III              1               2
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BUB1B MUTATED     0   5   3   4
  BUB1B WILD-TYPE  22  87 170  93
D1012V4, multiclass
    clus
vv   BUB1B MUTATED BUB1B WILD-TYPE
  T1             0              22
  T2             5              87
  T3             3             170
  T4             4              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
  BUB1B MUTATED     5   4   2   1
  BUB1B WILD-TYPE 113 100  75  76
D1012V5, multiclass
    clus
vv   BUB1B MUTATED BUB1B WILD-TYPE
  N0             5             113
  N1             4             100
  N2             2              75
  N3             1              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"
D1012V6, binary
                 cls
clus                0   1
  BUB1B MUTATED    11   1
  BUB1B WILD-TYPE 335  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUB1B MUTATED     11    1
  BUB1B WILD-TYPE  335   28
   clus
vv  BUB1B MUTATED BUB1B WILD-TYPE
  0            11             335
  1             1              28
[1] 2 2
[1] FALSE
D1012V7, binary
                 cls
clus                0   1
  BUB1B MUTATED     5   7
  BUB1B WILD-TYPE 140 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUB1B MUTATED      5    7
  BUB1B WILD-TYPE  140  241
        clus
vv       BUB1B MUTATED BUB1B WILD-TYPE
  FEMALE             5             140
  MALE               7             241
[1] 2 2
[1] FALSE
D1012V8, binary
                 cls
clus                0   1
  BUB1B MUTATED    11   1
  BUB1B WILD-TYPE 281  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUB1B MUTATED     11    1
  BUB1B WILD-TYPE  281   58
     clus
vv    BUB1B MUTATED BUB1B WILD-TYPE
  NO             11             281
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BUB1B MUTATED                                          0
  BUB1B WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BUB1B MUTATED                                       0
  BUB1B WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BUB1B MUTATED                                                        5
  BUB1B WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BUB1B MUTATED                                                   1
  BUB1B WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BUB1B MUTATED                                                                   3
  BUB1B WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BUB1B MUTATED                                                    0
  BUB1B WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BUB1B MUTATED                                                  3
  BUB1B WILD-TYPE                                               58
D1012V9, multiclass
                                                                   clus
vv                                                                  BUB1B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  BUB1B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BUB1B MUTATED    11   0   0   1
  BUB1B WILD-TYPE 300  14  15  23
D1012V10, multiclass
    clus
vv   BUB1B MUTATED BUB1B WILD-TYPE
  R0            11             300
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1012V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BUB1B MUTATED       2                         0
  BUB1B WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BUB1B MUTATED                                           0     8
  BUB1B WILD-TYPE                                         1   235
D1012V12, multiclass
                                           clus
vv                                          BUB1B MUTATED BUB1B WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1012V13, binary
                 cls
clus                0   1
  BUB1B MUTATED     0  10
  BUB1B WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUB1B MUTATED      0   10
  BUB1B WILD-TYPE    4  300
                        clus
vv                       BUB1B MUTATED BUB1B WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(1013) Variable = EEA1 MUTATION ANALYSIS
D1013V1, survival
                sevent
clus2              0   1
  EEA1 MUTATED    10   4
  EEA1 WILD-TYPE 220 135
  EEA1 MUTATED EEA1 WILD-TYPE 
            14            355 
  EEA1 MUTATED EEA1 WILD-TYPE 
             4            135 
$`EEA1 MUTATED`
TCGA-BR-4184 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8368 
        6.97        44.94        35.84        29.59         0.26         4.31 
TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CG-5728 TCGA-HF-7132 TCGA-HU-8238 
       27.12        31.96        16.14        65.10        77.29         1.51 
TCGA-HU-A4GU TCGA-RD-A7BW 
        6.58         5.13 

$`EEA1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-7703 TCGA-BR-7704 
       30.90        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-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-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-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-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-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-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 

  EEA1 MUTATED EEA1 WILD-TYPE 
          0.26           0.00 
  EEA1 MUTATED EEA1 WILD-TYPE 
         77.29         122.30 
  EEA1 MUTATED EEA1 WILD-TYPE 
         21.63          14.17 
[1] "0.3 - 77.3 (21.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D1013V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EEA1 MUTATED         0        0        5        1         1         2
  EEA1 WILD-TYPE       2       15       35       29        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EEA1 MUTATED           0          1          2          0        1
  EEA1 WILD-TYPE         3         69         51         32       37
D1013V3, multiclass
            clus
vv           EEA1 MUTATED EEA1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              5             35
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            2             51
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EEA1 MUTATED     0   6   5   3
  EEA1 WILD-TYPE  22  86 168  94
D1013V4, multiclass
    clus
vv   EEA1 MUTATED EEA1 WILD-TYPE
  T1            0             22
  T2            6             86
  T3            5            168
  T4            3             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
  EEA1 MUTATED     7   4   2   1
  EEA1 WILD-TYPE 111 100  75  76
D1013V5, multiclass
    clus
vv   EEA1 MUTATED EEA1 WILD-TYPE
  N0            7            111
  N1            4            100
  N2            2             75
  N3            1             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"
D1013V6, binary
                cls
clus               0   1
  EEA1 MUTATED    12   1
  EEA1 WILD-TYPE 334  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED     12    1
  EEA1 WILD-TYPE  334   28
   clus
vv  EEA1 MUTATED EEA1 WILD-TYPE
  0           12            334
  1            1             28
[1] 2 2
[1] FALSE
D1013V7, binary
                cls
clus               0   1
  EEA1 MUTATED     8   6
  EEA1 WILD-TYPE 137 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED      8    6
  EEA1 WILD-TYPE  137  242
        clus
vv       EEA1 MUTATED EEA1 WILD-TYPE
  FEMALE            8            137
  MALE              6            242
[1] 2 2
[1] FALSE
D1013V8, binary
                cls
clus               0   1
  EEA1 MUTATED    11   2
  EEA1 WILD-TYPE 281  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED     11    2
  EEA1 WILD-TYPE  281   57
     clus
vv    EEA1 MUTATED EEA1 WILD-TYPE
  NO            11            281
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EEA1 MUTATED                                          0
  EEA1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EEA1 MUTATED                                       2
  EEA1 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EEA1 MUTATED                                                        8
  EEA1 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EEA1 MUTATED                                                   1
  EEA1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EEA1 MUTATED                                                                   1
  EEA1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EEA1 MUTATED                                                    0
  EEA1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EEA1 MUTATED                                                  2
  EEA1 WILD-TYPE                                               59
D1013V9, multiclass
                                                                   clus
vv                                                                  EEA1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  EEA1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EEA1 MUTATED    13   0   0   1
  EEA1 WILD-TYPE 298  14  15  23
D1013V10, multiclass
    clus
vv   EEA1 MUTATED EEA1 WILD-TYPE
  R0           13            298
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1013V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  EEA1 MUTATED       3                         0
  EEA1 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EEA1 MUTATED                                           0     9
  EEA1 WILD-TYPE                                         1   234
D1013V12, multiclass
                                           clus
vv                                          EEA1 MUTATED EEA1 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1013V13, binary
                cls
clus               0   1
  EEA1 MUTATED     0  12
  EEA1 WILD-TYPE   4 298
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED      0   12
  EEA1 WILD-TYPE    4  298
                        clus
vv                       EEA1 MUTATED EEA1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           12            298
[1] 2 2
[1] FALSE

Clustering(1014) Variable = KCNH3 MUTATION ANALYSIS
D1014V1, survival
                 sevent
clus2               0   1
  KCNH3 MUTATED    13   4
  KCNH3 WILD-TYPE 217 135
  KCNH3 MUTATED KCNH3 WILD-TYPE 
             17             352 
  KCNH3 MUTATED KCNH3 WILD-TYPE 
              4             135 
$`KCNH3 MUTATED`
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8360 TCGA-BR-8487 
        9.34        34.68        32.78        35.84         6.18         1.12 
TCGA-BR-8591 TCGA-BR-A4QL TCGA-CD-8527 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4437 
       28.14        16.14         7.17         6.58        12.62         8.05 
TCGA-CG-5723 TCGA-CG-5728 TCGA-F1-6874 TCGA-HU-8602 TCGA-MX-A5UJ 
      105.07        65.10        14.47        22.32        19.73 

$`KCNH3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-F1-6875 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-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 

  KCNH3 MUTATED KCNH3 WILD-TYPE 
           1.12            0.00 
  KCNH3 MUTATED KCNH3 WILD-TYPE 
         105.07          122.30 
  KCNH3 MUTATED KCNH3 WILD-TYPE 
          16.14           14.12 
[1] "1.1 - 105.1 (16.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D1014V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNH3 MUTATED         0        0        4        3         5         1
  KCNH3 WILD-TYPE       2       15       36       27        32        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNH3 MUTATED           0          1          1          1        0
  KCNH3 WILD-TYPE         3         69         52         31       38
D1014V3, multiclass
            clus
vv           KCNH3 MUTATED KCNH3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               4              36
  STAGE II               3              27
  STAGE IIA              5              32
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNH3 MUTATED     0   7   7   2
  KCNH3 WILD-TYPE  22  85 166  95
D1014V4, multiclass
    clus
vv   KCNH3 MUTATED KCNH3 WILD-TYPE
  T1             0              22
  T2             7              85
  T3             7             166
  T4             2              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
  KCNH3 MUTATED    10   4   1   2
  KCNH3 WILD-TYPE 108 100  76  75
D1014V5, multiclass
    clus
vv   KCNH3 MUTATED KCNH3 WILD-TYPE
  N0            10             108
  N1             4             100
  N2             1              76
  N3             2              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"
D1014V6, binary
                 cls
clus                0   1
  KCNH3 MUTATED    17   0
  KCNH3 WILD-TYPE 329  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH3 MUTATED     17    0
  KCNH3 WILD-TYPE  329   29
   clus
vv  KCNH3 MUTATED KCNH3 WILD-TYPE
  0            17             329
  1             0              29
[1] 2 2
[1] FALSE
D1014V7, binary
                 cls
clus                0   1
  KCNH3 MUTATED     9   8
  KCNH3 WILD-TYPE 136 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH3 MUTATED      9    8
  KCNH3 WILD-TYPE  136  240
        clus
vv       KCNH3 MUTATED KCNH3 WILD-TYPE
  FEMALE             9             136
  MALE               8             240
[1] 2 2
[1] FALSE
D1014V8, binary
                 cls
clus                0   1
  KCNH3 MUTATED    16   0
  KCNH3 WILD-TYPE 276  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH3 MUTATED     16    0
  KCNH3 WILD-TYPE  276   59
     clus
vv    KCNH3 MUTATED KCNH3 WILD-TYPE
  NO             16             276
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KCNH3 MUTATED                                          0
  KCNH3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KCNH3 MUTATED                                       2
  KCNH3 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNH3 MUTATED                                                        9
  KCNH3 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KCNH3 MUTATED                                                   0
  KCNH3 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNH3 MUTATED                                                                   5
  KCNH3 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KCNH3 MUTATED                                                    0
  KCNH3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KCNH3 MUTATED                                                  1
  KCNH3 WILD-TYPE                                               60
D1014V9, multiclass
                                                                   clus
vv                                                                  KCNH3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  KCNH3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCNH3 MUTATED    14   0   0   1
  KCNH3 WILD-TYPE 297  14  15  23
D1014V10, multiclass
    clus
vv   KCNH3 MUTATED KCNH3 WILD-TYPE
  R0            14             297
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1014V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCNH3 MUTATED       4                         0
  KCNH3 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNH3 MUTATED                                           0    10
  KCNH3 WILD-TYPE                                         1   233
D1014V12, multiclass
                                           clus
vv                                          KCNH3 MUTATED KCNH3 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1014V13, binary
                 cls
clus                0   1
  KCNH3 MUTATED     0  14
  KCNH3 WILD-TYPE   4 296
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH3 MUTATED      0   14
  KCNH3 WILD-TYPE    4  296
                        clus
vv                       KCNH3 MUTATED KCNH3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             296
[1] 2 2
[1] FALSE

Clustering(1015) Variable = DIP2C MUTATION ANALYSIS
D1015V1, survival
                 sevent
clus2               0   1
  DIP2C MUTATED    15   6
  DIP2C WILD-TYPE 215 133
  DIP2C MUTATED DIP2C WILD-TYPE 
             21             348 
  DIP2C MUTATED DIP2C WILD-TYPE 
              6             133 
$`DIP2C MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-6566 
       21.99        26.70         6.97        34.68         9.17        32.78 
TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-A4QL 
       30.90        35.84        32.25         6.18        31.10        16.14 
TCGA-CD-5801 TCGA-CG-5721 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4GX 
       13.18         6.02        30.51        22.32        22.82        20.25 
TCGA-R5-A7ZI TCGA-VQ-A8P2 TCGA-VQ-AA64 
       74.53        38.14        18.41 

$`DIP2C WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       26.10        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-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-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-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-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-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-8608 TCGA-HU-8610 
        1.51         5.92        24.39        28.96        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-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-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 

  DIP2C MUTATED DIP2C WILD-TYPE 
           6.02            0.00 
  DIP2C MUTATED DIP2C WILD-TYPE 
          74.53          122.30 
  DIP2C MUTATED DIP2C WILD-TYPE 
         22.820          14.025 
[1] "6.0 - 74.5 (22.8)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.9"
D1015V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DIP2C MUTATED         0        0        1        0         4         4
  DIP2C WILD-TYPE       2       15       39       30        33        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DIP2C MUTATED           0          4          2          3        4
  DIP2C WILD-TYPE         3         66         51         29       34
D1015V3, multiclass
            clus
vv           DIP2C MUTATED DIP2C WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              4              33
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             2              51
  STAGE IIIC             3              29
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DIP2C MUTATED     0   1   9  12
  DIP2C WILD-TYPE  22  91 164  85
D1015V4, multiclass
    clus
vv   DIP2C MUTATED DIP2C WILD-TYPE
  T1             0              22
  T2             1              91
  T3             9             164
  T4            12              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
  DIP2C MUTATED     9   6   5   2
  DIP2C WILD-TYPE 109  98  72  75
D1015V5, multiclass
    clus
vv   DIP2C MUTATED DIP2C WILD-TYPE
  N0             9             109
  N1             6              98
  N2             5              72
  N3             2              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"
D1015V6, binary
                 cls
clus                0   1
  DIP2C MUTATED    19   2
  DIP2C WILD-TYPE 327  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIP2C MUTATED     19    2
  DIP2C WILD-TYPE  327   27
   clus
vv  DIP2C MUTATED DIP2C WILD-TYPE
  0            19             327
  1             2              27
[1] 2 2
[1] FALSE
D1015V7, binary
                 cls
clus                0   1
  DIP2C MUTATED    14   8
  DIP2C WILD-TYPE 131 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIP2C MUTATED     14    8
  DIP2C WILD-TYPE  131  240
        clus
vv       DIP2C MUTATED DIP2C WILD-TYPE
  FEMALE            14             131
  MALE               8             240
[1] 2 2
[1] FALSE
D1015V8, binary
                 cls
clus                0   1
  DIP2C MUTATED    18   3
  DIP2C WILD-TYPE 274  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIP2C MUTATED     18    3
  DIP2C WILD-TYPE  274   56
     clus
vv    DIP2C MUTATED DIP2C WILD-TYPE
  NO             18             274
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DIP2C MUTATED                                          0
  DIP2C WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DIP2C MUTATED                                       4
  DIP2C WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DIP2C MUTATED                                                       11
  DIP2C WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DIP2C MUTATED                                                   2
  DIP2C WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DIP2C MUTATED                                                                   4
  DIP2C WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DIP2C MUTATED                                                    0
  DIP2C WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DIP2C MUTATED                                                  1
  DIP2C WILD-TYPE                                               60
D1015V9, multiclass
                                                                   clus
vv                                                                  DIP2C MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  DIP2C WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DIP2C MUTATED    18   1   1   2
  DIP2C WILD-TYPE 293  13  14  22
D1015V10, multiclass
    clus
vv   DIP2C MUTATED DIP2C WILD-TYPE
  R0            18             293
  R1             1              13
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1015V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DIP2C MUTATED       4                         0
  DIP2C WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DIP2C MUTATED                                           0    15
  DIP2C WILD-TYPE                                         1   228
D1015V12, multiclass
                                           clus
vv                                          DIP2C MUTATED DIP2C WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                15             228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1015V13, binary
                 cls
clus                0   1
  DIP2C MUTATED     1  16
  DIP2C WILD-TYPE   3 294
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIP2C MUTATED      1   16
  DIP2C WILD-TYPE    3  294
                        clus
vv                       DIP2C MUTATED DIP2C WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            16             294
[1] 2 2
[1] FALSE

Clustering(1016) Variable = KLHL1 MUTATION ANALYSIS
D1016V1, survival
                 sevent
clus2               0   1
  KLHL1 MUTATED    10   4
  KLHL1 WILD-TYPE 220 135
  KLHL1 MUTATED KLHL1 WILD-TYPE 
             14             355 
  KLHL1 MUTATED KLHL1 WILD-TYPE 
              4             135 
$`KLHL1 MUTATED`
TCGA-CG-4460 TCGA-B7-5818 TCGA-BR-6563 TCGA-BR-8485 TCGA-CG-4438 TCGA-CG-5726 
       21.99        11.70        39.12         9.21        54.08        28.96 
TCGA-D7-5577 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-IN-A7NT TCGA-RD-A8N9 TCGA-VQ-A8DT 
       25.71         0.10         6.51        10.62        35.61        48.79 
TCGA-VQ-A8P2 TCGA-VQ-AA6A 
       38.14        38.93 

$`KLHL1 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       19.33        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-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-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-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-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-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-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        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-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 

  KLHL1 MUTATED KLHL1 WILD-TYPE 
            0.1             0.0 
  KLHL1 MUTATED KLHL1 WILD-TYPE 
          54.08          122.30 
  KLHL1 MUTATED KLHL1 WILD-TYPE 
         27.335          14.070 
[1] "0.1 - 54.1 (27.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D1016V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KLHL1 MUTATED         1        1        1        1         1         2
  KLHL1 WILD-TYPE       1       14       39       29        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLHL1 MUTATED           0          2          1          3        2
  KLHL1 WILD-TYPE         3         68         52         29       36
D1016V3, multiclass
            clus
vv           KLHL1 MUTATED KLHL1 WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLHL1 MUTATED     2   3   4   6
  KLHL1 WILD-TYPE  20  89 169  91
D1016V4, multiclass
    clus
vv   KLHL1 MUTATED KLHL1 WILD-TYPE
  T1             2              20
  T2             3              89
  T3             4             169
  T4             6              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
  KLHL1 MUTATED     3   6   2   4
  KLHL1 WILD-TYPE 115  98  75  73
D1016V5, multiclass
    clus
vv   KLHL1 MUTATED KLHL1 WILD-TYPE
  N0             3             115
  N1             6              98
  N2             2              75
  N3             4              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"
D1016V6, binary
                 cls
clus                0   1
  KLHL1 MUTATED    13   1
  KLHL1 WILD-TYPE 333  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL1 MUTATED     13    1
  KLHL1 WILD-TYPE  333   28
   clus
vv  KLHL1 MUTATED KLHL1 WILD-TYPE
  0            13             333
  1             1              28
[1] 2 2
[1] FALSE
D1016V7, binary
                 cls
clus                0   1
  KLHL1 MUTATED     6   9
  KLHL1 WILD-TYPE 139 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL1 MUTATED      6    9
  KLHL1 WILD-TYPE  139  239
        clus
vv       KLHL1 MUTATED KLHL1 WILD-TYPE
  FEMALE             6             139
  MALE               9             239
[1] 2 2
[1] FALSE
D1016V8, binary
                 cls
clus                0   1
  KLHL1 MUTATED     9   4
  KLHL1 WILD-TYPE 283  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL1 MUTATED      9    4
  KLHL1 WILD-TYPE  283   55
     clus
vv    KLHL1 MUTATED KLHL1 WILD-TYPE
  NO              9             283
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KLHL1 MUTATED                                          0
  KLHL1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KLHL1 MUTATED                                       2
  KLHL1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KLHL1 MUTATED                                                        4
  KLHL1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KLHL1 MUTATED                                                   1
  KLHL1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KLHL1 MUTATED                                                                   5
  KLHL1 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KLHL1 MUTATED                                                    0
  KLHL1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KLHL1 MUTATED                                                  3
  KLHL1 WILD-TYPE                                               58
D1016V9, multiclass
                                                                   clus
vv                                                                  KLHL1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  KLHL1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KLHL1 MUTATED    14   0   1   0
  KLHL1 WILD-TYPE 297  14  14  24
D1016V10, multiclass
    clus
vv   KLHL1 MUTATED KLHL1 WILD-TYPE
  R0            14             297
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1016V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KLHL1 MUTATED       3                         1
  KLHL1 WILD-TYPE    84                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KLHL1 MUTATED                                           0     7
  KLHL1 WILD-TYPE                                         1   236
D1016V12, multiclass
                                           clus
vv                                          KLHL1 MUTATED KLHL1 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1016V13, binary
                 cls
clus                0   1
  KLHL1 MUTATED     0   9
  KLHL1 WILD-TYPE   4 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL1 MUTATED      0    9
  KLHL1 WILD-TYPE    4  301
                        clus
vv                       KLHL1 MUTATED KLHL1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(1017) Variable = ZC3H3 MUTATION ANALYSIS
D1017V1, survival
                 sevent
clus2               0   1
  ZC3H3 MUTATED    14   4
  ZC3H3 WILD-TYPE 216 135
  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
             18             351 
  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
              4             135 
$`ZC3H3 MUTATED`
TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8368 TCGA-BR-8591 TCGA-CD-A48A 
       26.70         9.67        34.68         4.31        28.14        12.43 
TCGA-CD-A4MG TCGA-CG-4305 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-HF-A5NB TCGA-HU-8244 
        6.58        15.95        14.27         5.92        30.51        24.39 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-R5-A7ZE 
       22.32        22.68        24.20         6.51         6.58        18.21 

$`ZC3H3 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
       11.31        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-A4YU TCGA-D7-A4YX TCGA-D7-A4YY 
       14.66        21.14        20.91        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-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-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-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 

  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
           4.31            0.00 
  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
          34.68          122.30 
  ZC3H3 MUTATED ZC3H3 WILD-TYPE 
          17.08           14.07 
[1] "4.3 - 34.7 (17.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D1017V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZC3H3 MUTATED         0        2        1        1         4         5
  ZC3H3 WILD-TYPE       2       13       39       29        33        47
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H3 MUTATED           0          2          0          2        1
  ZC3H3 WILD-TYPE         3         68         53         30       37
D1017V3, multiclass
            clus
vv           ZC3H3 MUTATED ZC3H3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              4              33
  STAGE IIB              5              47
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZC3H3 MUTATED     2   3   8   5
  ZC3H3 WILD-TYPE  20  89 165  92
D1017V4, multiclass
    clus
vv   ZC3H3 MUTATED ZC3H3 WILD-TYPE
  T1             2              20
  T2             3              89
  T3             8             165
  T4             5              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
  ZC3H3 MUTATED     9   4   2   3
  ZC3H3 WILD-TYPE 109 100  75  74
D1017V5, multiclass
    clus
vv   ZC3H3 MUTATED ZC3H3 WILD-TYPE
  N0             9             109
  N1             4             100
  N2             2              75
  N3             3              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"
D1017V6, binary
                 cls
clus                0   1
  ZC3H3 MUTATED    19   0
  ZC3H3 WILD-TYPE 327  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H3 MUTATED     19    0
  ZC3H3 WILD-TYPE  327   29
   clus
vv  ZC3H3 MUTATED ZC3H3 WILD-TYPE
  0            19             327
  1             0              29
[1] 2 2
[1] FALSE
D1017V7, binary
                 cls
clus                0   1
  ZC3H3 MUTATED    13   6
  ZC3H3 WILD-TYPE 132 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H3 MUTATED     13    6
  ZC3H3 WILD-TYPE  132  242
        clus
vv       ZC3H3 MUTATED ZC3H3 WILD-TYPE
  FEMALE            13             132
  MALE               6             242
[1] 2 2
[1] FALSE
D1017V8, binary
                 cls
clus                0   1
  ZC3H3 MUTATED    16   2
  ZC3H3 WILD-TYPE 276  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H3 MUTATED     16    2
  ZC3H3 WILD-TYPE  276   57
     clus
vv    ZC3H3 MUTATED ZC3H3 WILD-TYPE
  NO             16             276
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZC3H3 MUTATED                                          0
  ZC3H3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZC3H3 MUTATED                                       5
  ZC3H3 WILD-TYPE                                    65
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZC3H3 MUTATED                                                        7
  ZC3H3 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZC3H3 MUTATED                                                   1
  ZC3H3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZC3H3 MUTATED                                                                   0
  ZC3H3 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZC3H3 MUTATED                                                    0
  ZC3H3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZC3H3 MUTATED                                                  6
  ZC3H3 WILD-TYPE                                               55
D1017V9, multiclass
                                                                   clus
vv                                                                  ZC3H3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              6
                                                                   clus
vv                                                                  ZC3H3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZC3H3 MUTATED    12   1   0   2
  ZC3H3 WILD-TYPE 299  13  15  22
D1017V10, multiclass
    clus
vv   ZC3H3 MUTATED ZC3H3 WILD-TYPE
  R0            12             299
  R1             1              13
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1017V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZC3H3 MUTATED       8                         0
  ZC3H3 WILD-TYPE    79                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZC3H3 MUTATED                                           0     9
  ZC3H3 WILD-TYPE                                         1   234
D1017V12, multiclass
                                           clus
vv                                          ZC3H3 MUTATED ZC3H3 WILD-TYPE
  ASIAN                                                 8              79
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1017V13, binary
                 cls
clus                0   1
  ZC3H3 MUTATED     0  17
  ZC3H3 WILD-TYPE   4 293
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H3 MUTATED      0   17
  ZC3H3 WILD-TYPE    4  293
                        clus
vv                       ZC3H3 MUTATED ZC3H3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            17             293
[1] 2 2
[1] FALSE

Clustering(1018) Variable = SLC22A16 MUTATION ANALYSIS
D1018V1, survival
                    sevent
clus2                  0   1
  SLC22A16 MUTATED     9   1
  SLC22A16 WILD-TYPE 221 138
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                10                359 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                 1                138 
$`SLC22A16 MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8372 TCGA-CD-8529 TCGA-F1-6874 
       11.70         6.97        34.68        31.27        12.30        14.47 
TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-VQ-A8P2 
       22.32        22.68        29.98        38.14 

$`SLC22A16 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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 

  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
              6.97               0.00 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             38.14             122.30 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             22.50              14.07 
[1] "7.0 - 38.1 (22.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "5"  
D1018V2, 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       2       15       38       30        35        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A16 MUTATED           0          2          0          1        1
  SLC22A16 WILD-TYPE         3         68         53         31       37
D1018V3, multiclass
            clus
vv           SLC22A16 MUTATED SLC22A16 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  2                 38
  STAGE II                  0                 30
  STAGE IIA                 2                 35
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                0                 53
  STAGE IIIC                1                 31
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC22A16 MUTATED     0   3   3   4
  SLC22A16 WILD-TYPE  22  89 170  93
D1018V4, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  T1                0                 22
  T2                3                 89
  T3                3                170
  T4                4                 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
  SLC22A16 MUTATED     5   4   0   1
  SLC22A16 WILD-TYPE 113 100  77  76
D1018V5, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  N0                5                113
  N1                4                100
  N2                0                 77
  N3                1                 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"
D1018V6, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED     9   1
  SLC22A16 WILD-TYPE 337  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      9    1
  SLC22A16 WILD-TYPE  337   28
   clus
vv  SLC22A16 MUTATED SLC22A16 WILD-TYPE
  0                9                337
  1                1                 28
[1] 2 2
[1] FALSE
D1018V7, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED     4   7
  SLC22A16 WILD-TYPE 141 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      4    7
  SLC22A16 WILD-TYPE  141  241
        clus
vv       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  FEMALE                4                141
  MALE                  7                241
[1] 2 2
[1] FALSE
D1018V8, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED     8   2
  SLC22A16 WILD-TYPE 284  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      8    2
  SLC22A16 WILD-TYPE  284   57
     clus
vv    SLC22A16 MUTATED SLC22A16 WILD-TYPE
  NO                 8                284
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC22A16 MUTATED                                          0
  SLC22A16 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC22A16 MUTATED                                       3
  SLC22A16 WILD-TYPE                                    67
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC22A16 MUTATED                                                        4
  SLC22A16 WILD-TYPE                                                    154
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC22A16 MUTATED                                                   2
  SLC22A16 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC22A16 MUTATED                                                                   1
  SLC22A16 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC22A16 MUTATED                                                    0
  SLC22A16 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC22A16 MUTATED                                                  1
  SLC22A16 WILD-TYPE                                               60
D1018V9, multiclass
                                                                   clus
vv                                                                  SLC22A16 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  SLC22A16 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SLC22A16 MUTATED     8   0   0   2
  SLC22A16 WILD-TYPE 303  14  15  22
D1018V10, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  R0                8                303
  R1                0                 14
  R2                0                 15
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1018V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SLC22A16 MUTATED       4                         0
  SLC22A16 WILD-TYPE    83                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC22A16 MUTATED                                           0     7
  SLC22A16 WILD-TYPE                                         1   236
D1018V12, multiclass
                                           clus
vv                                          SLC22A16 MUTATED SLC22A16 WILD-TYPE
  ASIAN                                                    4                 83
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1018V13, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED     0  10
  SLC22A16 WILD-TYPE   4 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      0   10
  SLC22A16 WILD-TYPE    4  300
                        clus
vv                       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               10                300
[1] 2 2
[1] FALSE

Clustering(1019) Variable = NHLRC2 MUTATION ANALYSIS
D1019V1, survival
                  sevent
clus2                0   1
  NHLRC2 MUTATED     4   2
  NHLRC2 WILD-TYPE 226 137
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               6              363 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               2              137 
$`NHLRC2 MUTATED`
TCGA-BR-6452 TCGA-BR-8680 TCGA-BR-A4QL TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4G3 
       34.68        31.96        16.14        11.44        22.32         5.59 

$`NHLRC2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
            5.59             0.00 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
           34.68           122.30 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
           19.23            14.17 
[1] "5.6 - 34.7 (19.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D1019V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NHLRC2 MUTATED         0        0        0        0         1         2
  NHLRC2 WILD-TYPE       2       15       40       30        36        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NHLRC2 MUTATED           0          1          2          0        1
  NHLRC2 WILD-TYPE         3         69         51         32       37
D1019V3, multiclass
            clus
vv           NHLRC2 MUTATED NHLRC2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              2               51
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NHLRC2 MUTATED     0   1   3   3
  NHLRC2 WILD-TYPE  22  91 170  94
D1019V4, multiclass
    clus
vv   NHLRC2 MUTATED NHLRC2 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              3              170
  T4              3               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
  NHLRC2 MUTATED     3   0   2   2
  NHLRC2 WILD-TYPE 115 104  75  75
D1019V5, multiclass
    clus
vv   NHLRC2 MUTATED NHLRC2 WILD-TYPE
  N0              3              115
  N1              0              104
  N2              2               75
  N3              2               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"
D1019V6, binary
                  cls
clus                 0   1
  NHLRC2 MUTATED     6   1
  NHLRC2 WILD-TYPE 340  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC2 MUTATED      6    1
  NHLRC2 WILD-TYPE  340   28
   clus
vv  NHLRC2 MUTATED NHLRC2 WILD-TYPE
  0              6              340
  1              1               28
[1] 2 2
[1] FALSE
D1019V7, binary
                  cls
clus                 0   1
  NHLRC2 MUTATED     5   2
  NHLRC2 WILD-TYPE 140 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC2 MUTATED      5    2
  NHLRC2 WILD-TYPE  140  246
        clus
vv       NHLRC2 MUTATED NHLRC2 WILD-TYPE
  FEMALE              5              140
  MALE                2              246
[1] 2 2
[1] FALSE
D1019V8, binary
                  cls
clus                 0   1
  NHLRC2 MUTATED     6   0
  NHLRC2 WILD-TYPE 286  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC2 MUTATED      6    0
  NHLRC2 WILD-TYPE  286   59
     clus
vv    NHLRC2 MUTATED NHLRC2 WILD-TYPE
  NO               6              286
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NHLRC2 MUTATED                                          0
  NHLRC2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NHLRC2 MUTATED                                       1
  NHLRC2 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NHLRC2 MUTATED                                                        3
  NHLRC2 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NHLRC2 MUTATED                                                   0
  NHLRC2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NHLRC2 MUTATED                                                                   0
  NHLRC2 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NHLRC2 MUTATED                                                    0
  NHLRC2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NHLRC2 MUTATED                                                  3
  NHLRC2 WILD-TYPE                                               58
D1019V9, multiclass
                                                                   clus
vv                                                                  NHLRC2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  NHLRC2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NHLRC2 MUTATED     6   0   0   1
  NHLRC2 WILD-TYPE 305  14  15  23
D1019V10, multiclass
    clus
vv   NHLRC2 MUTATED NHLRC2 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1019V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NHLRC2 MUTATED       3                         0
  NHLRC2 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NHLRC2 MUTATED                                           0     4
  NHLRC2 WILD-TYPE                                         1   239
D1019V12, multiclass
                                           clus
vv                                          NHLRC2 MUTATED NHLRC2 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1019V13, binary
                  cls
clus                 0   1
  NHLRC2 MUTATED     0   7
  NHLRC2 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC2 MUTATED      0    7
  NHLRC2 WILD-TYPE    4  303
                        clus
vv                       NHLRC2 MUTATED NHLRC2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(1020) Variable = CEACAM3 MUTATION ANALYSIS
D1020V1, survival
                   sevent
clus2                 0   1
  CEACAM3 MUTATED     4   4
  CEACAM3 WILD-TYPE 226 135
  CEACAM3 MUTATED CEACAM3 WILD-TYPE 
                8               361 
  CEACAM3 MUTATED CEACAM3 WILD-TYPE 
                4               135 
$`CEACAM3 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8591 TCGA-CD-A4MG TCGA-CG-5721 
        6.97        34.68         0.26        28.14         6.58         6.02 
TCGA-FP-A4BE TCGA-VQ-AA64 
       11.08        18.41 

$`CEACAM3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  CEACAM3 MUTATED CEACAM3 WILD-TYPE 
             0.26              0.00 
  CEACAM3 MUTATED CEACAM3 WILD-TYPE 
            34.68            122.30 
  CEACAM3 MUTATED CEACAM3 WILD-TYPE 
            9.025            14.430 
[1] "0.3 - 34.7 (9.0)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.8"
D1020V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CEACAM3 MUTATED         1        0        1        0         3         0
  CEACAM3 WILD-TYPE       1       15       39       30        34        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEACAM3 MUTATED           0          1          1          1        1
  CEACAM3 WILD-TYPE         3         69         52         31       37
D1020V3, multiclass
            clus
vv           CEACAM3 MUTATED CEACAM3 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                3                34
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CEACAM3 MUTATED     1   1   5   2
  CEACAM3 WILD-TYPE  21  91 168  95
D1020V4, multiclass
    clus
vv   CEACAM3 MUTATED CEACAM3 WILD-TYPE
  T1               1                21
  T2               1                91
  T3               5               168
  T4               2                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
  CEACAM3 MUTATED     4   3   1   1
  CEACAM3 WILD-TYPE 114 101  76  76
D1020V5, multiclass
    clus
vv   CEACAM3 MUTATED CEACAM3 WILD-TYPE
  N0               4               114
  N1               3               101
  N2               1                76
  N3               1                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"
D1020V6, binary
                   cls
clus                  0   1
  CEACAM3 MUTATED     7   0
  CEACAM3 WILD-TYPE 339  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM3 MUTATED      7    0
  CEACAM3 WILD-TYPE  339   29
   clus
vv  CEACAM3 MUTATED CEACAM3 WILD-TYPE
  0               7               339
  1               0                29
[1] 2 2
[1] FALSE
D1020V7, binary
                   cls
clus                  0   1
  CEACAM3 MUTATED     2   7
  CEACAM3 WILD-TYPE 143 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM3 MUTATED      2    7
  CEACAM3 WILD-TYPE  143  241
        clus
vv       CEACAM3 MUTATED CEACAM3 WILD-TYPE
  FEMALE               2               143
  MALE                 7               241
[1] 2 2
[1] FALSE
D1020V8, binary
                   cls
clus                  0   1
  CEACAM3 MUTATED     7   2
  CEACAM3 WILD-TYPE 285  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM3 MUTATED      7    2
  CEACAM3 WILD-TYPE  285   57
     clus
vv    CEACAM3 MUTATED CEACAM3 WILD-TYPE
  NO                7               285
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CEACAM3 MUTATED                                          0
  CEACAM3 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CEACAM3 MUTATED                                       1
  CEACAM3 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CEACAM3 MUTATED                                                        6
  CEACAM3 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CEACAM3 MUTATED                                                   0
  CEACAM3 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CEACAM3 MUTATED                                                                   2
  CEACAM3 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CEACAM3 MUTATED                                                    0
  CEACAM3 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CEACAM3 MUTATED                                                  0
  CEACAM3 WILD-TYPE                                               61
D1020V9, multiclass
                                                                   clus
vv                                                                  CEACAM3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  CEACAM3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CEACAM3 MUTATED     7   0   0   1
  CEACAM3 WILD-TYPE 304  14  15  23
D1020V10, multiclass
    clus
vv   CEACAM3 MUTATED CEACAM3 WILD-TYPE
  R0               7               304
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1020V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CEACAM3 MUTATED       1                         2
  CEACAM3 WILD-TYPE    86                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CEACAM3 MUTATED                                           0     5
  CEACAM3 WILD-TYPE                                         1   238
D1020V12, multiclass
                                           clus
vv                                          CEACAM3 MUTATED CEACAM3 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               2                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1020V13, binary
                   cls
clus                  0   1
  CEACAM3 MUTATED     0   7
  CEACAM3 WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM3 MUTATED      0    7
  CEACAM3 WILD-TYPE    4  303
                        clus
vv                       CEACAM3 MUTATED CEACAM3 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(1021) Variable = THBS3 MUTATION ANALYSIS
D1021V1, survival
                 sevent
clus2               0   1
  THBS3 MUTATED     6   4
  THBS3 WILD-TYPE 224 135
  THBS3 MUTATED THBS3 WILD-TYPE 
             10             359 
  THBS3 MUTATED THBS3 WILD-TYPE 
              4             135 
$`THBS3 MUTATED`
TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CG-5721 
        9.67         6.61        34.68        16.14         6.58         6.02 
TCGA-HF-7132 TCGA-HF-A5NB TCGA-HU-A4GU TCGA-HU-A4H4 
       77.29        30.51         6.58        23.84 

$`THBS3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  THBS3 MUTATED THBS3 WILD-TYPE 
           6.02            0.00 
  THBS3 MUTATED THBS3 WILD-TYPE 
          77.29          122.30 
  THBS3 MUTATED THBS3 WILD-TYPE 
         12.905          14.270 
[1] "6.0 - 77.3 (12.9)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D1021V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  THBS3 MUTATED         0        0        0        1         2         2
  THBS3 WILD-TYPE       2       15       40       29        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  THBS3 MUTATED           1          0          1          1        1
  THBS3 WILD-TYPE         2         70         52         31       37
D1021V3, multiclass
            clus
vv           THBS3 MUTATED THBS3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              1               2
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  THBS3 MUTATED     0   3   4   2
  THBS3 WILD-TYPE  22  89 169  95
D1021V4, multiclass
    clus
vv   THBS3 MUTATED THBS3 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             4             169
  T4             2              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
  THBS3 MUTATED     2   4   1   2
  THBS3 WILD-TYPE 116 100  76  75
D1021V5, multiclass
    clus
vv   THBS3 MUTATED THBS3 WILD-TYPE
  N0             2             116
  N1             4             100
  N2             1              76
  N3             2              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"
D1021V6, binary
                 cls
clus                0   1
  THBS3 MUTATED    10   0
  THBS3 WILD-TYPE 336  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS3 MUTATED     10    0
  THBS3 WILD-TYPE  336   29
   clus
vv  THBS3 MUTATED THBS3 WILD-TYPE
  0            10             336
  1             0              29
[1] 2 2
[1] FALSE
D1021V7, binary
                 cls
clus                0   1
  THBS3 MUTATED     6   4
  THBS3 WILD-TYPE 139 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS3 MUTATED      6    4
  THBS3 WILD-TYPE  139  244
        clus
vv       THBS3 MUTATED THBS3 WILD-TYPE
  FEMALE             6             139
  MALE               4             244
[1] 2 2
[1] FALSE
D1021V8, binary
                 cls
clus                0   1
  THBS3 MUTATED     8   2
  THBS3 WILD-TYPE 284  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS3 MUTATED      8    2
  THBS3 WILD-TYPE  284   57
     clus
vv    THBS3 MUTATED THBS3 WILD-TYPE
  NO              8             284
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  THBS3 MUTATED                                          0
  THBS3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  THBS3 MUTATED                                       2
  THBS3 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  THBS3 MUTATED                                                        4
  THBS3 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  THBS3 MUTATED                                                   2
  THBS3 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  THBS3 MUTATED                                                                   1
  THBS3 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  THBS3 MUTATED                                                    0
  THBS3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  THBS3 MUTATED                                                  1
  THBS3 WILD-TYPE                                               60
D1021V9, multiclass
                                                                   clus
vv                                                                  THBS3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  THBS3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  THBS3 MUTATED     6   1   0   2
  THBS3 WILD-TYPE 305  13  15  22
D1021V10, multiclass
    clus
vv   THBS3 MUTATED THBS3 WILD-TYPE
  R0             6             305
  R1             1              13
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1021V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  THBS3 MUTATED       3                         0
  THBS3 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  THBS3 MUTATED                                           0     4
  THBS3 WILD-TYPE                                         1   239
D1021V12, multiclass
                                           clus
vv                                          THBS3 MUTATED THBS3 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1021V13, binary
                 cls
clus                0   1
  THBS3 MUTATED     0   7
  THBS3 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS3 MUTATED      0    7
  THBS3 WILD-TYPE    4  303
                        clus
vv                       THBS3 MUTATED THBS3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(1022) Variable = GPC4 MUTATION ANALYSIS
D1022V1, survival
                sevent
clus2              0   1
  GPC4 MUTATED     7   0
  GPC4 WILD-TYPE 223 139
  GPC4 MUTATED GPC4 WILD-TYPE 
             7            362 
  GPC4 MUTATED GPC4 WILD-TYPE 
             0            139 
$`GPC4 MUTATED`
TCGA-BR-7703 TCGA-BR-8078 TCGA-BR-8368 TCGA-BR-8486 TCGA-CG-4437 TCGA-F1-A448 
       36.16        29.59         4.31        20.22         8.05        21.27 
TCGA-FP-A4BE 
       11.08 

$`GPC4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  GPC4 MUTATED GPC4 WILD-TYPE 
          4.31           0.00 
  GPC4 MUTATED GPC4 WILD-TYPE 
         36.16         122.30 
  GPC4 MUTATED GPC4 WILD-TYPE 
         20.22          14.22 
[1] "4.3 - 36.2 (20.2)"  "0.0 - 122.3 (14.2)"
[1] "hr="     "9200000"
D1022V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPC4 MUTATED         0        2        1        1         1         1
  GPC4 WILD-TYPE       2       13       39       29        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPC4 MUTATED           0          0          1          0        0
  GPC4 WILD-TYPE         3         70         52         32       38
D1022V3, multiclass
            clus
vv           GPC4 MUTATED GPC4 WILD-TYPE
  STAGE I               0              2
  STAGE IA              2             13
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GPC4 MUTATED     3   2   2   1
  GPC4 WILD-TYPE  19  90 171  96
D1022V4, multiclass
    clus
vv   GPC4 MUTATED GPC4 WILD-TYPE
  T1            3             19
  T2            2             90
  T3            2            171
  T4            1             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
  GPC4 MUTATED     5   1   0   1
  GPC4 WILD-TYPE 113 103  77  76
D1022V5, multiclass
    clus
vv   GPC4 MUTATED GPC4 WILD-TYPE
  N0            5            113
  N1            1            103
  N2            0             77
  N3            1             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"
D1022V6, binary
                cls
clus               0   1
  GPC4 MUTATED     8   0
  GPC4 WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC4 MUTATED      8    0
  GPC4 WILD-TYPE  338   29
   clus
vv  GPC4 MUTATED GPC4 WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D1022V7, binary
                cls
clus               0   1
  GPC4 MUTATED     4   4
  GPC4 WILD-TYPE 141 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC4 MUTATED      4    4
  GPC4 WILD-TYPE  141  244
        clus
vv       GPC4 MUTATED GPC4 WILD-TYPE
  FEMALE            4            141
  MALE              4            244
[1] 2 2
[1] FALSE
D1022V8, binary
                cls
clus               0   1
  GPC4 MUTATED     5   2
  GPC4 WILD-TYPE 287  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC4 MUTATED      5    2
  GPC4 WILD-TYPE  287   57
     clus
vv    GPC4 MUTATED GPC4 WILD-TYPE
  NO             5            287
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GPC4 MUTATED                                          0
  GPC4 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GPC4 MUTATED                                       0
  GPC4 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPC4 MUTATED                                                        5
  GPC4 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GPC4 MUTATED                                                   1
  GPC4 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPC4 MUTATED                                                                   1
  GPC4 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GPC4 MUTATED                                                    1
  GPC4 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GPC4 MUTATED                                                  0
  GPC4 WILD-TYPE                                               61
D1022V9, multiclass
                                                                   clus
vv                                                                  GPC4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  GPC4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GPC4 MUTATED     7   0   0   1
  GPC4 WILD-TYPE 304  14  15  23
D1022V10, multiclass
    clus
vv   GPC4 MUTATED GPC4 WILD-TYPE
  R0            7            304
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1022V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GPC4 MUTATED       0                         1
  GPC4 WILD-TYPE    87                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPC4 MUTATED                                           0     6
  GPC4 WILD-TYPE                                         1   237
D1022V12, multiclass
                                           clus
vv                                          GPC4 MUTATED GPC4 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1022V13, binary
                cls
clus               0   1
  GPC4 MUTATED     1   6
  GPC4 WILD-TYPE   3 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC4 MUTATED      1    6
  GPC4 WILD-TYPE    3  304
                        clus
vv                       GPC4 MUTATED GPC4 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(1023) Variable = ABTB1 MUTATION ANALYSIS
D1023V1, survival
                 sevent
clus2               0   1
  ABTB1 MUTATED     4   5
  ABTB1 WILD-TYPE 226 134
  ABTB1 MUTATED ABTB1 WILD-TYPE 
              9             360 
  ABTB1 MUTATED ABTB1 WILD-TYPE 
              5             134 
$`ABTB1 MUTATED`
TCGA-BR-4184 TCGA-BR-8361 TCGA-BR-A4QL TCGA-CG-5726 TCGA-CG-5728 TCGA-HU-A4GQ 
        6.97        31.10        16.14        28.96        65.10         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-R5-A7ZE 
        6.51         6.58        18.21 

$`ABTB1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  ABTB1 MUTATED ABTB1 WILD-TYPE 
            0.1             0.0 
  ABTB1 MUTATED ABTB1 WILD-TYPE 
           65.1           122.3 
  ABTB1 MUTATED ABTB1 WILD-TYPE 
          16.14           14.22 
[1] "0.1 - 65.1 (16.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.5"
D1023V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABTB1 MUTATED         0        1        1        0         1         1
  ABTB1 WILD-TYPE       2       14       39       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABTB1 MUTATED           0          2          1          2        1
  ABTB1 WILD-TYPE         3         68         52         30       37
D1023V3, multiclass
            clus
vv           ABTB1 MUTATED ABTB1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABTB1 MUTATED     1   1   5   3
  ABTB1 WILD-TYPE  21  91 168  94
D1023V4, multiclass
    clus
vv   ABTB1 MUTATED ABTB1 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             5             168
  T4             3              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
  ABTB1 MUTATED     3   2   4   1
  ABTB1 WILD-TYPE 115 102  73  76
D1023V5, multiclass
    clus
vv   ABTB1 MUTATED ABTB1 WILD-TYPE
  N0             3             115
  N1             2             102
  N2             4              73
  N3             1              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"
D1023V6, binary
                 cls
clus                0   1
  ABTB1 MUTATED     9   0
  ABTB1 WILD-TYPE 337  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABTB1 MUTATED      9    0
  ABTB1 WILD-TYPE  337   29
   clus
vv  ABTB1 MUTATED ABTB1 WILD-TYPE
  0             9             337
  1             0              29
[1] 2 2
[1] FALSE
D1023V7, binary
                 cls
clus                0   1
  ABTB1 MUTATED     6   4
  ABTB1 WILD-TYPE 139 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABTB1 MUTATED      6    4
  ABTB1 WILD-TYPE  139  244
        clus
vv       ABTB1 MUTATED ABTB1 WILD-TYPE
  FEMALE             6             139
  MALE               4             244
[1] 2 2
[1] FALSE
D1023V8, binary
                 cls
clus                0   1
  ABTB1 MUTATED     7   0
  ABTB1 WILD-TYPE 285  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABTB1 MUTATED      7    0
  ABTB1 WILD-TYPE  285   59
     clus
vv    ABTB1 MUTATED ABTB1 WILD-TYPE
  NO              7             285
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ABTB1 MUTATED                                          0
  ABTB1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ABTB1 MUTATED                                       1
  ABTB1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABTB1 MUTATED                                                        4
  ABTB1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ABTB1 MUTATED                                                   0
  ABTB1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABTB1 MUTATED                                                                   2
  ABTB1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ABTB1 MUTATED                                                    0
  ABTB1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ABTB1 MUTATED                                                  3
  ABTB1 WILD-TYPE                                               58
D1023V9, multiclass
                                                                   clus
vv                                                                  ABTB1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  ABTB1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABTB1 MUTATED     7   0   0   2
  ABTB1 WILD-TYPE 304  14  15  22
D1023V10, multiclass
    clus
vv   ABTB1 MUTATED ABTB1 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1023V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABTB1 MUTATED       3                         0
  ABTB1 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABTB1 MUTATED                                           0     5
  ABTB1 WILD-TYPE                                         1   238
D1023V12, multiclass
                                           clus
vv                                          ABTB1 MUTATED ABTB1 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1023V13, binary
                 cls
clus                0   1
  ABTB1 MUTATED     0   8
  ABTB1 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABTB1 MUTATED      0    8
  ABTB1 WILD-TYPE    4  302
                        clus
vv                       ABTB1 MUTATED ABTB1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(1024) Variable = NEK7 MUTATION ANALYSIS
D1024V1, survival
                sevent
clus2              0   1
  NEK7 MUTATED     3   2
  NEK7 WILD-TYPE 227 137
  NEK7 MUTATED NEK7 WILD-TYPE 
             5            364 
  NEK7 MUTATED NEK7 WILD-TYPE 
             2            137 
$`NEK7 MUTATED`
TCGA-CG-4460 TCGA-CG-4306 TCGA-F1-6874 TCGA-HF-A5NB TCGA-HU-A4GX 
       21.99         1.02        14.47        30.51        20.25 

$`NEK7 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  NEK7 MUTATED NEK7 WILD-TYPE 
          1.02           0.00 
  NEK7 MUTATED NEK7 WILD-TYPE 
         30.51         122.30 
  NEK7 MUTATED NEK7 WILD-TYPE 
         20.25          14.12 
[1] "1.0 - 30.5 (20.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D1024V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NEK7 MUTATED         1        0        1        0         0         0
  NEK7 WILD-TYPE       1       15       39       30        37        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NEK7 MUTATED           0          0          0          2        2
  NEK7 WILD-TYPE         3         70         53         30       36
D1024V3, multiclass
            clus
vv           NEK7 MUTATED NEK7 WILD-TYPE
  STAGE I               1              1
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NEK7 MUTATED     1   1   1   3
  NEK7 WILD-TYPE  21  91 172  94
D1024V4, multiclass
    clus
vv   NEK7 MUTATED NEK7 WILD-TYPE
  T1            1             21
  T2            1             91
  T3            1            172
  T4            3             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
  NEK7 MUTATED     1   2   2   1
  NEK7 WILD-TYPE 117 102  75  76
D1024V5, multiclass
    clus
vv   NEK7 MUTATED NEK7 WILD-TYPE
  N0            1            117
  N1            2            102
  N2            2             75
  N3            1             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"
D1024V6, binary
                cls
clus               0   1
  NEK7 MUTATED     3   2
  NEK7 WILD-TYPE 343  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK7 MUTATED      3    2
  NEK7 WILD-TYPE  343   27
   clus
vv  NEK7 MUTATED NEK7 WILD-TYPE
  0            3            343
  1            2             27
[1] 2 2
[1] FALSE
D1024V7, binary
                cls
clus               0   1
  NEK7 MUTATED     3   3
  NEK7 WILD-TYPE 142 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK7 MUTATED      3    3
  NEK7 WILD-TYPE  142  245
        clus
vv       NEK7 MUTATED NEK7 WILD-TYPE
  FEMALE            3            142
  MALE              3            245
[1] 2 2
[1] FALSE
D1024V8, binary
                cls
clus               0   1
  NEK7 MUTATED     4   1
  NEK7 WILD-TYPE 288  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK7 MUTATED      4    1
  NEK7 WILD-TYPE  288   58
     clus
vv    NEK7 MUTATED NEK7 WILD-TYPE
  NO             4            288
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NEK7 MUTATED                                          0
  NEK7 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NEK7 MUTATED                                       1
  NEK7 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NEK7 MUTATED                                                        2
  NEK7 WILD-TYPE                                                    156
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NEK7 MUTATED                                                   1
  NEK7 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NEK7 MUTATED                                                                   2
  NEK7 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NEK7 MUTATED                                                    0
  NEK7 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NEK7 MUTATED                                                  0
  NEK7 WILD-TYPE                                               61
D1024V9, multiclass
                                                                   clus
vv                                                                  NEK7 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  NEK7 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NEK7 MUTATED     3   1   2   0
  NEK7 WILD-TYPE 308  13  13  24
D1024V10, multiclass
    clus
vv   NEK7 MUTATED NEK7 WILD-TYPE
  R0            3            308
  R1            1             13
  R2            2             13
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1024V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NEK7 MUTATED       1                         1
  NEK7 WILD-TYPE    86                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NEK7 MUTATED                                           0     1
  NEK7 WILD-TYPE                                         1   242
D1024V12, multiclass
                                           clus
vv                                          NEK7 MUTATED NEK7 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                1            242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1024V13, binary
                cls
clus               0   1
  NEK7 MUTATED     0   3
  NEK7 WILD-TYPE   4 307
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK7 MUTATED      0    3
  NEK7 WILD-TYPE    4  307
                        clus
vv                       NEK7 MUTATED NEK7 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            3            307
[1] 2 2
[1] FALSE

Clustering(1025) Variable = QTRTD1 MUTATION ANALYSIS
D1025V1, survival
                  sevent
clus2                0   1
  QTRTD1 MUTATED     3   3
  QTRTD1 WILD-TYPE 227 136
  QTRTD1 MUTATED QTRTD1 WILD-TYPE 
               6              363 
  QTRTD1 MUTATED QTRTD1 WILD-TYPE 
               3              136 
$`QTRTD1 MUTATED`
TCGA-BR-4257 TCGA-BR-6452 TCGA-CG-4440 TCGA-F1-6874 TCGA-HF-A5NB TCGA-VQ-A8DU 
        9.67        34.68         4.01        14.47        30.51         5.46 

$`QTRTD1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  QTRTD1 MUTATED QTRTD1 WILD-TYPE 
            4.01             0.00 
  QTRTD1 MUTATED QTRTD1 WILD-TYPE 
           34.68           122.30 
  QTRTD1 MUTATED QTRTD1 WILD-TYPE 
           12.07            14.27 
[1] "4.0 - 34.7 (12.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.5"
D1025V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  QTRTD1 MUTATED         0        0        1        0         1         0
  QTRTD1 WILD-TYPE       2       15       39       30        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  QTRTD1 MUTATED           0          1          0          1        1
  QTRTD1 WILD-TYPE         3         69         53         31       37
D1025V3, multiclass
            clus
vv           QTRTD1 MUTATED QTRTD1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  QTRTD1 MUTATED     0   1   3   1
  QTRTD1 WILD-TYPE  22  91 170  96
D1025V4, multiclass
    clus
vv   QTRTD1 MUTATED QTRTD1 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              3              170
  T4              1               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
  QTRTD1 MUTATED     2   0   1   2
  QTRTD1 WILD-TYPE 116 104  76  75
D1025V5, multiclass
    clus
vv   QTRTD1 MUTATED QTRTD1 WILD-TYPE
  N0              2              116
  N1              0              104
  N2              1               76
  N3              2               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"
D1025V6, binary
                  cls
clus                 0   1
  QTRTD1 MUTATED     5   1
  QTRTD1 WILD-TYPE 341  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  QTRTD1 MUTATED      5    1
  QTRTD1 WILD-TYPE  341   28
   clus
vv  QTRTD1 MUTATED QTRTD1 WILD-TYPE
  0              5              341
  1              1               28
[1] 2 2
[1] FALSE
D1025V7, binary
                  cls
clus                 0   1
  QTRTD1 MUTATED     4   2
  QTRTD1 WILD-TYPE 141 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  QTRTD1 MUTATED      4    2
  QTRTD1 WILD-TYPE  141  246
        clus
vv       QTRTD1 MUTATED QTRTD1 WILD-TYPE
  FEMALE              4              141
  MALE                2              246
[1] 2 2
[1] FALSE
D1025V8, binary
                  cls
clus                 0   1
  QTRTD1 MUTATED     4   1
  QTRTD1 WILD-TYPE 288  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  QTRTD1 MUTATED      4    1
  QTRTD1 WILD-TYPE  288   58
     clus
vv    QTRTD1 MUTATED QTRTD1 WILD-TYPE
  NO               4              288
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  QTRTD1 MUTATED                                          0
  QTRTD1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  QTRTD1 MUTATED                                       0
  QTRTD1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  QTRTD1 MUTATED                                                        2
  QTRTD1 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  QTRTD1 MUTATED                                                   1
  QTRTD1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  QTRTD1 MUTATED                                                                   2
  QTRTD1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  QTRTD1 MUTATED                                                    0
  QTRTD1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  QTRTD1 MUTATED                                                  1
  QTRTD1 WILD-TYPE                                               60
D1025V9, multiclass
                                                                   clus
vv                                                                  QTRTD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  QTRTD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  QTRTD1 MUTATED     3   1   1   1
  QTRTD1 WILD-TYPE 308  13  14  23
D1025V10, multiclass
    clus
vv   QTRTD1 MUTATED QTRTD1 WILD-TYPE
  R0              3              308
  R1              1               13
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1025V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  QTRTD1 MUTATED       0                         0
  QTRTD1 WILD-TYPE    87                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  QTRTD1 MUTATED                                           0     4
  QTRTD1 WILD-TYPE                                         1   239
D1025V12, multiclass
                                           clus
vv                                          QTRTD1 MUTATED QTRTD1 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1025V13, binary
                  cls
clus                 0   1
  QTRTD1 MUTATED     0   3
  QTRTD1 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  QTRTD1 MUTATED      0    3
  QTRTD1 WILD-TYPE    4  307
                        clus
vv                       QTRTD1 MUTATED QTRTD1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(1026) Variable = UACA MUTATION ANALYSIS
D1026V1, survival
                sevent
clus2              0   1
  UACA MUTATED     8   3
  UACA WILD-TYPE 222 136
  UACA MUTATED UACA WILD-TYPE 
            11            358 
  UACA MUTATED UACA WILD-TYPE 
             3            136 
$`UACA MUTATED`
TCGA-BR-6852 TCGA-BR-8487 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4469 
       44.94         1.12        31.96         6.58         1.02         7.07 
TCGA-CG-5719 TCGA-D7-A4YY TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H8 
        1.02        13.78         6.51         6.58        14.07 

$`UACA WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-D7-6815 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-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-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 

  UACA MUTATED UACA WILD-TYPE 
          1.02           0.00 
  UACA MUTATED UACA WILD-TYPE 
         44.94         122.30 
  UACA MUTATED UACA WILD-TYPE 
          6.58          14.71 
[1] "1.0 - 44.9 (6.6)"   "0.0 - 122.3 (14.7)"
[1] "hr=" "1.2"
D1026V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  UACA MUTATED         0        0        1        0         4         2
  UACA WILD-TYPE       2       15       39       30        33        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UACA MUTATED           0          1          1          0        4
  UACA WILD-TYPE         3         69         52         32       34
D1026V3, multiclass
            clus
vv           UACA MUTATED UACA WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             4             33
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              4             34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  UACA MUTATED     2   0   8   4
  UACA WILD-TYPE  20  92 165  93
D1026V4, multiclass
    clus
vv   UACA MUTATED UACA WILD-TYPE
  T1            2             20
  T2            0             92
  T3            8            165
  T4            4             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
  UACA MUTATED     7   2   2   2
  UACA WILD-TYPE 111 102  75  75
D1026V5, multiclass
    clus
vv   UACA MUTATED UACA WILD-TYPE
  N0            7            111
  N1            2            102
  N2            2             75
  N3            2             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"
D1026V6, binary
                cls
clus               0   1
  UACA MUTATED    11   3
  UACA WILD-TYPE 335  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  UACA MUTATED     11    3
  UACA WILD-TYPE  335   26
   clus
vv  UACA MUTATED UACA WILD-TYPE
  0           11            335
  1            3             26
[1] 2 2
[1] FALSE
D1026V7, binary
                cls
clus               0   1
  UACA MUTATED     6   8
  UACA WILD-TYPE 139 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  UACA MUTATED      6    8
  UACA WILD-TYPE  139  240
        clus
vv       UACA MUTATED UACA WILD-TYPE
  FEMALE            6            139
  MALE              8            240
[1] 2 2
[1] FALSE
D1026V8, binary
                cls
clus               0   1
  UACA MUTATED     8   1
  UACA WILD-TYPE 284  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  UACA MUTATED      8    1
  UACA WILD-TYPE  284   58
     clus
vv    UACA MUTATED UACA WILD-TYPE
  NO             8            284
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  UACA MUTATED                                          0
  UACA WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  UACA MUTATED                                       2
  UACA WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UACA MUTATED                                                        6
  UACA WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  UACA MUTATED                                                   0
  UACA WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  UACA MUTATED                                                                   3
  UACA WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  UACA MUTATED                                                    0
  UACA WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  UACA MUTATED                                                  3
  UACA WILD-TYPE                                               58
D1026V9, multiclass
                                                                   clus
vv                                                                  UACA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  UACA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  UACA MUTATED     9   1   1   2
  UACA WILD-TYPE 302  13  14  22
D1026V10, multiclass
    clus
vv   UACA MUTATED UACA WILD-TYPE
  R0            9            302
  R1            1             13
  R2            1             14
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1026V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  UACA MUTATED       5                         0
  UACA WILD-TYPE    82                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  UACA MUTATED                                           0     6
  UACA WILD-TYPE                                         1   237
D1026V12, multiclass
                                           clus
vv                                          UACA MUTATED UACA WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1026V13, binary
                cls
clus               0   1
  UACA MUTATED     0  11
  UACA WILD-TYPE   4 299
[1] "tbl2"
                cls
clus             [,1] [,2]
  UACA MUTATED      0   11
  UACA WILD-TYPE    4  299
                        clus
vv                       UACA MUTATED UACA WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           11            299
[1] 2 2
[1] FALSE

Clustering(1027) Variable = TMEM206 MUTATION ANALYSIS
D1027V1, survival
                   sevent
clus2                 0   1
  TMEM206 MUTATED     3   3
  TMEM206 WILD-TYPE 227 136
  TMEM206 MUTATED TMEM206 WILD-TYPE 
                6               363 
  TMEM206 MUTATED TMEM206 WILD-TYPE 
                3               136 
$`TMEM206 MUTATED`
TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-8078 TCGA-CG-4306 TCGA-D7-A6EV 
       30.90         9.67        34.68        29.59         1.02        11.24 

$`TMEM206 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  TMEM206 MUTATED TMEM206 WILD-TYPE 
             1.02              0.00 
  TMEM206 MUTATED TMEM206 WILD-TYPE 
            34.68            122.30 
  TMEM206 MUTATED TMEM206 WILD-TYPE 
           20.415            14.270 
[1] "1.0 - 34.7 (20.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D1027V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEM206 MUTATED         1        0        0        0         1         2
  TMEM206 WILD-TYPE       1       15       40       30        36        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM206 MUTATED           0          0          0          0        1
  TMEM206 WILD-TYPE         3         70         53         32       37
D1027V3, multiclass
            clus
vv           TMEM206 MUTATED TMEM206 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM206 MUTATED     1   2   2   1
  TMEM206 WILD-TYPE  21  90 171  96
D1027V4, multiclass
    clus
vv   TMEM206 MUTATED TMEM206 WILD-TYPE
  T1               1                21
  T2               2                90
  T3               2               171
  T4               1                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
  TMEM206 MUTATED     2   1   2   0
  TMEM206 WILD-TYPE 116 103  75  77
D1027V5, multiclass
    clus
vv   TMEM206 MUTATED TMEM206 WILD-TYPE
  N0               2               116
  N1               1               103
  N2               2                75
  N3               0                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"
D1027V6, binary
                   cls
clus                  0   1
  TMEM206 MUTATED     5   1
  TMEM206 WILD-TYPE 341  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM206 MUTATED      5    1
  TMEM206 WILD-TYPE  341   28
   clus
vv  TMEM206 MUTATED TMEM206 WILD-TYPE
  0               5               341
  1               1                28
[1] 2 2
[1] FALSE
D1027V7, binary
                   cls
clus                  0   1
  TMEM206 MUTATED     5   2
  TMEM206 WILD-TYPE 140 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM206 MUTATED      5    2
  TMEM206 WILD-TYPE  140  246
        clus
vv       TMEM206 MUTATED TMEM206 WILD-TYPE
  FEMALE               5               140
  MALE                 2               246
[1] 2 2
[1] FALSE
D1027V8, binary
                   cls
clus                  0   1
  TMEM206 MUTATED     6   0
  TMEM206 WILD-TYPE 286  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM206 MUTATED      6    0
  TMEM206 WILD-TYPE  286   59
     clus
vv    TMEM206 MUTATED TMEM206 WILD-TYPE
  NO                6               286
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TMEM206 MUTATED                                          0
  TMEM206 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TMEM206 MUTATED                                       0
  TMEM206 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM206 MUTATED                                                        7
  TMEM206 WILD-TYPE                                                    151
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TMEM206 MUTATED                                                   0
  TMEM206 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM206 MUTATED                                                                   0
  TMEM206 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TMEM206 MUTATED                                                    0
  TMEM206 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TMEM206 MUTATED                                                  0
  TMEM206 WILD-TYPE                                               61
D1027V9, multiclass
                                                                   clus
vv                                                                  TMEM206 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  TMEM206 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM206 MUTATED     4   0   1   2
  TMEM206 WILD-TYPE 307  14  14  22
D1027V10, multiclass
    clus
vv   TMEM206 MUTATED TMEM206 WILD-TYPE
  R0               4               307
  R1               0                14
  R2               1                14
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1027V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM206 MUTATED       0                         1
  TMEM206 WILD-TYPE    87                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM206 MUTATED                                           0     5
  TMEM206 WILD-TYPE                                         1   238
D1027V12, multiclass
                                           clus
vv                                          TMEM206 MUTATED TMEM206 WILD-TYPE
  ASIAN                                                   0                87
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1027V13, binary
                   cls
clus                  0   1
  TMEM206 MUTATED     0   6
  TMEM206 WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM206 MUTATED      0    6
  TMEM206 WILD-TYPE    4  304
                        clus
vv                       TMEM206 MUTATED TMEM206 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(1028) Variable = CDKN2AIP MUTATION ANALYSIS
D1028V1, survival
                    sevent
clus2                  0   1
  CDKN2AIP MUTATED     3   0
  CDKN2AIP WILD-TYPE 227 139
  CDKN2AIP MUTATED CDKN2AIP WILD-TYPE 
                 3                366 
  CDKN2AIP MUTATED CDKN2AIP WILD-TYPE 
                 0                139 
$`CDKN2AIP MUTATED`
TCGA-BR-8487 TCGA-D7-A4YY TCGA-HU-A4H4 
        1.12        13.78        23.84 

$`CDKN2AIP WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  CDKN2AIP MUTATED CDKN2AIP WILD-TYPE 
              1.12               0.00 
  CDKN2AIP MUTATED CDKN2AIP WILD-TYPE 
             23.84             122.30 
  CDKN2AIP MUTATED CDKN2AIP WILD-TYPE 
             13.78              14.35 
[1] "1.1 - 23.8 (13.8)"  "0.0 - 122.3 (14.3)"
[1] "hr="     "3300000"
D1028V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CDKN2AIP MUTATED         0        0        0        0         1         1
  CDKN2AIP WILD-TYPE       2       15       40       30        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDKN2AIP MUTATED           0          0          1          0        0
  CDKN2AIP WILD-TYPE         3         70         52         32       38
D1028V3, multiclass
            clus
vv           CDKN2AIP MUTATED CDKN2AIP WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                1                 52
  STAGE IIIC                0                 32
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CDKN2AIP MUTATED     0   1   2   0
  CDKN2AIP WILD-TYPE  22  91 171  97
D1028V4, multiclass
    clus
vv   CDKN2AIP MUTATED CDKN2AIP WILD-TYPE
  T1                0                 22
  T2                1                 91
  T3                2                171
  T4                0                 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
  CDKN2AIP MUTATED     1   0   1   1
  CDKN2AIP WILD-TYPE 117 104  76  76
D1028V5, multiclass
    clus
vv   CDKN2AIP MUTATED CDKN2AIP WILD-TYPE
  N0                1                117
  N1                0                104
  N2                1                 76
  N3                1                 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"
D1028V6, binary
                    cls
clus                   0   1
  CDKN2AIP MUTATED     3   0
  CDKN2AIP WILD-TYPE 343  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDKN2AIP MUTATED      3    0
  CDKN2AIP WILD-TYPE  343   29
   clus
vv  CDKN2AIP MUTATED CDKN2AIP WILD-TYPE
  0                3                343
  1                0                 29
[1] 2 2
[1] FALSE
D1028V7, binary
                    cls
clus                   0   1
  CDKN2AIP MUTATED     2   1
  CDKN2AIP WILD-TYPE 143 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDKN2AIP MUTATED      2    1
  CDKN2AIP WILD-TYPE  143  247
        clus
vv       CDKN2AIP MUTATED CDKN2AIP WILD-TYPE
  FEMALE                2                143
  MALE                  1                247
[1] 2 2
[1] FALSE
D1028V8, binary
                    cls
clus                   0   1
  CDKN2AIP MUTATED     2   1
  CDKN2AIP WILD-TYPE 290  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDKN2AIP MUTATED      2    1
  CDKN2AIP WILD-TYPE  290   58
     clus
vv    CDKN2AIP MUTATED CDKN2AIP WILD-TYPE
  NO                 2                290
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CDKN2AIP MUTATED                                          0
  CDKN2AIP WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CDKN2AIP MUTATED                                       0
  CDKN2AIP WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDKN2AIP MUTATED                                                        2
  CDKN2AIP WILD-TYPE                                                    156
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CDKN2AIP MUTATED                                                   0
  CDKN2AIP WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CDKN2AIP MUTATED                                                                   0
  CDKN2AIP WILD-TYPE                                                                68
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CDKN2AIP MUTATED                                                    0
  CDKN2AIP WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CDKN2AIP MUTATED                                                  1
  CDKN2AIP WILD-TYPE                                               60
D1028V9, multiclass
                                                                   clus
vv                                                                  CDKN2AIP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  CDKN2AIP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  CDKN2AIP MUTATED     3   0   0   0
  CDKN2AIP WILD-TYPE 308  14  15  24
D1028V10, multiclass
    clus
vv   CDKN2AIP MUTATED CDKN2AIP WILD-TYPE
  R0                3                308
  R1                0                 14
  R2                0                 15
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1028V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  CDKN2AIP MUTATED       1                         0
  CDKN2AIP WILD-TYPE    86                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CDKN2AIP MUTATED                                           0     2
  CDKN2AIP WILD-TYPE                                         1   241
D1028V12, multiclass
                                           clus
vv                                          CDKN2AIP MUTATED CDKN2AIP WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    2                241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1028V13, binary
                    cls
clus                   0   1
  CDKN2AIP MUTATED     0   3
  CDKN2AIP WILD-TYPE   4 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDKN2AIP MUTATED      0    3
  CDKN2AIP WILD-TYPE    4  307
                        clus
vv                       CDKN2AIP MUTATED CDKN2AIP WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                3                307
[1] 2 2
[1] FALSE

Clustering(1029) Variable = CLGN MUTATION ANALYSIS
D1029V1, survival
                sevent
clus2              0   1
  CLGN MUTATED     4   3
  CLGN WILD-TYPE 226 136
  CLGN MUTATED CLGN WILD-TYPE 
             7            362 
  CLGN MUTATED CLGN WILD-TYPE 
             3            136 
$`CLGN MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-8360 TCGA-BR-8361 TCGA-CD-A4MI 
        6.97         6.61        34.68         6.18        31.10        11.77 
TCGA-CG-5721 
        6.02 

$`CLGN WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  CLGN MUTATED CLGN WILD-TYPE 
          6.02           0.00 
  CLGN MUTATED CLGN WILD-TYPE 
         34.68         122.30 
  CLGN MUTATED CLGN WILD-TYPE 
          6.97          14.45 
[1] "6.0 - 34.7 (7.0)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.5"
D1029V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CLGN MUTATED         0        0        0        0         2         0
  CLGN WILD-TYPE       2       15       40       30        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLGN MUTATED           1          3          0          1        1
  CLGN WILD-TYPE         2         67         53         31       37
D1029V3, multiclass
            clus
vv           CLGN MUTATED CLGN WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             1              2
  STAGE IIIA            3             67
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CLGN MUTATED     0   1   4   3
  CLGN WILD-TYPE  22  91 169  94
D1029V4, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  T1            0             22
  T2            1             91
  T3            4            169
  T4            3             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
  CLGN MUTATED     3   4   1   0
  CLGN WILD-TYPE 115 100  76  77
D1029V5, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  N0            3            115
  N1            4            100
  N2            1             76
  N3            0             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"
D1029V6, binary
                cls
clus               0   1
  CLGN MUTATED     8   0
  CLGN WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      8    0
  CLGN WILD-TYPE  338   29
   clus
vv  CLGN MUTATED CLGN WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D1029V7, binary
                cls
clus               0   1
  CLGN MUTATED     5   4
  CLGN WILD-TYPE 140 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      5    4
  CLGN WILD-TYPE  140  244
        clus
vv       CLGN MUTATED CLGN WILD-TYPE
  FEMALE            5            140
  MALE              4            244
[1] 2 2
[1] FALSE
D1029V8, binary
                cls
clus               0   1
  CLGN MUTATED     7   0
  CLGN WILD-TYPE 285  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      7    0
  CLGN WILD-TYPE  285   59
     clus
vv    CLGN MUTATED CLGN WILD-TYPE
  NO             7            285
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CLGN MUTATED                                          0
  CLGN WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CLGN MUTATED                                       0
  CLGN WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CLGN MUTATED                                                        7
  CLGN WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CLGN MUTATED                                                   0
  CLGN WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CLGN MUTATED                                                                   2
  CLGN WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CLGN MUTATED                                                    0
  CLGN WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CLGN MUTATED                                                  0
  CLGN WILD-TYPE                                               61
D1029V9, multiclass
                                                                   clus
vv                                                                  CLGN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  CLGN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CLGN MUTATED     4   0   0   4
  CLGN WILD-TYPE 307  14  15  20
D1029V10, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  R0            4            307
  R1            0             14
  R2            0             15
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1029V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CLGN MUTATED       1                         0
  CLGN WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CLGN MUTATED                                           0     7
  CLGN WILD-TYPE                                         1   236
D1029V12, multiclass
                                           clus
vv                                          CLGN MUTATED CLGN WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1029V13, binary
                cls
clus               0   1
  CLGN MUTATED     0   8
  CLGN WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      0    8
  CLGN WILD-TYPE    4  302
                        clus
vv                       CLGN MUTATED CLGN WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(1030) Variable = ACAA2 MUTATION ANALYSIS
D1030V1, survival
                 sevent
clus2               0   1
  ACAA2 MUTATED     4   4
  ACAA2 WILD-TYPE 226 135
  ACAA2 MUTATED ACAA2 WILD-TYPE 
              8             361 
  ACAA2 MUTATED ACAA2 WILD-TYPE 
              4             135 
$`ACAA2 MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-A4QL TCGA-CD-A4MG 
       19.56         6.97        32.78        35.84        16.14         6.58 
TCGA-IN-A6RL TCGA-VQ-A8P2 
       13.35        38.14 

$`ACAA2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       12.46        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 

  ACAA2 MUTATED ACAA2 WILD-TYPE 
           6.58            0.00 
  ACAA2 MUTATED ACAA2 WILD-TYPE 
          38.14          122.30 
  ACAA2 MUTATED ACAA2 WILD-TYPE 
          17.85           14.17 
[1] "6.6 - 38.1 (17.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D1030V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ACAA2 MUTATED         0        0        1        0         2         0
  ACAA2 WILD-TYPE       2       15       39       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACAA2 MUTATED           0          3          1          1        0
  ACAA2 WILD-TYPE         3         67         52         31       38
D1030V3, multiclass
            clus
vv           ACAA2 MUTATED ACAA2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACAA2 MUTATED     0   2   4   2
  ACAA2 WILD-TYPE  22  90 169  95
D1030V4, multiclass
    clus
vv   ACAA2 MUTATED ACAA2 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             4             169
  T4             2              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
  ACAA2 MUTATED     3   3   0   2
  ACAA2 WILD-TYPE 115 101  77  75
D1030V5, multiclass
    clus
vv   ACAA2 MUTATED ACAA2 WILD-TYPE
  N0             3             115
  N1             3             101
  N2             0              77
  N3             2              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"
D1030V6, binary
                 cls
clus                0   1
  ACAA2 MUTATED     7   0
  ACAA2 WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAA2 MUTATED      7    0
  ACAA2 WILD-TYPE  339   29
   clus
vv  ACAA2 MUTATED ACAA2 WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D1030V7, binary
                 cls
clus                0   1
  ACAA2 MUTATED     3   5
  ACAA2 WILD-TYPE 142 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAA2 MUTATED      3    5
  ACAA2 WILD-TYPE  142  243
        clus
vv       ACAA2 MUTATED ACAA2 WILD-TYPE
  FEMALE             3             142
  MALE               5             243
[1] 2 2
[1] FALSE
D1030V8, binary
                 cls
clus                0   1
  ACAA2 MUTATED     7   1
  ACAA2 WILD-TYPE 285  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAA2 MUTATED      7    1
  ACAA2 WILD-TYPE  285   58
     clus
vv    ACAA2 MUTATED ACAA2 WILD-TYPE
  NO              7             285
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ACAA2 MUTATED                                          0
  ACAA2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ACAA2 MUTATED                                       2
  ACAA2 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ACAA2 MUTATED                                                        5
  ACAA2 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ACAA2 MUTATED                                                   1
  ACAA2 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ACAA2 MUTATED                                                                   0
  ACAA2 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ACAA2 MUTATED                                                    0
  ACAA2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ACAA2 MUTATED                                                  0
  ACAA2 WILD-TYPE                                               61
D1030V9, multiclass
                                                                   clus
vv                                                                  ACAA2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  ACAA2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ACAA2 MUTATED     5   0   0   1
  ACAA2 WILD-TYPE 306  14  15  23
D1030V10, multiclass
    clus
vv   ACAA2 MUTATED ACAA2 WILD-TYPE
  R0             5             306
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1030V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ACAA2 MUTATED       1                         0
  ACAA2 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ACAA2 MUTATED                                           0     7
  ACAA2 WILD-TYPE                                         1   236
D1030V12, multiclass
                                           clus
vv                                          ACAA2 MUTATED ACAA2 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1030V13, binary
                 cls
clus                0   1
  ACAA2 MUTATED     0   7
  ACAA2 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAA2 MUTATED      0    7
  ACAA2 WILD-TYPE    4  303
                        clus
vv                       ACAA2 MUTATED ACAA2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(1031) Variable = SLC25A45 MUTATION ANALYSIS
D1031V1, survival
                    sevent
clus2                  0   1
  SLC25A45 MUTATED     8   0
  SLC25A45 WILD-TYPE 222 139
  SLC25A45 MUTATED SLC25A45 WILD-TYPE 
                 8                361 
  SLC25A45 MUTATED SLC25A45 WILD-TYPE 
                 0                139 
$`SLC25A45 MUTATED`
TCGA-B7-5816 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-A4CQ TCGA-CG-5721 TCGA-CG-5723 
       26.70        29.59         1.12        34.98         6.02       105.07 
TCGA-HU-8602 TCGA-HU-A4GH 
       22.32        11.77 

$`SLC25A45 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  SLC25A45 MUTATED SLC25A45 WILD-TYPE 
              1.12               0.00 
  SLC25A45 MUTATED SLC25A45 WILD-TYPE 
            105.07             122.30 
  SLC25A45 MUTATED SLC25A45 WILD-TYPE 
             24.51              14.17 
[1] "1.1 - 105.1 (24.5)" "0.0 - 122.3 (14.2)"
[1] "hr="     "2.6e+07"
D1031V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC25A45 MUTATED         0        1        0        1         1         3
  SLC25A45 WILD-TYPE       2       14       40       29        36        49
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A45 MUTATED           0          1          0          0        1
  SLC25A45 WILD-TYPE         3         69         53         32       37
D1031V3, multiclass
            clus
vv           SLC25A45 MUTATED SLC25A45 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  0                 40
  STAGE II                  1                 29
  STAGE IIA                 1                 36
  STAGE IIB                 3                 49
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                0                 53
  STAGE IIIC                0                 32
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC25A45 MUTATED     2   1   1   5
  SLC25A45 WILD-TYPE  20  91 172  92
D1031V4, multiclass
    clus
vv   SLC25A45 MUTATED SLC25A45 WILD-TYPE
  T1                2                 20
  T2                1                 91
  T3                1                172
  T4                5                 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
  SLC25A45 MUTATED     5   3   0   0
  SLC25A45 WILD-TYPE 113 101  77  77
D1031V5, multiclass
    clus
vv   SLC25A45 MUTATED SLC25A45 WILD-TYPE
  N0                5                113
  N1                3                101
  N2                0                 77
  N3                0                 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"
D1031V6, binary
                    cls
clus                   0   1
  SLC25A45 MUTATED     9   0
  SLC25A45 WILD-TYPE 337  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A45 MUTATED      9    0
  SLC25A45 WILD-TYPE  337   29
   clus
vv  SLC25A45 MUTATED SLC25A45 WILD-TYPE
  0                9                337
  1                0                 29
[1] 2 2
[1] FALSE
D1031V7, binary
                    cls
clus                   0   1
  SLC25A45 MUTATED     5   4
  SLC25A45 WILD-TYPE 140 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A45 MUTATED      5    4
  SLC25A45 WILD-TYPE  140  244
        clus
vv       SLC25A45 MUTATED SLC25A45 WILD-TYPE
  FEMALE                5                140
  MALE                  4                244
[1] 2 2
[1] FALSE
D1031V8, binary
                    cls
clus                   0   1
  SLC25A45 MUTATED     8   0
  SLC25A45 WILD-TYPE 284  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A45 MUTATED      8    0
  SLC25A45 WILD-TYPE  284   59
     clus
vv    SLC25A45 MUTATED SLC25A45 WILD-TYPE
  NO                 8                284
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC25A45 MUTATED                                          0
  SLC25A45 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC25A45 MUTATED                                       2
  SLC25A45 WILD-TYPE                                    68
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC25A45 MUTATED                                                        5
  SLC25A45 WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC25A45 MUTATED                                                   0
  SLC25A45 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC25A45 MUTATED                                                                   1
  SLC25A45 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC25A45 MUTATED                                                    0
  SLC25A45 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC25A45 MUTATED                                                  1
  SLC25A45 WILD-TYPE                                               60
D1031V9, multiclass
                                                                   clus
vv                                                                  SLC25A45 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  SLC25A45 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SLC25A45 MUTATED     8   0   0   1
  SLC25A45 WILD-TYPE 303  14  15  23
D1031V10, multiclass
    clus
vv   SLC25A45 MUTATED SLC25A45 WILD-TYPE
  R0                8                303
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1031V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SLC25A45 MUTATED       2                         0
  SLC25A45 WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC25A45 MUTATED                                           0     5
  SLC25A45 WILD-TYPE                                         1   238
D1031V12, multiclass
                                           clus
vv                                          SLC25A45 MUTATED SLC25A45 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1031V13, binary
                    cls
clus                   0   1
  SLC25A45 MUTATED     0   7
  SLC25A45 WILD-TYPE   4 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A45 MUTATED      0    7
  SLC25A45 WILD-TYPE    4  303
                        clus
vv                       SLC25A45 MUTATED SLC25A45 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                7                303
[1] 2 2
[1] FALSE

Clustering(1032) Variable = TMEFF2 MUTATION ANALYSIS
D1032V1, survival
                  sevent
clus2                0   1
  TMEFF2 MUTATED     8   1
  TMEFF2 WILD-TYPE 222 138
  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
               9              360 
  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
               1              138 
$`TMEFF2 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8361 TCGA-BR-8372 TCGA-CD-8536 TCGA-CG-5721 
       34.68        44.94        31.10        31.27        12.43         6.02 
TCGA-CG-5723 TCGA-HU-A4H4 TCGA-VQ-A91U 
      105.07        23.84         1.71 

$`TMEFF2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
            1.71             0.00 
  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
          105.07           122.30 
  TMEFF2 MUTATED TMEFF2 WILD-TYPE 
           31.10            14.12 
[1] "1.7 - 105.1 (31.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "5"  
D1032V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMEFF2 MUTATED         0        0        0        2         2         1
  TMEFF2 WILD-TYPE       2       15       40       28        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEFF2 MUTATED           0          1          0          2        2
  TMEFF2 WILD-TYPE         3         69         53         30       36
D1032V3, multiclass
            clus
vv           TMEFF2 MUTATED TMEFF2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                2               28
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TMEFF2 MUTATED     0   2   4   4
  TMEFF2 WILD-TYPE  22  90 169  93
D1032V4, multiclass
    clus
vv   TMEFF2 MUTATED TMEFF2 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              4              169
  T4              4               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
  TMEFF2 MUTATED     3   3   3   1
  TMEFF2 WILD-TYPE 115 101  74  76
D1032V5, multiclass
    clus
vv   TMEFF2 MUTATED TMEFF2 WILD-TYPE
  N0              3              115
  N1              3              101
  N2              3               74
  N3              1               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"
D1032V6, binary
                  cls
clus                 0   1
  TMEFF2 MUTATED    10   0
  TMEFF2 WILD-TYPE 336  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEFF2 MUTATED     10    0
  TMEFF2 WILD-TYPE  336   29
   clus
vv  TMEFF2 MUTATED TMEFF2 WILD-TYPE
  0             10              336
  1              0               29
[1] 2 2
[1] FALSE
D1032V7, binary
                  cls
clus                 0   1
  TMEFF2 MUTATED     5   5
  TMEFF2 WILD-TYPE 140 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEFF2 MUTATED      5    5
  TMEFF2 WILD-TYPE  140  243
        clus
vv       TMEFF2 MUTATED TMEFF2 WILD-TYPE
  FEMALE              5              140
  MALE                5              243
[1] 2 2
[1] FALSE
D1032V8, binary
                  cls
clus                 0   1
  TMEFF2 MUTATED     9   0
  TMEFF2 WILD-TYPE 283  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEFF2 MUTATED      9    0
  TMEFF2 WILD-TYPE  283   59
     clus
vv    TMEFF2 MUTATED TMEFF2 WILD-TYPE
  NO               9              283
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TMEFF2 MUTATED                                          0
  TMEFF2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TMEFF2 MUTATED                                       0
  TMEFF2 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEFF2 MUTATED                                                        7
  TMEFF2 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TMEFF2 MUTATED                                                   0
  TMEFF2 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEFF2 MUTATED                                                                   2
  TMEFF2 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TMEFF2 MUTATED                                                    0
  TMEFF2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TMEFF2 MUTATED                                                  1
  TMEFF2 WILD-TYPE                                               60
D1032V9, multiclass
                                                                   clus
vv                                                                  TMEFF2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  TMEFF2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TMEFF2 MUTATED     9   0   0   1
  TMEFF2 WILD-TYPE 302  14  15  23
D1032V10, multiclass
    clus
vv   TMEFF2 MUTATED TMEFF2 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1032V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TMEFF2 MUTATED       3                         0
  TMEFF2 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEFF2 MUTATED                                           0     5
  TMEFF2 WILD-TYPE                                         1   238
D1032V12, multiclass
                                           clus
vv                                          TMEFF2 MUTATED TMEFF2 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1032V13, binary
                  cls
clus                 0   1
  TMEFF2 MUTATED     0   7
  TMEFF2 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEFF2 MUTATED      0    7
  TMEFF2 WILD-TYPE    4  303
                        clus
vv                       TMEFF2 MUTATED TMEFF2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(1033) Variable = IFNA17 MUTATION ANALYSIS
D1033V1, survival
                  sevent
clus2                0   1
  IFNA17 MUTATED     1   2
  IFNA17 WILD-TYPE 229 137
  IFNA17 MUTATED IFNA17 WILD-TYPE 
               3              366 
  IFNA17 MUTATED IFNA17 WILD-TYPE 
               2              137 
$`IFNA17 MUTATED`
TCGA-BR-8687 TCGA-CG-5721 TCGA-D7-6527 
        8.22         6.02        10.26 

$`IFNA17 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-6528 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 

  IFNA17 MUTATED IFNA17 WILD-TYPE 
            6.02             0.00 
  IFNA17 MUTATED IFNA17 WILD-TYPE 
           10.26           122.30 
  IFNA17 MUTATED IFNA17 WILD-TYPE 
            8.22            14.45 
[1] "6.0 - 10.3 (8.2)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "4.3"
D1033V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  IFNA17 MUTATED         0        0        0        1         0         0
  IFNA17 WILD-TYPE       2       15       40       29        37        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFNA17 MUTATED           0          0          0          1        1
  IFNA17 WILD-TYPE         3         70         53         31       37
D1033V3, multiclass
            clus
vv           IFNA17 MUTATED IFNA17 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               0               37
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IFNA17 MUTATED     0   1   0   2
  IFNA17 WILD-TYPE  22  91 173  95
D1033V4, multiclass
    clus
vv   IFNA17 MUTATED IFNA17 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              0              173
  T4              2               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
  IFNA17 MUTATED     0   3   1   0
  IFNA17 WILD-TYPE 118 101  76  77
D1033V5, multiclass
    clus
vv   IFNA17 MUTATED IFNA17 WILD-TYPE
  N0              0              118
  N1              3              101
  N2              1               76
  N3              0               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"
D1033V6, binary
                  cls
clus                 0   1
  IFNA17 MUTATED     4   0
  IFNA17 WILD-TYPE 342  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNA17 MUTATED      4    0
  IFNA17 WILD-TYPE  342   29
   clus
vv  IFNA17 MUTATED IFNA17 WILD-TYPE
  0              4              342
  1              0               29
[1] 2 2
[1] FALSE
D1033V7, binary
                  cls
clus                 0   1
  IFNA17 MUTATED     2   2
  IFNA17 WILD-TYPE 143 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNA17 MUTATED      2    2
  IFNA17 WILD-TYPE  143  246
        clus
vv       IFNA17 MUTATED IFNA17 WILD-TYPE
  FEMALE              2              143
  MALE                2              246
[1] 2 2
[1] FALSE
D1033V8, binary
                  cls
clus                 0   1
  IFNA17 MUTATED     2   1
  IFNA17 WILD-TYPE 290  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNA17 MUTATED      2    1
  IFNA17 WILD-TYPE  290   58
     clus
vv    IFNA17 MUTATED IFNA17 WILD-TYPE
  NO               2              290
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IFNA17 MUTATED                                          0
  IFNA17 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IFNA17 MUTATED                                       0
  IFNA17 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IFNA17 MUTATED                                                        2
  IFNA17 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IFNA17 MUTATED                                                   0
  IFNA17 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IFNA17 MUTATED                                                                   1
  IFNA17 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IFNA17 MUTATED                                                    1
  IFNA17 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IFNA17 MUTATED                                                  0
  IFNA17 WILD-TYPE                                               61
D1033V9, multiclass
                                                                   clus
vv                                                                  IFNA17 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  IFNA17 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IFNA17 MUTATED     2   1   0   1
  IFNA17 WILD-TYPE 309  13  15  23
D1033V10, multiclass
    clus
vv   IFNA17 MUTATED IFNA17 WILD-TYPE
  R0              2              309
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1033V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  IFNA17 MUTATED       0                         0
  IFNA17 WILD-TYPE    87                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IFNA17 MUTATED                                           0     3
  IFNA17 WILD-TYPE                                         1   240
D1033V12, multiclass
                                           clus
vv                                          IFNA17 MUTATED IFNA17 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1033V13, binary
                  cls
clus                 0   1
  IFNA17 MUTATED     0   3
  IFNA17 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNA17 MUTATED      0    3
  IFNA17 WILD-TYPE    4  307
                        clus
vv                       IFNA17 MUTATED IFNA17 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(1034) Variable = PGBD1 MUTATION ANALYSIS
D1034V1, survival
                 sevent
clus2               0   1
  PGBD1 MUTATED     9   3
  PGBD1 WILD-TYPE 221 136
  PGBD1 MUTATED PGBD1 WILD-TYPE 
             12             357 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
              3             136 
$`PGBD1 MUTATED`
TCGA-MX-A663 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8372 TCGA-CD-A4MJ 
        9.86        11.70         6.97        34.68        31.27        12.62 
TCGA-CG-4305 TCGA-CG-5720 TCGA-CG-5728 TCGA-HU-8602 TCGA-HU-A4GX TCGA-VQ-A8P2 
       15.95         0.99        65.10        22.32        20.25        38.14 

$`PGBD1 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15        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-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-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-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         1.02         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-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-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 

  PGBD1 MUTATED PGBD1 WILD-TYPE 
           0.99            0.00 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
           65.1           122.3 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
          18.10           14.17 
[1] "1.0 - 65.1 (18.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.8"
D1034V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PGBD1 MUTATED         0        0        4        1         2         1
  PGBD1 WILD-TYPE       2       15       36       29        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PGBD1 MUTATED           0          2          0          2        0
  PGBD1 WILD-TYPE         3         68         53         30       38
D1034V3, multiclass
            clus
vv           PGBD1 MUTATED PGBD1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               4              36
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PGBD1 MUTATED     1   5   3   4
  PGBD1 WILD-TYPE  21  87 170  93
D1034V4, multiclass
    clus
vv   PGBD1 MUTATED PGBD1 WILD-TYPE
  T1             1              21
  T2             5              87
  T3             3             170
  T4             4              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
  PGBD1 MUTATED     7   3   1   1
  PGBD1 WILD-TYPE 111 101  76  76
D1034V5, multiclass
    clus
vv   PGBD1 MUTATED PGBD1 WILD-TYPE
  N0             7             111
  N1             3             101
  N2             1              76
  N3             1              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"
D1034V6, binary
                 cls
clus                0   1
  PGBD1 MUTATED    13   0
  PGBD1 WILD-TYPE 333  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED     13    0
  PGBD1 WILD-TYPE  333   29
   clus
vv  PGBD1 MUTATED PGBD1 WILD-TYPE
  0            13             333
  1             0              29
[1] 2 2
[1] FALSE
D1034V7, binary
                 cls
clus                0   1
  PGBD1 MUTATED     6   8
  PGBD1 WILD-TYPE 139 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED      6    8
  PGBD1 WILD-TYPE  139  240
        clus
vv       PGBD1 MUTATED PGBD1 WILD-TYPE
  FEMALE             6             139
  MALE               8             240
[1] 2 2
[1] FALSE
D1034V8, binary
                 cls
clus                0   1
  PGBD1 MUTATED     9   1
  PGBD1 WILD-TYPE 283  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED      9    1
  PGBD1 WILD-TYPE  283   58
     clus
vv    PGBD1 MUTATED PGBD1 WILD-TYPE
  NO              9             283
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PGBD1 MUTATED                                          0
  PGBD1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PGBD1 MUTATED                                       3
  PGBD1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PGBD1 MUTATED                                                        9
  PGBD1 WILD-TYPE                                                    149
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PGBD1 MUTATED                                                   1
  PGBD1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PGBD1 MUTATED                                                                   1
  PGBD1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PGBD1 MUTATED                                                    0
  PGBD1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PGBD1 MUTATED                                                  0
  PGBD1 WILD-TYPE                                               61
D1034V9, multiclass
                                                                   clus
vv                                                                  PGBD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  PGBD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PGBD1 MUTATED    10   0   0   3
  PGBD1 WILD-TYPE 301  14  15  21
D1034V10, multiclass
    clus
vv   PGBD1 MUTATED PGBD1 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1034V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PGBD1 MUTATED       3                         0
  PGBD1 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PGBD1 MUTATED                                           0     8
  PGBD1 WILD-TYPE                                         1   235
D1034V12, multiclass
                                           clus
vv                                          PGBD1 MUTATED PGBD1 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1034V13, binary
                 cls
clus                0   1
  PGBD1 MUTATED     0  10
  PGBD1 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED      0   10
  PGBD1 WILD-TYPE    4  300
                        clus
vv                       PGBD1 MUTATED PGBD1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(1035) Variable = FCN2 MUTATION ANALYSIS
D1035V1, survival
                sevent
clus2              0   1
  FCN2 MUTATED     6   2
  FCN2 WILD-TYPE 224 137
  FCN2 MUTATED FCN2 WILD-TYPE 
             8            361 
  FCN2 MUTATED FCN2 WILD-TYPE 
             2            137 
$`FCN2 MUTATED`
TCGA-BR-8060 TCGA-BR-8360 TCGA-BR-8487 TCGA-D7-A4YT TCGA-F1-A448 TCGA-HF-A5NB 
       11.44         6.18         1.12        14.27        21.27        30.51 
TCGA-HU-A4GQ TCGA-VQ-A8P2 
        0.10        38.14 

$`FCN2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  FCN2 MUTATED FCN2 WILD-TYPE 
           0.1            0.0 
  FCN2 MUTATED FCN2 WILD-TYPE 
         38.14         122.30 
  FCN2 MUTATED FCN2 WILD-TYPE 
        12.855         14.430 
[1] "0.1 - 38.1 (12.9)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.3"
D1035V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FCN2 MUTATED         0        0        0        0         2         2
  FCN2 WILD-TYPE       2       15       40       30        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FCN2 MUTATED           0          2          1          2        0
  FCN2 WILD-TYPE         3         68         52         30       38
D1035V3, multiclass
            clus
vv           FCN2 MUTATED FCN2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            2             30
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FCN2 MUTATED     0   2   3   4
  FCN2 WILD-TYPE  22  90 170  93
D1035V4, multiclass
    clus
vv   FCN2 MUTATED FCN2 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            3            170
  T4            4             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
  FCN2 MUTATED     3   2   2   3
  FCN2 WILD-TYPE 115 102  75  74
D1035V5, multiclass
    clus
vv   FCN2 MUTATED FCN2 WILD-TYPE
  N0            3            115
  N1            2            102
  N2            2             75
  N3            3             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"
D1035V6, binary
                cls
clus               0   1
  FCN2 MUTATED    10   0
  FCN2 WILD-TYPE 336  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  FCN2 MUTATED     10    0
  FCN2 WILD-TYPE  336   29
   clus
vv  FCN2 MUTATED FCN2 WILD-TYPE
  0           10            336
  1            0             29
[1] 2 2
[1] FALSE
D1035V7, binary
                cls
clus               0   1
  FCN2 MUTATED     4   6
  FCN2 WILD-TYPE 141 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  FCN2 MUTATED      4    6
  FCN2 WILD-TYPE  141  242
        clus
vv       FCN2 MUTATED FCN2 WILD-TYPE
  FEMALE            4            141
  MALE              6            242
[1] 2 2
[1] FALSE
D1035V8, binary
                cls
clus               0   1
  FCN2 MUTATED     6   3
  FCN2 WILD-TYPE 286  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  FCN2 MUTATED      6    3
  FCN2 WILD-TYPE  286   56
     clus
vv    FCN2 MUTATED FCN2 WILD-TYPE
  NO             6            286
  YES            3             56
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FCN2 MUTATED                                          0
  FCN2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FCN2 MUTATED                                       0
  FCN2 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FCN2 MUTATED                                                        3
  FCN2 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FCN2 MUTATED                                                   3
  FCN2 WILD-TYPE                                                18
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FCN2 MUTATED                                                                   2
  FCN2 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FCN2 MUTATED                                                    0
  FCN2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FCN2 MUTATED                                                  2
  FCN2 WILD-TYPE                                               59
D1035V9, multiclass
                                                                   clus
vv                                                                  FCN2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  FCN2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FCN2 MUTATED     8   1   0   1
  FCN2 WILD-TYPE 303  13  15  23
D1035V10, multiclass
    clus
vv   FCN2 MUTATED FCN2 WILD-TYPE
  R0            8            303
  R1            1             13
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1035V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  FCN2 MUTATED       1                         0
  FCN2 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FCN2 MUTATED                                           0     8
  FCN2 WILD-TYPE                                         1   235
D1035V12, multiclass
                                           clus
vv                                          FCN2 MUTATED FCN2 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1035V13, binary
                cls
clus               0   1
  FCN2 MUTATED     1   7
  FCN2 WILD-TYPE   3 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  FCN2 MUTATED      1    7
  FCN2 WILD-TYPE    3  303
                        clus
vv                       FCN2 MUTATED FCN2 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(1036) Variable = PTPRJ MUTATION ANALYSIS
D1036V1, survival
                 sevent
clus2               0   1
  PTPRJ MUTATED    16   8
  PTPRJ WILD-TYPE 214 131
  PTPRJ MUTATED PTPRJ WILD-TYPE 
             24             345 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
              8             131 
$`PTPRJ MUTATED`
TCGA-CG-5727 TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 
       79.07        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-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-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
        9.86        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-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-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-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-D7-8572 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-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-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-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-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-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.44        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-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-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-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Q 
       38.14        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 

  PTPRJ MUTATED PTPRJ WILD-TYPE 
            0.1             0.0 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
         105.07          122.30 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
          20.04           14.07 
[1] "0.1 - 105.1 (20.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D1036V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPRJ MUTATED         1        1        2        3         3         4
  PTPRJ WILD-TYPE       1       14       38       27        34        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPRJ MUTATED           0          4          4          2        1
  PTPRJ WILD-TYPE         3         66         49         30       37
D1036V3, multiclass
            clus
vv           PTPRJ MUTATED PTPRJ WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               3              27
  STAGE IIA              3              34
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             4              49
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRJ MUTATED     2   8  11   6
  PTPRJ WILD-TYPE  20  84 162  91
D1036V4, multiclass
    clus
vv   PTPRJ MUTATED PTPRJ WILD-TYPE
  T1             2              20
  T2             8              84
  T3            11             162
  T4             6              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
  PTPRJ MUTATED     9   9   3   4
  PTPRJ WILD-TYPE 109  95  74  73
D1036V5, multiclass
    clus
vv   PTPRJ MUTATED PTPRJ WILD-TYPE
  N0             9             109
  N1             9              95
  N2             3              74
  N3             4              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"
D1036V6, binary
                 cls
clus                0   1
  PTPRJ MUTATED    26   0
  PTPRJ WILD-TYPE 320  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED     26    0
  PTPRJ WILD-TYPE  320   29
   clus
vv  PTPRJ MUTATED PTPRJ WILD-TYPE
  0            26             320
  1             0              29
[1] 2 2
[1] FALSE
D1036V7, binary
                 cls
clus                0   1
  PTPRJ MUTATED     7  21
  PTPRJ WILD-TYPE 138 227
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED      7   21
  PTPRJ WILD-TYPE  138  227
        clus
vv       PTPRJ MUTATED PTPRJ WILD-TYPE
  FEMALE             7             138
  MALE              21             227
[1] 2 2
[1] FALSE
D1036V8, binary
                 cls
clus                0   1
  PTPRJ MUTATED    23   2
  PTPRJ WILD-TYPE 269  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED     23    2
  PTPRJ WILD-TYPE  269   57
     clus
vv    PTPRJ MUTATED PTPRJ WILD-TYPE
  NO             23             269
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PTPRJ MUTATED                                          0
  PTPRJ WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PTPRJ MUTATED                                       4
  PTPRJ WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTPRJ MUTATED                                                       12
  PTPRJ WILD-TYPE                                                    146
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PTPRJ MUTATED                                                   2
  PTPRJ WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTPRJ MUTATED                                                                   5
  PTPRJ WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PTPRJ MUTATED                                                    0
  PTPRJ WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PTPRJ MUTATED                                                  5
  PTPRJ WILD-TYPE                                               56
D1036V9, multiclass
                                                                   clus
vv                                                                  PTPRJ MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              5
                                                                   clus
vv                                                                  PTPRJ WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        146
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTPRJ MUTATED    21   0   0   5
  PTPRJ WILD-TYPE 290  14  15  19
D1036V10, multiclass
    clus
vv   PTPRJ MUTATED PTPRJ WILD-TYPE
  R0            21             290
  R1             0              14
  R2             0              15
  RX             5              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1036V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PTPRJ MUTATED       5                         1
  PTPRJ WILD-TYPE    82                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPRJ MUTATED                                           0    18
  PTPRJ WILD-TYPE                                         1   225
D1036V12, multiclass
                                           clus
vv                                          PTPRJ MUTATED PTPRJ WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                18             225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1036V13, binary
                 cls
clus                0   1
  PTPRJ MUTATED     1  22
  PTPRJ WILD-TYPE   3 288
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED      1   22
  PTPRJ WILD-TYPE    3  288
                        clus
vv                       PTPRJ MUTATED PTPRJ WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            22             288
[1] 2 2
[1] FALSE

Clustering(1037) Variable = C11ORF63 MUTATION ANALYSIS
D1037V1, survival
                    sevent
clus2                  0   1
  C11ORF63 MUTATED    14   5
  C11ORF63 WILD-TYPE 216 134
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                19                350 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                 5                134 
$`C11ORF63 MUTATED`
TCGA-B7-5816 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-8077 TCGA-BR-8081 
       26.70         9.34        34.68        19.33         0.69        32.25 
TCGA-BR-8372 TCGA-BR-A4QL TCGA-CG-4441 TCGA-D7-6528 TCGA-D7-A4YT TCGA-FP-A4BE 
       31.27        16.14        14.01        15.22        14.27        11.08 
TCGA-HF-7134 TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-IN-A6RL TCGA-SW-A7EA 
       52.21         6.58        12.95        23.84        13.35        19.04 
TCGA-VQ-A8P2 
       38.14 

$`C11ORF63 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-8078 
       29.56        33.21        37.25        14.43        11.44        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-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-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-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-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-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       13.58         0.56         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-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
       20.25         0.26         2.10        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-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-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 

  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
              0.69               0.00 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
             52.21             122.30 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
             16.14              14.07 
[1] "0.7 - 52.2 (16.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D1037V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C11ORF63 MUTATED         0        1        2        0         2         5
  C11ORF63 WILD-TYPE       2       14       38       30        35        47
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C11ORF63 MUTATED           0          5          3          1        0
  C11ORF63 WILD-TYPE         3         65         50         31       38
D1037V3, multiclass
            clus
vv           C11ORF63 MUTATED C11ORF63 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  2                 38
  STAGE II                  0                 30
  STAGE IIA                 2                 35
  STAGE IIB                 5                 47
  STAGE III                 0                  3
  STAGE IIIA                5                 65
  STAGE IIIB                3                 50
  STAGE IIIC                1                 31
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C11ORF63 MUTATED     1   6   6   6
  C11ORF63 WILD-TYPE  21  86 167  91
D1037V4, multiclass
    clus
vv   C11ORF63 MUTATED C11ORF63 WILD-TYPE
  T1                1                 21
  T2                6                 86
  T3                6                167
  T4                6                 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
  C11ORF63 MUTATED     8   6   2   4
  C11ORF63 WILD-TYPE 110  98  75  73
D1037V5, multiclass
    clus
vv   C11ORF63 MUTATED C11ORF63 WILD-TYPE
  N0                8                110
  N1                6                 98
  N2                2                 75
  N3                4                 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"
D1037V6, binary
                    cls
clus                   0   1
  C11ORF63 MUTATED    20   0
  C11ORF63 WILD-TYPE 326  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED     20    0
  C11ORF63 WILD-TYPE  326   29
   clus
vv  C11ORF63 MUTATED C11ORF63 WILD-TYPE
  0               20                326
  1                0                 29
[1] 2 2
[1] FALSE
D1037V7, binary
                    cls
clus                   0   1
  C11ORF63 MUTATED    11   9
  C11ORF63 WILD-TYPE 134 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED     11    9
  C11ORF63 WILD-TYPE  134  239
        clus
vv       C11ORF63 MUTATED C11ORF63 WILD-TYPE
  FEMALE               11                134
  MALE                  9                239
[1] 2 2
[1] FALSE
D1037V8, binary
                    cls
clus                   0   1
  C11ORF63 MUTATED    15   2
  C11ORF63 WILD-TYPE 277  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED     15    2
  C11ORF63 WILD-TYPE  277   57
     clus
vv    C11ORF63 MUTATED C11ORF63 WILD-TYPE
  NO                15                277
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C11ORF63 MUTATED                                          0
  C11ORF63 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C11ORF63 MUTATED                                       3
  C11ORF63 WILD-TYPE                                    67
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C11ORF63 MUTATED                                                        9
  C11ORF63 WILD-TYPE                                                    149
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C11ORF63 MUTATED                                                   1
  C11ORF63 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C11ORF63 MUTATED                                                                   3
  C11ORF63 WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C11ORF63 MUTATED                                                    0
  C11ORF63 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C11ORF63 MUTATED                                                  4
  C11ORF63 WILD-TYPE                                               57
D1037V9, multiclass
                                                                   clus
vv                                                                  C11ORF63 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 4
                                                                   clus
vv                                                                  C11ORF63 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C11ORF63 MUTATED    18   0   0   2
  C11ORF63 WILD-TYPE 293  14  15  22
D1037V10, multiclass
    clus
vv   C11ORF63 MUTATED C11ORF63 WILD-TYPE
  R0               18                293
  R1                0                 14
  R2                0                 15
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1037V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C11ORF63 MUTATED       3                         1
  C11ORF63 WILD-TYPE    84                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C11ORF63 MUTATED                                           0    14
  C11ORF63 WILD-TYPE                                         1   229
D1037V12, multiclass
                                           clus
vv                                          C11ORF63 MUTATED C11ORF63 WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1037V13, binary
                    cls
clus                   0   1
  C11ORF63 MUTATED     0  17
  C11ORF63 WILD-TYPE   4 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED      0   17
  C11ORF63 WILD-TYPE    4  293
                        clus
vv                       C11ORF63 MUTATED C11ORF63 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               17                293
[1] 2 2
[1] FALSE

Clustering(1038) Variable = HSF4 MUTATION ANALYSIS
D1038V1, survival
                sevent
clus2              0   1
  HSF4 MUTATED     4   4
  HSF4 WILD-TYPE 226 135
  HSF4 MUTATED HSF4 WILD-TYPE 
             8            361 
  HSF4 MUTATED HSF4 WILD-TYPE 
             4            135 
$`HSF4 MUTATED`
TCGA-BR-6852 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8382 TCGA-CD-8536 TCGA-CG-5733 
       44.94         0.26        31.27        25.05        12.43        21.07 
TCGA-HU-A4GQ TCGA-HU-A4GT 
        0.10         6.51 

$`HSF4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  HSF4 MUTATED HSF4 WILD-TYPE 
           0.1            0.0 
  HSF4 MUTATED HSF4 WILD-TYPE 
         44.94         122.30 
  HSF4 MUTATED HSF4 WILD-TYPE 
         16.75          14.27 
[1] "0.1 - 44.9 (16.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D1038V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HSF4 MUTATED         0        0        1        1         2         0
  HSF4 WILD-TYPE       2       15       39       29        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSF4 MUTATED           0          1          0          3        0
  HSF4 WILD-TYPE         3         69         53         29       38
D1038V3, multiclass
            clus
vv           HSF4 MUTATED HSF4 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            3             29
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HSF4 MUTATED     0   2   3   3
  HSF4 WILD-TYPE  22  90 170  94
D1038V4, multiclass
    clus
vv   HSF4 MUTATED HSF4 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            3            170
  T4            3             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
  HSF4 MUTATED     4   0   2   2
  HSF4 WILD-TYPE 114 104  75  75
D1038V5, multiclass
    clus
vv   HSF4 MUTATED HSF4 WILD-TYPE
  N0            4            114
  N1            0            104
  N2            2             75
  N3            2             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"
D1038V6, binary
                cls
clus               0   1
  HSF4 MUTATED     8   0
  HSF4 WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF4 MUTATED      8    0
  HSF4 WILD-TYPE  338   29
   clus
vv  HSF4 MUTATED HSF4 WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D1038V7, binary
                cls
clus               0   1
  HSF4 MUTATED     5   3
  HSF4 WILD-TYPE 140 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF4 MUTATED      5    3
  HSF4 WILD-TYPE  140  245
        clus
vv       HSF4 MUTATED HSF4 WILD-TYPE
  FEMALE            5            140
  MALE              3            245
[1] 2 2
[1] FALSE
D1038V8, binary
                cls
clus               0   1
  HSF4 MUTATED     8   0
  HSF4 WILD-TYPE 284  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF4 MUTATED      8    0
  HSF4 WILD-TYPE  284   59
     clus
vv    HSF4 MUTATED HSF4 WILD-TYPE
  NO             8            284
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HSF4 MUTATED                                          0
  HSF4 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HSF4 MUTATED                                       0
  HSF4 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HSF4 MUTATED                                                        5
  HSF4 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HSF4 MUTATED                                                   0
  HSF4 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HSF4 MUTATED                                                                   1
  HSF4 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HSF4 MUTATED                                                    0
  HSF4 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HSF4 MUTATED                                                  2
  HSF4 WILD-TYPE                                               59
D1038V9, multiclass
                                                                   clus
vv                                                                  HSF4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  HSF4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HSF4 MUTATED     8   0   0   0
  HSF4 WILD-TYPE 303  14  15  24
D1038V10, multiclass
    clus
vv   HSF4 MUTATED HSF4 WILD-TYPE
  R0            8            303
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1038V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  HSF4 MUTATED       3                         0
  HSF4 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HSF4 MUTATED                                           0     4
  HSF4 WILD-TYPE                                         1   239
D1038V12, multiclass
                                           clus
vv                                          HSF4 MUTATED HSF4 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1038V13, binary
                cls
clus               0   1
  HSF4 MUTATED     0   7
  HSF4 WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF4 MUTATED      0    7
  HSF4 WILD-TYPE    4  303
                        clus
vv                       HSF4 MUTATED HSF4 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(1039) Variable = CNPY4 MUTATION ANALYSIS
D1039V1, survival
                 sevent
clus2               0   1
  CNPY4 MUTATED     3   1
  CNPY4 WILD-TYPE 227 138
  CNPY4 MUTATED CNPY4 WILD-TYPE 
              4             365 
  CNPY4 MUTATED CNPY4 WILD-TYPE 
              1             138 
$`CNPY4 MUTATED`
TCGA-BR-8485 TCGA-CG-4306 TCGA-CG-4443 TCGA-VQ-A8E7 
        9.21         1.02        29.98        37.41 

$`CNPY4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PE TCGA-VQ-A8PK TCGA-VQ-A8PM 
       43.36        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 

  CNPY4 MUTATED CNPY4 WILD-TYPE 
           1.02            0.00 
  CNPY4 MUTATED CNPY4 WILD-TYPE 
          37.41          122.30 
  CNPY4 MUTATED CNPY4 WILD-TYPE 
         19.595          14.270 
[1] "1.0 - 37.4 (19.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.6"
D1039V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNPY4 MUTATED         0        1        0        0         0         0
  CNPY4 WILD-TYPE       2       14       40       30        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNPY4 MUTATED           0          0          0          1        2
  CNPY4 WILD-TYPE         3         70         53         31       36
D1039V3, multiclass
            clus
vv           CNPY4 MUTATED CNPY4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CNPY4 MUTATED     1   0   2   1
  CNPY4 WILD-TYPE  21  92 171  96
D1039V4, multiclass
    clus
vv   CNPY4 MUTATED CNPY4 WILD-TYPE
  T1             1              21
  T2             0              92
  T3             2             171
  T4             1              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
  CNPY4 MUTATED     1   1   1   1
  CNPY4 WILD-TYPE 117 103  76  76
D1039V5, multiclass
    clus
vv   CNPY4 MUTATED CNPY4 WILD-TYPE
  N0             1             117
  N1             1             103
  N2             1              76
  N3             1              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"
D1039V6, binary
                 cls
clus                0   1
  CNPY4 MUTATED     2   2
  CNPY4 WILD-TYPE 344  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNPY4 MUTATED      2    2
  CNPY4 WILD-TYPE  344   27
   clus
vv  CNPY4 MUTATED CNPY4 WILD-TYPE
  0             2             344
  1             2              27
[1] 2 2
[1] FALSE
D1039V7, binary
                 cls
clus                0   1
  CNPY4 MUTATED     1   3
  CNPY4 WILD-TYPE 144 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNPY4 MUTATED      1    3
  CNPY4 WILD-TYPE  144  245
        clus
vv       CNPY4 MUTATED CNPY4 WILD-TYPE
  FEMALE             1             144
  MALE               3             245
[1] 2 2
[1] FALSE
D1039V8, binary
                 cls
clus                0   1
  CNPY4 MUTATED     2   0
  CNPY4 WILD-TYPE 290  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNPY4 MUTATED      2    0
  CNPY4 WILD-TYPE  290   59
     clus
vv    CNPY4 MUTATED CNPY4 WILD-TYPE
  NO              2             290
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CNPY4 MUTATED                                          0
  CNPY4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CNPY4 MUTATED                                       0
  CNPY4 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CNPY4 MUTATED                                                        2
  CNPY4 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CNPY4 MUTATED                                                   0
  CNPY4 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CNPY4 MUTATED                                                                   1
  CNPY4 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CNPY4 MUTATED                                                    0
  CNPY4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CNPY4 MUTATED                                                  1
  CNPY4 WILD-TYPE                                               60
D1039V9, multiclass
                                                                   clus
vv                                                                  CNPY4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  CNPY4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CNPY4 MUTATED     3   0   1   0
  CNPY4 WILD-TYPE 308  14  14  24
D1039V10, multiclass
    clus
vv   CNPY4 MUTATED CNPY4 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1039V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CNPY4 MUTATED       0                         0
  CNPY4 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CNPY4 MUTATED                                           0     2
  CNPY4 WILD-TYPE                                         1   241
D1039V12, multiclass
[1] "Remove cluster labels:" "CNPY4 MUTATED"         
clus
  CNPY4 MUTATED CNPY4 WILD-TYPE 
              2             338 
     TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-FP-A8CX      TCGA-KB-A93G 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-MX-A663      TCGA-B7-5816      TCGA-B7-5818      TCGA-B7-A5TI 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-B7-A5TJ      TCGA-B7-A5TK      TCGA-B7-A5TN      TCGA-BR-4183 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-4184      TCGA-BR-4187      TCGA-BR-4188      TCGA-BR-4191 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-4201      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-4257      TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-4292      TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-4362      TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4368 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-4369      TCGA-BR-4370      TCGA-BR-4371      TCGA-BR-6452 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-6453      TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-6457      TCGA-BR-6458      TCGA-BR-6563      TCGA-BR-6564 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-6565      TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-6707      TCGA-BR-6709      TCGA-BR-6710      TCGA-BR-6801 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-6802      TCGA-BR-6803      TCGA-BR-6852      TCGA-BR-7196 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-7197      TCGA-BR-7703      TCGA-BR-7704      TCGA-BR-7707 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-7715      TCGA-BR-7716      TCGA-BR-7717      TCGA-BR-7722 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-7723      TCGA-BR-7851      TCGA-BR-7901      TCGA-BR-7957 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-7958      TCGA-BR-7959      TCGA-BR-8058      TCGA-BR-8059 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-8060      TCGA-BR-8077      TCGA-BR-8078      TCGA-BR-8080 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-8081      TCGA-BR-8284      TCGA-BR-8285      TCGA-BR-8286 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-8289      TCGA-BR-8291      TCGA-BR-8295      TCGA-BR-8297 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-8360      TCGA-BR-8361      TCGA-BR-8363      TCGA-BR-8364 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-8365      TCGA-BR-8366      TCGA-BR-8367      TCGA-BR-8368 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-8369      TCGA-BR-8370      TCGA-BR-8371      TCGA-BR-8372 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-8373      TCGA-BR-8380      TCGA-BR-8381      TCGA-BR-8382 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-8384      TCGA-BR-8483      TCGA-BR-8484      TCGA-BR-8486 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-8487      TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-8591      TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-8678      TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-8683      TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-A44T      TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-A4CQ      TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-A4IV      TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-A4J2      TCGA-BR-A4J4      TCGA-BR-A4J5      TCGA-BR-A4J6 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-A4J7      TCGA-BR-A4J8      TCGA-BR-A4PD      TCGA-BR-A4PE 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-BR-A4PF      TCGA-BR-A4QI      TCGA-BR-A4QL      TCGA-BR-A4QM 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-CD-5798      TCGA-CD-5799      TCGA-CD-5800      TCGA-CD-5801 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-CD-5802      TCGA-CD-5803      TCGA-CD-5804      TCGA-CD-5813 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-CD-8524      TCGA-CD-8525      TCGA-CD-8526      TCGA-CD-8527 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-CD-8528      TCGA-CD-8529      TCGA-CD-8530      TCGA-CD-8531 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-CD-8532      TCGA-CD-8533      TCGA-CD-8534      TCGA-CD-8535 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-CD-8536      TCGA-CD-A486      TCGA-CD-A487      TCGA-CD-A489 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-CD-A48A      TCGA-CD-A48C      TCGA-CD-A4MG      TCGA-CD-A4MH 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-CD-A4MI      TCGA-CD-A4MJ      TCGA-D7-5577      TCGA-D7-5578 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-D7-5579      TCGA-D7-6518      TCGA-D7-6519      TCGA-D7-6520 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-D7-6521      TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6525 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-D7-8570      TCGA-D7-8572      TCGA-D7-8573      TCGA-D7-8574 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-D7-8575      TCGA-D7-8576      TCGA-D7-8578      TCGA-D7-8579 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-D7-A4YT      TCGA-D7-A4YU      TCGA-D7-A4YV      TCGA-D7-A4YX 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-D7-A4YY      TCGA-D7-A4Z0      TCGA-D7-A6ET      TCGA-D7-A6EV 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-D7-A6EX      TCGA-D7-A6EY      TCGA-D7-A6EZ      TCGA-D7-A6F0 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-D7-A6F2      TCGA-D7-A747      TCGA-D7-A748      TCGA-D7-A74A 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-D7-A74B      TCGA-EQ-5647      TCGA-EQ-8122      TCGA-F1-6874 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-F1-6875      TCGA-F1-A448      TCGA-F1-A72C      TCGA-FP-7735 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-FP-7829      TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-FP-8209      TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-FP-A4BE      TCGA-FP-A4BF      TCGA-FP-A9TM      TCGA-HJ-7597 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-HU-8238      TCGA-HU-8243      TCGA-HU-8244      TCGA-HU-8249 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-HU-8602      TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-HU-A4G2      TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-HU-A4G9      TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-HU-A4GH      TCGA-HU-A4GJ      TCGA-HU-A4GN      TCGA-HU-A4GP 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-HU-A4GQ      TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-HU-A4GY      TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-HU-A4H4      TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-HU-A4HB      TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-IN-8462      TCGA-IN-8663      TCGA-IN-A6RI      TCGA-IN-A6RJ 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-IN-A6RL      TCGA-IN-A6RN      TCGA-IN-A6RO      TCGA-IN-A6RP 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-IN-A6RR      TCGA-IN-A6RS      TCGA-IN-A7NR      TCGA-IN-A7NT 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-IN-A7NU      TCGA-IN-AB1V      TCGA-IN-AB1X      TCGA-IP-7968 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-KB-A93J      TCGA-MX-A5UG      TCGA-MX-A5UJ      TCGA-MX-A666 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-R5-A7O7      TCGA-R5-A7ZE      TCGA-R5-A7ZF      TCGA-R5-A7ZI 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-R5-A7ZR      TCGA-R5-A804      TCGA-R5-A805      TCGA-RD-A7BS 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-RD-A7BT      TCGA-RD-A7BW      TCGA-RD-A7C1      TCGA-RD-A8MV 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-RD-A8MW      TCGA-RD-A8N0      TCGA-RD-A8N1      TCGA-RD-A8N2 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-RD-A8N4      TCGA-RD-A8N5      TCGA-RD-A8N6      TCGA-RD-A8N9 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-SW-A7EA      TCGA-SW-A7EB      TCGA-VQ-A8DL      TCGA-VQ-A8DU 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-VQ-A8DV      TCGA-VQ-A8DZ      TCGA-VQ-A8E2      TCGA-VQ-A8P2 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-VQ-A8P3      TCGA-VQ-A8PE      TCGA-VQ-A8PK      TCGA-VQ-A8PM 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-VQ-A8PQ      TCGA-VQ-A91U      TCGA-VQ-A92D      TCGA-VQ-AA64 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-VQ-AA68      TCGA-VQ-AA69      TCGA-VQ-AA6A      TCGA-VQ-AA6B 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-VQ-AA6F      TCGA-VQ-AA6G      TCGA-VQ-AA6I      TCGA-VQ-AA6J 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
     TCGA-VQ-AA6K      TCGA-ZA-A8F6 
"CNPY4 WILD-TYPE" "CNPY4 WILD-TYPE" 
D1039V13, binary
                 cls
clus                0   1
  CNPY4 MUTATED     0   1
  CNPY4 WILD-TYPE   4 309
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNPY4 MUTATED      0    1
  CNPY4 WILD-TYPE    4  309
                        clus
vv                       CNPY4 MUTATED CNPY4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             1             309
[1] 2 2
[1] FALSE

Clustering(1040) Variable = FAM167A MUTATION ANALYSIS
D1040V1, survival
                   sevent
clus2                 0   1
  FAM167A MUTATED     6   1
  FAM167A WILD-TYPE 224 138
  FAM167A MUTATED FAM167A WILD-TYPE 
                7               362 
  FAM167A MUTATED FAM167A WILD-TYPE 
                1               138 
$`FAM167A MUTATED`
TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8368 TCGA-CD-A4MG TCGA-MX-A5UJ 
       34.68        32.25         6.18         4.31         6.58        19.73 
TCGA-VQ-A8P2 
       38.14 

$`FAM167A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  FAM167A MUTATED FAM167A WILD-TYPE 
             4.31              0.00 
  FAM167A MUTATED FAM167A WILD-TYPE 
            38.14            122.30 
  FAM167A MUTATED FAM167A WILD-TYPE 
            19.73             14.22 
[1] "4.3 - 38.1 (19.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.9"
D1040V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAM167A MUTATED         0        0        1        0         3         1
  FAM167A WILD-TYPE       2       15       39       30        34        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM167A MUTATED           0          2          0          0        0
  FAM167A WILD-TYPE         3         68         53         32       38
D1040V3, multiclass
            clus
vv           FAM167A MUTATED FAM167A WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                3                34
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM167A MUTATED     1   1   4   2
  FAM167A WILD-TYPE  21  91 169  95
D1040V4, multiclass
    clus
vv   FAM167A MUTATED FAM167A WILD-TYPE
  T1               1                21
  T2               1                91
  T3               4               169
  T4               2                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
  FAM167A MUTATED     5   1   1   0
  FAM167A WILD-TYPE 113 103  76  77
D1040V5, multiclass
    clus
vv   FAM167A MUTATED FAM167A WILD-TYPE
  N0               5               113
  N1               1               103
  N2               1                76
  N3               0                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"
D1040V6, binary
                   cls
clus                  0   1
  FAM167A MUTATED     8   0
  FAM167A WILD-TYPE 338  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM167A MUTATED      8    0
  FAM167A WILD-TYPE  338   29
   clus
vv  FAM167A MUTATED FAM167A WILD-TYPE
  0               8               338
  1               0                29
[1] 2 2
[1] FALSE
D1040V7, binary
                   cls
clus                  0   1
  FAM167A MUTATED     5   3
  FAM167A WILD-TYPE 140 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM167A MUTATED      5    3
  FAM167A WILD-TYPE  140  245
        clus
vv       FAM167A MUTATED FAM167A WILD-TYPE
  FEMALE               5               140
  MALE                 3               245
[1] 2 2
[1] FALSE
D1040V8, binary
                   cls
clus                  0   1
  FAM167A MUTATED     6   1
  FAM167A WILD-TYPE 286  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM167A MUTATED      6    1
  FAM167A WILD-TYPE  286   58
     clus
vv    FAM167A MUTATED FAM167A WILD-TYPE
  NO                6               286
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM167A MUTATED                                          0
  FAM167A WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM167A MUTATED                                       1
  FAM167A WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM167A MUTATED                                                        4
  FAM167A WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM167A MUTATED                                                   1
  FAM167A WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM167A MUTATED                                                                   1
  FAM167A WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM167A MUTATED                                                    0
  FAM167A WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM167A MUTATED                                                  1
  FAM167A WILD-TYPE                                               60
D1040V9, multiclass
                                                                   clus
vv                                                                  FAM167A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  FAM167A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM167A MUTATED     6   0   0   1
  FAM167A WILD-TYPE 305  14  15  23
D1040V10, multiclass
    clus
vv   FAM167A MUTATED FAM167A WILD-TYPE
  R0               6               305
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1040V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  FAM167A MUTATED       1                         0
  FAM167A WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM167A MUTATED                                           0     7
  FAM167A WILD-TYPE                                         1   236
D1040V12, multiclass
                                           clus
vv                                          FAM167A MUTATED FAM167A WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1040V13, binary
                   cls
clus                  0   1
  FAM167A MUTATED     0   7
  FAM167A WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM167A MUTATED      0    7
  FAM167A WILD-TYPE    4  303
                        clus
vv                       FAM167A MUTATED FAM167A WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(1041) Variable = DMC1 MUTATION ANALYSIS
D1041V1, survival
                sevent
clus2              0   1
  DMC1 MUTATED     4   3
  DMC1 WILD-TYPE 226 136
  DMC1 MUTATED DMC1 WILD-TYPE 
             7            362 
  DMC1 MUTATED DMC1 WILD-TYPE 
             3            136 
$`DMC1 MUTATED`
TCGA-BR-8284 TCGA-BR-8363 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CG-5721 TCGA-FP-A4BE 
        8.05         0.26        20.42        21.44         6.02        11.08 
TCGA-VQ-A8P2 
       38.14 

$`DMC1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-A4PF 
       28.34         0.66        32.52        13.51        20.65         1.15 
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-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 

  DMC1 MUTATED DMC1 WILD-TYPE 
          0.26           0.00 
  DMC1 MUTATED DMC1 WILD-TYPE 
         38.14         122.30 
  DMC1 MUTATED DMC1 WILD-TYPE 
         11.08          14.35 
[1] "0.3 - 38.1 (11.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D1041V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DMC1 MUTATED         0        0        2        0         2         0
  DMC1 WILD-TYPE       2       15       38       30        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DMC1 MUTATED           0          1          0          1        1
  DMC1 WILD-TYPE         3         69         53         31       37
D1041V3, multiclass
            clus
vv           DMC1 MUTATED DMC1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DMC1 MUTATED     0   2   2   3
  DMC1 WILD-TYPE  22  90 171  94
D1041V4, multiclass
    clus
vv   DMC1 MUTATED DMC1 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            2            171
  T4            3             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
  DMC1 MUTATED     4   2   0   1
  DMC1 WILD-TYPE 114 102  77  76
D1041V5, multiclass
    clus
vv   DMC1 MUTATED DMC1 WILD-TYPE
  N0            4            114
  N1            2            102
  N2            0             77
  N3            1             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"
D1041V6, binary
                cls
clus               0   1
  DMC1 MUTATED     8   0
  DMC1 WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      8    0
  DMC1 WILD-TYPE  338   29
   clus
vv  DMC1 MUTATED DMC1 WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D1041V7, binary
                cls
clus               0   1
  DMC1 MUTATED     5   3
  DMC1 WILD-TYPE 140 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      5    3
  DMC1 WILD-TYPE  140  245
        clus
vv       DMC1 MUTATED DMC1 WILD-TYPE
  FEMALE            5            140
  MALE              3            245
[1] 2 2
[1] FALSE
D1041V8, binary
                cls
clus               0   1
  DMC1 MUTATED     5   2
  DMC1 WILD-TYPE 287  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      5    2
  DMC1 WILD-TYPE  287   57
     clus
vv    DMC1 MUTATED DMC1 WILD-TYPE
  NO             5            287
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DMC1 MUTATED                                          0
  DMC1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DMC1 MUTATED                                       0
  DMC1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DMC1 MUTATED                                                        5
  DMC1 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DMC1 MUTATED                                                   1
  DMC1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DMC1 MUTATED                                                                   2
  DMC1 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DMC1 MUTATED                                                    0
  DMC1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DMC1 MUTATED                                                  0
  DMC1 WILD-TYPE                                               61
D1041V9, multiclass
                                                                   clus
vv                                                                  DMC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  DMC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DMC1 MUTATED     7   0   0   1
  DMC1 WILD-TYPE 304  14  15  23
D1041V10, multiclass
    clus
vv   DMC1 MUTATED DMC1 WILD-TYPE
  R0            7            304
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1041V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  DMC1 MUTATED       0                         1
  DMC1 WILD-TYPE    87                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DMC1 MUTATED                                           0     6
  DMC1 WILD-TYPE                                         1   237
D1041V12, multiclass
                                           clus
vv                                          DMC1 MUTATED DMC1 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1041V13, binary
                cls
clus               0   1
  DMC1 MUTATED     0   6
  DMC1 WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  DMC1 MUTATED      0    6
  DMC1 WILD-TYPE    4  304
                        clus
vv                       DMC1 MUTATED DMC1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(1042) Variable = DENND4C MUTATION ANALYSIS
D1042V1, survival
                   sevent
clus2                 0   1
  DENND4C MUTATED    10   5
  DENND4C WILD-TYPE 220 134
  DENND4C MUTATED DENND4C WILD-TYPE 
               15               354 
  DENND4C MUTATED DENND4C WILD-TYPE 
                5               134 
$`DENND4C MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8485 TCGA-BR-8680 TCGA-CG-5724 
       21.99         6.97        34.68         9.21        31.96        12.03 
TCGA-CG-5728 TCGA-D7-6818 TCGA-D7-A4YY TCGA-FP-A4BF TCGA-HU-A4G8 TCGA-HU-A4G9 
       65.10        12.36        13.78         5.52        22.68        24.20 
TCGA-HU-A4H3 TCGA-IN-AB1X TCGA-MX-A5UJ 
       29.00        13.51        19.73 

$`DENND4C WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-5725 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
        0.99       105.07        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-D7-6820 
       17.19        10.26        15.22        15.98        12.79        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-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-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-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-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       10.62        11.70        15.75         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 

  DENND4C MUTATED DENND4C WILD-TYPE 
             5.52              0.00 
  DENND4C MUTATED DENND4C WILD-TYPE 
             65.1             122.3 
  DENND4C MUTATED DENND4C WILD-TYPE 
            19.73             14.22 
[1] "5.5 - 65.1 (19.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D1042V2, 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       2       14       39       30        35        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DENND4C MUTATED           0          5          1          2        3
  DENND4C WILD-TYPE         3         65         52         30       35
D1042V3, multiclass
            clus
vv           DENND4C MUTATED DENND4C WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               5                65
  STAGE IIIB               1                52
  STAGE IIIC               2                30
  STAGE IV                 3                35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DENND4C MUTATED     1   2   8   5
  DENND4C WILD-TYPE  21  90 165  92
D1042V4, multiclass
    clus
vv   DENND4C MUTATED DENND4C WILD-TYPE
  T1               1                21
  T2               2                90
  T3               8               165
  T4               5                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
  DENND4C MUTATED     5   3   3   5
  DENND4C WILD-TYPE 113 101  74  72
D1042V5, multiclass
    clus
vv   DENND4C MUTATED DENND4C WILD-TYPE
  N0               5               113
  N1               3               101
  N2               3                74
  N3               5                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"
D1042V6, binary
                   cls
clus                  0   1
  DENND4C MUTATED    12   3
  DENND4C WILD-TYPE 334  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4C MUTATED     12    3
  DENND4C WILD-TYPE  334   26
   clus
vv  DENND4C MUTATED DENND4C WILD-TYPE
  0              12               334
  1               3                26
[1] 2 2
[1] FALSE
D1042V7, binary
                   cls
clus                  0   1
  DENND4C MUTATED    10   6
  DENND4C WILD-TYPE 135 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4C MUTATED     10    6
  DENND4C WILD-TYPE  135  242
        clus
vv       DENND4C MUTATED DENND4C WILD-TYPE
  FEMALE              10               135
  MALE                 6               242
[1] 2 2
[1] FALSE
D1042V8, binary
                   cls
clus                  0   1
  DENND4C MUTATED    11   2
  DENND4C WILD-TYPE 281  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4C MUTATED     11    2
  DENND4C WILD-TYPE  281   57
     clus
vv    DENND4C MUTATED DENND4C WILD-TYPE
  NO               11               281
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DENND4C MUTATED                                          1
  DENND4C WILD-TYPE                                        7
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DENND4C MUTATED                                       4
  DENND4C WILD-TYPE                                    66
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DENND4C MUTATED                                                        6
  DENND4C WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DENND4C MUTATED                                                   0
  DENND4C WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DENND4C MUTATED                                                                   2
  DENND4C WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DENND4C MUTATED                                                    0
  DENND4C WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DENND4C MUTATED                                                  3
  DENND4C WILD-TYPE                                               58
D1042V9, multiclass
                                                                   clus
vv                                                                  DENND4C MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  DENND4C WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DENND4C MUTATED    10   1   2   2
  DENND4C WILD-TYPE 301  13  13  22
D1042V10, multiclass
    clus
vv   DENND4C MUTATED DENND4C WILD-TYPE
  R0              10               301
  R1               1                13
  R2               2                13
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1042V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  DENND4C MUTATED       4                         0
  DENND4C WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DENND4C MUTATED                                           0     9
  DENND4C WILD-TYPE                                         1   234
D1042V12, multiclass
                                           clus
vv                                          DENND4C MUTATED DENND4C WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1042V13, binary
                   cls
clus                  0   1
  DENND4C MUTATED     0  13
  DENND4C WILD-TYPE   4 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4C MUTATED      0   13
  DENND4C WILD-TYPE    4  297
                        clus
vv                       DENND4C MUTATED DENND4C WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              13               297
[1] 2 2
[1] FALSE

Clustering(1043) Variable = DEK MUTATION ANALYSIS
D1043V1, survival
               sevent
clus2             0   1
  DEK MUTATED     7   1
  DEK WILD-TYPE 223 138
  DEK MUTATED DEK WILD-TYPE 
            8           361 
  DEK MUTATED DEK WILD-TYPE 
            1           138 
$`DEK MUTATED`
TCGA-BR-8680 TCGA-CG-5723 TCGA-CG-5730 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-A4GX 
       31.96       105.07         4.01        30.51        26.47        20.25 
TCGA-IP-7968 TCGA-VQ-A8P2 
        2.53        38.14 

$`DEK WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  DEK MUTATED DEK WILD-TYPE 
         2.53          0.00 
  DEK MUTATED DEK WILD-TYPE 
       105.07        122.30 
  DEK MUTATED DEK WILD-TYPE 
        28.49         14.07 
[1] "2.5 - 105.1 (28.5)" "0.0 - 122.3 (14.1)"
[1] "hr=" "4.5"
D1043V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DEK MUTATED         0        0        1        1         0         0
  DEK WILD-TYPE       2       15       39       29        37        52
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEK MUTATED           0          1          1          2        2
  DEK WILD-TYPE         3         69         52         30       36
D1043V3, multiclass
            clus
vv           DEK MUTATED DEK WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             1            39
  STAGE II             1            29
  STAGE IIA            0            37
  STAGE IIB            0            52
  STAGE III            0             3
  STAGE IIIA           1            69
  STAGE IIIB           1            52
  STAGE IIIC           2            30
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  DEK MUTATED     0   3   1   4
  DEK WILD-TYPE  22  89 172  93
D1043V4, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  T1           0            22
  T2           3            89
  T3           1           172
  T4           4            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
  DEK MUTATED     1   3   3   1
  DEK WILD-TYPE 117 101  74  76
D1043V5, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  N0           1           117
  N1           3           101
  N2           3            74
  N3           1            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"
D1043V6, binary
               cls
clus              0   1
  DEK MUTATED     4   2
  DEK WILD-TYPE 342  27
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      4    2
  DEK WILD-TYPE  342   27
   clus
vv  DEK MUTATED DEK WILD-TYPE
  0           4           342
  1           2            27
[1] 2 2
[1] FALSE
D1043V7, binary
               cls
clus              0   1
  DEK MUTATED     4   4
  DEK WILD-TYPE 141 244
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      4    4
  DEK WILD-TYPE  141  244
        clus
vv       DEK MUTATED DEK WILD-TYPE
  FEMALE           4           141
  MALE             4           244
[1] 2 2
[1] FALSE
D1043V8, binary
               cls
clus              0   1
  DEK MUTATED     4   2
  DEK WILD-TYPE 288  57
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      4    2
  DEK WILD-TYPE  288   57
     clus
vv    DEK MUTATED DEK WILD-TYPE
  NO            4           288
  YES           2            57
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DEK MUTATED                                          1
  DEK WILD-TYPE                                        7
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DEK MUTATED                                       1
  DEK WILD-TYPE                                    69
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEK MUTATED                                                        2
  DEK WILD-TYPE                                                    156
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DEK MUTATED                                                   2
  DEK WILD-TYPE                                                19
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DEK MUTATED                                                                   1
  DEK WILD-TYPE                                                                67
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DEK MUTATED                                                    0
  DEK WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DEK MUTATED                                                  1
  DEK WILD-TYPE                                               60
D1043V9, multiclass
                                                                   clus
vv                                                                  DEK MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            1
                                                                   clus
vv                                                                  DEK WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  DEK MUTATED     6   1   1   0
  DEK WILD-TYPE 305  13  14  24
D1043V10, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  R0           6           305
  R1           1            13
  R2           1            14
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1043V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  DEK MUTATED       2                         0
  DEK WILD-TYPE    85                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEK MUTATED                                           0     3
  DEK WILD-TYPE                                         1   240
D1043V12, multiclass
                                           clus
vv                                          DEK MUTATED DEK WILD-TYPE
  ASIAN                                               2            85
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               3           240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1043V13, binary
               cls
clus              0   1
  DEK MUTATED     0   4
  DEK WILD-TYPE   4 306
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      0    4
  DEK WILD-TYPE    4  306
                        clus
vv                       DEK MUTATED DEK WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           4           306
[1] 2 2
[1] FALSE

Clustering(1044) Variable = SP140 MUTATION ANALYSIS
D1044V1, survival
                 sevent
clus2               0   1
  SP140 MUTATED    10   5
  SP140 WILD-TYPE 220 134
  SP140 MUTATED SP140 WILD-TYPE 
             15             354 
  SP140 MUTATED SP140 WILD-TYPE 
              5             134 
$`SP140 MUTATED`
TCGA-CG-4460 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-8060 TCGA-BR-8368 TCGA-BR-8485 
       21.99        11.70        34.68        11.44         4.31         9.21 
TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-4438 TCGA-F1-6875 TCGA-KB-A6F5 TCGA-KB-A93J 
        1.12         6.58        54.08        72.23         5.56        36.95 
TCGA-R5-A7ZI TCGA-VQ-A8P2 TCGA-VQ-A91U 
       74.53        38.14         1.71 

$`SP140 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-8486 TCGA-BR-8588 TCGA-BR-8589 
        3.72         5.39        25.18        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-4440 
       27.02        15.95         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-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-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-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-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A666 
       13.51         2.53        63.62         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-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 

  SP140 MUTATED SP140 WILD-TYPE 
           1.12            0.00 
  SP140 MUTATED SP140 WILD-TYPE 
          74.53          122.30 
  SP140 MUTATED SP140 WILD-TYPE 
          11.70           14.35 
[1] "1.1 - 74.5 (11.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D1044V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SP140 MUTATED         0        1        2        1         3         1
  SP140 WILD-TYPE       2       14       38       29        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SP140 MUTATED           0          4          0          1        3
  SP140 WILD-TYPE         3         66         53         31       35
D1044V3, multiclass
            clus
vv           SP140 MUTATED SP140 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             4              66
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SP140 MUTATED     0   5   5   6
  SP140 WILD-TYPE  22  87 168  91
D1044V4, multiclass
    clus
vv   SP140 MUTATED SP140 WILD-TYPE
  T1             0              22
  T2             5              87
  T3             5             168
  T4             6              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
  SP140 MUTATED     7   5   3   1
  SP140 WILD-TYPE 111  99  74  76
D1044V5, multiclass
    clus
vv   SP140 MUTATED SP140 WILD-TYPE
  N0             7             111
  N1             5              99
  N2             3              74
  N3             1              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"
D1044V6, binary
                 cls
clus                0   1
  SP140 MUTATED    14   2
  SP140 WILD-TYPE 332  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP140 MUTATED     14    2
  SP140 WILD-TYPE  332   27
   clus
vv  SP140 MUTATED SP140 WILD-TYPE
  0            14             332
  1             2              27
[1] 2 2
[1] FALSE
D1044V7, binary
                 cls
clus                0   1
  SP140 MUTATED     8   8
  SP140 WILD-TYPE 137 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP140 MUTATED      8    8
  SP140 WILD-TYPE  137  240
        clus
vv       SP140 MUTATED SP140 WILD-TYPE
  FEMALE             8             137
  MALE               8             240
[1] 2 2
[1] FALSE
D1044V8, binary
                 cls
clus                0   1
  SP140 MUTATED    12   2
  SP140 WILD-TYPE 280  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP140 MUTATED     12    2
  SP140 WILD-TYPE  280   57
     clus
vv    SP140 MUTATED SP140 WILD-TYPE
  NO             12             280
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SP140 MUTATED                                          0
  SP140 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SP140 MUTATED                                       4
  SP140 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SP140 MUTATED                                                        7
  SP140 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SP140 MUTATED                                                   1
  SP140 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SP140 MUTATED                                                                   4
  SP140 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SP140 MUTATED                                                    0
  SP140 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SP140 MUTATED                                                  0
  SP140 WILD-TYPE                                               61
D1044V9, multiclass
                                                                   clus
vv                                                                  SP140 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  SP140 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SP140 MUTATED    13   0   1   1
  SP140 WILD-TYPE 298  14  14  23
D1044V10, multiclass
    clus
vv   SP140 MUTATED SP140 WILD-TYPE
  R0            13             298
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1044V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SP140 MUTATED       2                         1
  SP140 WILD-TYPE    85                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SP140 MUTATED                                           0    10
  SP140 WILD-TYPE                                         1   233
D1044V12, multiclass
                                           clus
vv                                          SP140 MUTATED SP140 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1044V13, binary
                 cls
clus                0   1
  SP140 MUTATED     1   9
  SP140 WILD-TYPE   3 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP140 MUTATED      1    9
  SP140 WILD-TYPE    3  301
                        clus
vv                       SP140 MUTATED SP140 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             9             301
[1] 2 2
[1] FALSE

Clustering(1045) Variable = EGR1 MUTATION ANALYSIS
D1045V1, survival
                sevent
clus2              0   1
  EGR1 MUTATED    10   2
  EGR1 WILD-TYPE 220 137
  EGR1 MUTATED EGR1 WILD-TYPE 
            12            357 
  EGR1 MUTATED EGR1 WILD-TYPE 
             2            137 
$`EGR1 MUTATED`
TCGA-BR-6452 TCGA-BR-8078 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5723 TCGA-F1-6874 
       34.68        29.59        15.95         1.02       105.07        14.47 
TCGA-HF-A5NB TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-MX-A5UJ TCGA-VQ-A8P2 
       30.51        29.98         0.10         6.51        19.73        38.14 

$`EGR1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       11.77        21.37         8.98         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 

  EGR1 MUTATED EGR1 WILD-TYPE 
           0.1            0.0 
  EGR1 MUTATED EGR1 WILD-TYPE 
        105.07         122.30 
  EGR1 MUTATED EGR1 WILD-TYPE 
         24.66          14.07 
[1] "0.1 - 105.1 (24.7)" "0.0 - 122.3 (14.1)"
[1] "hr=" "3"  
D1045V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EGR1 MUTATED         0        0        1        2         3         1
  EGR1 WILD-TYPE       2       15       39       28        34        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EGR1 MUTATED           0          2          0          2        1
  EGR1 WILD-TYPE         3         68         53         30       37
D1045V3, multiclass
            clus
vv           EGR1 MUTATED EGR1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              2             28
  STAGE IIA             3             34
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EGR1 MUTATED     0   4   4   4
  EGR1 WILD-TYPE  22  88 169  93
D1045V4, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  T1            0             22
  T2            4             88
  T3            4            169
  T4            4             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
  EGR1 MUTATED     4   4   3   1
  EGR1 WILD-TYPE 114 100  74  76
D1045V5, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  N0            4            114
  N1            4            100
  N2            3             74
  N3            1             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"
D1045V6, binary
                cls
clus               0   1
  EGR1 MUTATED    11   1
  EGR1 WILD-TYPE 335  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED     11    1
  EGR1 WILD-TYPE  335   28
   clus
vv  EGR1 MUTATED EGR1 WILD-TYPE
  0           11            335
  1            1             28
[1] 2 2
[1] FALSE
D1045V7, binary
                cls
clus               0   1
  EGR1 MUTATED     5   7
  EGR1 WILD-TYPE 140 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      5    7
  EGR1 WILD-TYPE  140  241
        clus
vv       EGR1 MUTATED EGR1 WILD-TYPE
  FEMALE            5            140
  MALE              7            241
[1] 2 2
[1] FALSE
D1045V8, binary
                cls
clus               0   1
  EGR1 MUTATED     9   2
  EGR1 WILD-TYPE 283  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      9    2
  EGR1 WILD-TYPE  283   57
     clus
vv    EGR1 MUTATED EGR1 WILD-TYPE
  NO             9            283
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EGR1 MUTATED                                          0
  EGR1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EGR1 MUTATED                                       0
  EGR1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EGR1 MUTATED                                                        5
  EGR1 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EGR1 MUTATED                                                   2
  EGR1 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EGR1 MUTATED                                                                   1
  EGR1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EGR1 MUTATED                                                    0
  EGR1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EGR1 MUTATED                                                  4
  EGR1 WILD-TYPE                                               57
D1045V9, multiclass
                                                                   clus
vv                                                                  EGR1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  EGR1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EGR1 MUTATED    10   1   1   0
  EGR1 WILD-TYPE 301  13  14  24
D1045V10, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  R0           10            301
  R1            1             13
  R2            1             14
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1045V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  EGR1 MUTATED       3                         0
  EGR1 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EGR1 MUTATED                                           0     5
  EGR1 WILD-TYPE                                         1   238
D1045V12, multiclass
                                           clus
vv                                          EGR1 MUTATED EGR1 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1045V13, binary
                cls
clus               0   1
  EGR1 MUTATED     0   7
  EGR1 WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      0    7
  EGR1 WILD-TYPE    4  303
                        clus
vv                       EGR1 MUTATED EGR1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(1046) Variable = PKD2L2 MUTATION ANALYSIS
D1046V1, survival
                  sevent
clus2                0   1
  PKD2L2 MUTATED     8   1
  PKD2L2 WILD-TYPE 222 138
  PKD2L2 MUTATED PKD2L2 WILD-TYPE 
               9              360 
  PKD2L2 MUTATED PKD2L2 WILD-TYPE 
               1              138 
$`PKD2L2 MUTATED`
TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5721 TCGA-D7-5578 TCGA-D7-8572 TCGA-HU-A4G8 
        1.12        31.96         6.02        12.66        16.80        22.68 
TCGA-HU-A4GN TCGA-VQ-A8DL TCGA-VQ-A8P2 
       29.98         0.92        38.14 

$`PKD2L2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-D7-5579 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-D7-8573 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-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-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-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 

  PKD2L2 MUTATED PKD2L2 WILD-TYPE 
            0.92             0.00 
  PKD2L2 MUTATED PKD2L2 WILD-TYPE 
           38.14           122.30 
  PKD2L2 MUTATED PKD2L2 WILD-TYPE 
           16.80            14.22 
[1] "0.9 - 38.1 (16.8)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3.5"
D1046V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PKD2L2 MUTATED         0        0        0        0         3         2
  PKD2L2 WILD-TYPE       2       15       40       30        34        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PKD2L2 MUTATED           0          2          0          0        2
  PKD2L2 WILD-TYPE         3         68         53         32       36
D1046V3, multiclass
            clus
vv           PKD2L2 MUTATED PKD2L2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PKD2L2 MUTATED     0   2   4   3
  PKD2L2 WILD-TYPE  22  90 169  94
D1046V4, multiclass
    clus
vv   PKD2L2 MUTATED PKD2L2 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              4              169
  T4              3               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
  PKD2L2 MUTATED     2   5   3   0
  PKD2L2 WILD-TYPE 116  99  74  77
D1046V5, multiclass
    clus
vv   PKD2L2 MUTATED PKD2L2 WILD-TYPE
  N0              2              116
  N1              5               99
  N2              3               74
  N3              0               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"
D1046V6, binary
                  cls
clus                 0   1
  PKD2L2 MUTATED     9   1
  PKD2L2 WILD-TYPE 337  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L2 MUTATED      9    1
  PKD2L2 WILD-TYPE  337   28
   clus
vv  PKD2L2 MUTATED PKD2L2 WILD-TYPE
  0              9              337
  1              1               28
[1] 2 2
[1] FALSE
D1046V7, binary
                  cls
clus                 0   1
  PKD2L2 MUTATED     4   6
  PKD2L2 WILD-TYPE 141 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L2 MUTATED      4    6
  PKD2L2 WILD-TYPE  141  242
        clus
vv       PKD2L2 MUTATED PKD2L2 WILD-TYPE
  FEMALE              4              141
  MALE                6              242
[1] 2 2
[1] FALSE
D1046V8, binary
                  cls
clus                 0   1
  PKD2L2 MUTATED     8   1
  PKD2L2 WILD-TYPE 284  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L2 MUTATED      8    1
  PKD2L2 WILD-TYPE  284   58
     clus
vv    PKD2L2 MUTATED PKD2L2 WILD-TYPE
  NO               8              284
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PKD2L2 MUTATED                                          0
  PKD2L2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PKD2L2 MUTATED                                       1
  PKD2L2 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PKD2L2 MUTATED                                                        3
  PKD2L2 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PKD2L2 MUTATED                                                   1
  PKD2L2 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PKD2L2 MUTATED                                                                   1
  PKD2L2 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PKD2L2 MUTATED                                                    0
  PKD2L2 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PKD2L2 MUTATED                                                  4
  PKD2L2 WILD-TYPE                                               57
D1046V9, multiclass
                                                                   clus
vv                                                                  PKD2L2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  PKD2L2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PKD2L2 MUTATED     8   0   0   1
  PKD2L2 WILD-TYPE 303  14  15  23
D1046V10, multiclass
    clus
vv   PKD2L2 MUTATED PKD2L2 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1046V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PKD2L2 MUTATED       3                         0
  PKD2L2 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PKD2L2 MUTATED                                           0     6
  PKD2L2 WILD-TYPE                                         1   237
D1046V12, multiclass
                                           clus
vv                                          PKD2L2 MUTATED PKD2L2 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1046V13, binary
                  cls
clus                 0   1
  PKD2L2 MUTATED     0   7
  PKD2L2 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L2 MUTATED      0    7
  PKD2L2 WILD-TYPE    4  303
                        clus
vv                       PKD2L2 MUTATED PKD2L2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(1047) Variable = FGF13 MUTATION ANALYSIS
D1047V1, survival
                 sevent
clus2               0   1
  FGF13 MUTATED    10   3
  FGF13 WILD-TYPE 220 136
  FGF13 MUTATED FGF13 WILD-TYPE 
             13             356 
  FGF13 MUTATED FGF13 WILD-TYPE 
              3             136 
$`FGF13 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6852 TCGA-BR-8078 TCGA-CD-8531 TCGA-CG-5723 
       26.70        30.90        44.94        29.59        12.59       105.07 
TCGA-D7-A4Z0 TCGA-HF-A5NB TCGA-HU-A4H8 TCGA-R5-A7ZE TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       14.76        30.51        14.07        18.21        37.41        38.14 
TCGA-VQ-A8PK 
       17.85 

$`FGF13 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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 

  FGF13 MUTATED FGF13 WILD-TYPE 
          12.59            0.00 
  FGF13 MUTATED FGF13 WILD-TYPE 
         105.07          122.30 
  FGF13 MUTATED FGF13 WILD-TYPE 
         29.590          14.025 
[1] "12.6 - 105.1 (29.6)" "0.0 - 122.3 (14.0)" 
[1] "hr=" "2.7"
D1047V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FGF13 MUTATED         0        0        2        1         1         3
  FGF13 WILD-TYPE       2       15       38       29        36        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FGF13 MUTATED           0          3          1          1        1
  FGF13 WILD-TYPE         3         67         52         31       37
D1047V3, multiclass
            clus
vv           FGF13 MUTATED FGF13 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FGF13 MUTATED     2   4   5   4
  FGF13 WILD-TYPE  20  88 168  93
D1047V4, multiclass
    clus
vv   FGF13 MUTATED FGF13 WILD-TYPE
  T1             2              20
  T2             4              88
  T3             5             168
  T4             4              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
  FGF13 MUTATED     4   5   2   2
  FGF13 WILD-TYPE 114  99  75  75
D1047V5, multiclass
    clus
vv   FGF13 MUTATED FGF13 WILD-TYPE
  N0             4             114
  N1             5              99
  N2             2              75
  N3             2              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"
D1047V6, binary
                 cls
clus                0   1
  FGF13 MUTATED    14   1
  FGF13 WILD-TYPE 332  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF13 MUTATED     14    1
  FGF13 WILD-TYPE  332   28
   clus
vv  FGF13 MUTATED FGF13 WILD-TYPE
  0            14             332
  1             1              28
[1] 2 2
[1] FALSE
D1047V7, binary
                 cls
clus                0   1
  FGF13 MUTATED    10   5
  FGF13 WILD-TYPE 135 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF13 MUTATED     10    5
  FGF13 WILD-TYPE  135  243
        clus
vv       FGF13 MUTATED FGF13 WILD-TYPE
  FEMALE            10             135
  MALE               5             243
[1] 2 2
[1] FALSE
D1047V8, binary
                 cls
clus                0   1
  FGF13 MUTATED    10   4
  FGF13 WILD-TYPE 282  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF13 MUTATED     10    4
  FGF13 WILD-TYPE  282   55
     clus
vv    FGF13 MUTATED FGF13 WILD-TYPE
  NO             10             282
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FGF13 MUTATED                                          0
  FGF13 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FGF13 MUTATED                                       2
  FGF13 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FGF13 MUTATED                                                        6
  FGF13 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FGF13 MUTATED                                                   3
  FGF13 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FGF13 MUTATED                                                                   1
  FGF13 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FGF13 MUTATED                                                    0
  FGF13 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FGF13 MUTATED                                                  3
  FGF13 WILD-TYPE                                               58
D1047V9, multiclass
                                                                   clus
vv                                                                  FGF13 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  FGF13 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FGF13 MUTATED    11   1   0   2
  FGF13 WILD-TYPE 300  13  15  22
D1047V10, multiclass
    clus
vv   FGF13 MUTATED FGF13 WILD-TYPE
  R0            11             300
  R1             1              13
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1047V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FGF13 MUTATED       2                         0
  FGF13 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FGF13 MUTATED                                           0    11
  FGF13 WILD-TYPE                                         1   232
D1047V12, multiclass
                                           clus
vv                                          FGF13 MUTATED FGF13 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1047V13, binary
                 cls
clus                0   1
  FGF13 MUTATED     0  10
  FGF13 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF13 MUTATED      0   10
  FGF13 WILD-TYPE    4  300
                        clus
vv                       FGF13 MUTATED FGF13 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(1048) Variable = MAP4K5 MUTATION ANALYSIS
D1048V1, survival
                  sevent
clus2                0   1
  MAP4K5 MUTATED     2   1
  MAP4K5 WILD-TYPE 228 138
  MAP4K5 MUTATED MAP4K5 WILD-TYPE 
               3              366 
  MAP4K5 MUTATED MAP4K5 WILD-TYPE 
               1              138 
$`MAP4K5 MUTATED`
TCGA-BR-6452 TCGA-BR-8589 TCGA-CG-5733 
       34.68        27.12        21.07 

$`MAP4K5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  MAP4K5 MUTATED MAP4K5 WILD-TYPE 
           21.07             0.00 
  MAP4K5 MUTATED MAP4K5 WILD-TYPE 
           34.68           122.30 
  MAP4K5 MUTATED MAP4K5 WILD-TYPE 
           27.12            14.12 
[1] "21.1 - 34.7 (27.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D1048V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP4K5 MUTATED         0        0        0        0         1         0
  MAP4K5 WILD-TYPE       2       15       40       30        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP4K5 MUTATED           0          1          1          0        0
  MAP4K5 WILD-TYPE         3         69         52         32       38
D1048V3, multiclass
            clus
vv           MAP4K5 MUTATED MAP4K5 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP4K5 MUTATED     0   1   1   1
  MAP4K5 WILD-TYPE  22  91 172  96
D1048V4, multiclass
    clus
vv   MAP4K5 MUTATED MAP4K5 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              1              172
  T4              1               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
  MAP4K5 MUTATED     1   2   1   0
  MAP4K5 WILD-TYPE 117 102  76  77
D1048V5, multiclass
    clus
vv   MAP4K5 MUTATED MAP4K5 WILD-TYPE
  N0              1              117
  N1              2              102
  N2              1               76
  N3              0               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"
D1048V6, binary
                  cls
clus                 0   1
  MAP4K5 MUTATED     4   0
  MAP4K5 WILD-TYPE 342  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K5 MUTATED      4    0
  MAP4K5 WILD-TYPE  342   29
   clus
vv  MAP4K5 MUTATED MAP4K5 WILD-TYPE
  0              4              342
  1              0               29
[1] 2 2
[1] FALSE
D1048V7, binary
                  cls
clus                 0   1
  MAP4K5 MUTATED     3   1
  MAP4K5 WILD-TYPE 142 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K5 MUTATED      3    1
  MAP4K5 WILD-TYPE  142  247
        clus
vv       MAP4K5 MUTATED MAP4K5 WILD-TYPE
  FEMALE              3              142
  MALE                1              247
[1] 2 2
[1] FALSE
D1048V8, binary
                  cls
clus                 0   1
  MAP4K5 MUTATED     3   0
  MAP4K5 WILD-TYPE 289  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K5 MUTATED      3    0
  MAP4K5 WILD-TYPE  289   59
     clus
vv    MAP4K5 MUTATED MAP4K5 WILD-TYPE
  NO               3              289
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MAP4K5 MUTATED                                          0
  MAP4K5 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MAP4K5 MUTATED                                       0
  MAP4K5 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP4K5 MUTATED                                                        3
  MAP4K5 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MAP4K5 MUTATED                                                   0
  MAP4K5 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP4K5 MUTATED                                                                   1
  MAP4K5 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MAP4K5 MUTATED                                                    0
  MAP4K5 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MAP4K5 MUTATED                                                  0
  MAP4K5 WILD-TYPE                                               61
D1048V9, multiclass
                                                                   clus
vv                                                                  MAP4K5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  MAP4K5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP4K5 MUTATED     3   0   0   1
  MAP4K5 WILD-TYPE 308  14  15  23
D1048V10, multiclass
    clus
vv   MAP4K5 MUTATED MAP4K5 WILD-TYPE
  R0              3              308
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1048V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  MAP4K5 MUTATED       0                         0
  MAP4K5 WILD-TYPE    87                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP4K5 MUTATED                                           0     3
  MAP4K5 WILD-TYPE                                         1   240
D1048V12, multiclass
                                           clus
vv                                          MAP4K5 MUTATED MAP4K5 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1048V13, binary
                  cls
clus                 0   1
  MAP4K5 MUTATED     0   3
  MAP4K5 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K5 MUTATED      0    3
  MAP4K5 WILD-TYPE    4  307
                        clus
vv                       MAP4K5 MUTATED MAP4K5 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(1049) Variable = ARID5B MUTATION ANALYSIS
D1049V1, survival
                  sevent
clus2                0   1
  ARID5B MUTATED     9   2
  ARID5B WILD-TYPE 221 137
  ARID5B MUTATED ARID5B WILD-TYPE 
              11              358 
  ARID5B MUTATED ARID5B WILD-TYPE 
               2              137 
$`ARID5B MUTATED`
TCGA-B7-5816 TCGA-BR-8284 TCGA-BR-8361 TCGA-BR-8372 TCGA-CG-4305 TCGA-CG-4466 
       26.70         8.05        31.10        31.27        15.95        18.97 
TCGA-CG-5721 TCGA-HU-8602 TCGA-IN-A6RI TCGA-IN-A6RR TCGA-VQ-A92D 
        6.02        22.32        18.38         6.74        66.81 

$`ARID5B WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39        12.46        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
        6.44        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-A94T TCGA-VQ-AA64 
       15.65        20.81         1.71        42.64        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 

  ARID5B MUTATED ARID5B WILD-TYPE 
            6.02             0.00 
  ARID5B MUTATED ARID5B WILD-TYPE 
           66.81           122.30 
  ARID5B MUTATED ARID5B WILD-TYPE 
           18.97            14.07 
[1] "6.0 - 66.8 (19.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.6"
D1049V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARID5B MUTATED         2        0        2        1         0         3
  ARID5B WILD-TYPE       0       15       38       29        37        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID5B MUTATED           0          1          0          3        1
  ARID5B WILD-TYPE         3         69         53         29       37
D1049V3, multiclass
            clus
vv           ARID5B MUTATED ARID5B WILD-TYPE
  STAGE I                 2                0
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               0               37
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              3               29
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID5B MUTATED     2   3   1   7
  ARID5B WILD-TYPE  20  89 172  90
D1049V4, multiclass
    clus
vv   ARID5B MUTATED ARID5B WILD-TYPE
  T1              2               20
  T2              3               89
  T3              1              172
  T4              7               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
  ARID5B MUTATED     6   5   1   2
  ARID5B WILD-TYPE 112  99  76  75
D1049V5, multiclass
    clus
vv   ARID5B MUTATED ARID5B WILD-TYPE
  N0              6              112
  N1              5               99
  N2              1               76
  N3              2               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"
D1049V6, binary
                  cls
clus                 0   1
  ARID5B MUTATED    14   0
  ARID5B WILD-TYPE 332  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED     14    0
  ARID5B WILD-TYPE  332   29
   clus
vv  ARID5B MUTATED ARID5B WILD-TYPE
  0             14              332
  1              0               29
[1] 2 2
[1] FALSE
D1049V7, binary
                  cls
clus                 0   1
  ARID5B MUTATED     7   8
  ARID5B WILD-TYPE 138 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED      7    8
  ARID5B WILD-TYPE  138  240
        clus
vv       ARID5B MUTATED ARID5B WILD-TYPE
  FEMALE              7              138
  MALE                8              240
[1] 2 2
[1] FALSE
D1049V8, binary
                  cls
clus                 0   1
  ARID5B MUTATED    13   0
  ARID5B WILD-TYPE 279  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED     13    0
  ARID5B WILD-TYPE  279   59
     clus
vv    ARID5B MUTATED ARID5B WILD-TYPE
  NO              13              279
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARID5B MUTATED                                          0
  ARID5B WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARID5B MUTATED                                       2
  ARID5B WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARID5B MUTATED                                                        8
  ARID5B WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARID5B MUTATED                                                   0
  ARID5B WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARID5B MUTATED                                                                   4
  ARID5B WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARID5B MUTATED                                                    0
  ARID5B WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARID5B MUTATED                                                  1
  ARID5B WILD-TYPE                                               60
D1049V9, multiclass
                                                                   clus
vv                                                                  ARID5B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ARID5B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARID5B MUTATED    13   0   0   2
  ARID5B WILD-TYPE 298  14  15  22
D1049V10, multiclass
    clus
vv   ARID5B MUTATED ARID5B WILD-TYPE
  R0             13              298
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1049V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ARID5B MUTATED       1                         1
  ARID5B WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARID5B MUTATED                                           0    10
  ARID5B WILD-TYPE                                         1   233
D1049V12, multiclass
                                           clus
vv                                          ARID5B MUTATED ARID5B WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1049V13, binary
                  cls
clus                 0   1
  ARID5B MUTATED     0  11
  ARID5B WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5B MUTATED      0   11
  ARID5B WILD-TYPE    4  299
                        clus
vv                       ARID5B MUTATED ARID5B WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(1050) Variable = CCDC92 MUTATION ANALYSIS
D1050V1, survival
                  sevent
clus2                0   1
  CCDC92 MUTATED     4   3
  CCDC92 WILD-TYPE 226 136
  CCDC92 MUTATED CCDC92 WILD-TYPE 
               7              362 
  CCDC92 MUTATED CCDC92 WILD-TYPE 
               3              136 
$`CCDC92 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 TCGA-CD-A4MG TCGA-FP-A4BE 
        6.97        34.68        35.84         1.12         6.58        11.08 
TCGA-VQ-A8DZ 
       13.02 

$`CCDC92 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  CCDC92 MUTATED CCDC92 WILD-TYPE 
            1.12             0.00 
  CCDC92 MUTATED CCDC92 WILD-TYPE 
           35.84           122.30 
  CCDC92 MUTATED CCDC92 WILD-TYPE 
           11.08            14.45 
[1] "1.1 - 35.8 (11.1)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.4"
D1050V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC92 MUTATED         0        0        1        0         4         0
  CCDC92 WILD-TYPE       2       15       39       30        33        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC92 MUTATED           0          1          0          0        1
  CCDC92 WILD-TYPE         3         69         53         32       37
D1050V3, multiclass
            clus
vv           CCDC92 MUTATED CCDC92 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               4               33
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC92 MUTATED     0   1   5   1
  CCDC92 WILD-TYPE  22  91 168  96
D1050V4, multiclass
    clus
vv   CCDC92 MUTATED CCDC92 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              5              168
  T4              1               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
  CCDC92 MUTATED     5   1   0   1
  CCDC92 WILD-TYPE 113 103  77  76
D1050V5, multiclass
    clus
vv   CCDC92 MUTATED CCDC92 WILD-TYPE
  N0              5              113
  N1              1              103
  N2              0               77
  N3              1               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"
D1050V6, binary
                  cls
clus                 0   1
  CCDC92 MUTATED     5   1
  CCDC92 WILD-TYPE 341  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC92 MUTATED      5    1
  CCDC92 WILD-TYPE  341   28
   clus
vv  CCDC92 MUTATED CCDC92 WILD-TYPE
  0              5              341
  1              1               28
[1] 2 2
[1] FALSE
D1050V7, binary
                  cls
clus                 0   1
  CCDC92 MUTATED     3   4
  CCDC92 WILD-TYPE 142 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC92 MUTATED      3    4
  CCDC92 WILD-TYPE  142  244
        clus
vv       CCDC92 MUTATED CCDC92 WILD-TYPE
  FEMALE              3              142
  MALE                4              244
[1] 2 2
[1] FALSE
D1050V8, binary
                  cls
clus                 0   1
  CCDC92 MUTATED     6   1
  CCDC92 WILD-TYPE 286  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC92 MUTATED      6    1
  CCDC92 WILD-TYPE  286   58
     clus
vv    CCDC92 MUTATED CCDC92 WILD-TYPE
  NO               6              286
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CCDC92 MUTATED                                          1
  CCDC92 WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CCDC92 MUTATED                                       1
  CCDC92 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC92 MUTATED                                                        5
  CCDC92 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CCDC92 MUTATED                                                   0
  CCDC92 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC92 MUTATED                                                                   0
  CCDC92 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CCDC92 MUTATED                                                    0
  CCDC92 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CCDC92 MUTATED                                                  0
  CCDC92 WILD-TYPE                                               61
D1050V9, multiclass
                                                                   clus
vv                                                                  CCDC92 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  CCDC92 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CCDC92 MUTATED     4   0   1   1
  CCDC92 WILD-TYPE 307  14  14  23
D1050V10, multiclass
    clus
vv   CCDC92 MUTATED CCDC92 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1050V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CCDC92 MUTATED       1                         2
  CCDC92 WILD-TYPE    86                         7
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC92 MUTATED                                           0     4
  CCDC92 WILD-TYPE                                         1   239
D1050V12, multiclass
                                           clus
vv                                          CCDC92 MUTATED CCDC92 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              2                7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1050V13, binary
                  cls
clus                 0   1
  CCDC92 MUTATED     0   6
  CCDC92 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC92 MUTATED      0    6
  CCDC92 WILD-TYPE    4  304
                        clus
vv                       CCDC92 MUTATED CCDC92 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(1051) Variable = CNGA1 MUTATION ANALYSIS
D1051V1, survival
                 sevent
clus2               0   1
  CNGA1 MUTATED     6   4
  CNGA1 WILD-TYPE 224 135
  CNGA1 MUTATED CNGA1 WILD-TYPE 
             10             359 
  CNGA1 MUTATED CNGA1 WILD-TYPE 
              4             135 
$`CNGA1 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7715 TCGA-BR-8360 TCGA-BR-8680 
       21.99         6.97        34.68        33.63         6.18        31.96 
TCGA-CD-A4MG TCGA-CG-5733 TCGA-HU-A4GN TCGA-VQ-A8P2 
        6.58        21.07        29.98        38.14 

$`CNGA1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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 

  CNGA1 MUTATED CNGA1 WILD-TYPE 
           6.18            0.00 
  CNGA1 MUTATED CNGA1 WILD-TYPE 
          38.14          122.30 
  CNGA1 MUTATED CNGA1 WILD-TYPE 
         25.985          14.070 
[1] "6.2 - 38.1 (26.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D1051V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CNGA1 MUTATED         0        0        0        0         5         0
  CNGA1 WILD-TYPE       2       15       40       30        32        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNGA1 MUTATED           0          3          0          0        2
  CNGA1 WILD-TYPE         3         67         53         32       36
D1051V3, multiclass
            clus
vv           CNGA1 MUTATED CNGA1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              5              32
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CNGA1 MUTATED     0   2   5   3
  CNGA1 WILD-TYPE  22  90 168  94
D1051V4, multiclass
    clus
vv   CNGA1 MUTATED CNGA1 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             5             168
  T4             3              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
  CNGA1 MUTATED     4   4   2   0
  CNGA1 WILD-TYPE 114 100  75  77
D1051V5, multiclass
    clus
vv   CNGA1 MUTATED CNGA1 WILD-TYPE
  N0             4             114
  N1             4             100
  N2             2              75
  N3             0              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"
D1051V6, binary
                 cls
clus                0   1
  CNGA1 MUTATED     7   2
  CNGA1 WILD-TYPE 339  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA1 MUTATED      7    2
  CNGA1 WILD-TYPE  339   27
   clus
vv  CNGA1 MUTATED CNGA1 WILD-TYPE
  0             7             339
  1             2              27
[1] 2 2
[1] FALSE
D1051V7, binary
                 cls
clus                0   1
  CNGA1 MUTATED     3   7
  CNGA1 WILD-TYPE 142 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA1 MUTATED      3    7
  CNGA1 WILD-TYPE  142  241
        clus
vv       CNGA1 MUTATED CNGA1 WILD-TYPE
  FEMALE             3             142
  MALE               7             241
[1] 2 2
[1] FALSE
D1051V8, binary
                 cls
clus                0   1
  CNGA1 MUTATED     9   1
  CNGA1 WILD-TYPE 283  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA1 MUTATED      9    1
  CNGA1 WILD-TYPE  283   58
     clus
vv    CNGA1 MUTATED CNGA1 WILD-TYPE
  NO              9             283
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CNGA1 MUTATED                                          0
  CNGA1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CNGA1 MUTATED                                       1
  CNGA1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CNGA1 MUTATED                                                        3
  CNGA1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CNGA1 MUTATED                                                   1
  CNGA1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CNGA1 MUTATED                                                                   3
  CNGA1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CNGA1 MUTATED                                                    0
  CNGA1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CNGA1 MUTATED                                                  2
  CNGA1 WILD-TYPE                                               59
D1051V9, multiclass
                                                                   clus
vv                                                                  CNGA1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  CNGA1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CNGA1 MUTATED     7   0   1   1
  CNGA1 WILD-TYPE 304  14  14  23
D1051V10, multiclass
    clus
vv   CNGA1 MUTATED CNGA1 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1051V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CNGA1 MUTATED       3                         0
  CNGA1 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CNGA1 MUTATED                                           0     5
  CNGA1 WILD-TYPE                                         1   238
D1051V12, multiclass
                                           clus
vv                                          CNGA1 MUTATED CNGA1 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1051V13, binary
                 cls
clus                0   1
  CNGA1 MUTATED     0   7
  CNGA1 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA1 MUTATED      0    7
  CNGA1 WILD-TYPE    4  303
                        clus
vv                       CNGA1 MUTATED CNGA1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(1052) Variable = RAE1 MUTATION ANALYSIS
D1052V1, survival
                sevent
clus2              0   1
  RAE1 MUTATED     6   1
  RAE1 WILD-TYPE 224 138
  RAE1 MUTATED RAE1 WILD-TYPE 
             7            362 
  RAE1 MUTATED RAE1 WILD-TYPE 
             1            138 
$`RAE1 MUTATED`
TCGA-B7-A5TJ TCGA-BR-4256 TCGA-BR-8078 TCGA-BR-8297 TCGA-BR-8589 TCGA-BR-8678 
       11.01         9.34        29.59         7.40        27.12        24.79 
TCGA-HU-A4G9 
       24.20 

$`RAE1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15         9.86        26.70        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-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-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-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-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-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-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 

  RAE1 MUTATED RAE1 WILD-TYPE 
           7.4            0.0 
  RAE1 MUTATED RAE1 WILD-TYPE 
         29.59         122.30 
  RAE1 MUTATED RAE1 WILD-TYPE 
         24.20          14.22 
[1] "7.4 - 29.6 (24.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "3"  
D1052V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RAE1 MUTATED         0        1        1        0         0         2
  RAE1 WILD-TYPE       2       14       39       30        37        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAE1 MUTATED           0          0          1          1        0
  RAE1 WILD-TYPE         3         70         52         31       38
D1052V3, multiclass
            clus
vv           RAE1 MUTATED RAE1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RAE1 MUTATED     1   1   0   4
  RAE1 WILD-TYPE  21  91 173  93
D1052V4, multiclass
    clus
vv   RAE1 MUTATED RAE1 WILD-TYPE
  T1            1             21
  T2            1             91
  T3            0            173
  T4            4             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
  RAE1 MUTATED     3   2   0   1
  RAE1 WILD-TYPE 115 102  77  76
D1052V5, multiclass
    clus
vv   RAE1 MUTATED RAE1 WILD-TYPE
  N0            3            115
  N1            2            102
  N2            0             77
  N3            1             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"
D1052V6, binary
                cls
clus               0   1
  RAE1 MUTATED     8   0
  RAE1 WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED      8    0
  RAE1 WILD-TYPE  338   29
   clus
vv  RAE1 MUTATED RAE1 WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D1052V7, binary
                cls
clus               0   1
  RAE1 MUTATED     2   6
  RAE1 WILD-TYPE 143 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED      2    6
  RAE1 WILD-TYPE  143  242
        clus
vv       RAE1 MUTATED RAE1 WILD-TYPE
  FEMALE            2            143
  MALE              6            242
[1] 2 2
[1] FALSE
D1052V8, binary
                cls
clus               0   1
  RAE1 MUTATED     7   0
  RAE1 WILD-TYPE 285  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED      7    0
  RAE1 WILD-TYPE  285   59
     clus
vv    RAE1 MUTATED RAE1 WILD-TYPE
  NO             7            285
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RAE1 MUTATED                                          0
  RAE1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RAE1 MUTATED                                       1
  RAE1 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RAE1 MUTATED                                                        5
  RAE1 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RAE1 MUTATED                                                   0
  RAE1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RAE1 MUTATED                                                                   1
  RAE1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RAE1 MUTATED                                                    0
  RAE1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RAE1 MUTATED                                                  1
  RAE1 WILD-TYPE                                               60
D1052V9, multiclass
                                                                   clus
vv                                                                  RAE1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  RAE1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RAE1 MUTATED     5   0   0   2
  RAE1 WILD-TYPE 306  14  15  22
D1052V10, multiclass
    clus
vv   RAE1 MUTATED RAE1 WILD-TYPE
  R0            5            306
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1052V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RAE1 MUTATED       1                         0
  RAE1 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RAE1 MUTATED                                           0     7
  RAE1 WILD-TYPE                                         1   236
D1052V12, multiclass
                                           clus
vv                                          RAE1 MUTATED RAE1 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1052V13, binary
                cls
clus               0   1
  RAE1 MUTATED     0   8
  RAE1 WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED      0    8
  RAE1 WILD-TYPE    4  302
                        clus
vv                       RAE1 MUTATED RAE1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(1053) Variable = ZC3H8 MUTATION ANALYSIS
D1053V1, survival
                 sevent
clus2               0   1
  ZC3H8 MUTATED     1   3
  ZC3H8 WILD-TYPE 229 136
  ZC3H8 MUTATED ZC3H8 WILD-TYPE 
              4             365 
  ZC3H8 MUTATED ZC3H8 WILD-TYPE 
              3             136 
$`ZC3H8 MUTATED`
TCGA-CG-4460 TCGA-BR-8683 TCGA-D7-A4YY TCGA-RD-A7C1 
       21.99         9.86        13.78        16.67 

$`ZC3H8 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       31.96        32.58        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-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-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-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 

  ZC3H8 MUTATED ZC3H8 WILD-TYPE 
           9.86            0.00 
  ZC3H8 MUTATED ZC3H8 WILD-TYPE 
          21.99          122.30 
  ZC3H8 MUTATED ZC3H8 WILD-TYPE 
         15.225          14.270 
[1] "9.9 - 22.0 (15.2)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.1"
D1053V2, 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       2       15       39       30        37        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H8 MUTATED           0          0          2          0        1
  ZC3H8 WILD-TYPE         3         70         51         32       37
D1053V3, multiclass
            clus
vv           ZC3H8 MUTATED ZC3H8 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             2              51
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZC3H8 MUTATED     0   1   1   2
  ZC3H8 WILD-TYPE  22  91 172  95
D1053V4, multiclass
    clus
vv   ZC3H8 MUTATED ZC3H8 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             1             172
  T4             2              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
  ZC3H8 MUTATED     1   1   1   1
  ZC3H8 WILD-TYPE 117 103  76  76
D1053V5, multiclass
    clus
vv   ZC3H8 MUTATED ZC3H8 WILD-TYPE
  N0             1             117
  N1             1             103
  N2             1              76
  N3             1              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"
D1053V6, binary
                 cls
clus                0   1
  ZC3H8 MUTATED     3   1
  ZC3H8 WILD-TYPE 343  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H8 MUTATED      3    1
  ZC3H8 WILD-TYPE  343   28
   clus
vv  ZC3H8 MUTATED ZC3H8 WILD-TYPE
  0             3             343
  1             1              28
[1] 2 2
[1] FALSE
D1053V7, binary
                 cls
clus                0   1
  ZC3H8 MUTATED     1   3
  ZC3H8 WILD-TYPE 144 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H8 MUTATED      1    3
  ZC3H8 WILD-TYPE  144  245
        clus
vv       ZC3H8 MUTATED ZC3H8 WILD-TYPE
  FEMALE             1             144
  MALE               3             245
[1] 2 2
[1] FALSE
D1053V8, binary
                 cls
clus                0   1
  ZC3H8 MUTATED     3   1
  ZC3H8 WILD-TYPE 289  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H8 MUTATED      3    1
  ZC3H8 WILD-TYPE  289   58
     clus
vv    ZC3H8 MUTATED ZC3H8 WILD-TYPE
  NO              3             289
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZC3H8 MUTATED                                          0
  ZC3H8 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZC3H8 MUTATED                                       1
  ZC3H8 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZC3H8 MUTATED                                                        1
  ZC3H8 WILD-TYPE                                                    157
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZC3H8 MUTATED                                                   0
  ZC3H8 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZC3H8 MUTATED                                                                   1
  ZC3H8 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZC3H8 MUTATED                                                    0
  ZC3H8 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZC3H8 MUTATED                                                  1
  ZC3H8 WILD-TYPE                                               60
D1053V9, multiclass
                                                                   clus
vv                                                                  ZC3H8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  ZC3H8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZC3H8 MUTATED     3   0   1   0
  ZC3H8 WILD-TYPE 308  14  14  24
D1053V10, multiclass
    clus
vv   ZC3H8 MUTATED ZC3H8 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1053V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ZC3H8 MUTATED       1                         0
  ZC3H8 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZC3H8 MUTATED                                           0     2
  ZC3H8 WILD-TYPE                                         1   241
D1053V12, multiclass
                                           clus
vv                                          ZC3H8 MUTATED ZC3H8 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1053V13, binary
                 cls
clus                0   1
  ZC3H8 MUTATED     0   3
  ZC3H8 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H8 MUTATED      0    3
  ZC3H8 WILD-TYPE    4  307
                        clus
vv                       ZC3H8 MUTATED ZC3H8 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(1054) Variable = WDR53 MUTATION ANALYSIS
D1054V1, survival
                 sevent
clus2               0   1
  WDR53 MUTATED     5   1
  WDR53 WILD-TYPE 225 138
  WDR53 MUTATED WDR53 WILD-TYPE 
              6             363 
  WDR53 MUTATED WDR53 WILD-TYPE 
              1             138 
$`WDR53 MUTATED`
TCGA-B7-5818 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-HJ-7597 
       11.70        29.59         1.12        28.14        31.96        26.47 

$`WDR53 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  WDR53 MUTATED WDR53 WILD-TYPE 
           1.12            0.00 
  WDR53 MUTATED WDR53 WILD-TYPE 
          31.96          122.30 
  WDR53 MUTATED WDR53 WILD-TYPE 
         27.305          14.170 
[1] "1.1 - 32.0 (27.3)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.9"
D1054V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WDR53 MUTATED         0        0        2        0         1         1
  WDR53 WILD-TYPE       2       15       38       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WDR53 MUTATED           0          0          0          1        1
  WDR53 WILD-TYPE         3         70         53         31       37
D1054V3, multiclass
            clus
vv           WDR53 MUTATED WDR53 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WDR53 MUTATED     0   2   1   3
  WDR53 WILD-TYPE  22  90 172  94
D1054V4, multiclass
    clus
vv   WDR53 MUTATED WDR53 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             1             172
  T4             3              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
  WDR53 MUTATED     4   0   1   1
  WDR53 WILD-TYPE 114 104  76  76
D1054V5, multiclass
    clus
vv   WDR53 MUTATED WDR53 WILD-TYPE
  N0             4             114
  N1             0             104
  N2             1              76
  N3             1              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"
D1054V6, binary
                 cls
clus                0   1
  WDR53 MUTATED     4   1
  WDR53 WILD-TYPE 342  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR53 MUTATED      4    1
  WDR53 WILD-TYPE  342   28
   clus
vv  WDR53 MUTATED WDR53 WILD-TYPE
  0             4             342
  1             1              28
[1] 2 2
[1] FALSE
D1054V7, binary
                 cls
clus                0   1
  WDR53 MUTATED     3   3
  WDR53 WILD-TYPE 142 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR53 MUTATED      3    3
  WDR53 WILD-TYPE  142  245
        clus
vv       WDR53 MUTATED WDR53 WILD-TYPE
  FEMALE             3             142
  MALE               3             245
[1] 2 2
[1] FALSE
D1054V8, binary
                 cls
clus                0   1
  WDR53 MUTATED     6   0
  WDR53 WILD-TYPE 286  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR53 MUTATED      6    0
  WDR53 WILD-TYPE  286   59
     clus
vv    WDR53 MUTATED WDR53 WILD-TYPE
  NO              6             286
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  WDR53 MUTATED                                          1
  WDR53 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  WDR53 MUTATED                                       1
  WDR53 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WDR53 MUTATED                                                        3
  WDR53 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  WDR53 MUTATED                                                   0
  WDR53 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WDR53 MUTATED                                                                   0
  WDR53 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  WDR53 MUTATED                                                    0
  WDR53 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  WDR53 MUTATED                                                  1
  WDR53 WILD-TYPE                                               60
D1054V9, multiclass
                                                                   clus
vv                                                                  WDR53 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  WDR53 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WDR53 MUTATED     6   0   0   0
  WDR53 WILD-TYPE 305  14  15  24
D1054V10, multiclass
    clus
vv   WDR53 MUTATED WDR53 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1054V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  WDR53 MUTATED       1                         0
  WDR53 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WDR53 MUTATED                                           0     5
  WDR53 WILD-TYPE                                         1   238
D1054V12, multiclass
                                           clus
vv                                          WDR53 MUTATED WDR53 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1054V13, binary
                 cls
clus                0   1
  WDR53 MUTATED     0   6
  WDR53 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR53 MUTATED      0    6
  WDR53 WILD-TYPE    4  304
                        clus
vv                       WDR53 MUTATED WDR53 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(1055) Variable = EPB41L4B MUTATION ANALYSIS
D1055V1, survival
                    sevent
clus2                  0   1
  EPB41L4B MUTATED     9   4
  EPB41L4B WILD-TYPE 221 135
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
                13                356 
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
                 4                135 
$`EPB41L4B MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 TCGA-BR-8680 
        6.97         9.34        34.68        35.84         1.12        31.96 
TCGA-CG-5721 TCGA-FP-A4BE TCGA-HF-A5NB TCGA-HU-A4GQ TCGA-MX-A5UJ TCGA-VQ-A8P2 
        6.02        11.08        30.51         0.10        19.73        38.14 
TCGA-VQ-A91Q 
       20.81 

$`EPB41L4B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
               0.1                0.0 
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
             38.14             122.30 
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
             19.73              14.22 
[1] "0.1 - 38.1 (19.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D1055V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPB41L4B MUTATED         0        0        2        0         4         0
  EPB41L4B WILD-TYPE       2       15       38       30        33        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPB41L4B MUTATED           0          4          0          3        3
  EPB41L4B WILD-TYPE         3         66         53         29       35
D1055V3, multiclass
            clus
vv           EPB41L4B MUTATED EPB41L4B WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  2                 38
  STAGE II                  0                 30
  STAGE IIA                 4                 33
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                4                 66
  STAGE IIIB                0                 53
  STAGE IIIC                3                 29
  STAGE IV                  3                 35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  EPB41L4B MUTATED     1   2   7   7
  EPB41L4B WILD-TYPE  21  90 166  90
D1055V4, multiclass
    clus
vv   EPB41L4B MUTATED EPB41L4B WILD-TYPE
  T1                1                 21
  T2                2                 90
  T3                7                166
  T4                7                 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
  EPB41L4B MUTATED     7   4   3   3
  EPB41L4B WILD-TYPE 111 100  74  74
D1055V5, multiclass
    clus
vv   EPB41L4B MUTATED EPB41L4B WILD-TYPE
  N0                7                111
  N1                4                100
  N2                3                 74
  N3                3                 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"
D1055V6, binary
                    cls
clus                   0   1
  EPB41L4B MUTATED    16   1
  EPB41L4B WILD-TYPE 330  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4B MUTATED     16    1
  EPB41L4B WILD-TYPE  330   28
   clus
vv  EPB41L4B MUTATED EPB41L4B WILD-TYPE
  0               16                330
  1                1                 28
[1] 2 2
[1] FALSE
D1055V7, binary
                    cls
clus                   0   1
  EPB41L4B MUTATED     7  11
  EPB41L4B WILD-TYPE 138 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4B MUTATED      7   11
  EPB41L4B WILD-TYPE  138  237
        clus
vv       EPB41L4B MUTATED EPB41L4B WILD-TYPE
  FEMALE                7                138
  MALE                 11                237
[1] 2 2
[1] FALSE
D1055V8, binary
                    cls
clus                   0   1
  EPB41L4B MUTATED    10   4
  EPB41L4B WILD-TYPE 282  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4B MUTATED     10    4
  EPB41L4B WILD-TYPE  282   55
     clus
vv    EPB41L4B MUTATED EPB41L4B WILD-TYPE
  NO                10                282
  YES                4                 55
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EPB41L4B MUTATED                                          0
  EPB41L4B WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EPB41L4B MUTATED                                       0
  EPB41L4B WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPB41L4B MUTATED                                                       10
  EPB41L4B WILD-TYPE                                                    148
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EPB41L4B MUTATED                                                   2
  EPB41L4B WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPB41L4B MUTATED                                                                   2
  EPB41L4B WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EPB41L4B MUTATED                                                    0
  EPB41L4B WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EPB41L4B MUTATED                                                  4
  EPB41L4B WILD-TYPE                                               57
D1055V9, multiclass
                                                                   clus
vv                                                                  EPB41L4B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 4
                                                                   clus
vv                                                                  EPB41L4B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  EPB41L4B MUTATED    12   2   0   4
  EPB41L4B WILD-TYPE 299  12  15  20
D1055V10, multiclass
    clus
vv   EPB41L4B MUTATED EPB41L4B WILD-TYPE
  R0               12                299
  R1                2                 12
  R2                0                 15
  RX                4                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1055V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  EPB41L4B MUTATED       2                         1
  EPB41L4B WILD-TYPE    85                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPB41L4B MUTATED                                           0    11
  EPB41L4B WILD-TYPE                                         1   232
D1055V12, multiclass
                                           clus
vv                                          EPB41L4B MUTATED EPB41L4B WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   11                232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1055V13, binary
                    cls
clus                   0   1
  EPB41L4B MUTATED     0  13
  EPB41L4B WILD-TYPE   4 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4B MUTATED      0   13
  EPB41L4B WILD-TYPE    4  297
                        clus
vv                       EPB41L4B MUTATED EPB41L4B WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               13                297
[1] 2 2
[1] FALSE

Clustering(1056) Variable = RNMT MUTATION ANALYSIS
D1056V1, survival
                sevent
clus2              0   1
  RNMT MUTATED     6   1
  RNMT WILD-TYPE 224 138
  RNMT MUTATED RNMT WILD-TYPE 
             7            362 
  RNMT MUTATED RNMT WILD-TYPE 
             1            138 
$`RNMT MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5721 
       26.70        34.68        29.59        31.96         6.58         6.02 
TCGA-CG-5723 
      105.07 

$`RNMT WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  RNMT MUTATED RNMT WILD-TYPE 
          6.02           0.00 
  RNMT MUTATED RNMT WILD-TYPE 
        105.07         122.30 
  RNMT MUTATED RNMT WILD-TYPE 
         29.59          14.12 
[1] "6.0 - 105.1 (29.6)" "0.0 - 122.3 (14.1)"
[1] "hr=" "4.1"
D1056V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RNMT MUTATED         0        0        0        1         2         2
  RNMT WILD-TYPE       2       15       40       29        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNMT MUTATED           0          0          0          0        2
  RNMT WILD-TYPE         3         70         53         32       36
D1056V3, multiclass
            clus
vv           RNMT MUTATED RNMT WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              1             29
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RNMT MUTATED     0   1   2   4
  RNMT WILD-TYPE  22  91 171  93
D1056V4, multiclass
    clus
vv   RNMT MUTATED RNMT WILD-TYPE
  T1            0             22
  T2            1             91
  T3            2            171
  T4            4             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
  RNMT MUTATED     4   2   1   0
  RNMT WILD-TYPE 114 102  76  77
D1056V5, multiclass
    clus
vv   RNMT MUTATED RNMT WILD-TYPE
  N0            4            114
  N1            2            102
  N2            1             76
  N3            0             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"
D1056V6, binary
                cls
clus               0   1
  RNMT MUTATED     7   1
  RNMT WILD-TYPE 339  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNMT MUTATED      7    1
  RNMT WILD-TYPE  339   28
   clus
vv  RNMT MUTATED RNMT WILD-TYPE
  0            7            339
  1            1             28
[1] 2 2
[1] FALSE
D1056V7, binary
                cls
clus               0   1
  RNMT MUTATED     4   4
  RNMT WILD-TYPE 141 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNMT MUTATED      4    4
  RNMT WILD-TYPE  141  244
        clus
vv       RNMT MUTATED RNMT WILD-TYPE
  FEMALE            4            141
  MALE              4            244
[1] 2 2
[1] FALSE
D1056V8, binary
                cls
clus               0   1
  RNMT MUTATED     7   0
  RNMT WILD-TYPE 285  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNMT MUTATED      7    0
  RNMT WILD-TYPE  285   59
     clus
vv    RNMT MUTATED RNMT WILD-TYPE
  NO             7            285
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RNMT MUTATED                                          0
  RNMT WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RNMT MUTATED                                       2
  RNMT WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RNMT MUTATED                                                        4
  RNMT WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RNMT MUTATED                                                   0
  RNMT WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RNMT MUTATED                                                                   1
  RNMT WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RNMT MUTATED                                                    0
  RNMT WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RNMT MUTATED                                                  1
  RNMT WILD-TYPE                                               60
D1056V9, multiclass
                                                                   clus
vv                                                                  RNMT MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  RNMT WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RNMT MUTATED     6   0   0   1
  RNMT WILD-TYPE 305  14  15  23
D1056V10, multiclass
    clus
vv   RNMT MUTATED RNMT WILD-TYPE
  R0            6            305
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1056V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RNMT MUTATED       2                         0
  RNMT WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RNMT MUTATED                                           0     4
  RNMT WILD-TYPE                                         1   239
D1056V12, multiclass
                                           clus
vv                                          RNMT MUTATED RNMT WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                4            239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1056V13, binary
                cls
clus               0   1
  RNMT MUTATED     0   6
  RNMT WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNMT MUTATED      0    6
  RNMT WILD-TYPE    4  304
                        clus
vv                       RNMT MUTATED RNMT WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(1057) Variable = SUCNR1 MUTATION ANALYSIS
D1057V1, survival
                  sevent
clus2                0   1
  SUCNR1 MUTATED     2   1
  SUCNR1 WILD-TYPE 228 138
  SUCNR1 MUTATED SUCNR1 WILD-TYPE 
               3              366 
  SUCNR1 MUTATED SUCNR1 WILD-TYPE 
               1              138 
$`SUCNR1 MUTATED`
TCGA-BR-4201 TCGA-BR-8368 TCGA-VQ-A8P2 
       30.90         4.31        38.14 

$`SUCNR1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  SUCNR1 MUTATED SUCNR1 WILD-TYPE 
            4.31             0.00 
  SUCNR1 MUTATED SUCNR1 WILD-TYPE 
           38.14           122.30 
  SUCNR1 MUTATED SUCNR1 WILD-TYPE 
           30.90            14.22 
[1] "4.3 - 38.1 (30.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.5"
D1057V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SUCNR1 MUTATED         0        0        1        0         0         1
  SUCNR1 WILD-TYPE       2       15       39       30        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SUCNR1 MUTATED           0          1          0          0        0
  SUCNR1 WILD-TYPE         3         69         53         32       38
D1057V3, multiclass
            clus
vv           SUCNR1 MUTATED SUCNR1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SUCNR1 MUTATED     0   2   0   2
  SUCNR1 WILD-TYPE  22  90 173  95
D1057V4, multiclass
    clus
vv   SUCNR1 MUTATED SUCNR1 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              0              173
  T4              2               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
  SUCNR1 MUTATED     2   1   0   0
  SUCNR1 WILD-TYPE 116 103  77  77
D1057V5, multiclass
    clus
vv   SUCNR1 MUTATED SUCNR1 WILD-TYPE
  N0              2              116
  N1              1              103
  N2              0               77
  N3              0               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"
D1057V6, binary
                  cls
clus                 0   1
  SUCNR1 MUTATED     4   0
  SUCNR1 WILD-TYPE 342  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCNR1 MUTATED      4    0
  SUCNR1 WILD-TYPE  342   29
   clus
vv  SUCNR1 MUTATED SUCNR1 WILD-TYPE
  0              4              342
  1              0               29
[1] 2 2
[1] FALSE
D1057V7, binary
                  cls
clus                 0   1
  SUCNR1 MUTATED     2   2
  SUCNR1 WILD-TYPE 143 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCNR1 MUTATED      2    2
  SUCNR1 WILD-TYPE  143  246
        clus
vv       SUCNR1 MUTATED SUCNR1 WILD-TYPE
  FEMALE              2              143
  MALE                2              246
[1] 2 2
[1] FALSE
D1057V8, binary
                  cls
clus                 0   1
  SUCNR1 MUTATED     3   1
  SUCNR1 WILD-TYPE 289  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCNR1 MUTATED      3    1
  SUCNR1 WILD-TYPE  289   58
     clus
vv    SUCNR1 MUTATED SUCNR1 WILD-TYPE
  NO               3              289
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SUCNR1 MUTATED                                          0
  SUCNR1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SUCNR1 MUTATED                                       0
  SUCNR1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SUCNR1 MUTATED                                                        2
  SUCNR1 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SUCNR1 MUTATED                                                   1
  SUCNR1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SUCNR1 MUTATED                                                                   1
  SUCNR1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SUCNR1 MUTATED                                                    0
  SUCNR1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SUCNR1 MUTATED                                                  0
  SUCNR1 WILD-TYPE                                               61
D1057V9, multiclass
                                                                   clus
vv                                                                  SUCNR1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  SUCNR1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SUCNR1 MUTATED     3   0   0   1
  SUCNR1 WILD-TYPE 308  14  15  23
D1057V10, multiclass
    clus
vv   SUCNR1 MUTATED SUCNR1 WILD-TYPE
  R0              3              308
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1057V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SUCNR1 MUTATED       0                         0
  SUCNR1 WILD-TYPE    87                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SUCNR1 MUTATED                                           0     4
  SUCNR1 WILD-TYPE                                         1   239
D1057V12, multiclass
                                           clus
vv                                          SUCNR1 MUTATED SUCNR1 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1057V13, binary
                  cls
clus                 0   1
  SUCNR1 MUTATED     0   3
  SUCNR1 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUCNR1 MUTATED      0    3
  SUCNR1 WILD-TYPE    4  307
                        clus
vv                       SUCNR1 MUTATED SUCNR1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(1058) Variable = NYNRIN MUTATION ANALYSIS
D1058V1, survival
                  sevent
clus2                0   1
  NYNRIN MUTATED    10   5
  NYNRIN WILD-TYPE 220 134
  NYNRIN MUTATED NYNRIN WILD-TYPE 
              15              354 
  NYNRIN MUTATED NYNRIN WILD-TYPE 
               5              134 
$`NYNRIN MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-7707 TCGA-BR-8078 
       26.70        19.56         6.97        30.90        35.84        29.59 
TCGA-BR-8361 TCGA-BR-8487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4306 
       31.10         1.12        11.61         6.58        12.62         1.02 
TCGA-HF-A5NB TCGA-HU-A4GH TCGA-VQ-A8P2 
       30.51        11.77        38.14 

$`NYNRIN WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        11.70        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-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-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-A4MH 
       12.43         6.31        12.30        11.31        12.43        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-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-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 

  NYNRIN MUTATED NYNRIN WILD-TYPE 
            1.02             0.00 
  NYNRIN MUTATED NYNRIN WILD-TYPE 
           38.14           122.30 
  NYNRIN MUTATED NYNRIN WILD-TYPE 
           19.56            14.22 
[1] "1.0 - 38.1 (19.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D1058V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NYNRIN MUTATED         0        1        3        0         2         3
  NYNRIN WILD-TYPE       2       14       37       30        35        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NYNRIN MUTATED           0          2          0          3        1
  NYNRIN WILD-TYPE         3         68         53         29       37
D1058V3, multiclass
            clus
vv           NYNRIN MUTATED NYNRIN WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                3               37
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              3               29
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NYNRIN MUTATED     2   4   5   6
  NYNRIN WILD-TYPE  20  88 168  91
D1058V4, multiclass
    clus
vv   NYNRIN MUTATED NYNRIN WILD-TYPE
  T1              2               20
  T2              4               88
  T3              5              168
  T4              6               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
  NYNRIN MUTATED     8   3   2   2
  NYNRIN WILD-TYPE 110 101  75  75
D1058V5, multiclass
    clus
vv   NYNRIN MUTATED NYNRIN WILD-TYPE
  N0              8              110
  N1              3              101
  N2              2               75
  N3              2               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"
D1058V6, binary
                  cls
clus                 0   1
  NYNRIN MUTATED    15   1
  NYNRIN WILD-TYPE 331  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NYNRIN MUTATED     15    1
  NYNRIN WILD-TYPE  331   28
   clus
vv  NYNRIN MUTATED NYNRIN WILD-TYPE
  0             15              331
  1              1               28
[1] 2 2
[1] FALSE
D1058V7, binary
                  cls
clus                 0   1
  NYNRIN MUTATED     9   8
  NYNRIN WILD-TYPE 136 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NYNRIN MUTATED      9    8
  NYNRIN WILD-TYPE  136  240
        clus
vv       NYNRIN MUTATED NYNRIN WILD-TYPE
  FEMALE              9              136
  MALE                8              240
[1] 2 2
[1] FALSE
D1058V8, binary
                  cls
clus                 0   1
  NYNRIN MUTATED    12   2
  NYNRIN WILD-TYPE 280  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NYNRIN MUTATED     12    2
  NYNRIN WILD-TYPE  280   57
     clus
vv    NYNRIN MUTATED NYNRIN WILD-TYPE
  NO              12              280
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NYNRIN MUTATED                                          0
  NYNRIN WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NYNRIN MUTATED                                       3
  NYNRIN WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NYNRIN MUTATED                                                       10
  NYNRIN WILD-TYPE                                                    148
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NYNRIN MUTATED                                                   2
  NYNRIN WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NYNRIN MUTATED                                                                   1
  NYNRIN WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NYNRIN MUTATED                                                    0
  NYNRIN WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NYNRIN MUTATED                                                  1
  NYNRIN WILD-TYPE                                               60
D1058V9, multiclass
                                                                   clus
vv                                                                  NYNRIN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  NYNRIN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NYNRIN MUTATED     8   1   1   3
  NYNRIN WILD-TYPE 303  13  14  21
D1058V10, multiclass
    clus
vv   NYNRIN MUTATED NYNRIN WILD-TYPE
  R0              8              303
  R1              1               13
  R2              1               14
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1058V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NYNRIN MUTATED       4                         0
  NYNRIN WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NYNRIN MUTATED                                           0    10
  NYNRIN WILD-TYPE                                         1   233
D1058V12, multiclass
                                           clus
vv                                          NYNRIN MUTATED NYNRIN WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 10              233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1058V13, binary
                  cls
clus                 0   1
  NYNRIN MUTATED     0  13
  NYNRIN WILD-TYPE   4 297
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NYNRIN MUTATED      0   13
  NYNRIN WILD-TYPE    4  297
                        clus
vv                       NYNRIN MUTATED NYNRIN WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             13              297
[1] 2 2
[1] FALSE

Clustering(1059) Variable = PHTF1 MUTATION ANALYSIS
D1059V1, survival
                 sevent
clus2               0   1
  PHTF1 MUTATED     6   3
  PHTF1 WILD-TYPE 224 136
  PHTF1 MUTATED PHTF1 WILD-TYPE 
              9             360 
  PHTF1 MUTATED PHTF1 WILD-TYPE 
              3             136 
$`PHTF1 MUTATED`
TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8285 TCGA-BR-8680 TCGA-CD-A4MG 
        9.67        34.68        36.16         0.56        31.96         6.58 
TCGA-HU-A4GN TCGA-VQ-A8P2 TCGA-VQ-AA6A 
       29.98        38.14        38.93 

$`PHTF1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8286 
        0.69        29.59         9.60        32.25         8.05        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-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-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-AA6B 
       66.81        11.24        18.41        43.66        28.41        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 

  PHTF1 MUTATED PHTF1 WILD-TYPE 
           0.56            0.00 
  PHTF1 MUTATED PHTF1 WILD-TYPE 
          38.93          122.30 
  PHTF1 MUTATED PHTF1 WILD-TYPE 
          31.96           14.12 
[1] "0.6 - 38.9 (32.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D1059V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PHTF1 MUTATED         1        1        0        0         3         0
  PHTF1 WILD-TYPE       1       14       40       30        34        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHTF1 MUTATED           0          2          0          2        1
  PHTF1 WILD-TYPE         3         68         53         30       37
D1059V3, multiclass
            clus
vv           PHTF1 MUTATED PHTF1 WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PHTF1 MUTATED     2   1   3   4
  PHTF1 WILD-TYPE  20  91 170  93
D1059V4, multiclass
    clus
vv   PHTF1 MUTATED PHTF1 WILD-TYPE
  T1             2              20
  T2             1              91
  T3             3             170
  T4             4              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
  PHTF1 MUTATED     3   4   1   2
  PHTF1 WILD-TYPE 115 100  76  75
D1059V5, multiclass
    clus
vv   PHTF1 MUTATED PHTF1 WILD-TYPE
  N0             3             115
  N1             4             100
  N2             1              76
  N3             2              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"
D1059V6, binary
                 cls
clus                0   1
  PHTF1 MUTATED     9   1
  PHTF1 WILD-TYPE 337  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHTF1 MUTATED      9    1
  PHTF1 WILD-TYPE  337   28
   clus
vv  PHTF1 MUTATED PHTF1 WILD-TYPE
  0             9             337
  1             1              28
[1] 2 2
[1] FALSE
D1059V7, binary
                 cls
clus                0   1
  PHTF1 MUTATED     3   8
  PHTF1 WILD-TYPE 142 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHTF1 MUTATED      3    8
  PHTF1 WILD-TYPE  142  240
        clus
vv       PHTF1 MUTATED PHTF1 WILD-TYPE
  FEMALE             3             142
  MALE               8             240
[1] 2 2
[1] FALSE
D1059V8, binary
                 cls
clus                0   1
  PHTF1 MUTATED     8   3
  PHTF1 WILD-TYPE 284  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHTF1 MUTATED      8    3
  PHTF1 WILD-TYPE  284   56
     clus
vv    PHTF1 MUTATED PHTF1 WILD-TYPE
  NO              8             284
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PHTF1 MUTATED                                          0
  PHTF1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PHTF1 MUTATED                                       1
  PHTF1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PHTF1 MUTATED                                                        4
  PHTF1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PHTF1 MUTATED                                                   1
  PHTF1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PHTF1 MUTATED                                                                   2
  PHTF1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PHTF1 MUTATED                                                    1
  PHTF1 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PHTF1 MUTATED                                                  2
  PHTF1 WILD-TYPE                                               59
D1059V9, multiclass
                                                                   clus
vv                                                                  PHTF1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  PHTF1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PHTF1 MUTATED     8   1   0   1
  PHTF1 WILD-TYPE 303  13  15  23
D1059V10, multiclass
    clus
vv   PHTF1 MUTATED PHTF1 WILD-TYPE
  R0             8             303
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1059V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PHTF1 MUTATED       3                         1
  PHTF1 WILD-TYPE    84                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PHTF1 MUTATED                                           0     6
  PHTF1 WILD-TYPE                                         1   237
D1059V12, multiclass
                                           clus
vv                                          PHTF1 MUTATED PHTF1 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1059V13, binary
                 cls
clus                0   1
  PHTF1 MUTATED     0   8
  PHTF1 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHTF1 MUTATED      0    8
  PHTF1 WILD-TYPE    4  302
                        clus
vv                       PHTF1 MUTATED PHTF1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(1060) Variable = CARD14 MUTATION ANALYSIS
D1060V1, survival
                  sevent
clus2                0   1
  CARD14 MUTATED     7   5
  CARD14 WILD-TYPE 223 134
  CARD14 MUTATED CARD14 WILD-TYPE 
              12              357 
  CARD14 MUTATED CARD14 WILD-TYPE 
               5              134 
$`CARD14 MUTATED`
TCGA-CG-4460 TCGA-BR-4201 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8680 TCGA-CD-8536 
       21.99        30.90         0.26         4.31        31.96        12.43 
TCGA-CD-A4MH TCGA-CG-4465 TCGA-CG-5723 TCGA-D7-A4YV TCGA-FP-A4BE TCGA-HU-A4G9 
       12.20         9.01       105.07         5.92        11.08        24.20 

$`CARD14 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-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 

  CARD14 MUTATED CARD14 WILD-TYPE 
            0.26             0.00 
  CARD14 MUTATED CARD14 WILD-TYPE 
          105.07           122.30 
  CARD14 MUTATED CARD14 WILD-TYPE 
          12.315           14.430 
[1] "0.3 - 105.1 (12.3)" "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D1060V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CARD14 MUTATED         0        1        2        2         2         1
  CARD14 WILD-TYPE       2       14       38       28        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CARD14 MUTATED           0          1          0          0        3
  CARD14 WILD-TYPE         3         69         53         32       35
D1060V3, multiclass
            clus
vv           CARD14 MUTATED CARD14 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                2               28
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CARD14 MUTATED     1   4   4   4
  CARD14 WILD-TYPE  21  88 169  93
D1060V4, multiclass
    clus
vv   CARD14 MUTATED CARD14 WILD-TYPE
  T1              1               21
  T2              4               88
  T3              4              169
  T4              4               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
  CARD14 MUTATED     7   3   1   1
  CARD14 WILD-TYPE 111 101  76  76
D1060V5, multiclass
    clus
vv   CARD14 MUTATED CARD14 WILD-TYPE
  N0              7              111
  N1              3              101
  N2              1               76
  N3              1               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"
D1060V6, binary
                  cls
clus                 0   1
  CARD14 MUTATED    10   3
  CARD14 WILD-TYPE 336  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD14 MUTATED     10    3
  CARD14 WILD-TYPE  336   26
   clus
vv  CARD14 MUTATED CARD14 WILD-TYPE
  0             10              336
  1              3               26
[1] 2 2
[1] FALSE
D1060V7, binary
                  cls
clus                 0   1
  CARD14 MUTATED     9   4
  CARD14 WILD-TYPE 136 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD14 MUTATED      9    4
  CARD14 WILD-TYPE  136  244
        clus
vv       CARD14 MUTATED CARD14 WILD-TYPE
  FEMALE              9              136
  MALE                4              244
[1] 2 2
[1] FALSE
D1060V8, binary
                  cls
clus                 0   1
  CARD14 MUTATED     9   2
  CARD14 WILD-TYPE 283  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD14 MUTATED      9    2
  CARD14 WILD-TYPE  283   57
     clus
vv    CARD14 MUTATED CARD14 WILD-TYPE
  NO               9              283
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CARD14 MUTATED                                          0
  CARD14 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CARD14 MUTATED                                       1
  CARD14 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CARD14 MUTATED                                                        8
  CARD14 WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CARD14 MUTATED                                                   0
  CARD14 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CARD14 MUTATED                                                                   1
  CARD14 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CARD14 MUTATED                                                    0
  CARD14 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CARD14 MUTATED                                                  3
  CARD14 WILD-TYPE                                               58
D1060V9, multiclass
                                                                   clus
vv                                                                  CARD14 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  CARD14 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CARD14 MUTATED     8   0   2   2
  CARD14 WILD-TYPE 303  14  13  22
D1060V10, multiclass
    clus
vv   CARD14 MUTATED CARD14 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              2               13
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1060V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CARD14 MUTATED       4                         1
  CARD14 WILD-TYPE    83                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CARD14 MUTATED                                           0     5
  CARD14 WILD-TYPE                                         1   238
D1060V12, multiclass
                                           clus
vv                                          CARD14 MUTATED CARD14 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1060V13, binary
                  cls
clus                 0   1
  CARD14 MUTATED     0  10
  CARD14 WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD14 MUTATED      0   10
  CARD14 WILD-TYPE    4  300
                        clus
vv                       CARD14 MUTATED CARD14 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(1061) Variable = CASKIN1 MUTATION ANALYSIS
D1061V1, survival
                   sevent
clus2                 0   1
  CASKIN1 MUTATED    13   4
  CASKIN1 WILD-TYPE 217 135
  CASKIN1 MUTATED CASKIN1 WILD-TYPE 
               17               352 
  CASKIN1 MUTATED CASKIN1 WILD-TYPE 
                4               135 
$`CASKIN1 MUTATED`
TCGA-EQ-A4SO TCGA-BR-8059 TCGA-BR-8360 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8680 
       16.24        14.43         6.18        31.27         1.12        31.96 
TCGA-BR-A4QL TCGA-CD-A4MJ TCGA-CG-4437 TCGA-CG-5721 TCGA-D7-A4YV TCGA-HU-A4G9 
       16.14        12.62         8.05         6.02         5.92        24.20 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-IN-A7NT TCGA-MX-A5UJ TCGA-VQ-AA6G 
        6.51        20.25        10.62        19.73        26.04 

$`CASKIN1 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        22.98        79.07         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-A7NU 
       19.53         6.44         6.74        12.59         6.51        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-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       16.14        27.55        12.43        17.26 

  CASKIN1 MUTATED CASKIN1 WILD-TYPE 
             1.12              0.00 
  CASKIN1 MUTATED CASKIN1 WILD-TYPE 
            31.96            122.30 
  CASKIN1 MUTATED CASKIN1 WILD-TYPE 
            14.43             14.22 
[1] "1.1 - 32.0 (14.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D1061V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CASKIN1 MUTATED         0        1        1        1         4         2
  CASKIN1 WILD-TYPE       2       14       39       29        33        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASKIN1 MUTATED           1          1          2          2        2
  CASKIN1 WILD-TYPE         2         69         51         30       36
D1061V3, multiclass
            clus
vv           CASKIN1 MUTATED CASKIN1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                4                33
  STAGE IIB                2                50
  STAGE III                1                 2
  STAGE IIIA               1                69
  STAGE IIIB               2                51
  STAGE IIIC               2                30
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CASKIN1 MUTATED     1   2   8   6
  CASKIN1 WILD-TYPE  21  90 165  91
D1061V4, multiclass
    clus
vv   CASKIN1 MUTATED CASKIN1 WILD-TYPE
  T1               1                21
  T2               2                90
  T3               8               165
  T4               6                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
  CASKIN1 MUTATED     6   6   3   2
  CASKIN1 WILD-TYPE 112  98  74  75
D1061V5, multiclass
    clus
vv   CASKIN1 MUTATED CASKIN1 WILD-TYPE
  N0               6               112
  N1               6                98
  N2               3                74
  N3               2                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"
D1061V6, binary
                   cls
clus                  0   1
  CASKIN1 MUTATED    15   1
  CASKIN1 WILD-TYPE 331  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CASKIN1 MUTATED     15    1
  CASKIN1 WILD-TYPE  331   28
   clus
vv  CASKIN1 MUTATED CASKIN1 WILD-TYPE
  0              15               331
  1               1                28
[1] 2 2
[1] FALSE
D1061V7, binary
                   cls
clus                  0   1
  CASKIN1 MUTATED     8   9
  CASKIN1 WILD-TYPE 137 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CASKIN1 MUTATED      8    9
  CASKIN1 WILD-TYPE  137  239
        clus
vv       CASKIN1 MUTATED CASKIN1 WILD-TYPE
  FEMALE               8               137
  MALE                 9               239
[1] 2 2
[1] FALSE
D1061V8, binary
                   cls
clus                  0   1
  CASKIN1 MUTATED    16   1
  CASKIN1 WILD-TYPE 276  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CASKIN1 MUTATED     16    1
  CASKIN1 WILD-TYPE  276   58
     clus
vv    CASKIN1 MUTATED CASKIN1 WILD-TYPE
  NO               16               276
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CASKIN1 MUTATED                                          0
  CASKIN1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CASKIN1 MUTATED                                       1
  CASKIN1 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CASKIN1 MUTATED                                                        5
  CASKIN1 WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CASKIN1 MUTATED                                                   0
  CASKIN1 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CASKIN1 MUTATED                                                                   5
  CASKIN1 WILD-TYPE                                                                63
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CASKIN1 MUTATED                                                    0
  CASKIN1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CASKIN1 MUTATED                                                  5
  CASKIN1 WILD-TYPE                                               56
D1061V9, multiclass
                                                                   clus
vv                                                                  CASKIN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                5
                                                                   clus
vv                                                                  CASKIN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 56
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CASKIN1 MUTATED    16   0   0   0
  CASKIN1 WILD-TYPE 295  14  15  24
D1061V10, multiclass
    clus
vv   CASKIN1 MUTATED CASKIN1 WILD-TYPE
  R0              16               295
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1061V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CASKIN1 MUTATED       5                         0
  CASKIN1 WILD-TYPE    82                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CASKIN1 MUTATED                                           0    10
  CASKIN1 WILD-TYPE                                         1   233
D1061V12, multiclass
                                           clus
vv                                          CASKIN1 MUTATED CASKIN1 WILD-TYPE
  ASIAN                                                   5                82
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1061V13, binary
                   cls
clus                  0   1
  CASKIN1 MUTATED     0  14
  CASKIN1 WILD-TYPE   4 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CASKIN1 MUTATED      0   14
  CASKIN1 WILD-TYPE    4  296
                        clus
vv                       CASKIN1 MUTATED CASKIN1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              14               296
[1] 2 2
[1] FALSE

Clustering(1062) Variable = C13ORF18 MUTATION ANALYSIS
D1062V1, survival
                    sevent
clus2                  0   1
  C13ORF18 MUTATED     7   3
  C13ORF18 WILD-TYPE 223 136
  C13ORF18 MUTATED C13ORF18 WILD-TYPE 
                10                359 
  C13ORF18 MUTATED C13ORF18 WILD-TYPE 
                 3                136 
$`C13ORF18 MUTATED`
TCGA-BR-4256 TCGA-BR-6453 TCGA-BR-8369 TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-4437 
        9.34        15.95        14.04        16.14        15.95         8.05 
TCGA-D7-6527 TCGA-D7-A4YU TCGA-D7-A4Z0 TCGA-VQ-A91V 
       10.26        16.44        14.76        42.64 

$`C13ORF18 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        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-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-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 

  C13ORF18 MUTATED C13ORF18 WILD-TYPE 
              8.05               0.00 
  C13ORF18 MUTATED C13ORF18 WILD-TYPE 
             42.64             122.30 
  C13ORF18 MUTATED C13ORF18 WILD-TYPE 
            15.355             14.170 
[1] "8.1 - 42.6 (15.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D1062V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C13ORF18 MUTATED         0        0        0        3         1         1
  C13ORF18 WILD-TYPE       2       15       40       27        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C13ORF18 MUTATED           0          1          3          0        0
  C13ORF18 WILD-TYPE         3         69         50         32       38
D1062V3, multiclass
            clus
vv           C13ORF18 MUTATED C13ORF18 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  3                 27
  STAGE IIA                 1                 36
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                3                 50
  STAGE IIIC                0                 32
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C13ORF18 MUTATED     0   5   4   0
  C13ORF18 WILD-TYPE  22  87 169  97
D1062V4, multiclass
    clus
vv   C13ORF18 MUTATED C13ORF18 WILD-TYPE
  T1                0                 22
  T2                5                 87
  T3                4                169
  T4                0                 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
  C13ORF18 MUTATED     0   5   2   3
  C13ORF18 WILD-TYPE 118  99  75  74
D1062V5, multiclass
    clus
vv   C13ORF18 MUTATED C13ORF18 WILD-TYPE
  N0                0                118
  N1                5                 99
  N2                2                 75
  N3                3                 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"
D1062V6, binary
                    cls
clus                   0   1
  C13ORF18 MUTATED    10   0
  C13ORF18 WILD-TYPE 336  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF18 MUTATED     10    0
  C13ORF18 WILD-TYPE  336   29
   clus
vv  C13ORF18 MUTATED C13ORF18 WILD-TYPE
  0               10                336
  1                0                 29
[1] 2 2
[1] FALSE
D1062V7, binary
                    cls
clus                   0   1
  C13ORF18 MUTATED     3   7
  C13ORF18 WILD-TYPE 142 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF18 MUTATED      3    7
  C13ORF18 WILD-TYPE  142  241
        clus
vv       C13ORF18 MUTATED C13ORF18 WILD-TYPE
  FEMALE                3                142
  MALE                  7                241
[1] 2 2
[1] FALSE
D1062V8, binary
                    cls
clus                   0   1
  C13ORF18 MUTATED     7   3
  C13ORF18 WILD-TYPE 285  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF18 MUTATED      7    3
  C13ORF18 WILD-TYPE  285   56
     clus
vv    C13ORF18 MUTATED C13ORF18 WILD-TYPE
  NO                 7                285
  YES                3                 56
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C13ORF18 MUTATED                                          0
  C13ORF18 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C13ORF18 MUTATED                                       0
  C13ORF18 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C13ORF18 MUTATED                                                        5
  C13ORF18 WILD-TYPE                                                    153
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C13ORF18 MUTATED                                                   1
  C13ORF18 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C13ORF18 MUTATED                                                                   1
  C13ORF18 WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C13ORF18 MUTATED                                                    1
  C13ORF18 WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C13ORF18 MUTATED                                                  2
  C13ORF18 WILD-TYPE                                               59
D1062V9, multiclass
                                                                   clus
vv                                                                  C13ORF18 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  C13ORF18 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C13ORF18 MUTATED     9   0   0   1
  C13ORF18 WILD-TYPE 302  14  15  23
D1062V10, multiclass
    clus
vv   C13ORF18 MUTATED C13ORF18 WILD-TYPE
  R0                9                302
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1062V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C13ORF18 MUTATED       0                         0
  C13ORF18 WILD-TYPE    87                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C13ORF18 MUTATED                                           0     7
  C13ORF18 WILD-TYPE                                         1   236
D1062V12, multiclass
                                           clus
vv                                          C13ORF18 MUTATED C13ORF18 WILD-TYPE
  ASIAN                                                    0                 87
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    7                236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1062V13, binary
                    cls
clus                   0   1
  C13ORF18 MUTATED     0   7
  C13ORF18 WILD-TYPE   4 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF18 MUTATED      0    7
  C13ORF18 WILD-TYPE    4  303
                        clus
vv                       C13ORF18 MUTATED C13ORF18 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                7                303
[1] 2 2
[1] FALSE

Clustering(1063) Variable = CCDC37 MUTATION ANALYSIS
D1063V1, survival
                  sevent
clus2                0   1
  CCDC37 MUTATED     8   3
  CCDC37 WILD-TYPE 222 136
  CCDC37 MUTATED CCDC37 WILD-TYPE 
              11              358 
  CCDC37 MUTATED CCDC37 WILD-TYPE 
               3              136 
$`CCDC37 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8081 TCGA-BR-8372 TCGA-CG-5721 
        6.97        30.90        34.68        32.25        31.27         6.02 
TCGA-CG-5733 TCGA-FP-A4BE TCGA-HU-A4GT TCGA-HU-A4GU TCGA-VQ-A8P2 
       21.07        11.08         6.51         6.58        38.14 

$`CCDC37 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  CCDC37 MUTATED CCDC37 WILD-TYPE 
            6.02             0.00 
  CCDC37 MUTATED CCDC37 WILD-TYPE 
           38.14           122.30 
  CCDC37 MUTATED CCDC37 WILD-TYPE 
           21.07            14.22 
[1] "6.0 - 38.1 (21.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D1063V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CCDC37 MUTATED         0        0        1        0         3         3
  CCDC37 WILD-TYPE       2       15       39       30        34        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC37 MUTATED           0          3          0          1        1
  CCDC37 WILD-TYPE         3         67         53         31       37
D1063V3, multiclass
            clus
vv           CCDC37 MUTATED CCDC37 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC37 MUTATED     0   3   5   5
  CCDC37 WILD-TYPE  22  89 168  92
D1063V4, multiclass
    clus
vv   CCDC37 MUTATED CCDC37 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              5              168
  T4              5               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
  CCDC37 MUTATED     6   4   1   1
  CCDC37 WILD-TYPE 112 100  76  76
D1063V5, multiclass
    clus
vv   CCDC37 MUTATED CCDC37 WILD-TYPE
  N0              6              112
  N1              4              100
  N2              1               76
  N3              1               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"
D1063V6, binary
                  cls
clus                 0   1
  CCDC37 MUTATED    13   0
  CCDC37 WILD-TYPE 333  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC37 MUTATED     13    0
  CCDC37 WILD-TYPE  333   29
   clus
vv  CCDC37 MUTATED CCDC37 WILD-TYPE
  0             13              333
  1              0               29
[1] 2 2
[1] FALSE
D1063V7, binary
                  cls
clus                 0   1
  CCDC37 MUTATED     6   8
  CCDC37 WILD-TYPE 139 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC37 MUTATED      6    8
  CCDC37 WILD-TYPE  139  240
        clus
vv       CCDC37 MUTATED CCDC37 WILD-TYPE
  FEMALE              6              139
  MALE                8              240
[1] 2 2
[1] FALSE
D1063V8, binary
                  cls
clus                 0   1
  CCDC37 MUTATED    10   2
  CCDC37 WILD-TYPE 282  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC37 MUTATED     10    2
  CCDC37 WILD-TYPE  282   57
     clus
vv    CCDC37 MUTATED CCDC37 WILD-TYPE
  NO              10              282
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CCDC37 MUTATED                                          0
  CCDC37 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CCDC37 MUTATED                                       1
  CCDC37 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC37 MUTATED                                                        7
  CCDC37 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CCDC37 MUTATED                                                   1
  CCDC37 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CCDC37 MUTATED                                                                   4
  CCDC37 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CCDC37 MUTATED                                                    0
  CCDC37 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CCDC37 MUTATED                                                  1
  CCDC37 WILD-TYPE                                               60
D1063V9, multiclass
                                                                   clus
vv                                                                  CCDC37 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  CCDC37 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CCDC37 MUTATED    11   0   0   3
  CCDC37 WILD-TYPE 300  14  15  21
D1063V10, multiclass
    clus
vv   CCDC37 MUTATED CCDC37 WILD-TYPE
  R0             11              300
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1063V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CCDC37 MUTATED       2                         1
  CCDC37 WILD-TYPE    85                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CCDC37 MUTATED                                           0     8
  CCDC37 WILD-TYPE                                         1   235
D1063V12, multiclass
                                           clus
vv                                          CCDC37 MUTATED CCDC37 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1063V13, binary
                  cls
clus                 0   1
  CCDC37 MUTATED     0  10
  CCDC37 WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC37 MUTATED      0   10
  CCDC37 WILD-TYPE    4  300
                        clus
vv                       CCDC37 MUTATED CCDC37 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(1064) Variable = ETV1 MUTATION ANALYSIS
D1064V1, survival
                sevent
clus2              0   1
  ETV1 MUTATED     6   1
  ETV1 WILD-TYPE 224 138
  ETV1 MUTATED ETV1 WILD-TYPE 
             7            362 
  ETV1 MUTATED ETV1 WILD-TYPE 
             1            138 
$`ETV1 MUTATED`
TCGA-BR-4201 TCGA-BR-8360 TCGA-BR-8372 TCGA-BR-8680 TCGA-D7-6815 TCGA-D7-6822 
       30.90         6.18        31.27        31.96        15.98        12.33 
TCGA-VQ-A8P2 
       38.14 

$`ETV1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-D7-8570 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-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 

  ETV1 MUTATED ETV1 WILD-TYPE 
          6.18           0.00 
  ETV1 MUTATED ETV1 WILD-TYPE 
         38.14         122.30 
  ETV1 MUTATED ETV1 WILD-TYPE 
         30.90          14.12 
[1] "6.2 - 38.1 (30.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.6"
D1064V2, 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       2       15       39       30        36        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ETV1 MUTATED           0          1          0          1        1
  ETV1 WILD-TYPE         3         69         53         31       37
D1064V3, multiclass
            clus
vv           ETV1 MUTATED ETV1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ETV1 MUTATED     0   3   1   3
  ETV1 WILD-TYPE  22  89 172  94
D1064V4, multiclass
    clus
vv   ETV1 MUTATED ETV1 WILD-TYPE
  T1            0             22
  T2            3             89
  T3            1            172
  T4            3             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
  ETV1 MUTATED     2   2   2   1
  ETV1 WILD-TYPE 116 102  75  76
D1064V5, multiclass
    clus
vv   ETV1 MUTATED ETV1 WILD-TYPE
  N0            2            116
  N1            2            102
  N2            2             75
  N3            1             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"
D1064V6, binary
                cls
clus               0   1
  ETV1 MUTATED     7   1
  ETV1 WILD-TYPE 339  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED      7    1
  ETV1 WILD-TYPE  339   28
   clus
vv  ETV1 MUTATED ETV1 WILD-TYPE
  0            7            339
  1            1             28
[1] 2 2
[1] FALSE
D1064V7, binary
                cls
clus               0   1
  ETV1 MUTATED     3   5
  ETV1 WILD-TYPE 142 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED      3    5
  ETV1 WILD-TYPE  142  243
        clus
vv       ETV1 MUTATED ETV1 WILD-TYPE
  FEMALE            3            142
  MALE              5            243
[1] 2 2
[1] FALSE
D1064V8, binary
                cls
clus               0   1
  ETV1 MUTATED     6   1
  ETV1 WILD-TYPE 286  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED      6    1
  ETV1 WILD-TYPE  286   58
     clus
vv    ETV1 MUTATED ETV1 WILD-TYPE
  NO             6            286
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ETV1 MUTATED                                          0
  ETV1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ETV1 MUTATED                                       0
  ETV1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ETV1 MUTATED                                                        3
  ETV1 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ETV1 MUTATED                                                   1
  ETV1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ETV1 MUTATED                                                                   1
  ETV1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ETV1 MUTATED                                                    0
  ETV1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ETV1 MUTATED                                                  3
  ETV1 WILD-TYPE                                               58
D1064V9, multiclass
                                                                   clus
vv                                                                  ETV1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  ETV1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ETV1 MUTATED     6   0   0   2
  ETV1 WILD-TYPE 305  14  15  22
D1064V10, multiclass
    clus
vv   ETV1 MUTATED ETV1 WILD-TYPE
  R0            6            305
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1064V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ETV1 MUTATED       1                         0
  ETV1 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ETV1 MUTATED                                           0     7
  ETV1 WILD-TYPE                                         1   236
D1064V12, multiclass
                                           clus
vv                                          ETV1 MUTATED ETV1 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1064V13, binary
                cls
clus               0   1
  ETV1 MUTATED     0   7
  ETV1 WILD-TYPE   4 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED      0    7
  ETV1 WILD-TYPE    4  303
                        clus
vv                       ETV1 MUTATED ETV1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            303
[1] 2 2
[1] FALSE

Clustering(1065) Variable = TSPAN13 MUTATION ANALYSIS
D1065V1, survival
                   sevent
clus2                 0   1
  TSPAN13 MUTATED     3   1
  TSPAN13 WILD-TYPE 227 138
  TSPAN13 MUTATED TSPAN13 WILD-TYPE 
                4               365 
  TSPAN13 MUTATED TSPAN13 WILD-TYPE 
                1               138 
$`TSPAN13 MUTATED`
TCGA-BR-6452 TCGA-BR-8363 TCGA-CG-5721 TCGA-MX-A5UJ 
       34.68         0.26         6.02        19.73 

$`TSPAN13 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  TSPAN13 MUTATED TSPAN13 WILD-TYPE 
             0.26              0.00 
  TSPAN13 MUTATED TSPAN13 WILD-TYPE 
            34.68            122.30 
  TSPAN13 MUTATED TSPAN13 WILD-TYPE 
           12.875            14.270 
[1] "0.3 - 34.7 (12.9)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D1065V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TSPAN13 MUTATED         0        0        1        0         1         0
  TSPAN13 WILD-TYPE       2       15       39       30        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TSPAN13 MUTATED           0          1          0          0        1
  TSPAN13 WILD-TYPE         3         69         53         32       37
D1065V3, multiclass
            clus
vv           TSPAN13 MUTATED TSPAN13 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TSPAN13 MUTATED     0   1   2   1
  TSPAN13 WILD-TYPE  22  91 171  96
D1065V4, multiclass
    clus
vv   TSPAN13 MUTATED TSPAN13 WILD-TYPE
  T1               0                22
  T2               1                91
  T3               2               171
  T4               1                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
  TSPAN13 MUTATED     2   1   1   0
  TSPAN13 WILD-TYPE 116 103  76  77
D1065V5, multiclass
    clus
vv   TSPAN13 MUTATED TSPAN13 WILD-TYPE
  N0               2               116
  N1               1               103
  N2               1                76
  N3               0                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"
D1065V6, binary
                   cls
clus                  0   1
  TSPAN13 MUTATED     4   0
  TSPAN13 WILD-TYPE 342  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSPAN13 MUTATED      4    0
  TSPAN13 WILD-TYPE  342   29
   clus
vv  TSPAN13 MUTATED TSPAN13 WILD-TYPE
  0               4               342
  1               0                29
[1] 2 2
[1] FALSE
D1065V7, binary
                   cls
clus                  0   1
  TSPAN13 MUTATED     3   1
  TSPAN13 WILD-TYPE 142 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSPAN13 MUTATED      3    1
  TSPAN13 WILD-TYPE  142  247
        clus
vv       TSPAN13 MUTATED TSPAN13 WILD-TYPE
  FEMALE               3               142
  MALE                 1               247
[1] 2 2
[1] FALSE
D1065V8, binary
                   cls
clus                  0   1
  TSPAN13 MUTATED     4   0
  TSPAN13 WILD-TYPE 288  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSPAN13 MUTATED      4    0
  TSPAN13 WILD-TYPE  288   59
     clus
vv    TSPAN13 MUTATED TSPAN13 WILD-TYPE
  NO                4               288
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TSPAN13 MUTATED                                          0
  TSPAN13 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TSPAN13 MUTATED                                       0
  TSPAN13 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TSPAN13 MUTATED                                                        2
  TSPAN13 WILD-TYPE                                                    156
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TSPAN13 MUTATED                                                   0
  TSPAN13 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TSPAN13 MUTATED                                                                   1
  TSPAN13 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TSPAN13 MUTATED                                                    0
  TSPAN13 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TSPAN13 MUTATED                                                  1
  TSPAN13 WILD-TYPE                                               60
D1065V9, multiclass
                                                                   clus
vv                                                                  TSPAN13 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  TSPAN13 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TSPAN13 MUTATED     4   0   0   0
  TSPAN13 WILD-TYPE 307  14  15  24
D1065V10, multiclass
    clus
vv   TSPAN13 MUTATED TSPAN13 WILD-TYPE
  R0               4               307
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1065V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TSPAN13 MUTATED       0                         0
  TSPAN13 WILD-TYPE    87                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TSPAN13 MUTATED                                           0     3
  TSPAN13 WILD-TYPE                                         1   240
D1065V12, multiclass
                                           clus
vv                                          TSPAN13 MUTATED TSPAN13 WILD-TYPE
  ASIAN                                                   0                87
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1065V13, binary
                   cls
clus                  0   1
  TSPAN13 MUTATED     0   3
  TSPAN13 WILD-TYPE   4 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSPAN13 MUTATED      0    3
  TSPAN13 WILD-TYPE    4  307
                        clus
vv                       TSPAN13 MUTATED TSPAN13 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               3               307
[1] 2 2
[1] FALSE

Clustering(1066) Variable = MAP1A MUTATION ANALYSIS
D1066V1, survival
                 sevent
clus2               0   1
  MAP1A MUTATED    12   6
  MAP1A WILD-TYPE 218 133
  MAP1A MUTATED MAP1A WILD-TYPE 
             18             351 
  MAP1A MUTATED MAP1A WILD-TYPE 
              6             133 
$`MAP1A MUTATED`
TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7901 TCGA-BR-8361 
       11.01         6.97        34.68        44.94         3.45        31.10 
TCGA-BR-8372 TCGA-BR-8487 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4466 
       31.27         1.12        12.43         6.58         1.02        18.97 
TCGA-CG-5721 TCGA-CG-5726 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-VQ-A8P2 TCGA-VQ-AA6I 
        6.02        28.96        30.51        22.68        38.14        16.14 

$`MAP1A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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-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 

  MAP1A MUTATED MAP1A WILD-TYPE 
           1.02            0.00 
  MAP1A MUTATED MAP1A WILD-TYPE 
          44.94          122.30 
  MAP1A MUTATED MAP1A WILD-TYPE 
         17.555          14.170 
[1] "1.0 - 44.9 (17.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D1066V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MAP1A MUTATED         0        1        1        1         4         3
  MAP1A WILD-TYPE       2       14       39       29        33        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP1A MUTATED           0          2          1          3        2
  MAP1A WILD-TYPE         3         68         52         29       36
D1066V3, multiclass
            clus
vv           MAP1A MUTATED MAP1A WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              4              33
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MAP1A MUTATED     1   1  11   6
  MAP1A WILD-TYPE  21  91 162  91
D1066V4, multiclass
    clus
vv   MAP1A MUTATED MAP1A WILD-TYPE
  T1             1              21
  T2             1              91
  T3            11             162
  T4             6              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
  MAP1A MUTATED     7   5   2   3
  MAP1A WILD-TYPE 111  99  75  74
D1066V5, multiclass
    clus
vv   MAP1A MUTATED MAP1A WILD-TYPE
  N0             7             111
  N1             5              99
  N2             2              75
  N3             3              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"
D1066V6, binary
                 cls
clus                0   1
  MAP1A MUTATED    16   1
  MAP1A WILD-TYPE 330  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1A MUTATED     16    1
  MAP1A WILD-TYPE  330   28
   clus
vv  MAP1A MUTATED MAP1A WILD-TYPE
  0            16             330
  1             1              28
[1] 2 2
[1] FALSE
D1066V7, binary
                 cls
clus                0   1
  MAP1A MUTATED     8  11
  MAP1A WILD-TYPE 137 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1A MUTATED      8   11
  MAP1A WILD-TYPE  137  237
        clus
vv       MAP1A MUTATED MAP1A WILD-TYPE
  FEMALE             8             137
  MALE              11             237
[1] 2 2
[1] FALSE
D1066V8, binary
                 cls
clus                0   1
  MAP1A MUTATED    14   2
  MAP1A WILD-TYPE 278  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1A MUTATED     14    2
  MAP1A WILD-TYPE  278   57
     clus
vv    MAP1A MUTATED MAP1A WILD-TYPE
  NO             14             278
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MAP1A MUTATED                                          0
  MAP1A WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MAP1A MUTATED                                       2
  MAP1A WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP1A MUTATED                                                       10
  MAP1A WILD-TYPE                                                    148
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MAP1A MUTATED                                                   2
  MAP1A WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MAP1A MUTATED                                                                   5
  MAP1A WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MAP1A MUTATED                                                    0
  MAP1A WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MAP1A MUTATED                                                  0
  MAP1A WILD-TYPE                                               61
D1066V9, multiclass
                                                                   clus
vv                                                                  MAP1A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  MAP1A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MAP1A MUTATED    12   1   1   2
  MAP1A WILD-TYPE 299  13  14  22
D1066V10, multiclass
    clus
vv   MAP1A MUTATED MAP1A WILD-TYPE
  R0            12             299
  R1             1              13
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1066V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MAP1A MUTATED       3                         0
  MAP1A WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MAP1A MUTATED                                           0    11
  MAP1A WILD-TYPE                                         1   232
D1066V12, multiclass
                                           clus
vv                                          MAP1A MUTATED MAP1A WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1066V13, binary
                 cls
clus                0   1
  MAP1A MUTATED     0  12
  MAP1A WILD-TYPE   4 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAP1A MUTATED      0   12
  MAP1A WILD-TYPE    4  298
                        clus
vv                       MAP1A MUTATED MAP1A WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(1067) Variable = FBXO32 MUTATION ANALYSIS
D1067V1, survival
                  sevent
clus2                0   1
  FBXO32 MUTATED     6   0
  FBXO32 WILD-TYPE 224 139
  FBXO32 MUTATED FBXO32 WILD-TYPE 
               6              363 
  FBXO32 MUTATED FBXO32 WILD-TYPE 
               0              139 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  FBXO32 MUTATED FBXO32 WILD-TYPE 
            1.12             0.00 
  FBXO32 MUTATED FBXO32 WILD-TYPE 
           44.94           122.30 
  FBXO32 MUTATED FBXO32 WILD-TYPE 
           19.27            14.27 
[1] "1.1 - 44.9 (19.3)"  "0.0 - 122.3 (14.3)"
[1] "hr="     "9200000"
D1067V2, 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       2       15       40       30        34        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO32 MUTATED           0          2          0          0        1
  FBXO32 WILD-TYPE         3         68         53         32       37
D1067V3, multiclass
            clus
vv           FBXO32 MUTATED FBXO32 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO32 MUTATED     0   0   4   3
  FBXO32 WILD-TYPE  22  92 169  94
D1067V4, multiclass
    clus
vv   FBXO32 MUTATED FBXO32 WILD-TYPE
  T1              0               22
  T2              0               92
  T3              4              169
  T4              3               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
  FBXO32 MUTATED     4   2   1   0
  FBXO32 WILD-TYPE 114 102  76  77
D1067V5, multiclass
    clus
vv   FBXO32 MUTATED FBXO32 WILD-TYPE
  N0              4              114
  N1              2              102
  N2              1               76
  N3              0               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"
D1067V6, binary
                  cls
clus                 0   1
  FBXO32 MUTATED     6   1
  FBXO32 WILD-TYPE 340  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO32 MUTATED      6    1
  FBXO32 WILD-TYPE  340   28
   clus
vv  FBXO32 MUTATED FBXO32 WILD-TYPE
  0              6              340
  1              1               28
[1] 2 2
[1] FALSE
D1067V7, binary
                  cls
clus                 0   1
  FBXO32 MUTATED     4   3
  FBXO32 WILD-TYPE 141 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO32 MUTATED      4    3
  FBXO32 WILD-TYPE  141  245
        clus
vv       FBXO32 MUTATED FBXO32 WILD-TYPE
  FEMALE              4              141
  MALE                3              245
[1] 2 2
[1] FALSE
D1067V8, binary
                  cls
clus                 0   1
  FBXO32 MUTATED     5   1
  FBXO32 WILD-TYPE 287  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO32 MUTATED      5    1
  FBXO32 WILD-TYPE  287   58
     clus
vv    FBXO32 MUTATED FBXO32 WILD-TYPE
  NO               5              287
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FBXO32 MUTATED                                          0
  FBXO32 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FBXO32 MUTATED                                       1
  FBXO32 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBXO32 MUTATED                                                        3
  FBXO32 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FBXO32 MUTATED                                                   1
  FBXO32 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBXO32 MUTATED                                                                   0
  FBXO32 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FBXO32 MUTATED                                                    0
  FBXO32 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FBXO32 MUTATED                                                  2
  FBXO32 WILD-TYPE                                               59
D1067V9, multiclass
                                                                   clus
vv                                                                  FBXO32 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  FBXO32 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FBXO32 MUTATED     6   0   0   1
  FBXO32 WILD-TYPE 305  14  15  23
D1067V10, multiclass
    clus
vv   FBXO32 MUTATED FBXO32 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1067V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FBXO32 MUTATED       3                         0
  FBXO32 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXO32 MUTATED                                           0     4
  FBXO32 WILD-TYPE                                         1   239
D1067V12, multiclass
                                           clus
vv                                          FBXO32 MUTATED FBXO32 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1067V13, binary
                  cls
clus                 0   1
  FBXO32 MUTATED     0   6
  FBXO32 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO32 MUTATED      0    6
  FBXO32 WILD-TYPE    4  304
                        clus
vv                       FBXO32 MUTATED FBXO32 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(1068) Variable = PRAMEF2 MUTATION ANALYSIS
D1068V1, survival
                   sevent
clus2                 0   1
  PRAMEF2 MUTATED     8   2
  PRAMEF2 WILD-TYPE 222 137
  PRAMEF2 MUTATED PRAMEF2 WILD-TYPE 
               10               359 
  PRAMEF2 MUTATED PRAMEF2 WILD-TYPE 
                2               137 
$`PRAMEF2 MUTATED`
TCGA-BR-4280 TCGA-BR-7707 TCGA-BR-8361 TCGA-BR-8680 TCGA-CG-4436 TCGA-HU-A4GC 
        6.61        35.84        31.10        31.96         7.99         3.25 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4H5 TCGA-VQ-A91V 
        8.98         0.10        23.80        42.64 

$`PRAMEF2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-A4GT TCGA-HU-A4GU 
       25.81        11.77        21.37        29.98         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-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-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 

  PRAMEF2 MUTATED PRAMEF2 WILD-TYPE 
              0.1               0.0 
  PRAMEF2 MUTATED PRAMEF2 WILD-TYPE 
            42.64            122.30 
  PRAMEF2 MUTATED PRAMEF2 WILD-TYPE 
            16.39             14.27 
[1] "0.1 - 42.6 (16.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.9"
D1068V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PRAMEF2 MUTATED         0        0        3        0         1         0
  PRAMEF2 WILD-TYPE       2       15       37       30        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRAMEF2 MUTATED           1          1          1          2        1
  PRAMEF2 WILD-TYPE         2         69         52         30       37
D1068V3, multiclass
            clus
vv           PRAMEF2 MUTATED PRAMEF2 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 3                37
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                1                 2
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               2                30
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PRAMEF2 MUTATED     0   5   1   4
  PRAMEF2 WILD-TYPE  22  87 172  93
D1068V4, multiclass
    clus
vv   PRAMEF2 MUTATED PRAMEF2 WILD-TYPE
  T1               0                22
  T2               5                87
  T3               1               172
  T4               4                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
  PRAMEF2 MUTATED     3   2   5   0
  PRAMEF2 WILD-TYPE 115 102  72  77
D1068V5, multiclass
    clus
vv   PRAMEF2 MUTATED PRAMEF2 WILD-TYPE
  N0               3               115
  N1               2               102
  N2               5                72
  N3               0                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"
D1068V6, binary
                   cls
clus                  0   1
  PRAMEF2 MUTATED     9   1
  PRAMEF2 WILD-TYPE 337  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRAMEF2 MUTATED      9    1
  PRAMEF2 WILD-TYPE  337   28
   clus
vv  PRAMEF2 MUTATED PRAMEF2 WILD-TYPE
  0               9               337
  1               1                28
[1] 2 2
[1] FALSE
D1068V7, binary
                   cls
clus                  0   1
  PRAMEF2 MUTATED     4   6
  PRAMEF2 WILD-TYPE 141 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRAMEF2 MUTATED      4    6
  PRAMEF2 WILD-TYPE  141  242
        clus
vv       PRAMEF2 MUTATED PRAMEF2 WILD-TYPE
  FEMALE               4               141
  MALE                 6               242
[1] 2 2
[1] FALSE
D1068V8, binary
                   cls
clus                  0   1
  PRAMEF2 MUTATED     9   1
  PRAMEF2 WILD-TYPE 283  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRAMEF2 MUTATED      9    1
  PRAMEF2 WILD-TYPE  283   58
     clus
vv    PRAMEF2 MUTATED PRAMEF2 WILD-TYPE
  NO                9               283
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PRAMEF2 MUTATED                                          0
  PRAMEF2 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PRAMEF2 MUTATED                                       2
  PRAMEF2 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRAMEF2 MUTATED                                                        3
  PRAMEF2 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PRAMEF2 MUTATED                                                   0
  PRAMEF2 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PRAMEF2 MUTATED                                                                   1
  PRAMEF2 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PRAMEF2 MUTATED                                                    1
  PRAMEF2 WILD-TYPE                                                  4
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PRAMEF2 MUTATED                                                  3
  PRAMEF2 WILD-TYPE                                               58
D1068V9, multiclass
                                                                   clus
vv                                                                  PRAMEF2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  PRAMEF2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PRAMEF2 MUTATED     9   0   0   1
  PRAMEF2 WILD-TYPE 302  14  15  23
D1068V10, multiclass
    clus
vv   PRAMEF2 MUTATED PRAMEF2 WILD-TYPE
  R0               9               302
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1068V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  PRAMEF2 MUTATED       5                         0
  PRAMEF2 WILD-TYPE    82                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PRAMEF2 MUTATED                                           0     3
  PRAMEF2 WILD-TYPE                                         1   240
D1068V12, multiclass
                                           clus
vv                                          PRAMEF2 MUTATED PRAMEF2 WILD-TYPE
  ASIAN                                                   5                82
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   3               240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1068V13, binary
                   cls
clus                  0   1
  PRAMEF2 MUTATED     0   8
  PRAMEF2 WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRAMEF2 MUTATED      0    8
  PRAMEF2 WILD-TYPE    4  302
                        clus
vv                       PRAMEF2 MUTATED PRAMEF2 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(1069) Variable = C20ORF195 MUTATION ANALYSIS
D1069V1, survival
                     sevent
clus2                   0   1
  C20ORF195 MUTATED     4   2
  C20ORF195 WILD-TYPE 226 137
  C20ORF195 MUTATED C20ORF195 WILD-TYPE 
                  6                 363 
  C20ORF195 MUTATED C20ORF195 WILD-TYPE 
                  2                 137 
$`C20ORF195 MUTATED`
TCGA-BR-8285 TCGA-CG-4455 TCGA-F1-A448 TCGA-HU-A4H3 TCGA-IN-7806 TCGA-VQ-A91U 
        0.56        12.03        21.27        29.00        36.36         1.71 

$`C20ORF195 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-4462 
       54.08         4.01        14.01        29.98        19.07         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-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-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        33.40         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-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 

  C20ORF195 MUTATED C20ORF195 WILD-TYPE 
               0.56                0.00 
  C20ORF195 MUTATED C20ORF195 WILD-TYPE 
              36.36              122.30 
  C20ORF195 MUTATED C20ORF195 WILD-TYPE 
              16.65               14.27 
[1] "0.6 - 36.4 (16.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D1069V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C20ORF195 MUTATED         0        0        1        1         0         2
  C20ORF195 WILD-TYPE       2       15       39       29        37        50
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF195 MUTATED           0          1          1          3        0
  C20ORF195 WILD-TYPE         3         69         52         29       38
D1069V3, multiclass
            clus
vv           C20ORF195 MUTATED C20ORF195 WILD-TYPE
  STAGE I                    0                   2
  STAGE IA                   0                  15
  STAGE IB                   1                  39
  STAGE II                   1                  29
  STAGE IIA                  0                  37
  STAGE IIB                  2                  50
  STAGE III                  0                   3
  STAGE IIIA                 1                  69
  STAGE IIIB                 1                  52
  STAGE IIIC                 3                  29
  STAGE IV                   0                  38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C20ORF195 MUTATED     0   2   3   4
  C20ORF195 WILD-TYPE  22  90 170  93
D1069V4, multiclass
    clus
vv   C20ORF195 MUTATED C20ORF195 WILD-TYPE
  T1                 0                  22
  T2                 2                  90
  T3                 3                 170
  T4                 4                  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
  C20ORF195 MUTATED     2   3   0   4
  C20ORF195 WILD-TYPE 116 101  77  73
D1069V5, multiclass
    clus
vv   C20ORF195 MUTATED C20ORF195 WILD-TYPE
  N0                 2                 116
  N1                 3                 101
  N2                 0                  77
  N3                 4                  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"
D1069V6, binary
                     cls
clus                    0   1
  C20ORF195 MUTATED     8   0
  C20ORF195 WILD-TYPE 338  29
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF195 MUTATED      8    0
  C20ORF195 WILD-TYPE  338   29
   clus
vv  C20ORF195 MUTATED C20ORF195 WILD-TYPE
  0                 8                 338
  1                 0                  29
[1] 2 2
[1] FALSE
D1069V7, binary
                     cls
clus                    0   1
  C20ORF195 MUTATED     3   6
  C20ORF195 WILD-TYPE 142 242
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF195 MUTATED      3    6
  C20ORF195 WILD-TYPE  142  242
        clus
vv       C20ORF195 MUTATED C20ORF195 WILD-TYPE
  FEMALE                 3                 142
  MALE                   6                 242
[1] 2 2
[1] FALSE
D1069V8, binary
                     cls
clus                    0   1
  C20ORF195 MUTATED     6   2
  C20ORF195 WILD-TYPE 286  57
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF195 MUTATED      6    2
  C20ORF195 WILD-TYPE  286   57
     clus
vv    C20ORF195 MUTATED C20ORF195 WILD-TYPE
  NO                  6                 286
  YES                 2                  57
[1] 2 2
[1] FALSE
                     vv
clus                  STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C20ORF195 MUTATED                                          0
  C20ORF195 WILD-TYPE                                        8
                     vv
clus                  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C20ORF195 MUTATED                                       2
  C20ORF195 WILD-TYPE                                    68
                     vv
clus                  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C20ORF195 MUTATED                                                        2
  C20ORF195 WILD-TYPE                                                    156
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C20ORF195 MUTATED                                                   2
  C20ORF195 WILD-TYPE                                                19
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C20ORF195 MUTATED                                                                   3
  C20ORF195 WILD-TYPE                                                                65
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C20ORF195 MUTATED                                                    0
  C20ORF195 WILD-TYPE                                                  5
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C20ORF195 MUTATED                                                  0
  C20ORF195 WILD-TYPE                                               61
D1069V9, multiclass
                                                                   clus
vv                                                                  C20ORF195 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  0
                                                                   clus
vv                                                                  C20ORF195 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                            8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                              68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                  19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                  5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                   61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  C20ORF195 MUTATED     8   1   0   0
  C20ORF195 WILD-TYPE 303  13  15  24
D1069V10, multiclass
    clus
vv   C20ORF195 MUTATED C20ORF195 WILD-TYPE
  R0                 8                 303
  R1                 1                  13
  R2                 0                  15
  RX                 0                  24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1069V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN
  C20ORF195 MUTATED       2                         0
  C20ORF195 WILD-TYPE    85                         9
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C20ORF195 MUTATED                                           0     5
  C20ORF195 WILD-TYPE                                         1   238
D1069V12, multiclass
                                           clus
vv                                          C20ORF195 MUTATED
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                     5
                                           clus
vv                                          C20ORF195 WILD-TYPE
  ASIAN                                                      85
  BLACK OR AFRICAN AMERICAN                                   9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   1
  WHITE                                                     238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1069V13, binary
                     cls
clus                    0   1
  C20ORF195 MUTATED     1   5
  C20ORF195 WILD-TYPE   3 305
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF195 MUTATED      1    5
  C20ORF195 WILD-TYPE    3  305
                        clus
vv                       C20ORF195 MUTATED C20ORF195 WILD-TYPE
  HISPANIC OR LATINO                     1                   3
  NOT HISPANIC OR LATINO                 5                 305
[1] 2 2
[1] FALSE

Clustering(1070) Variable = RERE MUTATION ANALYSIS
D1070V1, survival
                sevent
clus2              0   1
  RERE MUTATED    11   8
  RERE WILD-TYPE 219 131
  RERE MUTATED RERE WILD-TYPE 
            19            350 
  RERE MUTATED RERE WILD-TYPE 
             8            131 
$`RERE MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8368 
       21.99        26.70         9.67        34.68        35.84         4.31 
TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-A4MG TCGA-CG-4306 TCGA-CG-4465 TCGA-CG-5723 
        1.12        28.14         6.58         1.02         9.01       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-D7-A6EY TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4H3 
       15.02        28.96        11.44        22.32        22.68        29.00 
TCGA-HU-A4H4 
       23.84 

$`RERE WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
        0.99        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-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-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-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        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 

  RERE MUTATED RERE WILD-TYPE 
          1.02           0.00 
  RERE MUTATED RERE WILD-TYPE 
        105.07         122.30 
  RERE MUTATED RERE WILD-TYPE 
         22.32          14.07 
[1] "1.0 - 105.1 (22.3)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D1070V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RERE MUTATED         1        1        4        1         3         4
  RERE WILD-TYPE       1       14       36       29        34        48
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RERE MUTATED           0          0          1          2        3
  RERE WILD-TYPE         3         70         52         30       35
D1070V3, multiclass
            clus
vv           RERE MUTATED RERE WILD-TYPE
  STAGE I               1              1
  STAGE IA              1             14
  STAGE IB              4             36
  STAGE II              1             29
  STAGE IIA             3             34
  STAGE IIB             4             48
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            1             52
  STAGE IIIC            2             30
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RERE MUTATED     3   6   7   6
  RERE WILD-TYPE  19  86 166  91
D1070V4, multiclass
    clus
vv   RERE MUTATED RERE WILD-TYPE
  T1            3             19
  T2            6             86
  T3            7            166
  T4            6             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
  RERE MUTATED    10   5   2   4
  RERE WILD-TYPE 108  99  75  73
D1070V5, multiclass
    clus
vv   RERE MUTATED RERE WILD-TYPE
  N0           10            108
  N1            5             99
  N2            2             75
  N3            4             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"
D1070V6, binary
                cls
clus               0   1
  RERE MUTATED    19   3
  RERE WILD-TYPE 327  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  RERE MUTATED     19    3
  RERE WILD-TYPE  327   26
   clus
vv  RERE MUTATED RERE WILD-TYPE
  0           19            327
  1            3             26
[1] 2 2
[1] FALSE
D1070V7, binary
                cls
clus               0   1
  RERE MUTATED    16   8
  RERE WILD-TYPE 129 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  RERE MUTATED     16    8
  RERE WILD-TYPE  129  240
        clus
vv       RERE MUTATED RERE WILD-TYPE
  FEMALE           16            129
  MALE              8            240
[1] 2 2
[1] FALSE
D1070V8, binary
                cls
clus               0   1
  RERE MUTATED    16   0
  RERE WILD-TYPE 276  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  RERE MUTATED     16    0
  RERE WILD-TYPE  276   59
     clus
vv    RERE MUTATED RERE WILD-TYPE
  NO            16            276
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RERE MUTATED                                          0
  RERE WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RERE MUTATED                                       6
  RERE WILD-TYPE                                    64
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RERE MUTATED                                                       13
  RERE WILD-TYPE                                                    145
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RERE MUTATED                                                   0
  RERE WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RERE MUTATED                                                                   3
  RERE WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RERE MUTATED                                                    0
  RERE WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RERE MUTATED                                                  2
  RERE WILD-TYPE                                               59
D1070V9, multiclass
                                                                   clus
vv                                                                  RERE MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  RERE WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RERE MUTATED    15   0   3   4
  RERE WILD-TYPE 296  14  12  20
D1070V10, multiclass
    clus
vv   RERE MUTATED RERE WILD-TYPE
  R0           15            296
  R1            0             14
  R2            3             12
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1070V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  RERE MUTATED       5                         1
  RERE WILD-TYPE    82                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RERE MUTATED                                           0    11
  RERE WILD-TYPE                                         1   232
D1070V12, multiclass
                                           clus
vv                                          RERE MUTATED RERE WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               11            232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1070V13, binary
                cls
clus               0   1
  RERE MUTATED     0  17
  RERE WILD-TYPE   4 293
[1] "tbl2"
                cls
clus             [,1] [,2]
  RERE MUTATED      0   17
  RERE WILD-TYPE    4  293
                        clus
vv                       RERE MUTATED RERE WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           17            293
[1] 2 2
[1] FALSE

Clustering(1071) Variable = WFIKKN2 MUTATION ANALYSIS
D1071V1, survival
                   sevent
clus2                 0   1
  WFIKKN2 MUTATED    11   4
  WFIKKN2 WILD-TYPE 219 135
  WFIKKN2 MUTATED WFIKKN2 WILD-TYPE 
               15               354 
  WFIKKN2 MUTATED WFIKKN2 WILD-TYPE 
                4               135 
$`WFIKKN2 MUTATED`
TCGA-BR-8295 TCGA-BR-8361 TCGA-CD-A4MI TCGA-CG-4306 TCGA-CG-5721 TCGA-D7-A6EV 
        2.20        31.10        11.77         1.02         6.02        11.24 
TCGA-D7-A6EY TCGA-HF-7134 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G8 TCGA-HU-A4GT 
       11.44        52.21        22.32        21.07        22.68         6.51 
TCGA-HU-A4H8 TCGA-R5-A7ZI TCGA-VQ-A8P2 
       14.07        74.53        38.14 

$`WFIKKN2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A747 
       26.43        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-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-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-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 

  WFIKKN2 MUTATED WFIKKN2 WILD-TYPE 
             1.02              0.00 
  WFIKKN2 MUTATED WFIKKN2 WILD-TYPE 
            74.53            122.30 
  WFIKKN2 MUTATED WFIKKN2 WILD-TYPE 
            14.07             14.35 
[1] "1.0 - 74.5 (14.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.6"
D1071V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WFIKKN2 MUTATED         0        1        1        0         1         5
  WFIKKN2 WILD-TYPE       2       14       39       30        36        47
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WFIKKN2 MUTATED           0          2          2          1        3
  WFIKKN2 WILD-TYPE         3         68         51         31       35
D1071V3, multiclass
            clus
vv           WFIKKN2 MUTATED WFIKKN2 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                5                47
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               2                51
  STAGE IIIC               1                31
  STAGE IV                 3                35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  WFIKKN2 MUTATED     2   1   5   8
  WFIKKN2 WILD-TYPE  20  91 168  89
D1071V4, multiclass
    clus
vv   WFIKKN2 MUTATED WFIKKN2 WILD-TYPE
  T1               2                20
  T2               1                91
  T3               5               168
  T4               8                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
  WFIKKN2 MUTATED     5   6   4   1
  WFIKKN2 WILD-TYPE 113  98  73  76
D1071V5, multiclass
    clus
vv   WFIKKN2 MUTATED WFIKKN2 WILD-TYPE
  N0               5               113
  N1               6                98
  N2               4                73
  N3               1                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"
D1071V6, binary
                   cls
clus                  0   1
  WFIKKN2 MUTATED    14   2
  WFIKKN2 WILD-TYPE 332  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WFIKKN2 MUTATED     14    2
  WFIKKN2 WILD-TYPE  332   27
   clus
vv  WFIKKN2 MUTATED WFIKKN2 WILD-TYPE
  0              14               332
  1               2                27
[1] 2 2
[1] FALSE
D1071V7, binary
                   cls
clus                  0   1
  WFIKKN2 MUTATED     8   8
  WFIKKN2 WILD-TYPE 137 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WFIKKN2 MUTATED      8    8
  WFIKKN2 WILD-TYPE  137  240
        clus
vv       WFIKKN2 MUTATED WFIKKN2 WILD-TYPE
  FEMALE               8               137
  MALE                 8               240
[1] 2 2
[1] FALSE
D1071V8, binary
                   cls
clus                  0   1
  WFIKKN2 MUTATED    13   2
  WFIKKN2 WILD-TYPE 279  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WFIKKN2 MUTATED     13    2
  WFIKKN2 WILD-TYPE  279   57
     clus
vv    WFIKKN2 MUTATED WFIKKN2 WILD-TYPE
  NO               13               279
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  WFIKKN2 MUTATED                                          0
  WFIKKN2 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  WFIKKN2 MUTATED                                       4
  WFIKKN2 WILD-TYPE                                    66
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WFIKKN2 MUTATED                                                        5
  WFIKKN2 WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  WFIKKN2 MUTATED                                                   1
  WFIKKN2 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WFIKKN2 MUTATED                                                                   3
  WFIKKN2 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  WFIKKN2 MUTATED                                                    0
  WFIKKN2 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  WFIKKN2 MUTATED                                                  3
  WFIKKN2 WILD-TYPE                                               58
D1071V9, multiclass
                                                                   clus
vv                                                                  WFIKKN2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  WFIKKN2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  WFIKKN2 MUTATED    13   0   1   0
  WFIKKN2 WILD-TYPE 298  14  14  24
D1071V10, multiclass
    clus
vv   WFIKKN2 MUTATED WFIKKN2 WILD-TYPE
  R0              13               298
  R1               0                14
  R2               1                14
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1071V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  WFIKKN2 MUTATED       6                         0
  WFIKKN2 WILD-TYPE    81                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WFIKKN2 MUTATED                                           0     7
  WFIKKN2 WILD-TYPE                                         1   236
D1071V12, multiclass
                                           clus
vv                                          WFIKKN2 MUTATED WFIKKN2 WILD-TYPE
  ASIAN                                                   6                81
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1071V13, binary
                   cls
clus                  0   1
  WFIKKN2 MUTATED     1  11
  WFIKKN2 WILD-TYPE   3 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WFIKKN2 MUTATED      1   11
  WFIKKN2 WILD-TYPE    3  299
                        clus
vv                       WFIKKN2 MUTATED WFIKKN2 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              11               299
[1] 2 2
[1] FALSE

Clustering(1072) Variable = OR1L3 MUTATION ANALYSIS
D1072V1, survival
                 sevent
clus2               0   1
  OR1L3 MUTATED     6   1
  OR1L3 WILD-TYPE 224 138
  OR1L3 MUTATED OR1L3 WILD-TYPE 
              7             362 
  OR1L3 MUTATED OR1L3 WILD-TYPE 
              1             138 
$`OR1L3 MUTATED`
TCGA-BR-7722 TCGA-BR-8680 TCGA-CG-4436 TCGA-FP-7829 TCGA-FP-8211 TCGA-HF-7132 
       15.32        31.96         7.99        19.53        13.58        77.29 
TCGA-VQ-A8P2 
       38.14 

$`OR1L3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  OR1L3 MUTATED OR1L3 WILD-TYPE 
           7.99            0.00 
  OR1L3 MUTATED OR1L3 WILD-TYPE 
          77.29          122.30 
  OR1L3 MUTATED OR1L3 WILD-TYPE 
          19.53           14.12 
[1] "8.0 - 77.3 (19.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.9"
D1072V2, 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       2       15       39       29        37        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR1L3 MUTATED           0          1          0          0        1
  OR1L3 WILD-TYPE         3         69         53         32       37
D1072V3, multiclass
            clus
vv           OR1L3 MUTATED OR1L3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR1L3 MUTATED     0   2   3   2
  OR1L3 WILD-TYPE  22  90 170  95
D1072V4, multiclass
    clus
vv   OR1L3 MUTATED OR1L3 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             3             170
  T4             2              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
  OR1L3 MUTATED     1   5   1   0
  OR1L3 WILD-TYPE 117  99  76  77
D1072V5, multiclass
    clus
vv   OR1L3 MUTATED OR1L3 WILD-TYPE
  N0             1             117
  N1             5              99
  N2             1              76
  N3             0              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"
D1072V6, binary
                 cls
clus                0   1
  OR1L3 MUTATED     5   1
  OR1L3 WILD-TYPE 341  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1L3 MUTATED      5    1
  OR1L3 WILD-TYPE  341   28
   clus
vv  OR1L3 MUTATED OR1L3 WILD-TYPE
  0             5             341
  1             1              28
[1] 2 2
[1] FALSE
D1072V7, binary
                 cls
clus                0   1
  OR1L3 MUTATED     0   7
  OR1L3 WILD-TYPE 145 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1L3 MUTATED      0    7
  OR1L3 WILD-TYPE  145  241
        clus
vv       OR1L3 MUTATED OR1L3 WILD-TYPE
  FEMALE             0             145
  MALE               7             241
[1] 2 2
[1] FALSE
D1072V8, binary
                 cls
clus                0   1
  OR1L3 MUTATED     3   4
  OR1L3 WILD-TYPE 289  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1L3 MUTATED      3    4
  OR1L3 WILD-TYPE  289   55
     clus
vv    OR1L3 MUTATED OR1L3 WILD-TYPE
  NO              3             289
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OR1L3 MUTATED                                          0
  OR1L3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OR1L3 MUTATED                                       0
  OR1L3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OR1L3 MUTATED                                                        2
  OR1L3 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OR1L3 MUTATED                                                   3
  OR1L3 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OR1L3 MUTATED                                                                   1
  OR1L3 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OR1L3 MUTATED                                                    0
  OR1L3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OR1L3 MUTATED                                                  1
  OR1L3 WILD-TYPE                                               60
D1072V9, multiclass
                                                                   clus
vv                                                                  OR1L3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  OR1L3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR1L3 MUTATED     6   1   0   0
  OR1L3 WILD-TYPE 305  13  15  24
D1072V10, multiclass
    clus
vv   OR1L3 MUTATED OR1L3 WILD-TYPE
  R0             6             305
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1072V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OR1L3 MUTATED       1                         0
  OR1L3 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OR1L3 MUTATED                                           0     4
  OR1L3 WILD-TYPE                                         1   239
D1072V12, multiclass
                                           clus
vv                                          OR1L3 MUTATED OR1L3 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1072V13, binary
                 cls
clus                0   1
  OR1L3 MUTATED     0   4
  OR1L3 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1L3 MUTATED      0    4
  OR1L3 WILD-TYPE    4  306
                        clus
vv                       OR1L3 MUTATED OR1L3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(1073) Variable = MORC1 MUTATION ANALYSIS
D1073V1, survival
                 sevent
clus2               0   1
  MORC1 MUTATED     8   4
  MORC1 WILD-TYPE 222 135
  MORC1 MUTATED MORC1 WILD-TYPE 
             12             357 
  MORC1 MUTATED MORC1 WILD-TYPE 
              4             135 
$`MORC1 MUTATED`
TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6566 TCGA-BR-8680 TCGA-BR-A4PE TCGA-CG-5721 
        9.67         6.61        32.78        31.96        20.42         6.02 
TCGA-CG-5723 TCGA-HU-8238 TCGA-HU-8602 TCGA-IN-A6RL TCGA-R5-A805 TCGA-VQ-A8P2 
      105.07         1.51        22.32        13.35         9.24        38.14 

$`MORC1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 
       30.51        26.47         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-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-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-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 

  MORC1 MUTATED MORC1 WILD-TYPE 
           1.51            0.00 
  MORC1 MUTATED MORC1 WILD-TYPE 
         105.07          122.30 
  MORC1 MUTATED MORC1 WILD-TYPE 
         16.885          14.270 
[1] "1.5 - 105.1 (16.9)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D1073V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MORC1 MUTATED         0        0        1        1         1         1
  MORC1 WILD-TYPE       2       15       39       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MORC1 MUTATED           1          3          1          0        2
  MORC1 WILD-TYPE         2         67         52         32       36
D1073V3, multiclass
            clus
vv           MORC1 MUTATED MORC1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MORC1 MUTATED     0   4   3   5
  MORC1 WILD-TYPE  22  88 170  92
D1073V4, multiclass
    clus
vv   MORC1 MUTATED MORC1 WILD-TYPE
  T1             0              22
  T2             4              88
  T3             3             170
  T4             5              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
  MORC1 MUTATED     4   5   3   0
  MORC1 WILD-TYPE 114  99  74  77
D1073V5, multiclass
    clus
vv   MORC1 MUTATED MORC1 WILD-TYPE
  N0             4             114
  N1             5              99
  N2             3              74
  N3             0              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"
D1073V6, binary
                 cls
clus                0   1
  MORC1 MUTATED    12   1
  MORC1 WILD-TYPE 334  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC1 MUTATED     12    1
  MORC1 WILD-TYPE  334   28
   clus
vv  MORC1 MUTATED MORC1 WILD-TYPE
  0            12             334
  1             1              28
[1] 2 2
[1] FALSE
D1073V7, binary
                 cls
clus                0   1
  MORC1 MUTATED     6   7
  MORC1 WILD-TYPE 139 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC1 MUTATED      6    7
  MORC1 WILD-TYPE  139  241
        clus
vv       MORC1 MUTATED MORC1 WILD-TYPE
  FEMALE             6             139
  MALE               7             241
[1] 2 2
[1] FALSE
D1073V8, binary
                 cls
clus                0   1
  MORC1 MUTATED    10   1
  MORC1 WILD-TYPE 282  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC1 MUTATED     10    1
  MORC1 WILD-TYPE  282   58
     clus
vv    MORC1 MUTATED MORC1 WILD-TYPE
  NO             10             282
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MORC1 MUTATED                                          0
  MORC1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MORC1 MUTATED                                       1
  MORC1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MORC1 MUTATED                                                        7
  MORC1 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MORC1 MUTATED                                                   1
  MORC1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MORC1 MUTATED                                                                   2
  MORC1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MORC1 MUTATED                                                    0
  MORC1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MORC1 MUTATED                                                  2
  MORC1 WILD-TYPE                                               59
D1073V9, multiclass
                                                                   clus
vv                                                                  MORC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  MORC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MORC1 MUTATED     9   0   0   3
  MORC1 WILD-TYPE 302  14  15  21
D1073V10, multiclass
    clus
vv   MORC1 MUTATED MORC1 WILD-TYPE
  R0             9             302
  R1             0              14
  R2             0              15
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1073V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MORC1 MUTATED       3                         0
  MORC1 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MORC1 MUTATED                                           0     8
  MORC1 WILD-TYPE                                         1   235
D1073V12, multiclass
                                           clus
vv                                          MORC1 MUTATED MORC1 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 8             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1073V13, binary
                 cls
clus                0   1
  MORC1 MUTATED     0  10
  MORC1 WILD-TYPE   4 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC1 MUTATED      0   10
  MORC1 WILD-TYPE    4  300
                        clus
vv                       MORC1 MUTATED MORC1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(1074) Variable = AP3B1 MUTATION ANALYSIS
D1074V1, survival
                 sevent
clus2               0   1
  AP3B1 MUTATED     3   6
  AP3B1 WILD-TYPE 227 133
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              9             360 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              6             133 
$`AP3B1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-8289 TCGA-BR-8382 TCGA-BR-8680 TCGA-BR-A4QL 
       26.70         6.97         2.66        25.05        31.96        16.14 
TCGA-CD-A4MG TCGA-CG-5726 TCGA-SW-A7EA 
        6.58        28.96        19.04 

$`AP3B1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  AP3B1 MUTATED AP3B1 WILD-TYPE 
           2.66            0.00 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
          31.96          122.30 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
          19.04           14.12 
[1] "2.7 - 32.0 (19.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D1074V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AP3B1 MUTATED         0        1        1        0         1         1
  AP3B1 WILD-TYPE       2       14       39       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AP3B1 MUTATED           0          1          1          1        2
  AP3B1 WILD-TYPE         3         69         52         31       36
D1074V3, multiclass
            clus
vv           AP3B1 MUTATED AP3B1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AP3B1 MUTATED     1   1   3   4
  AP3B1 WILD-TYPE  21  91 170  93
D1074V4, multiclass
    clus
vv   AP3B1 MUTATED AP3B1 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             3             170
  T4             4              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
  AP3B1 MUTATED     4   1   1   3
  AP3B1 WILD-TYPE 114 103  76  74
D1074V5, multiclass
    clus
vv   AP3B1 MUTATED AP3B1 WILD-TYPE
  N0             4             114
  N1             1             103
  N2             1              76
  N3             3              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"
D1074V6, binary
                 cls
clus                0   1
  AP3B1 MUTATED     6   2
  AP3B1 WILD-TYPE 340  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      6    2
  AP3B1 WILD-TYPE  340   27
   clus
vv  AP3B1 MUTATED AP3B1 WILD-TYPE
  0             6             340
  1             2              27
[1] 2 2
[1] FALSE
D1074V7, binary
                 cls
clus                0   1
  AP3B1 MUTATED     4   5
  AP3B1 WILD-TYPE 141 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      4    5
  AP3B1 WILD-TYPE  141  243
        clus
vv       AP3B1 MUTATED AP3B1 WILD-TYPE
  FEMALE             4             141
  MALE               5             243
[1] 2 2
[1] FALSE
D1074V8, binary
                 cls
clus                0   1
  AP3B1 MUTATED     8   0
  AP3B1 WILD-TYPE 284  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      8    0
  AP3B1 WILD-TYPE  284   59
     clus
vv    AP3B1 MUTATED AP3B1 WILD-TYPE
  NO              8             284
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AP3B1 MUTATED                                          0
  AP3B1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AP3B1 MUTATED                                       3
  AP3B1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AP3B1 MUTATED                                                        3
  AP3B1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AP3B1 MUTATED                                                   0
  AP3B1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AP3B1 MUTATED                                                                   2
  AP3B1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AP3B1 MUTATED                                                    0
  AP3B1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AP3B1 MUTATED                                                  1
  AP3B1 WILD-TYPE                                               60
D1074V9, multiclass
                                                                   clus
vv                                                                  AP3B1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  AP3B1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AP3B1 MUTATED     7   0   0   1
  AP3B1 WILD-TYPE 304  14  15  23
D1074V10, multiclass
    clus
vv   AP3B1 MUTATED AP3B1 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1074V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  AP3B1 MUTATED       2                         0
  AP3B1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AP3B1 MUTATED                                           0     6
  AP3B1 WILD-TYPE                                         1   237
D1074V12, multiclass
                                           clus
vv                                          AP3B1 MUTATED AP3B1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1074V13, binary
                 cls
clus                0   1
  AP3B1 MUTATED     0   8
  AP3B1 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      0    8
  AP3B1 WILD-TYPE    4  302
                        clus
vv                       AP3B1 MUTATED AP3B1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(1075) Variable = OSBPL6 MUTATION ANALYSIS
D1075V1, survival
                  sevent
clus2                0   1
  OSBPL6 MUTATED    11   6
  OSBPL6 WILD-TYPE 219 133
  OSBPL6 MUTATED OSBPL6 WILD-TYPE 
              17              352 
  OSBPL6 MUTATED OSBPL6 WILD-TYPE 
               6              133 
$`OSBPL6 MUTATED`
TCGA-B7-5818 TCGA-BR-4280 TCGA-BR-6566 TCGA-BR-8081 TCGA-BR-8589 TCGA-BR-8590 
       11.70         6.61        32.78        32.25        27.12         9.34 
TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A4J4 TCGA-CD-A4MG TCGA-D7-5579 TCGA-HU-8602 
       31.96         8.22         0.53         6.58        20.91        22.32 
TCGA-HU-A4GH TCGA-IN-7808 TCGA-IN-A6RL TCGA-RD-A8N9 TCGA-VQ-A8DT 
       11.77         3.45        13.35        35.61        48.79 

$`OSBPL6 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
        1.12        12.79        28.14         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-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-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-D7-6815 
       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-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-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
       36.36        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-SW-A7EA TCGA-SW-A7EB 
      116.38        71.38        57.44         8.94        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-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 

  OSBPL6 MUTATED OSBPL6 WILD-TYPE 
            0.53             0.00 
  OSBPL6 MUTATED OSBPL6 WILD-TYPE 
           48.79           122.30 
  OSBPL6 MUTATED OSBPL6 WILD-TYPE 
           13.35            14.35 
[1] "0.5 - 48.8 (13.3)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D1075V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OSBPL6 MUTATED         0        1        2        1         2         2
  OSBPL6 WILD-TYPE       2       14       38       29        35        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSBPL6 MUTATED           1          2          3          2        1
  OSBPL6 WILD-TYPE         2         68         50         30       37
D1075V3, multiclass
            clus
vv           OSBPL6 MUTATED OSBPL6 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               2               50
  STAGE III               1                2
  STAGE IIIA              2               68
  STAGE IIIB              3               50
  STAGE IIIC              2               30
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OSBPL6 MUTATED     1   5   5   7
  OSBPL6 WILD-TYPE  21  87 168  90
D1075V4, multiclass
    clus
vv   OSBPL6 MUTATED OSBPL6 WILD-TYPE
  T1              1               21
  T2              5               87
  T3              5              168
  T4              7               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
  OSBPL6 MUTATED     7   4   5   2
  OSBPL6 WILD-TYPE 111 100  72  75
D1075V5, multiclass
    clus
vv   OSBPL6 MUTATED OSBPL6 WILD-TYPE
  N0              7              111
  N1              4              100
  N2              5               72
  N3              2               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"
D1075V6, binary
                  cls
clus                 0   1
  OSBPL6 MUTATED    16   2
  OSBPL6 WILD-TYPE 330  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL6 MUTATED     16    2
  OSBPL6 WILD-TYPE  330   27
   clus
vv  OSBPL6 MUTATED OSBPL6 WILD-TYPE
  0             16              330
  1              2               27
[1] 2 2
[1] FALSE
D1075V7, binary
                  cls
clus                 0   1
  OSBPL6 MUTATED     7  11
  OSBPL6 WILD-TYPE 138 237
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL6 MUTATED      7   11
  OSBPL6 WILD-TYPE  138  237
        clus
vv       OSBPL6 MUTATED OSBPL6 WILD-TYPE
  FEMALE              7              138
  MALE               11              237
[1] 2 2
[1] FALSE
D1075V8, binary
                  cls
clus                 0   1
  OSBPL6 MUTATED    15   2
  OSBPL6 WILD-TYPE 277  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL6 MUTATED     15    2
  OSBPL6 WILD-TYPE  277   57
     clus
vv    OSBPL6 MUTATED OSBPL6 WILD-TYPE
  NO              15              277
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OSBPL6 MUTATED                                          0
  OSBPL6 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OSBPL6 MUTATED                                       5
  OSBPL6 WILD-TYPE                                    65
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OSBPL6 MUTATED                                                        9
  OSBPL6 WILD-TYPE                                                    149
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OSBPL6 MUTATED                                                   1
  OSBPL6 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OSBPL6 MUTATED                                                                   1
  OSBPL6 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OSBPL6 MUTATED                                                    0
  OSBPL6 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OSBPL6 MUTATED                                                  2
  OSBPL6 WILD-TYPE                                               59
D1075V9, multiclass
                                                                   clus
vv                                                                  OSBPL6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  OSBPL6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OSBPL6 MUTATED    13   2   0   1
  OSBPL6 WILD-TYPE 298  12  15  23
D1075V10, multiclass
    clus
vv   OSBPL6 MUTATED OSBPL6 WILD-TYPE
  R0             13              298
  R1              2               12
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1075V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  OSBPL6 MUTATED       6                         0
  OSBPL6 WILD-TYPE    81                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OSBPL6 MUTATED                                           0    11
  OSBPL6 WILD-TYPE                                         1   232
D1075V12, multiclass
                                           clus
vv                                          OSBPL6 MUTATED OSBPL6 WILD-TYPE
  ASIAN                                                  6               81
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1075V13, binary
                  cls
clus                 0   1
  OSBPL6 MUTATED     0  17
  OSBPL6 WILD-TYPE   4 293
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL6 MUTATED      0   17
  OSBPL6 WILD-TYPE    4  293
                        clus
vv                       OSBPL6 MUTATED OSBPL6 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             17              293
[1] 2 2
[1] FALSE

Clustering(1076) Variable = EFHC1 MUTATION ANALYSIS
D1076V1, survival
                 sevent
clus2               0   1
  EFHC1 MUTATED     7   3
  EFHC1 WILD-TYPE 223 136
  EFHC1 MUTATED EFHC1 WILD-TYPE 
             10             359 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
              3             136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-8244 
       77.29        63.06        52.21        26.47         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-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-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-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 

  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           14.07 
[1] "0.1 - 34.7 (26.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D1076V2, 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       2       15       40       30        35        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFHC1 MUTATED           0          0          0          3        1
  EFHC1 WILD-TYPE         3         70         53         29       37
D1076V3, multiclass
            clus
vv           EFHC1 MUTATED EFHC1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             3              29
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EFHC1 MUTATED     0   3   2   5
  EFHC1 WILD-TYPE  22  89 171  92
D1076V4, multiclass
    clus
vv   EFHC1 MUTATED EFHC1 WILD-TYPE
  T1             0              22
  T2             3              89
  T3             2             171
  T4             5              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
  EFHC1 MUTATED     2   3   2   2
  EFHC1 WILD-TYPE 116 101  75  75
D1076V5, multiclass
    clus
vv   EFHC1 MUTATED EFHC1 WILD-TYPE
  N0             2             116
  N1             3             101
  N2             2              75
  N3             2              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"
D1076V6, binary
                 cls
clus                0   1
  EFHC1 MUTATED    10   0
  EFHC1 WILD-TYPE 336  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED     10    0
  EFHC1 WILD-TYPE  336   29
   clus
vv  EFHC1 MUTATED EFHC1 WILD-TYPE
  0            10             336
  1             0              29
[1] 2 2
[1] FALSE
D1076V7, binary
                 cls
clus                0   1
  EFHC1 MUTATED     6   4
  EFHC1 WILD-TYPE 139 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED      6    4
  EFHC1 WILD-TYPE  139  244
        clus
vv       EFHC1 MUTATED EFHC1 WILD-TYPE
  FEMALE             6             139
  MALE               4             244
[1] 2 2
[1] FALSE
D1076V8, binary
                 cls
clus                0   1
  EFHC1 MUTATED     9   1
  EFHC1 WILD-TYPE 283  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED      9    1
  EFHC1 WILD-TYPE  283   58
     clus
vv    EFHC1 MUTATED EFHC1 WILD-TYPE
  NO              9             283
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EFHC1 MUTATED                                          0
  EFHC1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EFHC1 MUTATED                                       1
  EFHC1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EFHC1 MUTATED                                                        3
  EFHC1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EFHC1 MUTATED                                                   1
  EFHC1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EFHC1 MUTATED                                                                   1
  EFHC1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EFHC1 MUTATED                                                    0
  EFHC1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EFHC1 MUTATED                                                  4
  EFHC1 WILD-TYPE                                               57
D1076V9, multiclass
                                                                   clus
vv                                                                  EFHC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  EFHC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EFHC1 MUTATED     7   1   0   1
  EFHC1 WILD-TYPE 304  13  15  23
D1076V10, multiclass
    clus
vv   EFHC1 MUTATED EFHC1 WILD-TYPE
  R0             7             304
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1076V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EFHC1 MUTATED       5                         0
  EFHC1 WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EFHC1 MUTATED                                           0     3
  EFHC1 WILD-TYPE                                         1   240
D1076V12, multiclass
                                           clus
vv                                          EFHC1 MUTATED EFHC1 WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1076V13, binary
                 cls
clus                0   1
  EFHC1 MUTATED     0   8
  EFHC1 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED      0    8
  EFHC1 WILD-TYPE    4  302
                        clus
vv                       EFHC1 MUTATED EFHC1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(1077) Variable = DTNBP1 MUTATION ANALYSIS
D1077V1, survival
                  sevent
clus2                0   1
  DTNBP1 MUTATED     2   3
  DTNBP1 WILD-TYPE 228 136
  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
               5              364 
  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
               3              136 
$`DTNBP1 MUTATED`
TCGA-BR-4257 TCGA-BR-6802 TCGA-BR-8363 TCGA-BR-A4IY TCGA-D7-A4YV 
        9.67        30.90         0.26        12.89         5.92 

$`DTNBP1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
            0.26             0.00 
  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
            30.9            122.3 
  DTNBP1 MUTATED DTNBP1 WILD-TYPE 
            9.67            14.45 
[1] "0.3 - 30.9 (9.7)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "2.4"
D1077V2, 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       2       15       39       30        37        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DTNBP1 MUTATED           0          2          0          0        0
  DTNBP1 WILD-TYPE         3         68         53         32       38
D1077V3, multiclass
            clus
vv           DTNBP1 MUTATED DTNBP1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DTNBP1 MUTATED     0   1   2   2
  DTNBP1 WILD-TYPE  22  91 171  95
D1077V4, multiclass
    clus
vv   DTNBP1 MUTATED DTNBP1 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              2              171
  T4              2               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
  DTNBP1 MUTATED     3   1   1   0
  DTNBP1 WILD-TYPE 115 103  76  77
D1077V5, multiclass
    clus
vv   DTNBP1 MUTATED DTNBP1 WILD-TYPE
  N0              3              115
  N1              1              103
  N2              1               76
  N3              0               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"
D1077V6, binary
                  cls
clus                 0   1
  DTNBP1 MUTATED     6   0
  DTNBP1 WILD-TYPE 340  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DTNBP1 MUTATED      6    0
  DTNBP1 WILD-TYPE  340   29
   clus
vv  DTNBP1 MUTATED DTNBP1 WILD-TYPE
  0              6              340
  1              0               29
[1] 2 2
[1] FALSE
D1077V7, binary
                  cls
clus                 0   1
  DTNBP1 MUTATED     4   2
  DTNBP1 WILD-TYPE 141 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DTNBP1 MUTATED      4    2
  DTNBP1 WILD-TYPE  141  246
        clus
vv       DTNBP1 MUTATED DTNBP1 WILD-TYPE
  FEMALE              4              141
  MALE                2              246
[1] 2 2
[1] FALSE
D1077V8, binary
                  cls
clus                 0   1
  DTNBP1 MUTATED     5   0
  DTNBP1 WILD-TYPE 287  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DTNBP1 MUTATED      5    0
  DTNBP1 WILD-TYPE  287   59
     clus
vv    DTNBP1 MUTATED DTNBP1 WILD-TYPE
  NO               5              287
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DTNBP1 MUTATED                                          0
  DTNBP1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DTNBP1 MUTATED                                       0
  DTNBP1 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DTNBP1 MUTATED                                                        5
  DTNBP1 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DTNBP1 MUTATED                                                   0
  DTNBP1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DTNBP1 MUTATED                                                                   0
  DTNBP1 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DTNBP1 MUTATED                                                    0
  DTNBP1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DTNBP1 MUTATED                                                  1
  DTNBP1 WILD-TYPE                                               60
D1077V9, multiclass
                                                                   clus
vv                                                                  DTNBP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  DTNBP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DTNBP1 MUTATED     4   0   0   2
  DTNBP1 WILD-TYPE 307  14  15  22
D1077V10, multiclass
    clus
vv   DTNBP1 MUTATED DTNBP1 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1077V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  DTNBP1 MUTATED       1                         0
  DTNBP1 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DTNBP1 MUTATED                                           0     5
  DTNBP1 WILD-TYPE                                         1   238
D1077V12, multiclass
                                           clus
vv                                          DTNBP1 MUTATED DTNBP1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1077V13, binary
                  cls
clus                 0   1
  DTNBP1 MUTATED     0   6
  DTNBP1 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DTNBP1 MUTATED      0    6
  DTNBP1 WILD-TYPE    4  304
                        clus
vv                       DTNBP1 MUTATED DTNBP1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(1078) Variable = KCNH1 MUTATION ANALYSIS
D1078V1, survival
                 sevent
clus2               0   1
  KCNH1 MUTATED    16   3
  KCNH1 WILD-TYPE 214 136
  KCNH1 MUTATED KCNH1 WILD-TYPE 
             19             350 
  KCNH1 MUTATED KCNH1 WILD-TYPE 
              3             136 
$`KCNH1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-8381 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8680 
       26.70         6.97         7.36        28.14         7.53        31.96 
TCGA-CD-8536 TCGA-D7-A4Z0 TCGA-D7-A6F0 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-A5NB 
       12.43        14.76        22.29         6.21        77.29        30.51 
TCGA-HJ-7597 TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-RD-A7BT 
       26.47         6.51        20.25        23.84        14.07         8.61 
TCGA-SW-A7EA 
       19.04 

$`KCNH1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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-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-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-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 

  KCNH1 MUTATED KCNH1 WILD-TYPE 
           6.21            0.00 
  KCNH1 MUTATED KCNH1 WILD-TYPE 
          77.29          122.30 
  KCNH1 MUTATED KCNH1 WILD-TYPE 
          19.04           14.12 
[1] "6.2 - 77.3 (19.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.8"
D1078V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNH1 MUTATED         0        0        4        2         1         4
  KCNH1 WILD-TYPE       2       15       36       28        36        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNH1 MUTATED           0          1          1          3        3
  KCNH1 WILD-TYPE         3         69         52         29       35
D1078V3, multiclass
            clus
vv           KCNH1 MUTATED KCNH1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               4              36
  STAGE II               2              28
  STAGE IIA              1              36
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             3              29
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNH1 MUTATED     2   6   6   6
  KCNH1 WILD-TYPE  20  86 167  91
D1078V4, multiclass
    clus
vv   KCNH1 MUTATED KCNH1 WILD-TYPE
  T1             2              20
  T2             6              86
  T3             6             167
  T4             6              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
  KCNH1 MUTATED     6   5   5   4
  KCNH1 WILD-TYPE 112  99  72  73
D1078V5, multiclass
    clus
vv   KCNH1 MUTATED KCNH1 WILD-TYPE
  N0             6             112
  N1             5              99
  N2             5              72
  N3             4              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"
D1078V6, binary
                 cls
clus                0   1
  KCNH1 MUTATED    17   1
  KCNH1 WILD-TYPE 329  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH1 MUTATED     17    1
  KCNH1 WILD-TYPE  329   28
   clus
vv  KCNH1 MUTATED KCNH1 WILD-TYPE
  0            17             329
  1             1              28
[1] 2 2
[1] FALSE
D1078V7, binary
                 cls
clus                0   1
  KCNH1 MUTATED    10  10
  KCNH1 WILD-TYPE 135 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH1 MUTATED     10   10
  KCNH1 WILD-TYPE  135  238
        clus
vv       KCNH1 MUTATED KCNH1 WILD-TYPE
  FEMALE            10             135
  MALE              10             238
[1] 2 2
[1] FALSE
D1078V8, binary
                 cls
clus                0   1
  KCNH1 MUTATED    15   4
  KCNH1 WILD-TYPE 277  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH1 MUTATED     15    4
  KCNH1 WILD-TYPE  277   55
     clus
vv    KCNH1 MUTATED KCNH1 WILD-TYPE
  NO             15             277
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KCNH1 MUTATED                                          1
  KCNH1 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KCNH1 MUTATED                                       3
  KCNH1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNH1 MUTATED                                                        6
  KCNH1 WILD-TYPE                                                    152
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KCNH1 MUTATED                                                   3
  KCNH1 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNH1 MUTATED                                                                   3
  KCNH1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KCNH1 MUTATED                                                    0
  KCNH1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KCNH1 MUTATED                                                  4
  KCNH1 WILD-TYPE                                               57
D1078V9, multiclass
                                                                   clus
vv                                                                  KCNH1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  KCNH1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCNH1 MUTATED    16   1   1   2
  KCNH1 WILD-TYPE 295  13  14  22
D1078V10, multiclass
    clus
vv   KCNH1 MUTATED KCNH1 WILD-TYPE
  R0            16             295
  R1             1              13
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1078V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCNH1 MUTATED       6                         0
  KCNH1 WILD-TYPE    81                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNH1 MUTATED                                           1    11
  KCNH1 WILD-TYPE                                         0   232
D1078V12, multiclass
                                           clus
vv                                          KCNH1 MUTATED KCNH1 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               0
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1078V13, binary
                 cls
clus                0   1
  KCNH1 MUTATED     0  18
  KCNH1 WILD-TYPE   4 292
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH1 MUTATED      0   18
  KCNH1 WILD-TYPE    4  292
                        clus
vv                       KCNH1 MUTATED KCNH1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            18             292
[1] 2 2
[1] FALSE

Clustering(1079) Variable = BBS10 MUTATION ANALYSIS
D1079V1, survival
                 sevent
clus2               0   1
  BBS10 MUTATED     6   2
  BBS10 WILD-TYPE 224 137
  BBS10 MUTATED BBS10 WILD-TYPE 
              8             361 
  BBS10 MUTATED BBS10 WILD-TYPE 
              2             137 
$`BBS10 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-7707 TCGA-BR-A4J2 TCGA-HU-8602 
       26.70         6.97         9.34        35.84        14.17        22.32 
TCGA-HU-A4G8 TCGA-VQ-A8P2 
       22.68        38.14 

$`BBS10 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-D7-8575 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-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 

  BBS10 MUTATED BBS10 WILD-TYPE 
           6.97            0.00 
  BBS10 MUTATED BBS10 WILD-TYPE 
          38.14          122.30 
  BBS10 MUTATED BBS10 WILD-TYPE 
          22.50           14.07 
[1] "7.0 - 38.1 (22.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.9"
D1079V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BBS10 MUTATED         0        0        2        0         0         4
  BBS10 WILD-TYPE       2       15       38       30        37        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BBS10 MUTATED           0          2          0          0        0
  BBS10 WILD-TYPE         3         68         53         32       38
D1079V3, multiclass
            clus
vv           BBS10 MUTATED BBS10 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BBS10 MUTATED     0   2   2   4
  BBS10 WILD-TYPE  22  90 171  93
D1079V4, multiclass
    clus
vv   BBS10 MUTATED BBS10 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             2             171
  T4             4              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
  BBS10 MUTATED     5   4   0   0
  BBS10 WILD-TYPE 113 100  77  77
D1079V5, multiclass
    clus
vv   BBS10 MUTATED BBS10 WILD-TYPE
  N0             5             113
  N1             4             100
  N2             0              77
  N3             0              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"
D1079V6, binary
                 cls
clus                0   1
  BBS10 MUTATED     8   0
  BBS10 WILD-TYPE 338  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BBS10 MUTATED      8    0
  BBS10 WILD-TYPE  338   29
   clus
vv  BBS10 MUTATED BBS10 WILD-TYPE
  0             8             338
  1             0              29
[1] 2 2
[1] FALSE
D1079V7, binary
                 cls
clus                0   1
  BBS10 MUTATED     4   5
  BBS10 WILD-TYPE 141 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BBS10 MUTATED      4    5
  BBS10 WILD-TYPE  141  243
        clus
vv       BBS10 MUTATED BBS10 WILD-TYPE
  FEMALE             4             141
  MALE               5             243
[1] 2 2
[1] FALSE
D1079V8, binary
                 cls
clus                0   1
  BBS10 MUTATED     7   1
  BBS10 WILD-TYPE 285  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BBS10 MUTATED      7    1
  BBS10 WILD-TYPE  285   58
     clus
vv    BBS10 MUTATED BBS10 WILD-TYPE
  NO              7             285
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BBS10 MUTATED                                          0
  BBS10 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BBS10 MUTATED                                       4
  BBS10 WILD-TYPE                                    66
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BBS10 MUTATED                                                        3
  BBS10 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BBS10 MUTATED                                                   1
  BBS10 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BBS10 MUTATED                                                                   1
  BBS10 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BBS10 MUTATED                                                    0
  BBS10 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BBS10 MUTATED                                                  0
  BBS10 WILD-TYPE                                               61
D1079V9, multiclass
                                                                   clus
vv                                                                  BBS10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  BBS10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BBS10 MUTATED     6   0   0   2
  BBS10 WILD-TYPE 305  14  15  22
D1079V10, multiclass
    clus
vv   BBS10 MUTATED BBS10 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1079V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BBS10 MUTATED       3                         0
  BBS10 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BBS10 MUTATED                                           0     5
  BBS10 WILD-TYPE                                         1   238
D1079V12, multiclass
                                           clus
vv                                          BBS10 MUTATED BBS10 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1079V13, binary
                 cls
clus                0   1
  BBS10 MUTATED     0   7
  BBS10 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BBS10 MUTATED      0    7
  BBS10 WILD-TYPE    4  303
                        clus
vv                       BBS10 MUTATED BBS10 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(1080) Variable = SMARCC2 MUTATION ANALYSIS
D1080V1, survival
                   sevent
clus2                 0   1
  SMARCC2 MUTATED    10   7
  SMARCC2 WILD-TYPE 220 132
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
               17               352 
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
                7               132 
$`SMARCC2 MUTATED`
TCGA-CG-4460 TCGA-BR-4257 TCGA-BR-7707 TCGA-BR-7901 TCGA-BR-8078 TCGA-BR-8363 
       21.99         9.67        35.84         3.45        29.59         0.26 
TCGA-BR-8487 TCGA-BR-A4J2 TCGA-CD-8526 TCGA-CG-4443 TCGA-CG-5721 TCGA-CG-5728 
        1.12        14.17        12.53        29.98         6.02        65.10 
TCGA-D7-8572 TCGA-D7-A4YV TCGA-HF-7132 TCGA-HU-8243 TCGA-R5-A7ZF 
       16.80         5.92        77.29         5.92         8.52 

$`SMARCC2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       14.01        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-D7-8573 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-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-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-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-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 

  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             14.45 
[1] "0.3 - 77.3 (12.5)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D1080V2, 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       2       14       37       29        36        47
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCC2 MUTATED           0          1          0          1        3
  SMARCC2 WILD-TYPE         3         69         53         31       35
D1080V3, multiclass
            clus
vv           SMARCC2 MUTATED SMARCC2 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                14
  STAGE IB                 3                37
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                5                47
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 3                35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SMARCC2 MUTATED     1   5   4   6
  SMARCC2 WILD-TYPE  21  87 169  91
D1080V4, multiclass
    clus
vv   SMARCC2 MUTATED SMARCC2 WILD-TYPE
  T1               1                21
  T2               5                87
  T3               4               169
  T4               6                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
  SMARCC2 MUTATED     7   8   1   1
  SMARCC2 WILD-TYPE 111  96  76  76
D1080V5, multiclass
    clus
vv   SMARCC2 MUTATED SMARCC2 WILD-TYPE
  N0               7               111
  N1               8                96
  N2               1                76
  N3               1                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"
D1080V6, binary
                   cls
clus                  0   1
  SMARCC2 MUTATED    16   2
  SMARCC2 WILD-TYPE 330  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCC2 MUTATED     16    2
  SMARCC2 WILD-TYPE  330   27
   clus
vv  SMARCC2 MUTATED SMARCC2 WILD-TYPE
  0              16               330
  1               2                27
[1] 2 2
[1] FALSE
D1080V7, binary
                   cls
clus                  0   1
  SMARCC2 MUTATED    11   7
  SMARCC2 WILD-TYPE 134 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCC2 MUTATED     11    7
  SMARCC2 WILD-TYPE  134  241
        clus
vv       SMARCC2 MUTATED SMARCC2 WILD-TYPE
  FEMALE              11               134
  MALE                 7               241
[1] 2 2
[1] FALSE
D1080V8, binary
                   cls
clus                  0   1
  SMARCC2 MUTATED    14   1
  SMARCC2 WILD-TYPE 278  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCC2 MUTATED     14    1
  SMARCC2 WILD-TYPE  278   58
     clus
vv    SMARCC2 MUTATED SMARCC2 WILD-TYPE
  NO               14               278
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SMARCC2 MUTATED                                          0
  SMARCC2 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SMARCC2 MUTATED                                       1
  SMARCC2 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMARCC2 MUTATED                                                        8
  SMARCC2 WILD-TYPE                                                    150
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SMARCC2 MUTATED                                                   1
  SMARCC2 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMARCC2 MUTATED                                                                   5
  SMARCC2 WILD-TYPE                                                                63
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SMARCC2 MUTATED                                                    0
  SMARCC2 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SMARCC2 MUTATED                                                  3
  SMARCC2 WILD-TYPE                                               58
D1080V9, multiclass
                                                                   clus
vv                                                                  SMARCC2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  SMARCC2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SMARCC2 MUTATED    14   0   1   2
  SMARCC2 WILD-TYPE 297  14  14  22
D1080V10, multiclass
    clus
vv   SMARCC2 MUTATED SMARCC2 WILD-TYPE
  R0              14               297
  R1               0                14
  R2               1                14
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1080V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SMARCC2 MUTATED       3                         1
  SMARCC2 WILD-TYPE    84                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMARCC2 MUTATED                                           0     9
  SMARCC2 WILD-TYPE                                         1   234
D1080V12, multiclass
                                           clus
vv                                          SMARCC2 MUTATED SMARCC2 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1080V13, binary
                   cls
clus                  0   1
  SMARCC2 MUTATED     0  13
  SMARCC2 WILD-TYPE   4 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCC2 MUTATED      0   13
  SMARCC2 WILD-TYPE    4  297
                        clus
vv                       SMARCC2 MUTATED SMARCC2 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              13               297
[1] 2 2
[1] FALSE

Clustering(1081) Variable = NRK MUTATION ANALYSIS
D1081V1, survival
               sevent
clus2             0   1
  NRK MUTATED    13   8
  NRK WILD-TYPE 217 131
  NRK MUTATED NRK WILD-TYPE 
           21           348 
  NRK MUTATED NRK WILD-TYPE 
            8           131 
$`NRK MUTATED`
TCGA-CG-4444 TCGA-B7-A5TJ TCGA-BR-6852 TCGA-BR-8078 TCGA-BR-8289 TCGA-BR-8361 
       47.05        11.01        44.94        29.59         2.66        31.10 
TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8589 TCGA-CG-4469 TCGA-D7-6818 
        0.26         4.31         1.12        27.12         7.07        12.36 
TCGA-D7-A4YV TCGA-FP-8211 TCGA-HF-A5NB TCGA-IN-8663 TCGA-R5-A7ZI TCGA-RD-A7BT 
        5.92        13.58        30.51         3.39        74.53         8.61 
TCGA-SW-A7EA TCGA-VQ-A8PK TCGA-VQ-A91V 
       19.04        17.85        42.64 

$`NRK WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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 
        13.58         14.35 
[1] "0.3 - 74.5 (13.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D1081V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NRK MUTATED         0        1        3        0         2         5
  NRK WILD-TYPE       2       14       37       30        35        47
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NRK MUTATED           0          4          2          2        4
  NRK WILD-TYPE         3         66         51         30       34
D1081V3, multiclass
            clus
vv           NRK MUTATED NRK WILD-TYPE
  STAGE I              0             2
  STAGE IA             1            14
  STAGE IB             3            37
  STAGE II             0            30
  STAGE IIA            2            35
  STAGE IIB            5            47
  STAGE III            0             3
  STAGE IIIA           4            66
  STAGE IIIB           2            51
  STAGE IIIC           2            30
  STAGE IV             4            34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NRK MUTATED     2   6   9   8
  NRK WILD-TYPE  20  86 164  89
D1081V4, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  T1           2            20
  T2           6            86
  T3           9           164
  T4           8            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
  NRK MUTATED     8   5   4   6
  NRK WILD-TYPE 110  99  73  71
D1081V5, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  N0           8           110
  N1           5            99
  N2           4            73
  N3           6            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"
D1081V6, binary
               cls
clus              0   1
  NRK MUTATED    22   2
  NRK WILD-TYPE 324  27
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     22    2
  NRK WILD-TYPE  324   27
   clus
vv  NRK MUTATED NRK WILD-TYPE
  0          22           324
  1           2            27
[1] 2 2
[1] FALSE
D1081V7, binary
               cls
clus              0   1
  NRK MUTATED    13  13
  NRK WILD-TYPE 132 235
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     13   13
  NRK WILD-TYPE  132  235
        clus
vv       NRK MUTATED NRK WILD-TYPE
  FEMALE          13           132
  MALE            13           235
[1] 2 2
[1] FALSE
D1081V8, binary
               cls
clus              0   1
  NRK MUTATED    15   6
  NRK WILD-TYPE 277  53
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     15    6
  NRK WILD-TYPE  277   53
     clus
vv    NRK MUTATED NRK WILD-TYPE
  NO           15           277
  YES           6            53
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NRK MUTATED                                          0
  NRK WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NRK MUTATED                                       4
  NRK WILD-TYPE                                    66
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NRK MUTATED                                                       14
  NRK WILD-TYPE                                                    144
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NRK MUTATED                                                   1
  NRK WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NRK MUTATED                                                                   5
  NRK WILD-TYPE                                                                63
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NRK MUTATED                                                    0
  NRK WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NRK MUTATED                                                  2
  NRK WILD-TYPE                                               59
D1081V9, multiclass
                                                                   clus
vv                                                                  NRK MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                     14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            2
                                                                   clus
vv                                                                  NRK WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  NRK MUTATED    17   3   1   4
  NRK WILD-TYPE 294  11  14  20
D1081V10, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  R0          17           294
  R1           3            11
  R2           1            14
  RX           4            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1081V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  NRK MUTATED       1                         0
  NRK WILD-TYPE    86                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NRK MUTATED                                           1    20
  NRK WILD-TYPE                                         0   223
D1081V12, multiclass
                                           clus
vv                                          NRK MUTATED NRK WILD-TYPE
  ASIAN                                               1            86
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           1             0
  WHITE                                              20           223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1081V13, binary
               cls
clus              0   1
  NRK MUTATED     1  20
  NRK WILD-TYPE   3 290
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED      1   20
  NRK WILD-TYPE    3  290
                        clus
vv                       NRK MUTATED NRK WILD-TYPE
  HISPANIC OR LATINO               1             3
  NOT HISPANIC OR LATINO          20           290
[1] 2 2
[1] FALSE

Clustering(1082) Variable = WBP11 MUTATION ANALYSIS
D1082V1, survival
                 sevent
clus2               0   1
  WBP11 MUTATED     4   1
  WBP11 WILD-TYPE 226 138
  WBP11 MUTATED WBP11 WILD-TYPE 
              5             364 
  WBP11 MUTATED WBP11 WILD-TYPE 
              1             138 
$`WBP11 MUTATED`
TCGA-CG-4460 TCGA-BR-8360 TCGA-D7-5578 TCGA-HU-A4GT TCGA-R5-A7ZI 
       21.99         6.18        12.66         6.51        74.53 

$`WBP11 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-D7-5579 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-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-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 

  WBP11 MUTATED WBP11 WILD-TYPE 
           6.18            0.00 
  WBP11 MUTATED WBP11 WILD-TYPE 
          74.53          122.30 
  WBP11 MUTATED WBP11 WILD-TYPE 
          12.66           14.35 
[1] "6.2 - 74.5 (12.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.1"
D1082V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WBP11 MUTATED         0        0        0        0         2         0
  WBP11 WILD-TYPE       2       15       40       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WBP11 MUTATED           0          1          0          0        2
  WBP11 WILD-TYPE         3         69         53         32       36
D1082V3, multiclass
            clus
vv           WBP11 MUTATED WBP11 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WBP11 MUTATED     0   0   3   2
  WBP11 WILD-TYPE  22  92 170  95
D1082V4, multiclass
    clus
vv   WBP11 MUTATED WBP11 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             3             170
  T4             2              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
  WBP11 MUTATED     2   2   1   0
  WBP11 WILD-TYPE 116 102  76  77
D1082V5, multiclass
    clus
vv   WBP11 MUTATED WBP11 WILD-TYPE
  N0             2             116
  N1             2             102
  N2             1              76
  N3             0              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"
D1082V6, binary
                 cls
clus                0   1
  WBP11 MUTATED     3   2
  WBP11 WILD-TYPE 343  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WBP11 MUTATED      3    2
  WBP11 WILD-TYPE  343   27
   clus
vv  WBP11 MUTATED WBP11 WILD-TYPE
  0             3             343
  1             2              27
[1] 2 2
[1] FALSE
D1082V7, binary
                 cls
clus                0   1
  WBP11 MUTATED     3   2
  WBP11 WILD-TYPE 142 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WBP11 MUTATED      3    2
  WBP11 WILD-TYPE  142  246
        clus
vv       WBP11 MUTATED WBP11 WILD-TYPE
  FEMALE             3             142
  MALE               2             246
[1] 2 2
[1] FALSE
D1082V8, binary
                 cls
clus                0   1
  WBP11 MUTATED     5   0
  WBP11 WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WBP11 MUTATED      5    0
  WBP11 WILD-TYPE  287   59
     clus
vv    WBP11 MUTATED WBP11 WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  WBP11 MUTATED                                          0
  WBP11 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  WBP11 MUTATED                                       1
  WBP11 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WBP11 MUTATED                                                        0
  WBP11 WILD-TYPE                                                    158
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  WBP11 MUTATED                                                   0
  WBP11 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WBP11 MUTATED                                                                   2
  WBP11 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  WBP11 MUTATED                                                    0
  WBP11 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  WBP11 MUTATED                                                  2
  WBP11 WILD-TYPE                                               59
D1082V9, multiclass
                                                                   clus
vv                                                                  WBP11 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        0
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  WBP11 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        158
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WBP11 MUTATED     4   0   1   0
  WBP11 WILD-TYPE 307  14  14  24
D1082V10, multiclass
    clus
vv   WBP11 MUTATED WBP11 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1082V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  WBP11 MUTATED       1                         0
  WBP11 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WBP11 MUTATED                                           0     3
  WBP11 WILD-TYPE                                         1   240
D1082V12, multiclass
                                           clus
vv                                          WBP11 MUTATED WBP11 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1082V13, binary
                 cls
clus                0   1
  WBP11 MUTATED     1   3
  WBP11 WILD-TYPE   3 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WBP11 MUTATED      1    3
  WBP11 WILD-TYPE    3  307
                        clus
vv                       WBP11 MUTATED WBP11 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(1083) Variable = WSB2 MUTATION ANALYSIS
D1083V1, survival
                sevent
clus2              0   1
  WSB2 MUTATED     7   0
  WSB2 WILD-TYPE 223 139
  WSB2 MUTATED WSB2 WILD-TYPE 
             7            362 
  WSB2 MUTATED WSB2 WILD-TYPE 
             0            139 
$`WSB2 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8589 TCGA-BR-A4QM TCGA-CG-4437 
       34.68        44.94        36.16        27.12         5.13         8.05 
TCGA-CG-5723 
      105.07 

$`WSB2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  WSB2 MUTATED WSB2 WILD-TYPE 
          5.13           0.00 
  WSB2 MUTATED WSB2 WILD-TYPE 
        105.07         122.30 
  WSB2 MUTATED WSB2 WILD-TYPE 
         34.68          14.12 
[1] "5.1 - 105.1 (34.7)" "0.0 - 122.3 (14.1)"
[1] "hr="     "2.6e+07"
D1083V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  WSB2 MUTATED         1        1        1        2         2         0
  WSB2 WILD-TYPE       1       14       39       28        35        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WSB2 MUTATED           0          1          1          0        0
  WSB2 WILD-TYPE         3         69         52         32       38
D1083V3, multiclass
            clus
vv           WSB2 MUTATED WSB2 WILD-TYPE
  STAGE I               1              1
  STAGE IA              1             14
  STAGE IB              1             39
  STAGE II              2             28
  STAGE IIA             2             35
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            1             52
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WSB2 MUTATED     2   3   3   1
  WSB2 WILD-TYPE  20  89 170  96
D1083V4, multiclass
    clus
vv   WSB2 MUTATED WSB2 WILD-TYPE
  T1            2             20
  T2            3             89
  T3            3            170
  T4            1             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
  WSB2 MUTATED     4   4   1   0
  WSB2 WILD-TYPE 114 100  76  77
D1083V5, multiclass
    clus
vv   WSB2 MUTATED WSB2 WILD-TYPE
  N0            4            114
  N1            4            100
  N2            1             76
  N3            0             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"
D1083V6, binary
                cls
clus               0   1
  WSB2 MUTATED     8   0
  WSB2 WILD-TYPE 338  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  WSB2 MUTATED      8    0
  WSB2 WILD-TYPE  338   29
   clus
vv  WSB2 MUTATED WSB2 WILD-TYPE
  0            8            338
  1            0             29
[1] 2 2
[1] FALSE
D1083V7, binary
                cls
clus               0   1
  WSB2 MUTATED     2   7
  WSB2 WILD-TYPE 143 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  WSB2 MUTATED      2    7
  WSB2 WILD-TYPE  143  241
        clus
vv       WSB2 MUTATED WSB2 WILD-TYPE
  FEMALE            2            143
  MALE              7            241
[1] 2 2
[1] FALSE
D1083V8, binary
                cls
clus               0   1
  WSB2 MUTATED     8   0
  WSB2 WILD-TYPE 284  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  WSB2 MUTATED      8    0
  WSB2 WILD-TYPE  284   59
     clus
vv    WSB2 MUTATED WSB2 WILD-TYPE
  NO             8            284
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  WSB2 MUTATED                                          0
  WSB2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  WSB2 MUTATED                                       0
  WSB2 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WSB2 MUTATED                                                        6
  WSB2 WILD-TYPE                                                    152
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  WSB2 MUTATED                                                   0
  WSB2 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  WSB2 MUTATED                                                                   2
  WSB2 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  WSB2 MUTATED                                                    1
  WSB2 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  WSB2 MUTATED                                                  0
  WSB2 WILD-TYPE                                               61
D1083V9, multiclass
                                                                   clus
vv                                                                  WSB2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  WSB2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WSB2 MUTATED     9   0   0   0
  WSB2 WILD-TYPE 302  14  15  24
D1083V10, multiclass
    clus
vv   WSB2 MUTATED WSB2 WILD-TYPE
  R0            9            302
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1083V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  WSB2 MUTATED       0                         1
  WSB2 WILD-TYPE    87                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  WSB2 MUTATED                                           0     5
  WSB2 WILD-TYPE                                         1   238
D1083V12, multiclass
                                           clus
vv                                          WSB2 MUTATED WSB2 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1083V13, binary
                cls
clus               0   1
  WSB2 MUTATED     0   6
  WSB2 WILD-TYPE   4 304
[1] "tbl2"
                cls
clus             [,1] [,2]
  WSB2 MUTATED      0    6
  WSB2 WILD-TYPE    4  304
                        clus
vv                       WSB2 MUTATED WSB2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            304
[1] 2 2
[1] FALSE

Clustering(1084) Variable = SET MUTATION ANALYSIS
D1084V1, survival
               sevent
clus2             0   1
  SET MUTATED     4   3
  SET WILD-TYPE 226 136
  SET MUTATED SET WILD-TYPE 
            7           362 
  SET MUTATED SET WILD-TYPE 
            3           136 
$`SET MUTATED`
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-BR-8382 TCGA-CG-4306 TCGA-CG-5728 TCGA-D7-A74A 
       21.99        16.24        25.05         1.02        65.10        19.96 
TCGA-HU-8602 
       22.32 

$`SET WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       47.05        22.98        79.07         0.23        20.15         9.86 
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-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-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-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 

  SET MUTATED SET WILD-TYPE 
         1.02          0.00 
  SET MUTATED SET WILD-TYPE 
         65.1         122.3 
  SET MUTATED SET WILD-TYPE 
        21.99         14.07 
[1] "1.0 - 65.1 (22.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D1084V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SET MUTATED         0        0        1        0         0         1
  SET WILD-TYPE       2       15       39       30        37        51
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SET MUTATED           0          1          1          1        2
  SET WILD-TYPE         3         69         52         31       36
D1084V3, multiclass
            clus
vv           SET MUTATED SET WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             1            39
  STAGE II             0            30
  STAGE IIA            0            37
  STAGE IIB            1            51
  STAGE III            0             3
  STAGE IIIA           1            69
  STAGE IIIB           1            52
  STAGE IIIC           1            31
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SET MUTATED     0   1   2   4
  SET WILD-TYPE  22  91 171  93
D1084V4, multiclass
    clus
vv   SET MUTATED SET WILD-TYPE
  T1           0            22
  T2           1            91
  T3           2           171
  T4           4            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
  SET MUTATED     2   2   2   1
  SET WILD-TYPE 116 102  75  76
D1084V5, multiclass
    clus
vv   SET MUTATED SET WILD-TYPE
  N0           2           116
  N1           2           102
  N2           2            75
  N3           1            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"
D1084V6, binary
               cls
clus              0   1
  SET MUTATED     4   2
  SET WILD-TYPE 342  27
[1] "tbl2"
               cls
clus            [,1] [,2]
  SET MUTATED      4    2
  SET WILD-TYPE  342   27
   clus
vv  SET MUTATED SET WILD-TYPE
  0           4           342
  1           2            27
[1] 2 2
[1] FALSE
D1084V7, binary
               cls
clus              0   1
  SET MUTATED     5   2
  SET WILD-TYPE 140 246
[1] "tbl2"
               cls
clus            [,1] [,2]
  SET MUTATED      5    2
  SET WILD-TYPE  140  246
        clus
vv       SET MUTATED SET WILD-TYPE
  FEMALE           5           140
  MALE             2           246
[1] 2 2
[1] FALSE
D1084V8, binary
               cls
clus              0   1
  SET MUTATED     4   1
  SET WILD-TYPE 288  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  SET MUTATED      4    1
  SET WILD-TYPE  288   58
     clus
vv    SET MUTATED SET WILD-TYPE
  NO            4           288
  YES           1            58
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SET MUTATED                                          0
  SET WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SET MUTATED                                       1
  SET WILD-TYPE                                    69
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SET MUTATED                                                        2
  SET WILD-TYPE                                                    156
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SET MUTATED                                                   0
  SET WILD-TYPE                                                21
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SET MUTATED                                                                   2
  SET WILD-TYPE                                                                66
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SET MUTATED                                                    0
  SET WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SET MUTATED                                                  1
  SET WILD-TYPE                                               60
D1084V9, multiclass
                                                                   clus
vv                                                                  SET MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            1
                                                                   clus
vv                                                                  SET WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  SET MUTATED     5   0   2   0
  SET WILD-TYPE 306  14  13  24
D1084V10, multiclass
    clus
vv   SET MUTATED SET WILD-TYPE
  R0           5           306
  R1           0            14
  R2           2            13
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1084V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  SET MUTATED       1                         0
  SET WILD-TYPE    86                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SET MUTATED                                           0     3
  SET WILD-TYPE                                         1   240
D1084V12, multiclass
                                           clus
vv                                          SET MUTATED SET WILD-TYPE
  ASIAN                                               1            86
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               3           240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1084V13, binary
               cls
clus              0   1
  SET MUTATED     0   4
  SET WILD-TYPE   4 306
[1] "tbl2"
               cls
clus            [,1] [,2]
  SET MUTATED      0    4
  SET WILD-TYPE    4  306
                        clus
vv                       SET MUTATED SET WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           4           306
[1] 2 2
[1] FALSE

Clustering(1085) Variable = CASC5 MUTATION ANALYSIS
D1085V1, survival
                 sevent
clus2               0   1
  CASC5 MUTATED    14   4
  CASC5 WILD-TYPE 216 135
  CASC5 MUTATED CASC5 WILD-TYPE 
             18             351 
  CASC5 MUTATED CASC5 WILD-TYPE 
              4             135 
$`CASC5 MUTATED`
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-7197 TCGA-BR-7703 
       19.56         9.44         6.97        34.68         9.21        36.16 
TCGA-BR-8077 TCGA-BR-8081 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A452 TCGA-CD-8533 
        0.69        32.25        28.14        31.96         7.53        15.39 
TCGA-CD-A4MI TCGA-CG-4437 TCGA-CG-4441 TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-VQ-A8P2 
       11.77         8.05        14.01        11.77         2.10        38.14 

$`CASC5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        26.70        11.70        11.01         9.47 
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-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       21.90        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-8078 TCGA-BR-8080 TCGA-BR-8284 
       37.25        14.43        11.44        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-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-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-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-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-4438 
        3.02        27.02        15.95         1.02         7.99        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-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-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 

  CASC5 MUTATED CASC5 WILD-TYPE 
           0.69            0.00 
  CASC5 MUTATED CASC5 WILD-TYPE 
          38.14          122.30 
  CASC5 MUTATED CASC5 WILD-TYPE 
          12.89           14.43 
[1] "0.7 - 38.1 (12.9)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.7"
D1085V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CASC5 MUTATED         0        2        0        3         1         2
  CASC5 WILD-TYPE       2       13       40       27        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASC5 MUTATED           0          6          1          3        2
  CASC5 WILD-TYPE         3         64         52         29       36
D1085V3, multiclass
            clus
vv           CASC5 MUTATED CASC5 WILD-TYPE
  STAGE I                0               2
  STAGE IA               2              13
  STAGE IB               0              40
  STAGE II               3              27
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             6              64
  STAGE IIIB             1              52
  STAGE IIIC             3              29
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASC5 MUTATED     2   2   5  11
  CASC5 WILD-TYPE  20  90 168  86
D1085V4, multiclass
    clus
vv   CASC5 MUTATED CASC5 WILD-TYPE
  T1             2              20
  T2             2              90
  T3             5             168
  T4            11              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
  CASC5 MUTATED     7   7   3   3
  CASC5 WILD-TYPE 111  97  74  74
D1085V5, multiclass
    clus
vv   CASC5 MUTATED CASC5 WILD-TYPE
  N0             7             111
  N1             7              97
  N2             3              74
  N3             3              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"
D1085V6, binary
                 cls
clus                0   1
  CASC5 MUTATED    19   1
  CASC5 WILD-TYPE 327  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC5 MUTATED     19    1
  CASC5 WILD-TYPE  327   28
   clus
vv  CASC5 MUTATED CASC5 WILD-TYPE
  0            19             327
  1             1              28
[1] 2 2
[1] FALSE
D1085V7, binary
                 cls
clus                0   1
  CASC5 MUTATED     6  15
  CASC5 WILD-TYPE 139 233
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC5 MUTATED      6   15
  CASC5 WILD-TYPE  139  233
        clus
vv       CASC5 MUTATED CASC5 WILD-TYPE
  FEMALE             6             139
  MALE              15             233
[1] 2 2
[1] FALSE
D1085V8, binary
                 cls
clus                0   1
  CASC5 MUTATED    15   1
  CASC5 WILD-TYPE 277  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC5 MUTATED     15    1
  CASC5 WILD-TYPE  277   58
     clus
vv    CASC5 MUTATED CASC5 WILD-TYPE
  NO             15             277
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CASC5 MUTATED                                          0
  CASC5 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CASC5 MUTATED                                       2
  CASC5 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CASC5 MUTATED                                                       11
  CASC5 WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CASC5 MUTATED                                                   1
  CASC5 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CASC5 MUTATED                                                                   3
  CASC5 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CASC5 MUTATED                                                    1
  CASC5 WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CASC5 MUTATED                                                  3
  CASC5 WILD-TYPE                                               58
D1085V9, multiclass
                                                                   clus
vv                                                                  CASC5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  CASC5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CASC5 MUTATED    14   0   0   4
  CASC5 WILD-TYPE 297  14  15  20
D1085V10, multiclass
    clus
vv   CASC5 MUTATED CASC5 WILD-TYPE
  R0            14             297
  R1             0              14
  R2             0              15
  RX             4              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1085V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CASC5 MUTATED       6                         0
  CASC5 WILD-TYPE    81                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CASC5 MUTATED                                           0    13
  CASC5 WILD-TYPE                                         1   230
D1085V12, multiclass
                                           clus
vv                                          CASC5 MUTATED CASC5 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                13             230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1085V13, binary
                 cls
clus                0   1
  CASC5 MUTATED     0  18
  CASC5 WILD-TYPE   4 292
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC5 MUTATED      0   18
  CASC5 WILD-TYPE    4  292
                        clus
vv                       CASC5 MUTATED CASC5 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            18             292
[1] 2 2
[1] FALSE

Clustering(1086) Variable = BEND5 MUTATION ANALYSIS
D1086V1, survival
                 sevent
clus2               0   1
  BEND5 MUTATED     1   2
  BEND5 WILD-TYPE 229 137
  BEND5 MUTATED BEND5 WILD-TYPE 
              3             366 
  BEND5 MUTATED BEND5 WILD-TYPE 
              2             137 
$`BEND5 MUTATED`
TCGA-CG-4460 TCGA-CG-5727 TCGA-HJ-7597 
       21.99        79.07        26.47 

$`BEND5 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 
       47.05        22.98        16.24         0.23        20.15         9.86 
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 

  BEND5 MUTATED BEND5 WILD-TYPE 
          21.99            0.00 
  BEND5 MUTATED BEND5 WILD-TYPE 
          79.07          122.30 
  BEND5 MUTATED BEND5 WILD-TYPE 
          26.47           14.12 
[1] "22.0 - 79.1 (26.5)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D1086V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  BEND5 MUTATED         0        0        2        1         0         1
  BEND5 WILD-TYPE       2       15       38       29        37        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BEND5 MUTATED           0          0          0          0        1
  BEND5 WILD-TYPE         3         70         53         32       37
D1086V3, multiclass
            clus
vv           BEND5 MUTATED BEND5 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BEND5 MUTATED     0   2   1   2
  BEND5 WILD-TYPE  22  90 172  95
D1086V4, multiclass
    clus
vv   BEND5 MUTATED BEND5 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             1             172
  T4             2              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
  BEND5 MUTATED     4   1   0   0
  BEND5 WILD-TYPE 114 103  77  77
D1086V5, multiclass
    clus
vv   BEND5 MUTATED BEND5 WILD-TYPE
  N0             4             114
  N1             1             103
  N2             0              77
  N3             0              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"
D1086V6, binary
                 cls
clus                0   1
  BEND5 MUTATED     4   1
  BEND5 WILD-TYPE 342  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND5 MUTATED      4    1
  BEND5 WILD-TYPE  342   28
   clus
vv  BEND5 MUTATED BEND5 WILD-TYPE
  0             4             342
  1             1              28
[1] 2 2
[1] FALSE
D1086V7, binary
                 cls
clus                0   1
  BEND5 MUTATED     3   3
  BEND5 WILD-TYPE 142 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND5 MUTATED      3    3
  BEND5 WILD-TYPE  142  245
        clus
vv       BEND5 MUTATED BEND5 WILD-TYPE
  FEMALE             3             142
  MALE               3             245
[1] 2 2
[1] FALSE
D1086V8, binary
                 cls
clus                0   1
  BEND5 MUTATED     4   0
  BEND5 WILD-TYPE 288  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND5 MUTATED      4    0
  BEND5 WILD-TYPE  288   59
     clus
vv    BEND5 MUTATED BEND5 WILD-TYPE
  NO              4             288
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  BEND5 MUTATED                                          1
  BEND5 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  BEND5 MUTATED                                       0
  BEND5 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BEND5 MUTATED                                                        1
  BEND5 WILD-TYPE                                                    157
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  BEND5 MUTATED                                                   0
  BEND5 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  BEND5 MUTATED                                                                   4
  BEND5 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  BEND5 MUTATED                                                    0
  BEND5 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  BEND5 MUTATED                                                  0
  BEND5 WILD-TYPE                                               61
D1086V9, multiclass
                                                                   clus
vv                                                                  BEND5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  BEND5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BEND5 MUTATED     4   0   1   1
  BEND5 WILD-TYPE 307  14  14  23
D1086V10, multiclass
    clus
vv   BEND5 MUTATED BEND5 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1086V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  BEND5 MUTATED       0                         0
  BEND5 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  BEND5 MUTATED                                           0     3
  BEND5 WILD-TYPE                                         1   240
D1086V12, multiclass
                                           clus
vv                                          BEND5 MUTATED BEND5 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1086V13, binary
                 cls
clus                0   1
  BEND5 MUTATED     0   3
  BEND5 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND5 MUTATED      0    3
  BEND5 WILD-TYPE    4  307
                        clus
vv                       BEND5 MUTATED BEND5 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(1087) Variable = FGF22 MUTATION ANALYSIS
D1087V1, survival
                 sevent
clus2               0   1
  FGF22 MUTATED     4   0
  FGF22 WILD-TYPE 226 139
  FGF22 MUTATED FGF22 WILD-TYPE 
              4             365 
  FGF22 MUTATED FGF22 WILD-TYPE 
              0             139 
$`FGF22 MUTATED`
TCGA-CD-8536 TCGA-HF-A5NB TCGA-HU-A4G8 TCGA-HU-A4GN 
       12.43        30.51        22.68        29.98 

$`FGF22 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  FGF22 MUTATED FGF22 WILD-TYPE 
          12.43            0.00 
  FGF22 MUTATED FGF22 WILD-TYPE 
          30.51          122.30 
  FGF22 MUTATED FGF22 WILD-TYPE 
          26.33           14.17 
[1] "12.4 - 30.5 (26.3)" "0.0 - 122.3 (14.2)"
[1] "hr="     "9100000"
D1087V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FGF22 MUTATED         0        0        0        1         1         1
  FGF22 WILD-TYPE       2       15       40       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FGF22 MUTATED           0          0          0          1        0
  FGF22 WILD-TYPE         3         70         53         31       38
D1087V3, multiclass
            clus
vv           FGF22 MUTATED FGF22 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FGF22 MUTATED     0   1   2   1
  FGF22 WILD-TYPE  22  91 171  96
D1087V4, multiclass
    clus
vv   FGF22 MUTATED FGF22 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             2             171
  T4             1              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
  FGF22 MUTATED     1   2   0   1
  FGF22 WILD-TYPE 117 102  77  76
D1087V5, multiclass
    clus
vv   FGF22 MUTATED FGF22 WILD-TYPE
  N0             1             117
  N1             2             102
  N2             0              77
  N3             1              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"
D1087V6, binary
                 cls
clus                0   1
  FGF22 MUTATED     4   0
  FGF22 WILD-TYPE 342  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF22 MUTATED      4    0
  FGF22 WILD-TYPE  342   29
   clus
vv  FGF22 MUTATED FGF22 WILD-TYPE
  0             4             342
  1             0              29
[1] 2 2
[1] FALSE
D1087V7, binary
                 cls
clus                0   1
  FGF22 MUTATED     2   2
  FGF22 WILD-TYPE 143 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF22 MUTATED      2    2
  FGF22 WILD-TYPE  143  246
        clus
vv       FGF22 MUTATED FGF22 WILD-TYPE
  FEMALE             2             143
  MALE               2             246
[1] 2 2
[1] FALSE
D1087V8, binary
                 cls
clus                0   1
  FGF22 MUTATED     3   1
  FGF22 WILD-TYPE 289  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF22 MUTATED      3    1
  FGF22 WILD-TYPE  289   58
     clus
vv    FGF22 MUTATED FGF22 WILD-TYPE
  NO              3             289
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FGF22 MUTATED                                          0
  FGF22 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FGF22 MUTATED                                       1
  FGF22 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FGF22 MUTATED                                                        1
  FGF22 WILD-TYPE                                                    157
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FGF22 MUTATED                                                   1
  FGF22 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FGF22 MUTATED                                                                   0
  FGF22 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FGF22 MUTATED                                                    0
  FGF22 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FGF22 MUTATED                                                  1
  FGF22 WILD-TYPE                                               60
D1087V9, multiclass
                                                                   clus
vv                                                                  FGF22 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  FGF22 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FGF22 MUTATED     2   1   0   0
  FGF22 WILD-TYPE 309  13  15  24
D1087V10, multiclass
    clus
vv   FGF22 MUTATED FGF22 WILD-TYPE
  R0             2             309
  R1             1              13
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1087V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  FGF22 MUTATED       3                         0
  FGF22 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FGF22 MUTATED                                           0     0
  FGF22 WILD-TYPE                                         1   243
D1087V12, multiclass
                                           clus
vv                                          FGF22 MUTATED FGF22 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 0             243
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1087V13, binary
                 cls
clus                0   1
  FGF22 MUTATED     0   3
  FGF22 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF22 MUTATED      0    3
  FGF22 WILD-TYPE    4  307
                        clus
vv                       FGF22 MUTATED FGF22 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(1088) Variable = EIF2AK3 MUTATION ANALYSIS
D1088V1, survival
                   sevent
clus2                 0   1
  EIF2AK3 MUTATED    13   3
  EIF2AK3 WILD-TYPE 217 136
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
               16               353 
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
                3               136 
$`EIF2AK3 MUTATED`
TCGA-B7-5816 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8059 TCGA-BR-8360 
       26.70         9.67        34.68        36.16        14.43         6.18 
TCGA-BR-A4PD TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-6528 TCGA-D7-A74A TCGA-FP-8631 
       20.65         6.02        65.10        15.22        19.96         0.56 
TCGA-HU-8604 TCGA-IN-A6RJ TCGA-VQ-A8DL TCGA-VQ-A8P2 
       22.82        12.46         0.92        38.14 

$`EIF2AK3 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-D7-6815 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-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-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-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-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 

  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
             0.56              0.00 
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
             65.1             122.3 
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
            17.59             14.07 
[1] "0.6 - 65.1 (17.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.2"
D1088V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EIF2AK3 MUTATED         1        2        2        0         4         2
  EIF2AK3 WILD-TYPE       1       13       38       30        33        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF2AK3 MUTATED           1          3          0          0        2
  EIF2AK3 WILD-TYPE         2         67         53         32       36
D1088V3, multiclass
            clus
vv           EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 2                13
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                4                33
  STAGE IIB                2                50
  STAGE III                1                 2
  STAGE IIIA               3                67
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  EIF2AK3 MUTATED     3   2   6   6
  EIF2AK3 WILD-TYPE  19  90 167  91
D1088V4, multiclass
    clus
vv   EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  T1               3                19
  T2               2                90
  T3               6               167
  T4               6                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
  EIF2AK3 MUTATED    10   5   3   0
  EIF2AK3 WILD-TYPE 108  99  74  77
D1088V5, multiclass
    clus
vv   EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  N0              10               108
  N1               5                99
  N2               3                74
  N3               0                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"
D1088V6, binary
                   cls
clus                  0   1
  EIF2AK3 MUTATED    16   1
  EIF2AK3 WILD-TYPE 330  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK3 MUTATED     16    1
  EIF2AK3 WILD-TYPE  330   28
   clus
vv  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  0              16               330
  1               1                28
[1] 2 2
[1] FALSE
D1088V7, binary
                   cls
clus                  0   1
  EIF2AK3 MUTATED    11   8
  EIF2AK3 WILD-TYPE 134 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK3 MUTATED     11    8
  EIF2AK3 WILD-TYPE  134  240
        clus
vv       EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  FEMALE              11               134
  MALE                 8               240
[1] 2 2
[1] FALSE
D1088V8, binary
                   cls
clus                  0   1
  EIF2AK3 MUTATED    14   1
  EIF2AK3 WILD-TYPE 278  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK3 MUTATED     14    1
  EIF2AK3 WILD-TYPE  278   58
     clus
vv    EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  NO               14               278
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EIF2AK3 MUTATED                                          0
  EIF2AK3 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EIF2AK3 MUTATED                                       2
  EIF2AK3 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EIF2AK3 MUTATED                                                        6
  EIF2AK3 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EIF2AK3 MUTATED                                                   1
  EIF2AK3 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EIF2AK3 MUTATED                                                                   5
  EIF2AK3 WILD-TYPE                                                                63
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EIF2AK3 MUTATED                                                    1
  EIF2AK3 WILD-TYPE                                                  4
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EIF2AK3 MUTATED                                                  4
  EIF2AK3 WILD-TYPE                                               57
D1088V9, multiclass
                                                                   clus
vv                                                                  EIF2AK3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                4
                                                                   clus
vv                                                                  EIF2AK3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  EIF2AK3 MUTATED    16   0   1   2
  EIF2AK3 WILD-TYPE 295  14  14  22
D1088V10, multiclass
    clus
vv   EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  R0              16               295
  R1               0                14
  R2               1                14
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1088V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  EIF2AK3 MUTATED       1                         1
  EIF2AK3 WILD-TYPE    86                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EIF2AK3 MUTATED                                           0    14
  EIF2AK3 WILD-TYPE                                         1   229
D1088V12, multiclass
                                           clus
vv                                          EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  14               229
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1088V13, binary
                   cls
clus                  0   1
  EIF2AK3 MUTATED     0  14
  EIF2AK3 WILD-TYPE   4 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK3 MUTATED      0   14
  EIF2AK3 WILD-TYPE    4  296
                        clus
vv                       EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              14               296
[1] 2 2
[1] FALSE

Clustering(1089) Variable = GALK1 MUTATION ANALYSIS
D1089V1, survival
                 sevent
clus2               0   1
  GALK1 MUTATED     1   1
  GALK1 WILD-TYPE 229 138
  GALK1 MUTATED GALK1 WILD-TYPE 
              2             367 
  GALK1 MUTATED GALK1 WILD-TYPE 
              1             138 
$`GALK1 MUTATED`
TCGA-CD-A4MG TCGA-FP-A4BE 
        6.58        11.08 

$`GALK1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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 

  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           14.43 
[1] "6.6 - 11.1 (8.8)"   "0.0 - 122.3 (14.4)"
[1] "Remove cluster labels:" "GALK1 MUTATED"         
D1089V2, 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       2       15       40       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GALK1 MUTATED           0          1          0          0        0
  GALK1 WILD-TYPE         3         69         53         32       38
D1089V3, multiclass
            clus
vv           GALK1 MUTATED GALK1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GALK1 MUTATED     0   0   2   1
  GALK1 WILD-TYPE  22  92 171  96
D1089V4, multiclass
    clus
vv   GALK1 MUTATED GALK1 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             2             171
  T4             1              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
  GALK1 MUTATED     3   0   0   0
  GALK1 WILD-TYPE 115 104  77  77
D1089V5, multiclass
    clus
vv   GALK1 MUTATED GALK1 WILD-TYPE
  N0             3             115
  N1             0             104
  N2             0              77
  N3             0              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"
D1089V6, binary
                 cls
clus                0   1
  GALK1 MUTATED     4   0
  GALK1 WILD-TYPE 342  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GALK1 MUTATED      4    0
  GALK1 WILD-TYPE  342   29
   clus
vv  GALK1 MUTATED GALK1 WILD-TYPE
  0             4             342
  1             0              29
[1] 2 2
[1] FALSE
D1089V7, binary
                 cls
clus                0   1
  GALK1 MUTATED     2   2
  GALK1 WILD-TYPE 143 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GALK1 MUTATED      2    2
  GALK1 WILD-TYPE  143  246
        clus
vv       GALK1 MUTATED GALK1 WILD-TYPE
  FEMALE             2             143
  MALE               2             246
[1] 2 2
[1] FALSE
D1089V8, binary
                 cls
clus                0   1
  GALK1 MUTATED     1   1
  GALK1 WILD-TYPE 291  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GALK1 MUTATED      1    1
  GALK1 WILD-TYPE  291   58
     clus
vv    GALK1 MUTATED GALK1 WILD-TYPE
  NO              1             291
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GALK1 MUTATED                                          0
  GALK1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GALK1 MUTATED                                       1
  GALK1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GALK1 MUTATED                                                        3
  GALK1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GALK1 MUTATED                                                   0
  GALK1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GALK1 MUTATED                                                                   0
  GALK1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GALK1 MUTATED                                                    0
  GALK1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GALK1 MUTATED                                                  0
  GALK1 WILD-TYPE                                               61
D1089V9, multiclass
                                                                   clus
vv                                                                  GALK1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  GALK1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GALK1 MUTATED     1   0   0   2
  GALK1 WILD-TYPE 310  14  15  22
D1089V10, multiclass
    clus
vv   GALK1 MUTATED GALK1 WILD-TYPE
  R0             1             310
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1089V11, continuous
[1] "Remove cluster labels:" "GALK1 MUTATED"         
clus
  GALK1 MUTATED GALK1 WILD-TYPE 
              2             341 
     TCGA-CG-4444      TCGA-CG-4460      TCGA-CG-4475      TCGA-CG-4476 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-5727      TCGA-EQ-A4SO      TCGA-F1-6177      TCGA-FP-A8CX 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HF-7131      TCGA-KB-A93G      TCGA-MX-A663      TCGA-B7-5816 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-B7-A5TI      TCGA-BR-4183      TCGA-BR-4184      TCGA-BR-4188 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-4191      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4362 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-4368      TCGA-BR-6452      TCGA-BR-6453      TCGA-BR-6454 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457      TCGA-BR-6458 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-6563      TCGA-BR-6564      TCGA-BR-6565      TCGA-BR-6566 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707      TCGA-BR-6709 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-6852      TCGA-BR-7196      TCGA-BR-7197      TCGA-BR-7703 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-7704      TCGA-BR-7707      TCGA-BR-7715      TCGA-BR-7716 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-7717      TCGA-BR-7722      TCGA-BR-7723      TCGA-BR-7851 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-7901      TCGA-BR-7957      TCGA-BR-7958      TCGA-BR-7959 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8058      TCGA-BR-8059      TCGA-BR-8060      TCGA-BR-8077 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8078      TCGA-BR-8080      TCGA-BR-8081      TCGA-BR-8284 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8285      TCGA-BR-8286      TCGA-BR-8289      TCGA-BR-8291 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8295      TCGA-BR-8297      TCGA-BR-8360      TCGA-BR-8361 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8363      TCGA-BR-8364      TCGA-BR-8365      TCGA-BR-8366 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8367      TCGA-BR-8368      TCGA-BR-8369      TCGA-BR-8370 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8371      TCGA-BR-8372      TCGA-BR-8373      TCGA-BR-8380 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8381      TCGA-BR-8382      TCGA-BR-8384      TCGA-BR-8483 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8484      TCGA-BR-8485      TCGA-BR-8486      TCGA-BR-8487 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8588      TCGA-BR-8589      TCGA-BR-8590      TCGA-BR-8591 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8592      TCGA-BR-8676      TCGA-BR-8677      TCGA-BR-8678 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8679      TCGA-BR-8680      TCGA-BR-8682      TCGA-BR-8683 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-8686      TCGA-BR-8687      TCGA-BR-8690      TCGA-BR-A44T 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-A44U      TCGA-BR-A452      TCGA-BR-A453      TCGA-BR-A4CQ 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-A4CR      TCGA-BR-A4CS      TCGA-BR-A4IU      TCGA-BR-A4IV 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-A4IY      TCGA-BR-A4IZ      TCGA-BR-A4J1      TCGA-BR-A4J2 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-A4J4      TCGA-BR-A4J5      TCGA-BR-A4J6      TCGA-BR-A4J8 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-A4PD      TCGA-BR-A4PE      TCGA-BR-A4PF      TCGA-BR-A4QI 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-BR-A4QL      TCGA-BR-A4QM      TCGA-CD-5804      TCGA-CD-8525 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CD-8526      TCGA-CD-8531      TCGA-CD-8535      TCGA-CD-A487 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4436 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-4437      TCGA-CG-4438      TCGA-CG-4440      TCGA-CG-4441 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-4442      TCGA-CG-4443      TCGA-CG-4449      TCGA-CG-4455 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-4462      TCGA-CG-4465      TCGA-CG-4466      TCGA-CG-4469 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-4474      TCGA-CG-4477      TCGA-CG-5717      TCGA-CG-5718 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-5719      TCGA-CG-5720      TCGA-CG-5721      TCGA-CG-5722 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-5723      TCGA-CG-5724      TCGA-CG-5725      TCGA-CG-5726 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-5728      TCGA-CG-5730      TCGA-CG-5732      TCGA-CG-5733 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-CG-5734      TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-5579 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-6518      TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6525      TCGA-D7-6526 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815      TCGA-D7-6817 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822      TCGA-D7-8570 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-8572      TCGA-D7-8573      TCGA-D7-8574      TCGA-D7-8575 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-8576      TCGA-D7-8578      TCGA-D7-8579      TCGA-D7-A4YT 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-A4YU      TCGA-D7-A4YV      TCGA-D7-A4YX      TCGA-D7-A4YY 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-A4Z0      TCGA-D7-A6ET      TCGA-D7-A6EV      TCGA-D7-A6EX 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-A6EY      TCGA-D7-A6EZ      TCGA-D7-A6F0      TCGA-D7-A6F2 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-D7-A747      TCGA-D7-A748      TCGA-D7-A74A      TCGA-D7-A74B 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-EQ-5647      TCGA-EQ-8122      TCGA-F1-6874      TCGA-F1-6875 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-F1-A448      TCGA-F1-A72C      TCGA-FP-7735      TCGA-FP-7829 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-FP-7916      TCGA-FP-7998      TCGA-FP-8099      TCGA-FP-8209 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-FP-8210      TCGA-FP-8211      TCGA-FP-8631      TCGA-FP-A4BF 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-FP-A9TM      TCGA-HF-7132      TCGA-HF-7133      TCGA-HF-7134 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HF-7136      TCGA-HF-A5NB      TCGA-HJ-7597      TCGA-HU-8238 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-8243      TCGA-HU-8244      TCGA-HU-8249      TCGA-HU-8602 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-8604      TCGA-HU-8608      TCGA-HU-8610      TCGA-HU-A4G2 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-A4G3      TCGA-HU-A4G6      TCGA-HU-A4G8      TCGA-HU-A4G9 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-A4GC      TCGA-HU-A4GD      TCGA-HU-A4GF      TCGA-HU-A4GH 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-A4GJ      TCGA-HU-A4GN      TCGA-HU-A4GP      TCGA-HU-A4GQ 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-A4GT      TCGA-HU-A4GU      TCGA-HU-A4GX      TCGA-HU-A4GY 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-A4H0      TCGA-HU-A4H2      TCGA-HU-A4H3      TCGA-HU-A4H4 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-A4H5      TCGA-HU-A4H6      TCGA-HU-A4H8      TCGA-HU-A4HB 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-HU-A4HD      TCGA-IN-7806      TCGA-IN-7808      TCGA-IN-8462 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-IN-8663      TCGA-IN-A6RI      TCGA-IN-A6RJ      TCGA-IN-A6RL 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-IN-A6RN      TCGA-IN-A6RO      TCGA-IN-A6RP      TCGA-IN-A6RR 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-IN-A6RS      TCGA-IN-A7NR      TCGA-IN-A7NT      TCGA-IN-A7NU 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-IN-AB1V      TCGA-IN-AB1X      TCGA-IP-7968      TCGA-KB-A6F5 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-KB-A6F7      TCGA-KB-A93J      TCGA-MX-A5UG      TCGA-MX-A5UJ 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-R5-A7ZI      TCGA-RD-A7BS      TCGA-RD-A7BT      TCGA-RD-A7BW 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-RD-A7C1      TCGA-RD-A8MV      TCGA-RD-A8MW      TCGA-RD-A8N0 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-RD-A8N1      TCGA-RD-A8N2      TCGA-RD-A8N4      TCGA-RD-A8N5 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-RD-A8N6      TCGA-RD-A8N9      TCGA-SW-A7EA      TCGA-SW-A7EB 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-VQ-A8DL      TCGA-VQ-A8DT      TCGA-VQ-A8DU      TCGA-VQ-A8DV 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-VQ-A8DZ      TCGA-VQ-A8E2      TCGA-VQ-A8E7      TCGA-VQ-A8P2 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-VQ-A8P3      TCGA-VQ-A8PE      TCGA-VQ-A8PK      TCGA-VQ-A8PM 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-VQ-A8PQ      TCGA-VQ-A91Q      TCGA-VQ-A91U      TCGA-VQ-A91V 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-VQ-A92D      TCGA-VQ-A94T      TCGA-VQ-AA64      TCGA-VQ-AA68 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-VQ-AA69      TCGA-VQ-AA6A      TCGA-VQ-AA6B      TCGA-VQ-AA6F 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-VQ-AA6G      TCGA-VQ-AA6I      TCGA-VQ-AA6J      TCGA-VQ-AA6K 
"GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" "GALK1 WILD-TYPE" 
     TCGA-ZA-A8F6 
"GALK1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GALK1 MUTATED       1                         1
  GALK1 WILD-TYPE    86                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GALK1 MUTATED                                           0     2
  GALK1 WILD-TYPE                                         1   241
D1089V12, multiclass
                                           clus
vv                                          GALK1 MUTATED GALK1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1089V13, binary
                 cls
clus                0   1
  GALK1 MUTATED     0   4
  GALK1 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GALK1 MUTATED      0    4
  GALK1 WILD-TYPE    4  306
                        clus
vv                       GALK1 MUTATED GALK1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(1090) Variable = ZNF334 MUTATION ANALYSIS
D1090V1, survival
                  sevent
clus2                0   1
  ZNF334 MUTATED    10   1
  ZNF334 WILD-TYPE 220 138
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              11              358 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
               1              138 
$`ZNF334 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8680 TCGA-CG-5723 
        6.97        34.68        44.94        32.25        31.96       105.07 
TCGA-HU-8602 TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4GU TCGA-VQ-A8P2 
       22.32        11.77         6.51         6.58        38.14 

$`ZNF334 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  ZNF334 MUTATED ZNF334 WILD-TYPE 
            6.51             0.00 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
          105.07           122.30 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
           31.96            14.12 
[1] "6.5 - 105.1 (32.0)" "0.0 - 122.3 (14.1)"
[1] "hr=" "6"  
D1090V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF334 MUTATED         0        1        1        1         3         3
  ZNF334 WILD-TYPE       2       14       39       29        34        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF334 MUTATED           0          2          0          0        2
  ZNF334 WILD-TYPE         3         68         53         32       36
D1090V3, multiclass
            clus
vv           ZNF334 MUTATED ZNF334 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF334 MUTATED     1   2   5   5
  ZNF334 WILD-TYPE  21  90 168  92
D1090V4, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  T1              1               21
  T2              2               90
  T3              5              168
  T4              5               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
  ZNF334 MUTATED     7   4   2   0
  ZNF334 WILD-TYPE 111 100  75  77
D1090V5, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  N0              7              111
  N1              4              100
  N2              2               75
  N3              0               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"
D1090V6, binary
                  cls
clus                 0   1
  ZNF334 MUTATED    11   1
  ZNF334 WILD-TYPE 335  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED     11    1
  ZNF334 WILD-TYPE  335   28
   clus
vv  ZNF334 MUTATED ZNF334 WILD-TYPE
  0             11              335
  1              1               28
[1] 2 2
[1] FALSE
D1090V7, binary
                  cls
clus                 0   1
  ZNF334 MUTATED     6   7
  ZNF334 WILD-TYPE 139 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED      6    7
  ZNF334 WILD-TYPE  139  241
        clus
vv       ZNF334 MUTATED ZNF334 WILD-TYPE
  FEMALE              6              139
  MALE                7              241
[1] 2 2
[1] FALSE
D1090V8, binary
                  cls
clus                 0   1
  ZNF334 MUTATED    10   1
  ZNF334 WILD-TYPE 282  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED     10    1
  ZNF334 WILD-TYPE  282   58
     clus
vv    ZNF334 MUTATED ZNF334 WILD-TYPE
  NO              10              282
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF334 MUTATED                                          0
  ZNF334 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF334 MUTATED                                       2
  ZNF334 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF334 MUTATED                                                        6
  ZNF334 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF334 MUTATED                                                   1
  ZNF334 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF334 MUTATED                                                                   1
  ZNF334 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF334 MUTATED                                                    0
  ZNF334 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF334 MUTATED                                                  3
  ZNF334 WILD-TYPE                                               58
D1090V9, multiclass
                                                                   clus
vv                                                                  ZNF334 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  ZNF334 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF334 MUTATED    11   0   0   2
  ZNF334 WILD-TYPE 300  14  15  22
D1090V10, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  R0             11              300
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1090V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF334 MUTATED       5                         0
  ZNF334 WILD-TYPE    82                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF334 MUTATED                                           0     6
  ZNF334 WILD-TYPE                                         1   237
D1090V12, multiclass
                                           clus
vv                                          ZNF334 MUTATED ZNF334 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1090V13, binary
                  cls
clus                 0   1
  ZNF334 MUTATED     0  10
  ZNF334 WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED      0   10
  ZNF334 WILD-TYPE    4  300
                        clus
vv                       ZNF334 MUTATED ZNF334 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(1091) Variable = HORMAD1 MUTATION ANALYSIS
D1091V1, survival
                   sevent
clus2                 0   1
  HORMAD1 MUTATED     4   3
  HORMAD1 WILD-TYPE 226 136
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
                7               362 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
                3               136 
$`HORMAD1 MUTATED`
TCGA-CG-4460 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-8361 TCGA-CD-A4MJ TCGA-D7-A6EY 
       21.99        11.70         6.97        31.10        12.62        11.44 
TCGA-HF-7132 
       77.29 

$`HORMAD1 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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 

  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
             6.97              0.00 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
            77.29            122.30 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
            12.62             14.35 
[1] "7.0 - 77.3 (12.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D1091V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HORMAD1 MUTATED         0        0        2        1         0         0
  HORMAD1 WILD-TYPE       2       15       38       29        37        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HORMAD1 MUTATED           0          1          1          1        1
  HORMAD1 WILD-TYPE         3         69         52         31       37
D1091V3, multiclass
            clus
vv           HORMAD1 MUTATED HORMAD1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 1                29
  STAGE IIA                0                37
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  HORMAD1 MUTATED     0   3   2   2
  HORMAD1 WILD-TYPE  22  89 171  95
D1091V4, multiclass
    clus
vv   HORMAD1 MUTATED HORMAD1 WILD-TYPE
  T1               0                22
  T2               3                89
  T3               2               171
  T4               2                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
  HORMAD1 MUTATED     2   3   1   1
  HORMAD1 WILD-TYPE 116 101  76  76
D1091V5, multiclass
    clus
vv   HORMAD1 MUTATED HORMAD1 WILD-TYPE
  N0               2               116
  N1               3               101
  N2               1                76
  N3               1                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"
D1091V6, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     5   1
  HORMAD1 WILD-TYPE 341  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      5    1
  HORMAD1 WILD-TYPE  341   28
   clus
vv  HORMAD1 MUTATED HORMAD1 WILD-TYPE
  0               5               341
  1               1                28
[1] 2 2
[1] FALSE
D1091V7, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     3   4
  HORMAD1 WILD-TYPE 142 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      3    4
  HORMAD1 WILD-TYPE  142  244
        clus
vv       HORMAD1 MUTATED HORMAD1 WILD-TYPE
  FEMALE               3               142
  MALE                 4               244
[1] 2 2
[1] FALSE
D1091V8, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     6   1
  HORMAD1 WILD-TYPE 286  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      6    1
  HORMAD1 WILD-TYPE  286   58
     clus
vv    HORMAD1 MUTATED HORMAD1 WILD-TYPE
  NO                6               286
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HORMAD1 MUTATED                                          0
  HORMAD1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HORMAD1 MUTATED                                       1
  HORMAD1 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HORMAD1 MUTATED                                                        3
  HORMAD1 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HORMAD1 MUTATED                                                   1
  HORMAD1 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HORMAD1 MUTATED                                                                   1
  HORMAD1 WILD-TYPE                                                                67
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HORMAD1 MUTATED                                                    0
  HORMAD1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HORMAD1 MUTATED                                                  1
  HORMAD1 WILD-TYPE                                               60
D1091V9, multiclass
                                                                   clus
vv                                                                  HORMAD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  HORMAD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  HORMAD1 MUTATED     4   0   1   1
  HORMAD1 WILD-TYPE 307  14  14  23
D1091V10, multiclass
    clus
vv   HORMAD1 MUTATED HORMAD1 WILD-TYPE
  R0               4               307
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1091V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  HORMAD1 MUTATED       1                         0
  HORMAD1 WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HORMAD1 MUTATED                                           0     4
  HORMAD1 WILD-TYPE                                         1   239
D1091V12, multiclass
                                           clus
vv                                          HORMAD1 MUTATED HORMAD1 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1091V13, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     0   5
  HORMAD1 WILD-TYPE   4 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      0    5
  HORMAD1 WILD-TYPE    4  305
                        clus
vv                       HORMAD1 MUTATED HORMAD1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(1092) Variable = CSNK1G1 MUTATION ANALYSIS
D1092V1, survival
                   sevent
clus2                 0   1
  CSNK1G1 MUTATED     5   1
  CSNK1G1 WILD-TYPE 225 138
  CSNK1G1 MUTATED CSNK1G1 WILD-TYPE 
                6               363 
  CSNK1G1 MUTATED CSNK1G1 WILD-TYPE 
                1               138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  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            14.430 
[1] "1.0 - 38.1 (7.7)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.8"
D1092V2, 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       2       15       39       30        35        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK1G1 MUTATED           0          1          0          1        1
  CSNK1G1 WILD-TYPE         3         69         53         31       37
D1092V3, multiclass
            clus
vv           CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CSNK1G1 MUTATED     0   1   4   2
  CSNK1G1 WILD-TYPE  22  91 169  95
D1092V4, multiclass
    clus
vv   CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  T1               0                22
  T2               1                91
  T3               4               169
  T4               2                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
  CSNK1G1 MUTATED     3   1   2   0
  CSNK1G1 WILD-TYPE 115 103  75  77
D1092V5, multiclass
    clus
vv   CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  N0               3               115
  N1               1               103
  N2               2                75
  N3               0                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"
D1092V6, binary
                   cls
clus                  0   1
  CSNK1G1 MUTATED     5   1
  CSNK1G1 WILD-TYPE 341  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G1 MUTATED      5    1
  CSNK1G1 WILD-TYPE  341   28
   clus
vv  CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  0               5               341
  1               1                28
[1] 2 2
[1] FALSE
D1092V7, binary
                   cls
clus                  0   1
  CSNK1G1 MUTATED     4   3
  CSNK1G1 WILD-TYPE 141 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G1 MUTATED      4    3
  CSNK1G1 WILD-TYPE  141  245
        clus
vv       CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  FEMALE               4               141
  MALE                 3               245
[1] 2 2
[1] FALSE
D1092V8, binary
                   cls
clus                  0   1
  CSNK1G1 MUTATED     3   2
  CSNK1G1 WILD-TYPE 289  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G1 MUTATED      3    2
  CSNK1G1 WILD-TYPE  289   57
     clus
vv    CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  NO                3               289
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CSNK1G1 MUTATED                                          0
  CSNK1G1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CSNK1G1 MUTATED                                       0
  CSNK1G1 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CSNK1G1 MUTATED                                                        6
  CSNK1G1 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CSNK1G1 MUTATED                                                   1
  CSNK1G1 WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CSNK1G1 MUTATED                                                                   0
  CSNK1G1 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CSNK1G1 MUTATED                                                    0
  CSNK1G1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CSNK1G1 MUTATED                                                  0
  CSNK1G1 WILD-TYPE                                               61
D1092V9, multiclass
                                                                   clus
vv                                                                  CSNK1G1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  CSNK1G1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CSNK1G1 MUTATED     5   0   1   1
  CSNK1G1 WILD-TYPE 306  14  14  23
D1092V10, multiclass
    clus
vv   CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  R0               5               306
  R1               0                14
  R2               1                14
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1092V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  CSNK1G1 MUTATED       0                         1
  CSNK1G1 WILD-TYPE    87                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CSNK1G1 MUTATED                                           0     5
  CSNK1G1 WILD-TYPE                                         1   238
D1092V12, multiclass
                                           clus
vv                                          CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  ASIAN                                                   0                87
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1092V13, binary
                   cls
clus                  0   1
  CSNK1G1 MUTATED     0   5
  CSNK1G1 WILD-TYPE   4 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G1 MUTATED      0    5
  CSNK1G1 WILD-TYPE    4  305
                        clus
vv                       CSNK1G1 MUTATED CSNK1G1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               305
[1] 2 2
[1] FALSE

Clustering(1093) Variable = HIST1H1B MUTATION ANALYSIS
D1093V1, survival
                    sevent
clus2                  0   1
  HIST1H1B MUTATED     5   4
  HIST1H1B WILD-TYPE 225 135
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 9                360 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 4                135 
$`HIST1H1B MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8284 TCGA-BR-A4J1 TCGA-CG-4300 TCGA-CG-5726 
       34.68        36.16         8.05         0.72        20.02        28.96 
TCGA-HU-A4GT TCGA-IN-AB1V TCGA-SW-A7EA 
        6.51        15.75        19.04 

$`HIST1H1B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       11.77        12.62         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-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-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       10.62        11.70        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 

  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
              0.72               0.00 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
             36.16             122.30 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
             19.04              14.12 
[1] "0.7 - 36.2 (19.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.1"
D1093V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HIST1H1B MUTATED         1        3        1        0         2         0
  HIST1H1B WILD-TYPE       1       12       39       30        35        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1B MUTATED           0          2          1          1        0
  HIST1H1B WILD-TYPE         3         68         52         31       38
D1093V3, multiclass
            clus
vv           HIST1H1B MUTATED HIST1H1B WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  3                 12
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 2                 35
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                1                 52
  STAGE IIIC                1                 31
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H1B MUTATED     4   1   3   3
  HIST1H1B WILD-TYPE  18  91 170  94
D1093V4, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  T1                4                 18
  T2                1                 91
  T3                3                170
  T4                3                 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
  HIST1H1B MUTATED     7   2   1   1
  HIST1H1B WILD-TYPE 111 102  76  76
D1093V5, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  N0                7                111
  N1                2                102
  N2                1                 76
  N3                1                 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"
D1093V6, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED    10   0
  HIST1H1B WILD-TYPE 336  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED     10    0
  HIST1H1B WILD-TYPE  336   29
   clus
vv  HIST1H1B MUTATED HIST1H1B WILD-TYPE
  0               10                336
  1                0                 29
[1] 2 2
[1] FALSE
D1093V7, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     5   6
  HIST1H1B WILD-TYPE 140 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      5    6
  HIST1H1B WILD-TYPE  140  242
        clus
vv       HIST1H1B MUTATED HIST1H1B WILD-TYPE
  FEMALE                5                140
  MALE                  6                242
[1] 2 2
[1] FALSE
D1093V8, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     7   0
  HIST1H1B WILD-TYPE 285  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      7    0
  HIST1H1B WILD-TYPE  285   59
     clus
vv    HIST1H1B MUTATED HIST1H1B WILD-TYPE
  NO                 7                285
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HIST1H1B MUTATED                                          0
  HIST1H1B WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HIST1H1B MUTATED                                       1
  HIST1H1B WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HIST1H1B MUTATED                                                        6
  HIST1H1B WILD-TYPE                                                    152
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HIST1H1B MUTATED                                                   0
  HIST1H1B WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HIST1H1B MUTATED                                                                   2
  HIST1H1B WILD-TYPE                                                                66
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HIST1H1B MUTATED                                                    1
  HIST1H1B WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HIST1H1B MUTATED                                                  1
  HIST1H1B WILD-TYPE                                               60
D1093V9, multiclass
                                                                   clus
vv                                                                  HIST1H1B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  HIST1H1B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HIST1H1B MUTATED    10   0   0   1
  HIST1H1B WILD-TYPE 301  14  15  23
D1093V10, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  R0               10                301
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1093V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  HIST1H1B MUTATED       2                         1
  HIST1H1B WILD-TYPE    85                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HIST1H1B MUTATED                                           0     6
  HIST1H1B WILD-TYPE                                         1   237
D1093V12, multiclass
                                           clus
vv                                          HIST1H1B MUTATED HIST1H1B WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1093V13, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     0   9
  HIST1H1B WILD-TYPE   4 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      0    9
  HIST1H1B WILD-TYPE    4  301
                        clus
vv                       HIST1H1B MUTATED HIST1H1B WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                9                301
[1] 2 2
[1] FALSE

Clustering(1094) Variable = KIF20B MUTATION ANALYSIS
D1094V1, survival
                  sevent
clus2                0   1
  KIF20B MUTATED     7   3
  KIF20B WILD-TYPE 223 136
  KIF20B MUTATED KIF20B WILD-TYPE 
              10              359 
  KIF20B MUTATED KIF20B WILD-TYPE 
               3              136 
$`KIF20B MUTATED`
TCGA-B7-A5TJ TCGA-BR-4201 TCGA-BR-8078 TCGA-BR-8680 TCGA-CD-8536 TCGA-CD-A4MJ 
       11.01        30.90        29.59        31.96        12.43        12.62 
TCGA-CG-5728 TCGA-F1-A448 TCGA-VQ-A8PE TCGA-VQ-AA64 
       65.10        21.27        22.19        18.41 

$`KIF20B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15         9.86        26.70        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-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-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-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-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-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-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-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 

  KIF20B MUTATED KIF20B WILD-TYPE 
           11.01             0.00 
  KIF20B MUTATED KIF20B WILD-TYPE 
            65.1            122.3 
  KIF20B MUTATED KIF20B WILD-TYPE 
           21.73            14.07 
[1] "11.0 - 65.1 (21.7)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D1094V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIF20B MUTATED         1        0        2        1         0         2
  KIF20B WILD-TYPE       1       15       38       29        37        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF20B MUTATED           0          0          3          0        1
  KIF20B WILD-TYPE         3         70         50         32       37
D1094V3, multiclass
            clus
vv           KIF20B MUTATED KIF20B WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               0               37
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              3               50
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIF20B MUTATED     2   3   5   3
  KIF20B WILD-TYPE  20  89 168  94
D1094V4, multiclass
    clus
vv   KIF20B MUTATED KIF20B WILD-TYPE
  T1              2               20
  T2              3               89
  T3              5              168
  T4              3               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
  KIF20B MUTATED     4   1   2   2
  KIF20B WILD-TYPE 114 103  75  75
D1094V5, multiclass
    clus
vv   KIF20B MUTATED KIF20B WILD-TYPE
  N0              4              114
  N1              1              103
  N2              2               75
  N3              2               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"
D1094V6, binary
                  cls
clus                 0   1
  KIF20B MUTATED    10   1
  KIF20B WILD-TYPE 336  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED     10    1
  KIF20B WILD-TYPE  336   28
   clus
vv  KIF20B MUTATED KIF20B WILD-TYPE
  0             10              336
  1              1               28
[1] 2 2
[1] FALSE
D1094V7, binary
                  cls
clus                 0   1
  KIF20B MUTATED     5   8
  KIF20B WILD-TYPE 140 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED      5    8
  KIF20B WILD-TYPE  140  240
        clus
vv       KIF20B MUTATED KIF20B WILD-TYPE
  FEMALE              5              140
  MALE                8              240
[1] 2 2
[1] FALSE
D1094V8, binary
                  cls
clus                 0   1
  KIF20B MUTATED     8   2
  KIF20B WILD-TYPE 284  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED      8    2
  KIF20B WILD-TYPE  284   57
     clus
vv    KIF20B MUTATED KIF20B WILD-TYPE
  NO               8              284
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIF20B MUTATED                                          0
  KIF20B WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIF20B MUTATED                                       0
  KIF20B WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIF20B MUTATED                                                        7
  KIF20B WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIF20B MUTATED                                                   1
  KIF20B WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIF20B MUTATED                                                                   3
  KIF20B WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIF20B MUTATED                                                    0
  KIF20B WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIF20B MUTATED                                                  2
  KIF20B WILD-TYPE                                               59
D1094V9, multiclass
                                                                   clus
vv                                                                  KIF20B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  KIF20B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KIF20B MUTATED     8   0   0   3
  KIF20B WILD-TYPE 303  14  15  21
D1094V10, multiclass
    clus
vv   KIF20B MUTATED KIF20B WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1094V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  KIF20B MUTATED       3                         1
  KIF20B WILD-TYPE    84                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIF20B MUTATED                                           0     8
  KIF20B WILD-TYPE                                         1   235
D1094V12, multiclass
                                           clus
vv                                          KIF20B MUTATED KIF20B WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1094V13, binary
                  cls
clus                 0   1
  KIF20B MUTATED     1   9
  KIF20B WILD-TYPE   3 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED      1    9
  KIF20B WILD-TYPE    3  301
                        clus
vv                       KIF20B MUTATED KIF20B WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(1095) Variable = SASH3 MUTATION ANALYSIS
D1095V1, survival
                 sevent
clus2               0   1
  SASH3 MUTATED     6   1
  SASH3 WILD-TYPE 224 138
  SASH3 MUTATED SASH3 WILD-TYPE 
              7             362 
  SASH3 MUTATED SASH3 WILD-TYPE 
              1             138 
$`SASH3 MUTATED`
TCGA-BR-8360 TCGA-BR-8680 TCGA-CG-5726 TCGA-HF-7132 TCGA-HU-A4G8 TCGA-HU-A4GX 
        6.18        31.96        28.96        77.29        22.68        20.25 
TCGA-VQ-A8P2 
       38.14 

$`SASH3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  SASH3 MUTATED SASH3 WILD-TYPE 
           6.18            0.00 
  SASH3 MUTATED SASH3 WILD-TYPE 
          77.29          122.30 
  SASH3 MUTATED SASH3 WILD-TYPE 
          28.96           14.07 
[1] "6.2 - 77.3 (29.0)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "4.4"
D1095V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SASH3 MUTATED         0        1        0        1         1         1
  SASH3 WILD-TYPE       2       14       40       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SASH3 MUTATED           0          1          0          1        1
  SASH3 WILD-TYPE         3         69         53         31       37
D1095V3, multiclass
            clus
vv           SASH3 MUTATED SASH3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SASH3 MUTATED     2   1   2   3
  SASH3 WILD-TYPE  20  91 171  94
D1095V4, multiclass
    clus
vv   SASH3 MUTATED SASH3 WILD-TYPE
  T1             2              20
  T2             1              91
  T3             2             171
  T4             3              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
  SASH3 MUTATED     2   3   2   0
  SASH3 WILD-TYPE 116 101  75  77
D1095V5, multiclass
    clus
vv   SASH3 MUTATED SASH3 WILD-TYPE
  N0             2             116
  N1             3             101
  N2             2              75
  N3             0              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"
D1095V6, binary
                 cls
clus                0   1
  SASH3 MUTATED     7   1
  SASH3 WILD-TYPE 339  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SASH3 MUTATED      7    1
  SASH3 WILD-TYPE  339   28
   clus
vv  SASH3 MUTATED SASH3 WILD-TYPE
  0             7             339
  1             1              28
[1] 2 2
[1] FALSE
D1095V7, binary
                 cls
clus                0   1
  SASH3 MUTATED     3   5
  SASH3 WILD-TYPE 142 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SASH3 MUTATED      3    5
  SASH3 WILD-TYPE  142  243
        clus
vv       SASH3 MUTATED SASH3 WILD-TYPE
  FEMALE             3             142
  MALE               5             243
[1] 2 2
[1] FALSE
D1095V8, binary
                 cls
clus                0   1
  SASH3 MUTATED     4   2
  SASH3 WILD-TYPE 288  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SASH3 MUTATED      4    2
  SASH3 WILD-TYPE  288   57
     clus
vv    SASH3 MUTATED SASH3 WILD-TYPE
  NO              4             288
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SASH3 MUTATED                                          0
  SASH3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SASH3 MUTATED                                       2
  SASH3 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SASH3 MUTATED                                                        1
  SASH3 WILD-TYPE                                                    157
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SASH3 MUTATED                                                   2
  SASH3 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SASH3 MUTATED                                                                   2
  SASH3 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SASH3 MUTATED                                                    0
  SASH3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SASH3 MUTATED                                                  1
  SASH3 WILD-TYPE                                               60
D1095V9, multiclass
                                                                   clus
vv                                                                  SASH3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  SASH3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SASH3 MUTATED     6   0   0   1
  SASH3 WILD-TYPE 305  14  15  23
D1095V10, multiclass
    clus
vv   SASH3 MUTATED SASH3 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1095V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SASH3 MUTATED       3                         0
  SASH3 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SASH3 MUTATED                                           0     3
  SASH3 WILD-TYPE                                         1   240
D1095V12, multiclass
                                           clus
vv                                          SASH3 MUTATED SASH3 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1095V13, binary
                 cls
clus                0   1
  SASH3 MUTATED     0   5
  SASH3 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SASH3 MUTATED      0    5
  SASH3 WILD-TYPE    4  305
                        clus
vv                       SASH3 MUTATED SASH3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(1096) Variable = TCERG1 MUTATION ANALYSIS
D1096V1, survival
                  sevent
clus2                0   1
  TCERG1 MUTATED     7   4
  TCERG1 WILD-TYPE 223 135
  TCERG1 MUTATED TCERG1 WILD-TYPE 
              11              358 
  TCERG1 MUTATED TCERG1 WILD-TYPE 
               4              135 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  TCERG1 MUTATED TCERG1 WILD-TYPE 
            0.26             0.00 
  TCERG1 MUTATED TCERG1 WILD-TYPE 
           74.53           122.30 
  TCERG1 MUTATED TCERG1 WILD-TYPE 
          30.900           14.055 
[1] "0.3 - 74.5 (30.9)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D1096V2, 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       2       14       39       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TCERG1 MUTATED           0          1          1          1        3
  TCERG1 WILD-TYPE         3         69         52         31       35
D1096V3, multiclass
            clus
vv           TCERG1 MUTATED TCERG1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TCERG1 MUTATED     1   3   3   5
  TCERG1 WILD-TYPE  21  89 170  92
D1096V4, multiclass
    clus
vv   TCERG1 MUTATED TCERG1 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              3              170
  T4              5               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
  TCERG1 MUTATED     3   4   1   2
  TCERG1 WILD-TYPE 115 100  76  75
D1096V5, multiclass
    clus
vv   TCERG1 MUTATED TCERG1 WILD-TYPE
  N0              3              115
  N1              4              100
  N2              1               76
  N3              2               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"
D1096V6, binary
                  cls
clus                 0   1
  TCERG1 MUTATED     9   2
  TCERG1 WILD-TYPE 337  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCERG1 MUTATED      9    2
  TCERG1 WILD-TYPE  337   27
   clus
vv  TCERG1 MUTATED TCERG1 WILD-TYPE
  0              9              337
  1              2               27
[1] 2 2
[1] FALSE
D1096V7, binary
                  cls
clus                 0   1
  TCERG1 MUTATED     5   7
  TCERG1 WILD-TYPE 140 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCERG1 MUTATED      5    7
  TCERG1 WILD-TYPE  140  241
        clus
vv       TCERG1 MUTATED TCERG1 WILD-TYPE
  FEMALE              5              140
  MALE                7              241
[1] 2 2
[1] FALSE
D1096V8, binary
                  cls
clus                 0   1
  TCERG1 MUTATED     9   1
  TCERG1 WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCERG1 MUTATED      9    1
  TCERG1 WILD-TYPE  283   58
     clus
vv    TCERG1 MUTATED TCERG1 WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TCERG1 MUTATED                                          0
  TCERG1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TCERG1 MUTATED                                       1
  TCERG1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TCERG1 MUTATED                                                        7
  TCERG1 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TCERG1 MUTATED                                                   1
  TCERG1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TCERG1 MUTATED                                                                   2
  TCERG1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TCERG1 MUTATED                                                    0
  TCERG1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TCERG1 MUTATED                                                  1
  TCERG1 WILD-TYPE                                               60
D1096V9, multiclass
                                                                   clus
vv                                                                  TCERG1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  TCERG1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TCERG1 MUTATED    10   0   0   2
  TCERG1 WILD-TYPE 301  14  15  22
D1096V10, multiclass
    clus
vv   TCERG1 MUTATED TCERG1 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1096V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TCERG1 MUTATED       1                         0
  TCERG1 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TCERG1 MUTATED                                           0     9
  TCERG1 WILD-TYPE                                         1   234
D1096V12, multiclass
                                           clus
vv                                          TCERG1 MUTATED TCERG1 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1096V13, binary
                  cls
clus                 0   1
  TCERG1 MUTATED     1   8
  TCERG1 WILD-TYPE   3 302
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCERG1 MUTATED      1    8
  TCERG1 WILD-TYPE    3  302
                        clus
vv                       TCERG1 MUTATED TCERG1 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              8              302
[1] 2 2
[1] FALSE

Clustering(1097) Variable = FBXL22 MUTATION ANALYSIS
D1097V1, survival
                  sevent
clus2                0   1
  FBXL22 MUTATED     2   3
  FBXL22 WILD-TYPE 228 136
  FBXL22 MUTATED FBXL22 WILD-TYPE 
               5              364 
  FBXL22 MUTATED FBXL22 WILD-TYPE 
               3              136 
$`FBXL22 MUTATED`
TCGA-BR-4201 TCGA-BR-8487 TCGA-CG-5733 TCGA-HU-A4GQ TCGA-HU-A4GX 
       30.90         1.12        21.07         0.10        20.25 

$`FBXL22 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  FBXL22 MUTATED FBXL22 WILD-TYPE 
             0.1              0.0 
  FBXL22 MUTATED FBXL22 WILD-TYPE 
            30.9            122.3 
  FBXL22 MUTATED FBXL22 WILD-TYPE 
           20.25            14.22 
[1] "0.1 - 30.9 (20.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.8"
D1097V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FBXL22 MUTATED         0        0        0        0         1         0
  FBXL22 WILD-TYPE       2       15       40       30        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXL22 MUTATED           0          1          0          2        0
  FBXL22 WILD-TYPE         3         69         53         30       38
D1097V3, multiclass
            clus
vv           FBXL22 MUTATED FBXL22 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              2               30
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXL22 MUTATED     0   2   1   2
  FBXL22 WILD-TYPE  22  90 172  95
D1097V4, multiclass
    clus
vv   FBXL22 MUTATED FBXL22 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              1              172
  T4              2               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
  FBXL22 MUTATED     1   0   3   0
  FBXL22 WILD-TYPE 117 104  74  77
D1097V5, multiclass
    clus
vv   FBXL22 MUTATED FBXL22 WILD-TYPE
  N0              1              117
  N1              0              104
  N2              3               74
  N3              0               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"
D1097V6, binary
                  cls
clus                 0   1
  FBXL22 MUTATED     5   0
  FBXL22 WILD-TYPE 341  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL22 MUTATED      5    0
  FBXL22 WILD-TYPE  341   29
   clus
vv  FBXL22 MUTATED FBXL22 WILD-TYPE
  0              5              341
  1              0               29
[1] 2 2
[1] FALSE
D1097V7, binary
                  cls
clus                 0   1
  FBXL22 MUTATED     4   1
  FBXL22 WILD-TYPE 141 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL22 MUTATED      4    1
  FBXL22 WILD-TYPE  141  247
        clus
vv       FBXL22 MUTATED FBXL22 WILD-TYPE
  FEMALE              4              141
  MALE                1              247
[1] 2 2
[1] FALSE
D1097V8, binary
                  cls
clus                 0   1
  FBXL22 MUTATED     5   0
  FBXL22 WILD-TYPE 287  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL22 MUTATED      5    0
  FBXL22 WILD-TYPE  287   59
     clus
vv    FBXL22 MUTATED FBXL22 WILD-TYPE
  NO               5              287
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FBXL22 MUTATED                                          0
  FBXL22 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FBXL22 MUTATED                                       1
  FBXL22 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBXL22 MUTATED                                                        2
  FBXL22 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FBXL22 MUTATED                                                   0
  FBXL22 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FBXL22 MUTATED                                                                   1
  FBXL22 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FBXL22 MUTATED                                                    0
  FBXL22 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FBXL22 MUTATED                                                  1
  FBXL22 WILD-TYPE                                               60
D1097V9, multiclass
                                                                   clus
vv                                                                  FBXL22 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  FBXL22 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FBXL22 MUTATED     4   0   0   1
  FBXL22 WILD-TYPE 307  14  15  23
D1097V10, multiclass
    clus
vv   FBXL22 MUTATED FBXL22 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1097V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FBXL22 MUTATED       2                         0
  FBXL22 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FBXL22 MUTATED                                           0     2
  FBXL22 WILD-TYPE                                         1   241
D1097V12, multiclass
                                           clus
vv                                          FBXL22 MUTATED FBXL22 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1097V13, binary
                  cls
clus                 0   1
  FBXL22 MUTATED     0   4
  FBXL22 WILD-TYPE   4 306
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL22 MUTATED      0    4
  FBXL22 WILD-TYPE    4  306
                        clus
vv                       FBXL22 MUTATED FBXL22 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              306
[1] 2 2
[1] FALSE

Clustering(1098) Variable = PARP15 MUTATION ANALYSIS
D1098V1, survival
                  sevent
clus2                0   1
  PARP15 MUTATED     5   0
  PARP15 WILD-TYPE 225 139
  PARP15 MUTATED PARP15 WILD-TYPE 
               5              364 
  PARP15 MUTATED PARP15 WILD-TYPE 
               0              139 
$`PARP15 MUTATED`
TCGA-BR-6852 TCGA-BR-8680 TCGA-CG-5721 TCGA-CG-5728 TCGA-HU-A4GU 
       44.94        31.96         6.02        65.10         6.58 

$`PARP15 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  PARP15 MUTATED PARP15 WILD-TYPE 
            6.02             0.00 
  PARP15 MUTATED PARP15 WILD-TYPE 
            65.1            122.3 
  PARP15 MUTATED PARP15 WILD-TYPE 
           31.96            14.22 
[1] "6.0 - 65.1 (32.0)"  "0.0 - 122.3 (14.2)"
[1] "hr="     "9200000"
D1098V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PARP15 MUTATED         0        0        1        0         1         1
  PARP15 WILD-TYPE       2       15       39       30        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PARP15 MUTATED           0          0          0          0        2
  PARP15 WILD-TYPE         3         70         53         32       36
D1098V3, multiclass
            clus
vv           PARP15 MUTATED PARP15 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PARP15 MUTATED     0   1   2   2
  PARP15 WILD-TYPE  22  91 171  95
D1098V4, multiclass
    clus
vv   PARP15 MUTATED PARP15 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              2              171
  T4              2               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
  PARP15 MUTATED     2   2   1   0
  PARP15 WILD-TYPE 116 102  76  77
D1098V5, multiclass
    clus
vv   PARP15 MUTATED PARP15 WILD-TYPE
  N0              2              116
  N1              2              102
  N2              1               76
  N3              0               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"
D1098V6, binary
                  cls
clus                 0   1
  PARP15 MUTATED     4   1
  PARP15 WILD-TYPE 342  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP15 MUTATED      4    1
  PARP15 WILD-TYPE  342   28
   clus
vv  PARP15 MUTATED PARP15 WILD-TYPE
  0              4              342
  1              1               28
[1] 2 2
[1] FALSE
D1098V7, binary
                  cls
clus                 0   1
  PARP15 MUTATED     2   3
  PARP15 WILD-TYPE 143 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP15 MUTATED      2    3
  PARP15 WILD-TYPE  143  245
        clus
vv       PARP15 MUTATED PARP15 WILD-TYPE
  FEMALE              2              143
  MALE                3              245
[1] 2 2
[1] FALSE
D1098V8, binary
                  cls
clus                 0   1
  PARP15 MUTATED     4   0
  PARP15 WILD-TYPE 288  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP15 MUTATED      4    0
  PARP15 WILD-TYPE  288   59
     clus
vv    PARP15 MUTATED PARP15 WILD-TYPE
  NO               4              288
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PARP15 MUTATED                                          0
  PARP15 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PARP15 MUTATED                                       1
  PARP15 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PARP15 MUTATED                                                        1
  PARP15 WILD-TYPE                                                    157
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PARP15 MUTATED                                                   0
  PARP15 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PARP15 MUTATED                                                                   2
  PARP15 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PARP15 MUTATED                                                    0
  PARP15 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PARP15 MUTATED                                                  1
  PARP15 WILD-TYPE                                               60
D1098V9, multiclass
                                                                   clus
vv                                                                  PARP15 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  PARP15 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PARP15 MUTATED     5   0   0   0
  PARP15 WILD-TYPE 306  14  15  24
D1098V10, multiclass
    clus
vv   PARP15 MUTATED PARP15 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1098V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PARP15 MUTATED       2                         0
  PARP15 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PARP15 MUTATED                                           0     1
  PARP15 WILD-TYPE                                         1   242
D1098V12, multiclass
                                           clus
vv                                          PARP15 MUTATED PARP15 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  1              242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1098V13, binary
                  cls
clus                 0   1
  PARP15 MUTATED     0   3
  PARP15 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP15 MUTATED      0    3
  PARP15 WILD-TYPE    4  307
                        clus
vv                       PARP15 MUTATED PARP15 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(1099) Variable = NCAN MUTATION ANALYSIS
D1099V1, survival
                sevent
clus2              0   1
  NCAN MUTATED    11   6
  NCAN WILD-TYPE 219 133
  NCAN MUTATED NCAN WILD-TYPE 
            17            352 
  NCAN MUTATED NCAN WILD-TYPE 
             6            133 
$`NCAN MUTATED`
TCGA-CG-4460 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6566 TCGA-BR-6802 TCGA-BR-7707 
       21.99        30.90         9.34        32.78        30.90        35.84 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-A4PE TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-5723 
        6.18        31.10        20.42         6.58        15.95       105.07 
TCGA-D7-6822 TCGA-D7-A6EZ TCGA-FP-A4BE TCGA-HU-A4GQ TCGA-MX-A5UJ 
       12.33        20.32        11.08         0.10        19.73 

$`NCAN WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-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-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-D7-8570 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-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-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-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-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 

  NCAN MUTATED NCAN WILD-TYPE 
           0.1            0.0 
  NCAN MUTATED NCAN WILD-TYPE 
        105.07         122.30 
  NCAN MUTATED NCAN WILD-TYPE 
         20.32          14.07 
[1] "0.1 - 105.1 (20.3)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D1099V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NCAN MUTATED         1        0        4        2         4         1
  NCAN WILD-TYPE       1       15       36       28        33        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NCAN MUTATED           0          3          0          3        1
  NCAN WILD-TYPE         3         67         53         29       37
D1099V3, multiclass
            clus
vv           NCAN MUTATED NCAN WILD-TYPE
  STAGE I               1              1
  STAGE IA              0             15
  STAGE IB              4             36
  STAGE II              2             28
  STAGE IIA             4             33
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            0             53
  STAGE IIIC            3             29
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NCAN MUTATED     2   8   8   5
  NCAN WILD-TYPE  20  84 165  92
D1099V4, multiclass
    clus
vv   NCAN MUTATED NCAN WILD-TYPE
  T1            2             20
  T2            8             84
  T3            8            165
  T4            5             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
  NCAN MUTATED     9   6   5   1
  NCAN WILD-TYPE 109  98  72  76
D1099V5, multiclass
    clus
vv   NCAN MUTATED NCAN WILD-TYPE
  N0            9            109
  N1            6             98
  N2            5             72
  N3            1             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"
D1099V6, binary
                cls
clus               0   1
  NCAN MUTATED    22   1
  NCAN WILD-TYPE 324  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCAN MUTATED     22    1
  NCAN WILD-TYPE  324   28
   clus
vv  NCAN MUTATED NCAN WILD-TYPE
  0           22            324
  1            1             28
[1] 2 2
[1] FALSE
D1099V7, binary
                cls
clus               0   1
  NCAN MUTATED    11  14
  NCAN WILD-TYPE 134 234
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCAN MUTATED     11   14
  NCAN WILD-TYPE  134  234
        clus
vv       NCAN MUTATED NCAN WILD-TYPE
  FEMALE           11            134
  MALE             14            234
[1] 2 2
[1] FALSE
D1099V8, binary
                cls
clus               0   1
  NCAN MUTATED    20   1
  NCAN WILD-TYPE 272  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCAN MUTATED     20    1
  NCAN WILD-TYPE  272   58
     clus
vv    NCAN MUTATED NCAN WILD-TYPE
  NO            20            272
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NCAN MUTATED                                          0
  NCAN WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NCAN MUTATED                                       1
  NCAN WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NCAN MUTATED                                                       16
  NCAN WILD-TYPE                                                    142
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NCAN MUTATED                                                   0
  NCAN WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NCAN MUTATED                                                                   4
  NCAN WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NCAN MUTATED                                                    0
  NCAN WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NCAN MUTATED                                                  4
  NCAN WILD-TYPE                                               57
D1099V9, multiclass
                                                                   clus
vv                                                                  NCAN MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  NCAN WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NCAN MUTATED    16   1   1   6
  NCAN WILD-TYPE 295  13  14  18
D1099V10, multiclass
    clus
vv   NCAN MUTATED NCAN WILD-TYPE
  R0           16            295
  R1            1             13
  R2            1             14
  RX            6             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1099V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  NCAN MUTATED       2                         2
  NCAN WILD-TYPE    85                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NCAN MUTATED                                           0    18
  NCAN WILD-TYPE                                         1   225
D1099V12, multiclass
                                           clus
vv                                          NCAN MUTATED NCAN WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               18            225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1099V13, binary
                cls
clus               0   1
  NCAN MUTATED     0  22
  NCAN WILD-TYPE   4 288
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCAN MUTATED      0   22
  NCAN WILD-TYPE    4  288
                        clus
vv                       NCAN MUTATED NCAN WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           22            288
[1] 2 2
[1] FALSE

Clustering(1100) Variable = SLC30A3 MUTATION ANALYSIS
D1100V1, survival
                   sevent
clus2                 0   1
  SLC30A3 MUTATED     5   2
  SLC30A3 WILD-TYPE 225 137
  SLC30A3 MUTATED SLC30A3 WILD-TYPE 
                7               362 
  SLC30A3 MUTATED SLC30A3 WILD-TYPE 
                2               137 
$`SLC30A3 MUTATED`
TCGA-CG-4460 TCGA-BR-8360 TCGA-BR-8381 TCGA-BR-8680 TCGA-CD-A4MG TCGA-HU-A4GF 
       21.99         6.18         7.36        31.96         6.58        25.81 
TCGA-HU-A4GX 
       20.25 

$`SLC30A3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        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 

  SLC30A3 MUTATED SLC30A3 WILD-TYPE 
             6.18              0.00 
  SLC30A3 MUTATED SLC30A3 WILD-TYPE 
            31.96            122.30 
  SLC30A3 MUTATED SLC30A3 WILD-TYPE 
            20.25             14.22 
[1] "6.2 - 32.0 (20.2)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D1100V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC30A3 MUTATED         0        0        0        0         3         1
  SLC30A3 WILD-TYPE       2       15       40       30        34        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC30A3 MUTATED           0          1          0          1        2
  SLC30A3 WILD-TYPE         3         69         53         31       36
D1100V3, multiclass
            clus
vv           SLC30A3 MUTATED SLC30A3 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                3                34
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC30A3 MUTATED     0   0   4   4
  SLC30A3 WILD-TYPE  22  92 169  93
D1100V4, multiclass
    clus
vv   SLC30A3 MUTATED SLC30A3 WILD-TYPE
  T1               0                22
  T2               0                92
  T3               4               169
  T4               4                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
  SLC30A3 MUTATED     4   3   2   0
  SLC30A3 WILD-TYPE 114 101  75  77
D1100V5, multiclass
    clus
vv   SLC30A3 MUTATED SLC30A3 WILD-TYPE
  N0               4               114
  N1               3               101
  N2               2                75
  N3               0                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"
D1100V6, binary
                   cls
clus                  0   1
  SLC30A3 MUTATED     7   2
  SLC30A3 WILD-TYPE 339  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A3 MUTATED      7    2
  SLC30A3 WILD-TYPE  339   27
   clus
vv  SLC30A3 MUTATED SLC30A3 WILD-TYPE
  0               7               339
  1               2                27
[1] 2 2
[1] FALSE
D1100V7, binary
                   cls
clus                  0   1
  SLC30A3 MUTATED     4   5
  SLC30A3 WILD-TYPE 141 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A3 MUTATED      4    5
  SLC30A3 WILD-TYPE  141  243
        clus
vv       SLC30A3 MUTATED SLC30A3 WILD-TYPE
  FEMALE               4               141
  MALE                 5               243
[1] 2 2
[1] FALSE
D1100V8, binary
                   cls
clus                  0   1
  SLC30A3 MUTATED     7   0
  SLC30A3 WILD-TYPE 285  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A3 MUTATED      7    0
  SLC30A3 WILD-TYPE  285   59
     clus
vv    SLC30A3 MUTATED SLC30A3 WILD-TYPE
  NO                7               285
  YES               0                59
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC30A3 MUTATED                                          0
  SLC30A3 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC30A3 MUTATED                                       2
  SLC30A3 WILD-TYPE                                    68
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC30A3 MUTATED                                                        3
  SLC30A3 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC30A3 MUTATED                                                   0
  SLC30A3 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC30A3 MUTATED                                                                   2
  SLC30A3 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC30A3 MUTATED                                                    0
  SLC30A3 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC30A3 MUTATED                                                  2
  SLC30A3 WILD-TYPE                                               59
D1100V9, multiclass
                                                                   clus
vv                                                                  SLC30A3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                2
                                                                   clus
vv                                                                  SLC30A3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC30A3 MUTATED     5   0   1   2
  SLC30A3 WILD-TYPE 306  14  14  22
D1100V10, multiclass
    clus
vv   SLC30A3 MUTATED SLC30A3 WILD-TYPE
  R0               5               306
  R1               0                14
  R2               1                14
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1100V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC30A3 MUTATED       4                         0
  SLC30A3 WILD-TYPE    83                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC30A3 MUTATED                                           0     4
  SLC30A3 WILD-TYPE                                         1   239
D1100V12, multiclass
                                           clus
vv                                          SLC30A3 MUTATED SLC30A3 WILD-TYPE
  ASIAN                                                   4                83
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1100V13, binary
                   cls
clus                  0   1
  SLC30A3 MUTATED     0   8
  SLC30A3 WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A3 MUTATED      0    8
  SLC30A3 WILD-TYPE    4  302
                        clus
vv                       SLC30A3 MUTATED SLC30A3 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(1101) Variable = LRP1B MUTATION ANALYSIS
D1101V1, survival
                 sevent
clus2               0   1
  LRP1B MUTATED    62  35
  LRP1B WILD-TYPE 168 104
  LRP1B MUTATED LRP1B WILD-TYPE 
             97             272 
  LRP1B MUTATED LRP1B WILD-TYPE 
             35             104 
$`LRP1B MUTATED`
TCGA-CG-4444 TCGA-CG-4460 TCGA-MX-A663 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4201 
       47.05        21.99         9.86        26.70         6.97        30.90 
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6565 TCGA-BR-6566 
        9.34         9.67        34.68        15.95         9.17        32.78 
TCGA-BR-6706 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7723 TCGA-BR-7958 TCGA-BR-7959 
       18.05         9.21        36.16        28.73        29.56        33.21 
TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       14.43         9.60         2.66         7.40         6.18        31.10 
TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8591 
       14.04         5.39         9.21        20.22         1.12        28.14 
TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A4J5 
        7.53        24.79        31.96         9.86        13.87        28.34 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8527 
       20.42         1.15        21.44        13.18        12.76         7.17 
TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48C TCGA-CD-A4MG 
       12.39        15.39        12.82         6.31        11.61         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4469 TCGA-CG-5721 TCGA-CG-5723 
       11.77        12.62         1.02         7.07         6.02       105.07 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5732 TCGA-D7-6528 TCGA-D7-A4YU 
       12.03        28.96        65.10        69.04        15.22        16.44 
TCGA-D7-A4YY TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-D7-A747 TCGA-FP-7829 
       13.78        11.24        11.44        15.65         8.38        19.53 
TCGA-FP-A4BE TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8602 
       11.08         6.21        77.29        52.21        30.51        22.32 
TCGA-HU-8604 TCGA-HU-A4GC TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX 
       22.82         3.25        29.98         0.10         6.58        20.25 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A7NR 
       29.00        23.84        14.07        12.46        13.35         6.51 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-R5-A7ZI TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A7BT 
       10.62        11.70        74.53         9.24        11.05         8.61 
TCGA-SW-A7EA TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I 
       19.04        38.14        37.22        32.94        26.04        16.14 
TCGA-VQ-AA6J 
       27.55 

$`LRP1B WILD-TYPE`
TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-B7-5818 
       22.98        79.07        16.24         0.23        20.15        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-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-6705 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       26.10        25.61        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-7901 TCGA-BR-7957 
       33.63        39.78        18.15        15.32         3.45         9.07 
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-8291 TCGA-BR-8295 TCGA-BR-8363 TCGA-BR-8364 
        0.56        29.42        19.96         2.20         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-8484 
       31.27        14.79         7.36        25.05         3.72        25.18 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 
       12.79        27.12         9.34         6.28        26.73        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-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53         0.66        32.52        13.51 
TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       20.65        16.14         5.13        13.41        13.02        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8525 TCGA-CD-8526 
       13.35        11.21        12.10        12.39        12.59        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-8536 
       12.33        12.30        12.59        11.64        12.07        12.43 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 
       12.30        11.31        12.43        12.20        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-5725 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
        0.99        15.02         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-D7-6815 
       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-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX 
       14.27         5.92        36.43        14.76        26.43        11.31 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       20.32        22.29         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-HF-7133 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        0.56         5.52        63.06        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-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       24.26        22.68        24.20        22.75        25.81        11.77 
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-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.81         3.39        18.38        19.53         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       12.59        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-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        8.52         6.08         4.60         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-A8PE TCGA-VQ-A8PK 
       13.25        13.02        43.36        37.41        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-AA6F 
       11.24        18.41        43.66        28.41        38.93        54.12 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

  LRP1B MUTATED LRP1B WILD-TYPE 
            0.1             0.0 
  LRP1B MUTATED LRP1B WILD-TYPE 
         105.07          122.30 
  LRP1B MUTATED LRP1B WILD-TYPE 
         14.040          14.565 
[1] "0.1 - 105.1 (14.0)" "0.0 - 122.3 (14.6)"
[1] "hr=" "1.1"
D1101V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRP1B MUTATED         1        6        9        7        13        11
  LRP1B WILD-TYPE       1        9       31       23        24        41
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRP1B MUTATED           1         14         16         10       11
  LRP1B WILD-TYPE         2         56         37         22       27
D1101V3, multiclass
            clus
vv           LRP1B MUTATED LRP1B WILD-TYPE
  STAGE I                1               1
  STAGE IA               6               9
  STAGE IB               9              31
  STAGE II               7              23
  STAGE IIA             13              24
  STAGE IIB             11              41
  STAGE III              1               2
  STAGE IIIA            14              56
  STAGE IIIB            16              37
  STAGE IIIC            10              22
  STAGE IV              11              27
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LRP1B MUTATED     9  19  43  30
  LRP1B WILD-TYPE  13  73 130  67
D1101V4, multiclass
    clus
vv   LRP1B MUTATED LRP1B WILD-TYPE
  T1             9              13
  T2            19              73
  T3            43             130
  T4            30              67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  LRP1B MUTATED   35 29 15 22
  LRP1B WILD-TYPE 83 75 62 55
D1101V5, multiclass
    clus
vv   LRP1B MUTATED LRP1B WILD-TYPE
  N0            35              83
  N1            29              75
  N2            15              62
  N3            22              55
[1] 4 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
  LRP1B MUTATED    95   7
  LRP1B WILD-TYPE 251  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP1B MUTATED     95    7
  LRP1B WILD-TYPE  251   22
   clus
vv  LRP1B MUTATED LRP1B WILD-TYPE
  0            95             251
  1             7              22
[1] 2 2
[1] FALSE
D1101V7, binary
                 cls
clus                0   1
  LRP1B MUTATED    32  72
  LRP1B WILD-TYPE 113 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP1B MUTATED     32   72
  LRP1B WILD-TYPE  113  176
        clus
vv       LRP1B MUTATED LRP1B WILD-TYPE
  FEMALE            32             113
  MALE              72             176
[1] 2 2
[1] FALSE
D1101V8, binary
                 cls
clus                0   1
  LRP1B MUTATED    81  13
  LRP1B WILD-TYPE 211  46
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP1B MUTATED     81   13
  LRP1B WILD-TYPE  211   46
     clus
vv    LRP1B MUTATED LRP1B WILD-TYPE
  NO             81             211
  YES            13              46
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LRP1B MUTATED                                          0
  LRP1B WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LRP1B MUTATED                                      16
  LRP1B WILD-TYPE                                    54
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LRP1B MUTATED                                                       46
  LRP1B WILD-TYPE                                                    112
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LRP1B MUTATED                                                   7
  LRP1B WILD-TYPE                                                14
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LRP1B MUTATED                                                                  22
  LRP1B WILD-TYPE                                                                46
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LRP1B MUTATED                                                    1
  LRP1B WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LRP1B MUTATED                                                 12
  LRP1B WILD-TYPE                                               49
D1101V9, multiclass
                                                                   clus
vv                                                                  LRP1B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        16
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       46
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            22
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             12
                                                                   clus
vv                                                                  LRP1B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          54
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        112
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              14
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              46
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               49
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LRP1B MUTATED    86   2   4   6
  LRP1B WILD-TYPE 225  12  11  18
D1101V10, multiclass
    clus
vv   LRP1B MUTATED LRP1B WILD-TYPE
  R0            86             225
  R1             2              12
  R2             4              11
  RX             6              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1101V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LRP1B MUTATED      25                         3
  LRP1B WILD-TYPE    62                         6
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LRP1B MUTATED                                           1    60
  LRP1B WILD-TYPE                                         0   183
D1101V12, multiclass
                                           clus
vv                                          LRP1B MUTATED LRP1B WILD-TYPE
  ASIAN                                                25              62
  BLACK OR AFRICAN AMERICAN                             3               6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             1               0
  WHITE                                                60             183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1101V13, binary
                 cls
clus                0   1
  LRP1B MUTATED     1  82
  LRP1B WILD-TYPE   3 228
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRP1B MUTATED      1   82
  LRP1B WILD-TYPE    3  228
                        clus
vv                       LRP1B MUTATED LRP1B WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            82             228
[1] 2 2
[1] FALSE

Clustering(1102) Variable = GNAS MUTATION ANALYSIS
D1102V1, survival
                sevent
clus2              0   1
  GNAS MUTATED    23   9
  GNAS WILD-TYPE 207 130
  GNAS MUTATED GNAS WILD-TYPE 
            32            337 
  GNAS MUTATED GNAS WILD-TYPE 
             9            130 
$`GNAS MUTATED`
TCGA-CG-4460 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6452 
       21.99        19.56        11.01         6.97        30.90        34.68 
TCGA-BR-7958 TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A4QL TCGA-CD-5800 
       29.56         5.39         1.12        31.96        16.14        13.15 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4465 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5728 
        6.58        12.62         9.01         6.02        28.96        65.10 
TCGA-D7-8574 TCGA-EQ-8122 TCGA-FP-A4BE TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 
       17.19         7.99        11.08         6.21        77.29        52.21 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4HB TCGA-IN-A7NT 
       22.68        29.98         0.26         2.10        15.68        10.62 
TCGA-SW-A7EA TCGA-VQ-A8P2 
       19.04        38.14 

$`GNAS WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4183 
        9.86        26.70        11.70         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-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-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-8484 
       31.27        14.79         7.36        25.05         3.72        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-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-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-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-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-D7-6525 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-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-F1-6874 TCGA-F1-6875 
        4.34        19.96         7.13         0.62        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-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-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-A4GU 
       11.77        21.37         8.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
       20.25        12.95        29.00        23.84        23.80        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        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-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 

  GNAS MUTATED GNAS WILD-TYPE 
          0.26           0.00 
  GNAS MUTATED GNAS WILD-TYPE 
         77.29         122.30 
  GNAS MUTATED GNAS WILD-TYPE 
         15.91          14.17 
[1] "0.3 - 77.3 (15.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D1102V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GNAS MUTATED         1        3        3        2         5         5
  GNAS WILD-TYPE       1       12       37       28        32        47
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GNAS MUTATED           0          5          2          2        4
  GNAS WILD-TYPE         3         65         51         30       34
D1102V3, multiclass
            clus
vv           GNAS MUTATED GNAS WILD-TYPE
  STAGE I               1              1
  STAGE IA              3             12
  STAGE IB              3             37
  STAGE II              2             28
  STAGE IIA             5             32
  STAGE IIB             5             47
  STAGE III             0              3
  STAGE IIIA            5             65
  STAGE IIIB            2             51
  STAGE IIIC            2             30
  STAGE IV              4             34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GNAS MUTATED     5   8  11  10
  GNAS WILD-TYPE  17  84 162  87
D1102V4, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  T1            5             17
  T2            8             84
  T3           11            162
  T4           10             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
  GNAS MUTATED    12  12   3   5
  GNAS WILD-TYPE 106  92  74  72
D1102V5, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  N0           12            106
  N1           12             92
  N2            3             74
  N3            5             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"
D1102V6, binary
                cls
clus               0   1
  GNAS MUTATED    28   3
  GNAS WILD-TYPE 318  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     28    3
  GNAS WILD-TYPE  318   26
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0           28            318
  1            3             26
[1] 2 2
[1] FALSE
D1102V7, binary
                cls
clus               0   1
  GNAS MUTATED    13  21
  GNAS WILD-TYPE 132 227
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     13   21
  GNAS WILD-TYPE  132  227
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  FEMALE           13            132
  MALE             21            227
[1] 2 2
[1] FALSE
D1102V8, binary
                cls
clus               0   1
  GNAS MUTATED    25   6
  GNAS WILD-TYPE 267  53
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     25    6
  GNAS WILD-TYPE  267   53
     clus
vv    GNAS MUTATED GNAS WILD-TYPE
  NO            25            267
  YES            6             53
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GNAS MUTATED                                          0
  GNAS WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GNAS MUTATED                                       8
  GNAS WILD-TYPE                                    62
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GNAS MUTATED                                                       13
  GNAS WILD-TYPE                                                    145
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GNAS MUTATED                                                   2
  GNAS WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GNAS MUTATED                                                                   8
  GNAS WILD-TYPE                                                                60
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GNAS MUTATED                                                    1
  GNAS WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GNAS MUTATED                                                  2
  GNAS WILD-TYPE                                               59
D1102V9, multiclass
                                                                   clus
vv                                                                  GNAS MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            8
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  GNAS WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         62
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             60
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GNAS MUTATED    24   0   2   2
  GNAS WILD-TYPE 287  14  13  22
D1102V10, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  R0           24            287
  R1            0             14
  R2            2             13
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1102V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  GNAS MUTATED      10                         2
  GNAS WILD-TYPE    77                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GNAS MUTATED                                           0    15
  GNAS WILD-TYPE                                         1   228
D1102V12, multiclass
                                           clus
vv                                          GNAS MUTATED GNAS WILD-TYPE
  ASIAN                                               10             77
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               15            228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1102V13, binary
                cls
clus               0   1
  GNAS MUTATED     0  26
  GNAS WILD-TYPE   4 284
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      0   26
  GNAS WILD-TYPE    4  284
                        clus
vv                       GNAS MUTATED GNAS WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           26            284
[1] 2 2
[1] FALSE

Clustering(1103) Variable = FER MUTATION ANALYSIS
D1103V1, survival
               sevent
clus2             0   1
  FER MUTATED    10   2
  FER WILD-TYPE 220 137
  FER MUTATED FER WILD-TYPE 
           12           357 
  FER MUTATED FER WILD-TYPE 
            2           137 
$`FER MUTATED`
TCGA-BR-6452 TCGA-BR-8077 TCGA-BR-8680 TCGA-BR-A4PE TCGA-CD-A4MJ TCGA-CG-5721 
       34.68         0.69        31.96        20.42        12.62         6.02 
TCGA-CG-5723 TCGA-D7-A4YT TCGA-HF-7132 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-IN-A6RL 
      105.07        14.27        77.29         0.10         6.51        13.35 

$`FER WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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 

  FER MUTATED FER WILD-TYPE 
          0.1           0.0 
  FER MUTATED FER WILD-TYPE 
       105.07        122.30 
  FER MUTATED FER WILD-TYPE 
        13.81         14.43 
[1] "0.1 - 105.1 (13.8)" "0.0 - 122.3 (14.4)"
[1] "hr=" "2.7"
D1103V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FER MUTATED         0        0        3        2         2         0
  FER WILD-TYPE       2       15       37       28        35        52
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FER MUTATED           0          2          1          1        2
  FER WILD-TYPE         3         68         52         31       36
D1103V3, multiclass
            clus
vv           FER MUTATED FER WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             3            37
  STAGE II             2            28
  STAGE IIA            2            35
  STAGE IIB            0            52
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           1            52
  STAGE IIIC           1            31
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  FER MUTATED     0   7   2   4
  FER WILD-TYPE  22  85 171  93
D1103V4, multiclass
    clus
vv   FER MUTATED FER WILD-TYPE
  T1           0            22
  T2           7            85
  T3           2           171
  T4           4            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
  FER MUTATED     5   5   2   1
  FER WILD-TYPE 113  99  75  76
D1103V5, multiclass
    clus
vv   FER MUTATED FER WILD-TYPE
  N0           5           113
  N1           5            99
  N2           2            75
  N3           1            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"
D1103V6, binary
               cls
clus              0   1
  FER MUTATED    12   1
  FER WILD-TYPE 334  28
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED     12    1
  FER WILD-TYPE  334   28
   clus
vv  FER MUTATED FER WILD-TYPE
  0          12           334
  1           1            28
[1] 2 2
[1] FALSE
D1103V7, binary
               cls
clus              0   1
  FER MUTATED     4   9
  FER WILD-TYPE 141 239
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED      4    9
  FER WILD-TYPE  141  239
        clus
vv       FER MUTATED FER WILD-TYPE
  FEMALE           4           141
  MALE             9           239
[1] 2 2
[1] FALSE
D1103V8, binary
               cls
clus              0   1
  FER MUTATED    10   1
  FER WILD-TYPE 282  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED     10    1
  FER WILD-TYPE  282   58
     clus
vv    FER MUTATED FER WILD-TYPE
  NO           10           282
  YES           1            58
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FER MUTATED                                          0
  FER WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FER MUTATED                                       0
  FER WILD-TYPE                                    70
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FER MUTATED                                                        5
  FER WILD-TYPE                                                    153
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FER MUTATED                                                   1
  FER WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FER MUTATED                                                                   3
  FER WILD-TYPE                                                                65
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FER MUTATED                                                    0
  FER WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FER MUTATED                                                  4
  FER WILD-TYPE                                               57
D1103V9, multiclass
                                                                   clus
vv                                                                  FER MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            4
                                                                   clus
vv                                                                  FER WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  FER MUTATED    12   0   0   0
  FER WILD-TYPE 299  14  15  24
D1103V10, multiclass
    clus
vv   FER MUTATED FER WILD-TYPE
  R0          12           299
  R1           0            14
  R2           0            15
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1103V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  FER MUTATED       4                         0
  FER WILD-TYPE    83                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FER MUTATED                                           0     5
  FER WILD-TYPE                                         1   238
D1103V12, multiclass
                                           clus
vv                                          FER MUTATED FER WILD-TYPE
  ASIAN                                               4            83
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               5           238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1103V13, binary
               cls
clus              0   1
  FER MUTATED     0   9
  FER WILD-TYPE   4 301
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED      0    9
  FER WILD-TYPE    4  301
                        clus
vv                       FER MUTATED FER WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           9           301
[1] 2 2
[1] FALSE

Clustering(1104) Variable = GPATCH2 MUTATION ANALYSIS
D1104V1, survival
                   sevent
clus2                 0   1
  GPATCH2 MUTATED     4   2
  GPATCH2 WILD-TYPE 226 137
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
                6               363 
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
                2               137 
$`GPATCH2 MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8060 TCGA-CG-5721 TCGA-HU-A4GQ TCGA-KB-A93J 
       34.68        44.94        11.44         6.02         0.10        36.95 

$`GPATCH2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
              0.1               0.0 
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
            44.94            122.30 
  GPATCH2 MUTATED GPATCH2 WILD-TYPE 
            23.06             14.27 
[1] "0.1 - 44.9 (23.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D1104V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GPATCH2 MUTATED         1        0        1        1         2         1
  GPATCH2 WILD-TYPE       1       15       39       29        35        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPATCH2 MUTATED           0          0          0          1        1
  GPATCH2 WILD-TYPE         3         70         53         31       37
D1104V3, multiclass
            clus
vv           GPATCH2 MUTATED GPATCH2 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                2                35
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GPATCH2 MUTATED     2   3   2   2
  GPATCH2 WILD-TYPE  20  89 171  95
D1104V4, multiclass
    clus
vv   GPATCH2 MUTATED GPATCH2 WILD-TYPE
  T1               2                20
  T2               3                89
  T3               2               171
  T4               2                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
  GPATCH2 MUTATED     3   3   2   0
  GPATCH2 WILD-TYPE 115 101  75  77
D1104V5, multiclass
    clus
vv   GPATCH2 MUTATED GPATCH2 WILD-TYPE
  N0               3               115
  N1               3               101
  N2               2                75
  N3               0                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"
D1104V6, binary
                   cls
clus                  0   1
  GPATCH2 MUTATED     8   0
  GPATCH2 WILD-TYPE 338  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH2 MUTATED      8    0
  GPATCH2 WILD-TYPE  338   29
   clus
vv  GPATCH2 MUTATED GPATCH2 WILD-TYPE
  0               8               338
  1               0                29
[1] 2 2
[1] FALSE
D1104V7, binary
                   cls
clus                  0   1
  GPATCH2 MUTATED     4   5
  GPATCH2 WILD-TYPE 141 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH2 MUTATED      4    5
  GPATCH2 WILD-TYPE  141  243
        clus
vv       GPATCH2 MUTATED GPATCH2 WILD-TYPE
  FEMALE               4               141
  MALE                 5               243
[1] 2 2
[1] FALSE
D1104V8, binary
                   cls
clus                  0   1
  GPATCH2 MUTATED     6   1
  GPATCH2 WILD-TYPE 286  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH2 MUTATED      6    1
  GPATCH2 WILD-TYPE  286   58
     clus
vv    GPATCH2 MUTATED GPATCH2 WILD-TYPE
  NO                6               286
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GPATCH2 MUTATED                                          0
  GPATCH2 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GPATCH2 MUTATED                                       1
  GPATCH2 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPATCH2 MUTATED                                                        5
  GPATCH2 WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GPATCH2 MUTATED                                                   0
  GPATCH2 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPATCH2 MUTATED                                                                   2
  GPATCH2 WILD-TYPE                                                                66
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GPATCH2 MUTATED                                                    0
  GPATCH2 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GPATCH2 MUTATED                                                  1
  GPATCH2 WILD-TYPE                                               60
D1104V9, multiclass
                                                                   clus
vv                                                                  GPATCH2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  GPATCH2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GPATCH2 MUTATED     8   0   0   1
  GPATCH2 WILD-TYPE 303  14  15  23
D1104V10, multiclass
    clus
vv   GPATCH2 MUTATED GPATCH2 WILD-TYPE
  R0               8               303
  R1               0                14
  R2               0                15
  RX               1                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1104V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  GPATCH2 MUTATED       1                         1
  GPATCH2 WILD-TYPE    86                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPATCH2 MUTATED                                           0     5
  GPATCH2 WILD-TYPE                                         1   238
D1104V12, multiclass
                                           clus
vv                                          GPATCH2 MUTATED GPATCH2 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               1                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1104V13, binary
                   cls
clus                  0   1
  GPATCH2 MUTATED     0   6
  GPATCH2 WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH2 MUTATED      0    6
  GPATCH2 WILD-TYPE    4  304
                        clus
vv                       GPATCH2 MUTATED GPATCH2 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(1105) Variable = GFOD1 MUTATION ANALYSIS
D1105V1, survival
                 sevent
clus2               0   1
  GFOD1 MUTATED     7   3
  GFOD1 WILD-TYPE 223 136
  GFOD1 MUTATED GFOD1 WILD-TYPE 
             10             359 
  GFOD1 MUTATED GFOD1 WILD-TYPE 
              3             136 
$`GFOD1 MUTATED`
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8297 TCGA-CG-4306 TCGA-CG-4469 TCGA-CG-5723 
       30.90        44.94         7.40         1.02         7.07       105.07 
TCGA-CG-5726 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-IP-7968 
       28.96        22.32        22.68         2.53 

$`GFOD1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  GFOD1 MUTATED GFOD1 WILD-TYPE 
           1.02            0.00 
  GFOD1 MUTATED GFOD1 WILD-TYPE 
         105.07          122.30 
  GFOD1 MUTATED GFOD1 WILD-TYPE 
          22.50           14.17 
[1] "1.0 - 105.1 (22.5)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.5"
D1105V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GFOD1 MUTATED         0        1        1        1         1         2
  GFOD1 WILD-TYPE       2       14       39       29        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GFOD1 MUTATED           0          2          1          1        2
  GFOD1 WILD-TYPE         3         68         52         31       36
D1105V3, multiclass
            clus
vv           GFOD1 MUTATED GFOD1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GFOD1 MUTATED     1   2   6   3
  GFOD1 WILD-TYPE  21  90 167  94
D1105V4, multiclass
    clus
vv   GFOD1 MUTATED GFOD1 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             6             167
  T4             3              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
  GFOD1 MUTATED     5   2   3   2
  GFOD1 WILD-TYPE 113 102  74  75
D1105V5, multiclass
    clus
vv   GFOD1 MUTATED GFOD1 WILD-TYPE
  N0             5             113
  N1             2             102
  N2             3              74
  N3             2              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"
D1105V6, binary
                 cls
clus                0   1
  GFOD1 MUTATED    11   1
  GFOD1 WILD-TYPE 335  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFOD1 MUTATED     11    1
  GFOD1 WILD-TYPE  335   28
   clus
vv  GFOD1 MUTATED GFOD1 WILD-TYPE
  0            11             335
  1             1              28
[1] 2 2
[1] FALSE
D1105V7, binary
                 cls
clus                0   1
  GFOD1 MUTATED     5   8
  GFOD1 WILD-TYPE 140 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFOD1 MUTATED      5    8
  GFOD1 WILD-TYPE  140  240
        clus
vv       GFOD1 MUTATED GFOD1 WILD-TYPE
  FEMALE             5             140
  MALE               8             240
[1] 2 2
[1] FALSE
D1105V8, binary
                 cls
clus                0   1
  GFOD1 MUTATED     6   0
  GFOD1 WILD-TYPE 286  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFOD1 MUTATED      6    0
  GFOD1 WILD-TYPE  286   59
     clus
vv    GFOD1 MUTATED GFOD1 WILD-TYPE
  NO              6             286
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GFOD1 MUTATED                                          0
  GFOD1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GFOD1 MUTATED                                       3
  GFOD1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GFOD1 MUTATED                                                        7
  GFOD1 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GFOD1 MUTATED                                                   0
  GFOD1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GFOD1 MUTATED                                                                   3
  GFOD1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GFOD1 MUTATED                                                    0
  GFOD1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GFOD1 MUTATED                                                  0
  GFOD1 WILD-TYPE                                               61
D1105V9, multiclass
                                                                   clus
vv                                                                  GFOD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  GFOD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GFOD1 MUTATED     8   1   1   2
  GFOD1 WILD-TYPE 303  13  14  22
D1105V10, multiclass
    clus
vv   GFOD1 MUTATED GFOD1 WILD-TYPE
  R0             8             303
  R1             1              13
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1105V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  GFOD1 MUTATED       2                         0
  GFOD1 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GFOD1 MUTATED                                           0     6
  GFOD1 WILD-TYPE                                         1   237
D1105V12, multiclass
                                           clus
vv                                          GFOD1 MUTATED GFOD1 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1105V13, binary
                 cls
clus                0   1
  GFOD1 MUTATED     0   8
  GFOD1 WILD-TYPE   4 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFOD1 MUTATED      0    8
  GFOD1 WILD-TYPE    4  302
                        clus
vv                       GFOD1 MUTATED GFOD1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(1106) Variable = C3ORF33 MUTATION ANALYSIS
D1106V1, survival
                   sevent
clus2                 0   1
  C3ORF33 MUTATED     5   1
  C3ORF33 WILD-TYPE 225 138
  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
                6               363 
  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
                1               138 
$`C3ORF33 MUTATED`
TCGA-B7-5818 TCGA-BR-6566 TCGA-BR-7707 TCGA-BR-8060 TCGA-BR-8591 TCGA-FP-A4BE 
       11.70        32.78        35.84        11.44        28.14        11.08 

$`C3ORF33 WILD-TYPE`
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-B7-5816 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
            11.08              0.00 
  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
            35.84            122.30 
  C3ORF33 MUTATED C3ORF33 WILD-TYPE 
            19.92             14.27 
[1] "11.1 - 35.8 (19.9)" "0.0 - 122.3 (14.3)"
[1] "hr=" "2.7"
D1106V2, 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       1       15       38       30        35        51
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C3ORF33 MUTATED           0          0          0          1        0
  C3ORF33 WILD-TYPE         3         70         53         31       38
D1106V3, multiclass
            clus
vv           C3ORF33 MUTATED C3ORF33 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                2                35
  STAGE IIB                1                51
  STAGE III                0                 3
  STAGE IIIA               0                70
  STAGE IIIB               0                53
  STAGE IIIC               1                31
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C3ORF33 MUTATED     1   3   2   1
  C3ORF33 WILD-TYPE  21  89 171  96
D1106V4, multiclass
    clus
vv   C3ORF33 MUTATED C3ORF33 WILD-TYPE
  T1               1                21
  T2               3                89
  T3               2               171
  T4               1                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
  C3ORF33 MUTATED     4   1   1   1
  C3ORF33 WILD-TYPE 114 103  76  76
D1106V5, multiclass
    clus
vv   C3ORF33 MUTATED C3ORF33 WILD-TYPE
  N0               4               114
  N1               1               103
  N2               1                76
  N3               1                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"
D1106V6, binary
                   cls
clus                  0   1
  C3ORF33 MUTATED     6   0
  C3ORF33 WILD-TYPE 340  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF33 MUTATED      6    0
  C3ORF33 WILD-TYPE  340   29
   clus
vv  C3ORF33 MUTATED C3ORF33 WILD-TYPE
  0               6               340
  1               0                29
[1] 2 2
[1] FALSE
D1106V7, binary
                   cls
clus                  0   1
  C3ORF33 MUTATED     3   4
  C3ORF33 WILD-TYPE 142 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF33 MUTATED      3    4
  C3ORF33 WILD-TYPE  142  244
        clus
vv       C3ORF33 MUTATED C3ORF33 WILD-TYPE
  FEMALE               3               142
  MALE                 4               244
[1] 2 2
[1] FALSE
D1106V8, binary
                   cls
clus                  0   1
  C3ORF33 MUTATED     6   1
  C3ORF33 WILD-TYPE 286  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF33 MUTATED      6    1
  C3ORF33 WILD-TYPE  286   58
     clus
vv    C3ORF33 MUTATED C3ORF33 WILD-TYPE
  NO                6               286
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C3ORF33 MUTATED                                          0
  C3ORF33 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C3ORF33 MUTATED                                       1
  C3ORF33 WILD-TYPE                                    69
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C3ORF33 MUTATED                                                        6
  C3ORF33 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C3ORF33 MUTATED                                                   0
  C3ORF33 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C3ORF33 MUTATED                                                                   0
  C3ORF33 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C3ORF33 MUTATED                                                    0
  C3ORF33 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C3ORF33 MUTATED                                                  0
  C3ORF33 WILD-TYPE                                               61
D1106V9, multiclass
                                                                   clus
vv                                                                  C3ORF33 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                0
                                                                   clus
vv                                                                  C3ORF33 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C3ORF33 MUTATED     7   0   0   0
  C3ORF33 WILD-TYPE 304  14  15  24
D1106V10, multiclass
    clus
vv   C3ORF33 MUTATED C3ORF33 WILD-TYPE
  R0               7               304
  R1               0                14
  R2               0                15
  RX               0                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1106V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  C3ORF33 MUTATED       0                         2
  C3ORF33 WILD-TYPE    87                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C3ORF33 MUTATED                                           0     5
  C3ORF33 WILD-TYPE                                         1   238
D1106V12, multiclass
                                           clus
vv                                          C3ORF33 MUTATED C3ORF33 WILD-TYPE
  ASIAN                                                   0                87
  BLACK OR AFRICAN AMERICAN                               2                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1106V13, binary
                   cls
clus                  0   1
  C3ORF33 MUTATED     0   7
  C3ORF33 WILD-TYPE   4 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF33 MUTATED      0    7
  C3ORF33 WILD-TYPE    4  303
                        clus
vv                       C3ORF33 MUTATED C3ORF33 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               303
[1] 2 2
[1] FALSE

Clustering(1107) Variable = MYCL1 MUTATION ANALYSIS
D1107V1, survival
                 sevent
clus2               0   1
  MYCL1 MUTATED     5   3
  MYCL1 WILD-TYPE 225 136
  MYCL1 MUTATED MYCL1 WILD-TYPE 
              8             361 
  MYCL1 MUTATED MYCL1 WILD-TYPE 
              3             136 
$`MYCL1 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-CD-5813 TCGA-CG-4465 TCGA-FP-8211 TCGA-HU-A4GU 
        6.97        34.68        12.39         9.01        13.58         6.58 
TCGA-HU-A4GX TCGA-VQ-AA68 
       20.25        43.66 

$`MYCL1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-AA69 TCGA-VQ-AA6A 
       42.64        66.81        11.24        18.41        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 

  MYCL1 MUTATED MYCL1 WILD-TYPE 
           6.58            0.00 
  MYCL1 MUTATED MYCL1 WILD-TYPE 
          43.66          122.30 
  MYCL1 MUTATED MYCL1 WILD-TYPE 
         12.985          14.430 
[1] "6.6 - 43.7 (13.0)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1"  
D1107V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MYCL1 MUTATED         0        0        0        1         1         2
  MYCL1 WILD-TYPE       2       15       40       29        36        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MYCL1 MUTATED           0          1          0          2        1
  MYCL1 WILD-TYPE         3         69         53         30       37
D1107V3, multiclass
            clus
vv           MYCL1 MUTATED MYCL1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYCL1 MUTATED     0   0   5   3
  MYCL1 WILD-TYPE  22  92 168  94
D1107V4, multiclass
    clus
vv   MYCL1 MUTATED MYCL1 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             5             168
  T4             3              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
  MYCL1 MUTATED     2   3   1   2
  MYCL1 WILD-TYPE 116 101  76  75
D1107V5, multiclass
    clus
vv   MYCL1 MUTATED MYCL1 WILD-TYPE
  N0             2             116
  N1             3             101
  N2             1              76
  N3             2              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"
D1107V6, binary
                 cls
clus                0   1
  MYCL1 MUTATED     5   1
  MYCL1 WILD-TYPE 341  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCL1 MUTATED      5    1
  MYCL1 WILD-TYPE  341   28
   clus
vv  MYCL1 MUTATED MYCL1 WILD-TYPE
  0             5             341
  1             1              28
[1] 2 2
[1] FALSE
D1107V7, binary
                 cls
clus                0   1
  MYCL1 MUTATED     4   4
  MYCL1 WILD-TYPE 141 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCL1 MUTATED      4    4
  MYCL1 WILD-TYPE  141  244
        clus
vv       MYCL1 MUTATED MYCL1 WILD-TYPE
  FEMALE             4             141
  MALE               4             244
[1] 2 2
[1] FALSE
D1107V8, binary
                 cls
clus                0   1
  MYCL1 MUTATED     5   2
  MYCL1 WILD-TYPE 287  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCL1 MUTATED      5    2
  MYCL1 WILD-TYPE  287   57
     clus
vv    MYCL1 MUTATED MYCL1 WILD-TYPE
  NO              5             287
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MYCL1 MUTATED                                          0
  MYCL1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MYCL1 MUTATED                                       3
  MYCL1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MYCL1 MUTATED                                                        3
  MYCL1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MYCL1 MUTATED                                                   1
  MYCL1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MYCL1 MUTATED                                                                   0
  MYCL1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MYCL1 MUTATED                                                    0
  MYCL1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MYCL1 MUTATED                                                  1
  MYCL1 WILD-TYPE                                               60
D1107V9, multiclass
                                                                   clus
vv                                                                  MYCL1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  MYCL1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYCL1 MUTATED     4   1   1   1
  MYCL1 WILD-TYPE 307  13  14  23
D1107V10, multiclass
    clus
vv   MYCL1 MUTATED MYCL1 WILD-TYPE
  R0             4             307
  R1             1              13
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1107V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MYCL1 MUTATED       3                         0
  MYCL1 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MYCL1 MUTATED                                           0     4
  MYCL1 WILD-TYPE                                         1   239
D1107V12, multiclass
                                           clus
vv                                          MYCL1 MUTATED MYCL1 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1107V13, binary
                 cls
clus                0   1
  MYCL1 MUTATED     0   6
  MYCL1 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYCL1 MUTATED      0    6
  MYCL1 WILD-TYPE    4  304
                        clus
vv                       MYCL1 MUTATED MYCL1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(1108) Variable = SERPING1 MUTATION ANALYSIS
D1108V1, survival
                    sevent
clus2                  0   1
  SERPING1 MUTATED     3   4
  SERPING1 WILD-TYPE 227 135
  SERPING1 MUTATED SERPING1 WILD-TYPE 
                 7                362 
  SERPING1 MUTATED SERPING1 WILD-TYPE 
                 4                135 
$`SERPING1 MUTATED`
TCGA-CG-4460 TCGA-BR-8059 TCGA-BR-8677 TCGA-CD-8532 TCGA-CD-A4MG TCGA-CD-A4MJ 
       21.99        14.43        26.73        11.64         6.58        12.62 
TCGA-D7-A4YX 
       36.43 

$`SERPING1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-8678 TCGA-BR-8680 TCGA-BR-8682 
       28.14         6.28         7.53        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-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-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-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-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 

  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              14.22 
[1] "6.6 - 36.4 (14.4)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D1108V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SERPING1 MUTATED         0        0        1        1         1         2
  SERPING1 WILD-TYPE       2       15       39       29        36        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPING1 MUTATED           1          0          1          0        1
  SERPING1 WILD-TYPE         2         70         52         32       37
D1108V3, multiclass
            clus
vv           SERPING1 MUTATED SERPING1 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  1                 29
  STAGE IIA                 1                 36
  STAGE IIB                 2                 50
  STAGE III                 1                  2
  STAGE IIIA                0                 70
  STAGE IIIB                1                 52
  STAGE IIIC                0                 32
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SERPING1 MUTATED     0   1   4   3
  SERPING1 WILD-TYPE  22  91 169  94
D1108V4, multiclass
    clus
vv   SERPING1 MUTATED SERPING1 WILD-TYPE
  T1                0                 22
  T2                1                 91
  T3                4                169
  T4                3                 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
  SERPING1 MUTATED     4   3   0   1
  SERPING1 WILD-TYPE 114 101  77  76
D1108V5, multiclass
    clus
vv   SERPING1 MUTATED SERPING1 WILD-TYPE
  N0                4                114
  N1                3                101
  N2                0                 77
  N3                1                 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"
D1108V6, binary
                    cls
clus                   0   1
  SERPING1 MUTATED     7   1
  SERPING1 WILD-TYPE 339  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPING1 MUTATED      7    1
  SERPING1 WILD-TYPE  339   28
   clus
vv  SERPING1 MUTATED SERPING1 WILD-TYPE
  0                7                339
  1                1                 28
[1] 2 2
[1] FALSE
D1108V7, binary
                    cls
clus                   0   1
  SERPING1 MUTATED     2   6
  SERPING1 WILD-TYPE 143 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPING1 MUTATED      2    6
  SERPING1 WILD-TYPE  143  242
        clus
vv       SERPING1 MUTATED SERPING1 WILD-TYPE
  FEMALE                2                143
  MALE                  6                242
[1] 2 2
[1] FALSE
D1108V8, binary
                    cls
clus                   0   1
  SERPING1 MUTATED     8   0
  SERPING1 WILD-TYPE 284  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPING1 MUTATED      8    0
  SERPING1 WILD-TYPE  284   59
     clus
vv    SERPING1 MUTATED SERPING1 WILD-TYPE
  NO                 8                284
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SERPING1 MUTATED                                          0
  SERPING1 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SERPING1 MUTATED                                       1
  SERPING1 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SERPING1 MUTATED                                                        4
  SERPING1 WILD-TYPE                                                    154
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SERPING1 MUTATED                                                   0
  SERPING1 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SERPING1 MUTATED                                                                   3
  SERPING1 WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SERPING1 MUTATED                                                    0
  SERPING1 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SERPING1 MUTATED                                                  0
  SERPING1 WILD-TYPE                                               61
D1108V9, multiclass
                                                                   clus
vv                                                                  SERPING1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 0
                                                                   clus
vv                                                                  SERPING1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SERPING1 MUTATED     5   0   1   0
  SERPING1 WILD-TYPE 306  14  14  24
D1108V10, multiclass
    clus
vv   SERPING1 MUTATED SERPING1 WILD-TYPE
  R0                5                306
  R1                0                 14
  R2                1                 14
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1108V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SERPING1 MUTATED       3                         0
  SERPING1 WILD-TYPE    84                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SERPING1 MUTATED                                           0     4
  SERPING1 WILD-TYPE                                         1   239
D1108V12, multiclass
                                           clus
vv                                          SERPING1 MUTATED SERPING1 WILD-TYPE
  ASIAN                                                    3                 84
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1108V13, binary
                    cls
clus                   0   1
  SERPING1 MUTATED     0   7
  SERPING1 WILD-TYPE   4 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPING1 MUTATED      0    7
  SERPING1 WILD-TYPE    4  303
                        clus
vv                       SERPING1 MUTATED SERPING1 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                7                303
[1] 2 2
[1] FALSE

Clustering(1109) Variable = TNFRSF13B MUTATION ANALYSIS
D1109V1, survival
                     sevent
clus2                   0   1
  TNFRSF13B MUTATED     6   1
  TNFRSF13B WILD-TYPE 224 138
  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE 
                  7                 362 
  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE 
                  1                 138 
$`TNFRSF13B MUTATED`
TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8486 TCGA-BR-8487 TCGA-CD-8536 TCGA-HU-A4GH 
       44.94        36.16        20.22         1.12        12.43        11.77 
TCGA-RD-A7BS 
       11.05 

$`TNFRSF13B WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        9.21        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-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-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
        9.24         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 

  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE 
               1.12                0.00 
  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE 
              44.94              122.30 
  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE 
              12.43               14.35 
[1] "1.1 - 44.9 (12.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "2.7"
D1109V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNFRSF13B MUTATED         0        3        0        1         2         0
  TNFRSF13B WILD-TYPE       2       12       40       29        35        52
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFRSF13B MUTATED           0          1          0          0        0
  TNFRSF13B WILD-TYPE         3         69         53         32       38
D1109V3, multiclass
            clus
vv           TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  STAGE I                    0                   2
  STAGE IA                   3                  12
  STAGE IB                   0                  40
  STAGE II                   1                  29
  STAGE IIA                  2                  35
  STAGE IIB                  0                  52
  STAGE III                  0                   3
  STAGE IIIA                 1                  69
  STAGE IIIB                 0                  53
  STAGE IIIC                 0                  32
  STAGE IV                   0                  38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  TNFRSF13B MUTATED     3   0   4   0
  TNFRSF13B WILD-TYPE  19  92 169  97
D1109V4, multiclass
    clus
vv   TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  T1                 3                  19
  T2                 0                  92
  T3                 4                 169
  T4                 0                  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
  TNFRSF13B MUTATED     6   1   0   0
  TNFRSF13B WILD-TYPE 112 103  77  77
D1109V5, multiclass
    clus
vv   TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  N0                 6                 112
  N1                 1                 103
  N2                 0                  77
  N3                 0                  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"
D1109V6, binary
                     cls
clus                    0   1
  TNFRSF13B MUTATED     7   0
  TNFRSF13B WILD-TYPE 339  29
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF13B MUTATED      7    0
  TNFRSF13B WILD-TYPE  339   29
   clus
vv  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  0                 7                 339
  1                 0                  29
[1] 2 2
[1] FALSE
D1109V7, binary
                     cls
clus                    0   1
  TNFRSF13B MUTATED     3   4
  TNFRSF13B WILD-TYPE 142 244
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF13B MUTATED      3    4
  TNFRSF13B WILD-TYPE  142  244
        clus
vv       TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  FEMALE                 3                 142
  MALE                   4                 244
[1] 2 2
[1] FALSE
D1109V8, binary
                     cls
clus                    0   1
  TNFRSF13B MUTATED     6   1
  TNFRSF13B WILD-TYPE 286  58
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF13B MUTATED      6    1
  TNFRSF13B WILD-TYPE  286   58
     clus
vv    TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  NO                  6                 286
  YES                 1                  58
[1] 2 2
[1] FALSE
                     vv
clus                  STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TNFRSF13B MUTATED                                          0
  TNFRSF13B WILD-TYPE                                        8
                     vv
clus                  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TNFRSF13B MUTATED                                       1
  TNFRSF13B WILD-TYPE                                    69
                     vv
clus                  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNFRSF13B MUTATED                                                        4
  TNFRSF13B WILD-TYPE                                                    154
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TNFRSF13B MUTATED                                                   0
  TNFRSF13B WILD-TYPE                                                21
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNFRSF13B MUTATED                                                                   0
  TNFRSF13B WILD-TYPE                                                                68
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TNFRSF13B MUTATED                                                    1
  TNFRSF13B WILD-TYPE                                                  4
                     vv
clus                  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TNFRSF13B MUTATED                                                  1
  TNFRSF13B WILD-TYPE                                               60
D1109V9, multiclass
                                                                   clus
vv                                                                  TNFRSF13B MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  1
                                                                   clus
vv                                                                  TNFRSF13B WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                            8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                              69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                            154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                  21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                  4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                   60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  TNFRSF13B MUTATED     7   0   0   0
  TNFRSF13B WILD-TYPE 304  14  15  24
D1109V10, multiclass
    clus
vv   TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  R0                 7                 304
  R1                 0                  14
  R2                 0                  15
  RX                 0                  24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1109V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN
  TNFRSF13B MUTATED       2                         0
  TNFRSF13B WILD-TYPE    85                         9
                     vv
clus                  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNFRSF13B MUTATED                                           0     5
  TNFRSF13B WILD-TYPE                                         1   238
D1109V12, multiclass
                                           clus
vv                                          TNFRSF13B MUTATED
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                 0
  WHITE                                                     5
                                           clus
vv                                          TNFRSF13B WILD-TYPE
  ASIAN                                                      85
  BLACK OR AFRICAN AMERICAN                                   9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                   1
  WHITE                                                     238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1109V13, binary
                     cls
clus                    0   1
  TNFRSF13B MUTATED     0   7
  TNFRSF13B WILD-TYPE   4 303
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF13B MUTATED      0    7
  TNFRSF13B WILD-TYPE    4  303
                        clus
vv                       TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  HISPANIC OR LATINO                     0                   4
  NOT HISPANIC OR LATINO                 7                 303
[1] 2 2
[1] FALSE

Clustering(1110) Variable = ABCC1 MUTATION ANALYSIS
D1110V1, survival
                 sevent
clus2               0   1
  ABCC1 MUTATED     7   6
  ABCC1 WILD-TYPE 223 133
  ABCC1 MUTATED ABCC1 WILD-TYPE 
             13             356 
  ABCC1 MUTATED ABCC1 WILD-TYPE 
              6             133 
$`ABCC1 MUTATED`
TCGA-BR-4184 TCGA-BR-6802 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-8284 TCGA-BR-8372 
        6.97        30.90        35.84        33.63         8.05        31.27 
TCGA-BR-A4QL TCGA-CD-A4MG TCGA-CD-A4MI TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GT 
       16.14         6.58        11.77        22.32         0.10         6.51 
TCGA-HU-A4GU 
        6.58 

$`ABCC1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        8.98        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 

  ABCC1 MUTATED ABCC1 WILD-TYPE 
            0.1             0.0 
  ABCC1 MUTATED ABCC1 WILD-TYPE 
          35.84          122.30 
  ABCC1 MUTATED ABCC1 WILD-TYPE 
          11.77           14.35 
[1] "0.1 - 35.8 (11.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.3"
D1110V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ABCC1 MUTATED         0        0        2        0         3         2
  ABCC1 WILD-TYPE       2       15       38       30        34        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABCC1 MUTATED           0          3          1          3        0
  ABCC1 WILD-TYPE         3         67         52         29       38
D1110V3, multiclass
            clus
vv           ABCC1 MUTATED ABCC1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             3              29
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCC1 MUTATED     0   2   8   4
  ABCC1 WILD-TYPE  22  90 165  93
D1110V4, multiclass
    clus
vv   ABCC1 MUTATED ABCC1 WILD-TYPE
  T1             0              22
  T2             2              90
  T3             8             165
  T4             4              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
  ABCC1 MUTATED     6   3   2   3
  ABCC1 WILD-TYPE 112 101  75  74
D1110V5, multiclass
    clus
vv   ABCC1 MUTATED ABCC1 WILD-TYPE
  N0             6             112
  N1             3             101
  N2             2              75
  N3             3              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"
D1110V6, binary
                 cls
clus                0   1
  ABCC1 MUTATED    13   0
  ABCC1 WILD-TYPE 333  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC1 MUTATED     13    0
  ABCC1 WILD-TYPE  333   29
   clus
vv  ABCC1 MUTATED ABCC1 WILD-TYPE
  0            13             333
  1             0              29
[1] 2 2
[1] FALSE
D1110V7, binary
                 cls
clus                0   1
  ABCC1 MUTATED     5   9
  ABCC1 WILD-TYPE 140 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC1 MUTATED      5    9
  ABCC1 WILD-TYPE  140  239
        clus
vv       ABCC1 MUTATED ABCC1 WILD-TYPE
  FEMALE             5             140
  MALE               9             239
[1] 2 2
[1] FALSE
D1110V8, binary
                 cls
clus                0   1
  ABCC1 MUTATED    13   0
  ABCC1 WILD-TYPE 279  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC1 MUTATED     13    0
  ABCC1 WILD-TYPE  279   59
     clus
vv    ABCC1 MUTATED ABCC1 WILD-TYPE
  NO             13             279
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ABCC1 MUTATED                                          0
  ABCC1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ABCC1 MUTATED                                       3
  ABCC1 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCC1 MUTATED                                                        7
  ABCC1 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ABCC1 MUTATED                                                   0
  ABCC1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ABCC1 MUTATED                                                                   2
  ABCC1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ABCC1 MUTATED                                                    0
  ABCC1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ABCC1 MUTATED                                                  2
  ABCC1 WILD-TYPE                                               59
D1110V9, multiclass
                                                                   clus
vv                                                                  ABCC1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  ABCC1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCC1 MUTATED    11   0   0   1
  ABCC1 WILD-TYPE 300  14  15  23
D1110V10, multiclass
    clus
vv   ABCC1 MUTATED ABCC1 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1110V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ABCC1 MUTATED       6                         0
  ABCC1 WILD-TYPE    81                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ABCC1 MUTATED                                           0     7
  ABCC1 WILD-TYPE                                         1   236
D1110V12, multiclass
                                           clus
vv                                          ABCC1 MUTATED ABCC1 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1110V13, binary
                 cls
clus                0   1
  ABCC1 MUTATED     0  13
  ABCC1 WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC1 MUTATED      0   13
  ABCC1 WILD-TYPE    4  297
                        clus
vv                       ABCC1 MUTATED ABCC1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(1111) Variable = CD1E MUTATION ANALYSIS
D1111V1, survival
                sevent
clus2              0   1
  CD1E MUTATED     7   2
  CD1E WILD-TYPE 223 137
  CD1E MUTATED CD1E WILD-TYPE 
             9            360 
  CD1E MUTATED CD1E WILD-TYPE 
             2            137 
$`CD1E MUTATED`
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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-D7-6519 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-D7-8570 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-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-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 
        6.51        10.62        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-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-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 

  CD1E MUTATED CD1E WILD-TYPE 
           4.6            0.0 
  CD1E MUTATED CD1E WILD-TYPE 
         42.64         122.30 
  CD1E MUTATED CD1E WILD-TYPE 
         15.95          14.22 
[1] "4.6 - 42.6 (15.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.7"
D1111V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD1E MUTATED         0        0        2        0         1         2
  CD1E WILD-TYPE       2       15       38       30        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CD1E MUTATED           0          2          2          0        1
  CD1E WILD-TYPE         3         68         51         32       37
D1111V3, multiclass
            clus
vv           CD1E MUTATED CD1E WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            2             51
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD1E MUTATED     0   4   5   1
  CD1E WILD-TYPE  22  88 168  96
D1111V4, multiclass
    clus
vv   CD1E MUTATED CD1E WILD-TYPE
  T1            0             22
  T2            4             88
  T3            5            168
  T4            1             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
  CD1E MUTATED     3   2   2   3
  CD1E WILD-TYPE 115 102  75  74
D1111V5, multiclass
    clus
vv   CD1E MUTATED CD1E WILD-TYPE
  N0            3            115
  N1            2            102
  N2            2             75
  N3            3             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"
D1111V6, binary
                cls
clus               0   1
  CD1E MUTATED    10   1
  CD1E WILD-TYPE 336  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1E MUTATED     10    1
  CD1E WILD-TYPE  336   28
   clus
vv  CD1E MUTATED CD1E WILD-TYPE
  0           10            336
  1            1             28
[1] 2 2
[1] FALSE
D1111V7, binary
                cls
clus               0   1
  CD1E MUTATED     1  10
  CD1E WILD-TYPE 144 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1E MUTATED      1   10
  CD1E WILD-TYPE  144  238
        clus
vv       CD1E MUTATED CD1E WILD-TYPE
  FEMALE            1            144
  MALE             10            238
[1] 2 2
[1] FALSE
D1111V8, binary
                cls
clus               0   1
  CD1E MUTATED     8   1
  CD1E WILD-TYPE 284  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1E MUTATED      8    1
  CD1E WILD-TYPE  284   58
     clus
vv    CD1E MUTATED CD1E WILD-TYPE
  NO             8            284
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CD1E MUTATED                                          0
  CD1E WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CD1E MUTATED                                       3
  CD1E WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD1E MUTATED                                                        5
  CD1E WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CD1E MUTATED                                                   0
  CD1E WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD1E MUTATED                                                                   1
  CD1E WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CD1E MUTATED                                                    0
  CD1E WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CD1E MUTATED                                                  2
  CD1E WILD-TYPE                                               59
D1111V9, multiclass
                                                                   clus
vv                                                                  CD1E MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  CD1E WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CD1E MUTATED     8   1   0   1
  CD1E WILD-TYPE 303  13  15  23
D1111V10, multiclass
    clus
vv   CD1E MUTATED CD1E WILD-TYPE
  R0            8            303
  R1            1             13
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1111V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CD1E MUTATED       1                         1
  CD1E WILD-TYPE    86                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD1E MUTATED                                           0     7
  CD1E WILD-TYPE                                         1   236
D1111V12, multiclass
                                           clus
vv                                          CD1E MUTATED CD1E WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1111V13, binary
                cls
clus               0   1
  CD1E MUTATED     0   9
  CD1E WILD-TYPE   4 301
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1E MUTATED      0    9
  CD1E WILD-TYPE    4  301
                        clus
vv                       CD1E MUTATED CD1E WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            9            301
[1] 2 2
[1] FALSE

Clustering(1112) Variable = ATG9A MUTATION ANALYSIS
D1112V1, survival
                 sevent
clus2               0   1
  ATG9A MUTATED     7   3
  ATG9A WILD-TYPE 223 136
  ATG9A MUTATED ATG9A WILD-TYPE 
             10             359 
  ATG9A MUTATED ATG9A WILD-TYPE 
              3             136 
$`ATG9A MUTATED`
TCGA-BR-8680 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-5723 TCGA-HU-A4GQ 
       31.96         6.58        12.62        20.02       105.07         0.10 
TCGA-HU-A4GT TCGA-MX-A5UJ TCGA-VQ-A8P2 TCGA-VQ-AA6F 
        6.51        19.73        38.14        54.12 

$`ATG9A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.61        12.20        11.77         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-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-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       26.04        16.14        27.55        12.43        17.26 

  ATG9A MUTATED ATG9A WILD-TYPE 
            0.1             0.0 
  ATG9A MUTATED ATG9A WILD-TYPE 
         105.07          122.30 
  ATG9A MUTATED ATG9A WILD-TYPE 
         19.875          14.170 
[1] "0.1 - 105.1 (19.9)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D1112V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATG9A MUTATED         0        0        1        1         2         1
  ATG9A WILD-TYPE       2       15       39       29        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATG9A MUTATED           0          3          1          1        1
  ATG9A WILD-TYPE         3         67         52         31       37
D1112V3, multiclass
            clus
vv           ATG9A MUTATED ATG9A WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATG9A MUTATED     0   2   5   4
  ATG9A WILD-TYPE  22  90 168  93
D1112V4, multiclass
    clus
vv   ATG9A MUTATED ATG9A WILD-TYPE
  T1             0              22
  T2             2              90
  T3             5             168
  T4             4              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
  ATG9A MUTATED     4   3   4   0
  ATG9A WILD-TYPE 114 101  73  77
D1112V5, multiclass
    clus
vv   ATG9A MUTATED ATG9A WILD-TYPE
  N0             4             114
  N1             3             101
  N2             4              73
  N3             0              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"
D1112V6, binary
                 cls
clus                0   1
  ATG9A MUTATED    10   1
  ATG9A WILD-TYPE 336  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG9A MUTATED     10    1
  ATG9A WILD-TYPE  336   28
   clus
vv  ATG9A MUTATED ATG9A WILD-TYPE
  0            10             336
  1             1              28
[1] 2 2
[1] FALSE
D1112V7, binary
                 cls
clus                0   1
  ATG9A MUTATED     3   8
  ATG9A WILD-TYPE 142 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG9A MUTATED      3    8
  ATG9A WILD-TYPE  142  240
        clus
vv       ATG9A MUTATED ATG9A WILD-TYPE
  FEMALE             3             142
  MALE               8             240
[1] 2 2
[1] FALSE
D1112V8, binary
                 cls
clus                0   1
  ATG9A MUTATED     7   2
  ATG9A WILD-TYPE 285  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG9A MUTATED      7    2
  ATG9A WILD-TYPE  285   57
     clus
vv    ATG9A MUTATED ATG9A WILD-TYPE
  NO              7             285
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ATG9A MUTATED                                          0
  ATG9A WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ATG9A MUTATED                                       1
  ATG9A WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATG9A MUTATED                                                        4
  ATG9A WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ATG9A MUTATED                                                   1
  ATG9A WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATG9A MUTATED                                                                   1
  ATG9A WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ATG9A MUTATED                                                    0
  ATG9A WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ATG9A MUTATED                                                  4
  ATG9A WILD-TYPE                                               57
D1112V9, multiclass
                                                                   clus
vv                                                                  ATG9A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  ATG9A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ATG9A MUTATED     8   0   0   1
  ATG9A WILD-TYPE 303  14  15  23
D1112V10, multiclass
    clus
vv   ATG9A MUTATED ATG9A WILD-TYPE
  R0             8             303
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1112V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ATG9A MUTATED       5                         0
  ATG9A WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATG9A MUTATED                                           0     4
  ATG9A WILD-TYPE                                         1   239
D1112V12, multiclass
                                           clus
vv                                          ATG9A MUTATED ATG9A WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1112V13, binary
                 cls
clus                0   1
  ATG9A MUTATED     0   7
  ATG9A WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG9A MUTATED      0    7
  ATG9A WILD-TYPE    4  303
                        clus
vv                       ATG9A MUTATED ATG9A WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(1113) Variable = IGBP1 MUTATION ANALYSIS
D1113V1, survival
                 sevent
clus2               0   1
  IGBP1 MUTATED     4   2
  IGBP1 WILD-TYPE 226 137
  IGBP1 MUTATED IGBP1 WILD-TYPE 
              6             363 
  IGBP1 MUTATED IGBP1 WILD-TYPE 
              2             137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8677 TCGA-BR-8678 TCGA-BR-8680 
        9.34        28.14         6.28        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-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-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-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-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        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 

  IGBP1 MUTATED IGBP1 WILD-TYPE 
           7.13            0.00 
  IGBP1 MUTATED IGBP1 WILD-TYPE 
          44.94          122.30 
  IGBP1 MUTATED IGBP1 WILD-TYPE 
          15.47           14.27 
[1] "7.1 - 44.9 (15.5)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D1113V2, 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       2       15       40       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGBP1 MUTATED           0          2          2          0        0
  IGBP1 WILD-TYPE         3         68         51         32       38
D1113V3, multiclass
            clus
vv           IGBP1 MUTATED IGBP1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             2              51
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IGBP1 MUTATED     0   0   6   0
  IGBP1 WILD-TYPE  22  92 167  97
D1113V4, multiclass
    clus
vv   IGBP1 MUTATED IGBP1 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             6             167
  T4             0              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
  IGBP1 MUTATED     1   1   2   2
  IGBP1 WILD-TYPE 117 103  75  75
D1113V5, multiclass
    clus
vv   IGBP1 MUTATED IGBP1 WILD-TYPE
  N0             1             117
  N1             1             103
  N2             2              75
  N3             2              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"
D1113V6, binary
                 cls
clus                0   1
  IGBP1 MUTATED     6   0
  IGBP1 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGBP1 MUTATED      6    0
  IGBP1 WILD-TYPE  340   29
   clus
vv  IGBP1 MUTATED IGBP1 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D1113V7, binary
                 cls
clus                0   1
  IGBP1 MUTATED     3   3
  IGBP1 WILD-TYPE 142 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGBP1 MUTATED      3    3
  IGBP1 WILD-TYPE  142  245
        clus
vv       IGBP1 MUTATED IGBP1 WILD-TYPE
  FEMALE             3             142
  MALE               3             245
[1] 2 2
[1] FALSE
D1113V8, binary
                 cls
clus                0   1
  IGBP1 MUTATED     5   1
  IGBP1 WILD-TYPE 287  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGBP1 MUTATED      5    1
  IGBP1 WILD-TYPE  287   58
     clus
vv    IGBP1 MUTATED IGBP1 WILD-TYPE
  NO              5             287
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  IGBP1 MUTATED                                          0
  IGBP1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  IGBP1 MUTATED                                       1
  IGBP1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IGBP1 MUTATED                                                        2
  IGBP1 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  IGBP1 MUTATED                                                   0
  IGBP1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  IGBP1 MUTATED                                                                   3
  IGBP1 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  IGBP1 MUTATED                                                    0
  IGBP1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  IGBP1 MUTATED                                                  0
  IGBP1 WILD-TYPE                                               61
D1113V9, multiclass
                                                                   clus
vv                                                                  IGBP1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  IGBP1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IGBP1 MUTATED     6   0   0   0
  IGBP1 WILD-TYPE 305  14  15  24
D1113V10, multiclass
    clus
vv   IGBP1 MUTATED IGBP1 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1113V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  IGBP1 MUTATED       0                         0
  IGBP1 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  IGBP1 MUTATED                                           0     6
  IGBP1 WILD-TYPE                                         1   237
D1113V12, multiclass
                                           clus
vv                                          IGBP1 MUTATED IGBP1 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1113V13, binary
                 cls
clus                0   1
  IGBP1 MUTATED     0   5
  IGBP1 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGBP1 MUTATED      0    5
  IGBP1 WILD-TYPE    4  305
                        clus
vv                       IGBP1 MUTATED IGBP1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(1114) Variable = HIVEP2 MUTATION ANALYSIS
D1114V1, survival
                  sevent
clus2                0   1
  HIVEP2 MUTATED    18   8
  HIVEP2 WILD-TYPE 212 131
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
              26              343 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
               8              131 
$`HIVEP2 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6709 TCGA-BR-6852 
       21.99         6.97         9.67        34.68        12.16        44.94 
TCGA-BR-7703 TCGA-BR-8081 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-8680 
       36.16        32.25         1.12        12.79        28.14        31.96 
TCGA-BR-A4QL TCGA-CD-8524 TCGA-CD-8536 TCGA-CG-4300 TCGA-CG-5721 TCGA-D7-A6EY 
       16.14        12.76        12.43        20.02         6.02        11.44 
TCGA-HU-A4G8 TCGA-HU-A4GP TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-R5-A7O7 
       22.68         8.98        29.00        23.84        14.07        45.67 
TCGA-R5-A7ZE TCGA-VQ-A8P2 
       18.21        38.14 

$`HIVEP2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-7196 TCGA-BR-7197 
        8.98        40.21        30.90        31.20        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-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-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-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-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-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        12.62         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-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-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         0.10         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H6 
       20.25         0.26         2.10        12.95        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-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
       14.04         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 

  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
            1.12             0.00 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
           45.67           122.30 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
          19.115           14.070 
[1] "1.1 - 45.7 (19.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D1114V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  HIVEP2 MUTATED         0        1        1        2         4         4
  HIVEP2 WILD-TYPE       2       14       39       28        33        48
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIVEP2 MUTATED           0          4          4          2        4
  HIVEP2 WILD-TYPE         3         66         49         30       34
D1114V3, multiclass
            clus
vv           HIVEP2 MUTATED HIVEP2 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               4               33
  STAGE IIB               4               48
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              4               49
  STAGE IIIC              2               30
  STAGE IV                4               34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HIVEP2 MUTATED     2   2  13   9
  HIVEP2 WILD-TYPE  20  90 160  88
D1114V4, multiclass
    clus
vv   HIVEP2 MUTATED HIVEP2 WILD-TYPE
  T1              2               20
  T2              2               90
  T3             13              160
  T4              9               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
  HIVEP2 MUTATED     9   8   4   5
  HIVEP2 WILD-TYPE 109  96  73  72
D1114V5, multiclass
    clus
vv   HIVEP2 MUTATED HIVEP2 WILD-TYPE
  N0              9              109
  N1              8               96
  N2              4               73
  N3              5               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"
D1114V6, binary
                  cls
clus                 0   1
  HIVEP2 MUTATED    23   3
  HIVEP2 WILD-TYPE 323  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP2 MUTATED     23    3
  HIVEP2 WILD-TYPE  323   26
   clus
vv  HIVEP2 MUTATED HIVEP2 WILD-TYPE
  0             23              323
  1              3               26
[1] 2 2
[1] FALSE
D1114V7, binary
                  cls
clus                 0   1
  HIVEP2 MUTATED    17  10
  HIVEP2 WILD-TYPE 128 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP2 MUTATED     17   10
  HIVEP2 WILD-TYPE  128  238
        clus
vv       HIVEP2 MUTATED HIVEP2 WILD-TYPE
  FEMALE             17              128
  MALE               10              238
[1] 2 2
[1] FALSE
D1114V8, binary
                  cls
clus                 0   1
  HIVEP2 MUTATED    23   1
  HIVEP2 WILD-TYPE 269  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP2 MUTATED     23    1
  HIVEP2 WILD-TYPE  269   58
     clus
vv    HIVEP2 MUTATED HIVEP2 WILD-TYPE
  NO              23              269
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  HIVEP2 MUTATED                                          0
  HIVEP2 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  HIVEP2 MUTATED                                       3
  HIVEP2 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HIVEP2 MUTATED                                                       13
  HIVEP2 WILD-TYPE                                                    145
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  HIVEP2 MUTATED                                                   1
  HIVEP2 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  HIVEP2 MUTATED                                                                   3
  HIVEP2 WILD-TYPE                                                                65
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  HIVEP2 MUTATED                                                    1
  HIVEP2 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  HIVEP2 MUTATED                                                  6
  HIVEP2 WILD-TYPE                                               55
D1114V9, multiclass
                                                                   clus
vv                                                                  HIVEP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               6
                                                                   clus
vv                                                                  HIVEP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HIVEP2 MUTATED    19   1   1   3
  HIVEP2 WILD-TYPE 292  13  14  21
D1114V10, multiclass
    clus
vv   HIVEP2 MUTATED HIVEP2 WILD-TYPE
  R0             19              292
  R1              1               13
  R2              1               14
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1114V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  HIVEP2 MUTATED       8                         0
  HIVEP2 WILD-TYPE    79                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  HIVEP2 MUTATED                                           0    16
  HIVEP2 WILD-TYPE                                         1   227
D1114V12, multiclass
                                           clus
vv                                          HIVEP2 MUTATED HIVEP2 WILD-TYPE
  ASIAN                                                  8               79
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 16              227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1114V13, binary
                  cls
clus                 0   1
  HIVEP2 MUTATED     1  22
  HIVEP2 WILD-TYPE   3 288
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP2 MUTATED      1   22
  HIVEP2 WILD-TYPE    3  288
                        clus
vv                       HIVEP2 MUTATED HIVEP2 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             22              288
[1] 2 2
[1] FALSE

Clustering(1115) Variable = FAM60A MUTATION ANALYSIS
D1115V1, survival
                  sevent
clus2                0   1
  FAM60A MUTATED     1   1
  FAM60A WILD-TYPE 229 138
  FAM60A MUTATED FAM60A WILD-TYPE 
               2              367 
  FAM60A MUTATED FAM60A WILD-TYPE 
               1              138 
$`FAM60A MUTATED`
TCGA-BR-A4QL TCGA-IP-7968 
       16.14         2.53 

$`FAM60A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-KB-A6F5 TCGA-KB-A6F7 
       10.62        11.70        15.75        13.51         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 

  FAM60A MUTATED FAM60A WILD-TYPE 
            2.53             0.00 
  FAM60A MUTATED FAM60A WILD-TYPE 
           16.14           122.30 
  FAM60A MUTATED FAM60A WILD-TYPE 
           9.335           14.270 
[1] "2.5 - 16.1 (9.3)"   "0.0 - 122.3 (14.3)"
[1] "Remove cluster labels:" "FAM60A MUTATED"        
D1115V2, 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       2       15       40       30        37        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM60A MUTATED           0          0          2          0        1
  FAM60A WILD-TYPE         3         70         51         32       37
D1115V3, multiclass
            clus
vv           FAM60A MUTATED FAM60A WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              2               51
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM60A MUTATED     0   0   2   1
  FAM60A WILD-TYPE  22  92 171  96
D1115V4, multiclass
    clus
vv   FAM60A MUTATED FAM60A WILD-TYPE
  T1              0               22
  T2              0               92
  T3              2              171
  T4              1               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
  FAM60A MUTATED     0   0   2   1
  FAM60A WILD-TYPE 118 104  75  76
D1115V5, multiclass
    clus
vv   FAM60A MUTATED FAM60A WILD-TYPE
  N0              0              118
  N1              0              104
  N2              2               75
  N3              1               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"
D1115V6, binary
                  cls
clus                 0   1
  FAM60A MUTATED     2   0
  FAM60A WILD-TYPE 344  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM60A MUTATED      2    0
  FAM60A WILD-TYPE  344   29
   clus
vv  FAM60A MUTATED FAM60A WILD-TYPE
  0              2              344
  1              0               29
[1] 2 2
[1] FALSE
D1115V7, binary
                  cls
clus                 0   1
  FAM60A MUTATED     2   1
  FAM60A WILD-TYPE 143 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM60A MUTATED      2    1
  FAM60A WILD-TYPE  143  247
        clus
vv       FAM60A MUTATED FAM60A WILD-TYPE
  FEMALE              2              143
  MALE                1              247
[1] 2 2
[1] FALSE
D1115V8, binary
                  cls
clus                 0   1
  FAM60A MUTATED     1   0
  FAM60A WILD-TYPE 291  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM60A MUTATED      1    0
  FAM60A WILD-TYPE  291   59
     clus
vv    FAM60A MUTATED FAM60A WILD-TYPE
  NO               1              291
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAM60A MUTATED                                          0
  FAM60A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAM60A MUTATED                                       0
  FAM60A WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM60A MUTATED                                                        3
  FAM60A WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAM60A MUTATED                                                   0
  FAM60A WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAM60A MUTATED                                                                   0
  FAM60A WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAM60A MUTATED                                                    0
  FAM60A WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAM60A MUTATED                                                  0
  FAM60A WILD-TYPE                                               61
D1115V9, multiclass
                                                                   clus
vv                                                                  FAM60A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  FAM60A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAM60A MUTATED     2   0   0   1
  FAM60A WILD-TYPE 309  14  15  23
D1115V10, multiclass
    clus
vv   FAM60A MUTATED FAM60A WILD-TYPE
  R0              2              309
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1115V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FAM60A MUTATED       0                         0
  FAM60A WILD-TYPE    87                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAM60A MUTATED                                           0     3
  FAM60A WILD-TYPE                                         1   240
D1115V12, multiclass
                                           clus
vv                                          FAM60A MUTATED FAM60A WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1115V13, binary
                  cls
clus                 0   1
  FAM60A MUTATED     0   3
  FAM60A WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM60A MUTATED      0    3
  FAM60A WILD-TYPE    4  307
                        clus
vv                       FAM60A MUTATED FAM60A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(1116) Variable = ARV1 MUTATION ANALYSIS
D1116V1, survival
                sevent
clus2              0   1
  ARV1 MUTATED     4   1
  ARV1 WILD-TYPE 226 138
  ARV1 MUTATED ARV1 WILD-TYPE 
             5            364 
  ARV1 MUTATED ARV1 WILD-TYPE 
             1            138 
$`ARV1 MUTATED`
TCGA-BR-8372 TCGA-CD-A4MJ TCGA-CG-5734 TCGA-HU-A4G8 TCGA-MX-A5UJ 
       31.27        12.62         7.99        22.68        19.73 

$`ARV1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  ARV1 MUTATED ARV1 WILD-TYPE 
          7.99           0.00 
  ARV1 MUTATED ARV1 WILD-TYPE 
         31.27         122.30 
  ARV1 MUTATED ARV1 WILD-TYPE 
         19.73          14.22 
[1] "8.0 - 31.3 (19.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2.1"
D1116V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARV1 MUTATED         0        0        1        0         0         1
  ARV1 WILD-TYPE       2       15       39       30        37        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARV1 MUTATED           0          2          0          1        0
  ARV1 WILD-TYPE         3         68         53         31       38
D1116V3, multiclass
            clus
vv           ARV1 MUTATED ARV1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ARV1 MUTATED     0   1   3   1
  ARV1 WILD-TYPE  22  91 170  96
D1116V4, multiclass
    clus
vv   ARV1 MUTATED ARV1 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            3            170
  T4            1             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
  ARV1 MUTATED     1   2   1   1
  ARV1 WILD-TYPE 117 102  76  76
D1116V5, multiclass
    clus
vv   ARV1 MUTATED ARV1 WILD-TYPE
  N0            1            117
  N1            2            102
  N2            1             76
  N3            1             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"
D1116V6, binary
                cls
clus               0   1
  ARV1 MUTATED     5   0
  ARV1 WILD-TYPE 341  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARV1 MUTATED      5    0
  ARV1 WILD-TYPE  341   29
   clus
vv  ARV1 MUTATED ARV1 WILD-TYPE
  0            5            341
  1            0             29
[1] 2 2
[1] FALSE
D1116V7, binary
                cls
clus               0   1
  ARV1 MUTATED     2   3
  ARV1 WILD-TYPE 143 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARV1 MUTATED      2    3
  ARV1 WILD-TYPE  143  245
        clus
vv       ARV1 MUTATED ARV1 WILD-TYPE
  FEMALE            2            143
  MALE              3            245
[1] 2 2
[1] FALSE
D1116V8, binary
                cls
clus               0   1
  ARV1 MUTATED     4   0
  ARV1 WILD-TYPE 288  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARV1 MUTATED      4    0
  ARV1 WILD-TYPE  288   59
     clus
vv    ARV1 MUTATED ARV1 WILD-TYPE
  NO             4            288
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARV1 MUTATED                                          0
  ARV1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARV1 MUTATED                                       1
  ARV1 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARV1 MUTATED                                                        2
  ARV1 WILD-TYPE                                                    156
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARV1 MUTATED                                                   0
  ARV1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARV1 MUTATED                                                                   1
  ARV1 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARV1 MUTATED                                                    0
  ARV1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARV1 MUTATED                                                  1
  ARV1 WILD-TYPE                                               60
D1116V9, multiclass
                                                                   clus
vv                                                                  ARV1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  ARV1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ARV1 MUTATED     3   0   0   0
  ARV1 WILD-TYPE 308  14  15  24
D1116V10, multiclass
    clus
vv   ARV1 MUTATED ARV1 WILD-TYPE
  R0            3            308
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1116V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ARV1 MUTATED       2                         0
  ARV1 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARV1 MUTATED                                           0     2
  ARV1 WILD-TYPE                                         1   241
D1116V12, multiclass
                                           clus
vv                                          ARV1 MUTATED ARV1 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                2            241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1116V13, binary
                cls
clus               0   1
  ARV1 MUTATED     0   4
  ARV1 WILD-TYPE   4 306
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARV1 MUTATED      0    4
  ARV1 WILD-TYPE    4  306
                        clus
vv                       ARV1 MUTATED ARV1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            4            306
[1] 2 2
[1] FALSE

Clustering(1117) Variable = ERI1 MUTATION ANALYSIS
D1117V1, survival
                sevent
clus2              0   1
  ERI1 MUTATED     2   2
  ERI1 WILD-TYPE 228 137
  ERI1 MUTATED ERI1 WILD-TYPE 
             4            365 
  ERI1 MUTATED ERI1 WILD-TYPE 
             2            137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 
       54.12        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         14.270 
[1] "0.9 - 31.0 (13.5)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.6"
D1117V2, 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       2       15       38       30        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERI1 MUTATED           0          0          0          0        0
  ERI1 WILD-TYPE         3         70         53         32       38
D1117V3, multiclass
            clus
vv           ERI1 MUTATED ERI1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ERI1 MUTATED     0   2   1   0
  ERI1 WILD-TYPE  22  90 172  97
D1117V4, multiclass
    clus
vv   ERI1 MUTATED ERI1 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            1            172
  T4            0             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
  ERI1 MUTATED     3   0   0   0
  ERI1 WILD-TYPE 115 104  77  77
D1117V5, multiclass
    clus
vv   ERI1 MUTATED ERI1 WILD-TYPE
  N0            3            115
  N1            0            104
  N2            0             77
  N3            0             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"
D1117V6, binary
                cls
clus               0   1
  ERI1 MUTATED     3   0
  ERI1 WILD-TYPE 343  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERI1 MUTATED      3    0
  ERI1 WILD-TYPE  343   29
   clus
vv  ERI1 MUTATED ERI1 WILD-TYPE
  0            3            343
  1            0             29
[1] 2 2
[1] FALSE
D1117V7, binary
                cls
clus               0   1
  ERI1 MUTATED     3   1
  ERI1 WILD-TYPE 142 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERI1 MUTATED      3    1
  ERI1 WILD-TYPE  142  247
        clus
vv       ERI1 MUTATED ERI1 WILD-TYPE
  FEMALE            3            142
  MALE              1            247
[1] 2 2
[1] FALSE
D1117V8, binary
                cls
clus               0   1
  ERI1 MUTATED     3   1
  ERI1 WILD-TYPE 289  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERI1 MUTATED      3    1
  ERI1 WILD-TYPE  289   58
     clus
vv    ERI1 MUTATED ERI1 WILD-TYPE
  NO             3            289
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ERI1 MUTATED                                          0
  ERI1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ERI1 MUTATED                                       0
  ERI1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ERI1 MUTATED                                                        1
  ERI1 WILD-TYPE                                                    157
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ERI1 MUTATED                                                   0
  ERI1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ERI1 MUTATED                                                                   2
  ERI1 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ERI1 MUTATED                                                    0
  ERI1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ERI1 MUTATED                                                  1
  ERI1 WILD-TYPE                                               60
D1117V9, multiclass
                                                                   clus
vv                                                                  ERI1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  ERI1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ERI1 MUTATED     3   0   0   1
  ERI1 WILD-TYPE 308  14  15  23
D1117V10, multiclass
    clus
vv   ERI1 MUTATED ERI1 WILD-TYPE
  R0            3            308
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1117V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ERI1 MUTATED       0                         0
  ERI1 WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ERI1 MUTATED                                           0     3
  ERI1 WILD-TYPE                                         1   240
D1117V12, multiclass
                                           clus
vv                                          ERI1 MUTATED ERI1 WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1117V13, binary
                cls
clus               0   1
  ERI1 MUTATED     0   2
  ERI1 WILD-TYPE   4 308
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERI1 MUTATED      0    2
  ERI1 WILD-TYPE    4  308
                        clus
vv                       ERI1 MUTATED ERI1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            2            308
[1] 2 2
[1] FALSE

Clustering(1118) Variable = TM9SF3 MUTATION ANALYSIS
D1118V1, survival
                  sevent
clus2                0   1
  TM9SF3 MUTATED     7   3
  TM9SF3 WILD-TYPE 223 136
  TM9SF3 MUTATED TM9SF3 WILD-TYPE 
              10              359 
  TM9SF3 MUTATED TM9SF3 WILD-TYPE 
               3              136 
$`TM9SF3 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 
       21.99        34.68        35.84         1.12        27.12        28.14 
TCGA-BR-8680 TCGA-CD-8529 TCGA-RD-A7C1 TCGA-VQ-AA6I 
       31.96        12.30        16.67        16.14 

$`TM9SF3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-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 

  TM9SF3 MUTATED TM9SF3 WILD-TYPE 
            1.12             0.00 
  TM9SF3 MUTATED TM9SF3 WILD-TYPE 
           35.84           122.30 
  TM9SF3 MUTATED TM9SF3 WILD-TYPE 
          24.555           14.070 
[1] "1.1 - 35.8 (24.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D1118V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TM9SF3 MUTATED         0        0        3        0         2         1
  TM9SF3 WILD-TYPE       2       15       37       30        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TM9SF3 MUTATED           0          1          2          1        3
  TM9SF3 WILD-TYPE         3         69         51         31       35
D1118V3, multiclass
            clus
vv           TM9SF3 MUTATED TM9SF3 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                3               37
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              2               51
  STAGE IIIC              1               31
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TM9SF3 MUTATED     0   3   4   6
  TM9SF3 WILD-TYPE  22  89 169  91
D1118V4, multiclass
    clus
vv   TM9SF3 MUTATED TM9SF3 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              4              169
  T4              6               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
  TM9SF3 MUTATED     7   3   1   2
  TM9SF3 WILD-TYPE 111 101  76  75
D1118V5, multiclass
    clus
vv   TM9SF3 MUTATED TM9SF3 WILD-TYPE
  N0              7              111
  N1              3              101
  N2              1               76
  N3              2               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"
D1118V6, binary
                  cls
clus                 0   1
  TM9SF3 MUTATED    10   3
  TM9SF3 WILD-TYPE 336  26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM9SF3 MUTATED     10    3
  TM9SF3 WILD-TYPE  336   26
   clus
vv  TM9SF3 MUTATED TM9SF3 WILD-TYPE
  0             10              336
  1              3               26
[1] 2 2
[1] FALSE
D1118V7, binary
                  cls
clus                 0   1
  TM9SF3 MUTATED     4   9
  TM9SF3 WILD-TYPE 141 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM9SF3 MUTATED      4    9
  TM9SF3 WILD-TYPE  141  239
        clus
vv       TM9SF3 MUTATED TM9SF3 WILD-TYPE
  FEMALE              4              141
  MALE                9              239
[1] 2 2
[1] FALSE
D1118V8, binary
                  cls
clus                 0   1
  TM9SF3 MUTATED    10   2
  TM9SF3 WILD-TYPE 282  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM9SF3 MUTATED     10    2
  TM9SF3 WILD-TYPE  282   57
     clus
vv    TM9SF3 MUTATED TM9SF3 WILD-TYPE
  NO              10              282
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TM9SF3 MUTATED                                          0
  TM9SF3 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TM9SF3 MUTATED                                       1
  TM9SF3 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TM9SF3 MUTATED                                                        6
  TM9SF3 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TM9SF3 MUTATED                                                   1
  TM9SF3 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TM9SF3 MUTATED                                                                   4
  TM9SF3 WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TM9SF3 MUTATED                                                    0
  TM9SF3 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TM9SF3 MUTATED                                                  1
  TM9SF3 WILD-TYPE                                               60
D1118V9, multiclass
                                                                   clus
vv                                                                  TM9SF3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  TM9SF3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TM9SF3 MUTATED    11   1   1   0
  TM9SF3 WILD-TYPE 300  13  14  24
D1118V10, multiclass
    clus
vv   TM9SF3 MUTATED TM9SF3 WILD-TYPE
  R0             11              300
  R1              1               13
  R2              1               14
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1118V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TM9SF3 MUTATED       2                         0
  TM9SF3 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TM9SF3 MUTATED                                           0     8
  TM9SF3 WILD-TYPE                                         1   235
D1118V12, multiclass
                                           clus
vv                                          TM9SF3 MUTATED TM9SF3 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1118V13, binary
                  cls
clus                 0   1
  TM9SF3 MUTATED     0   9
  TM9SF3 WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM9SF3 MUTATED      0    9
  TM9SF3 WILD-TYPE    4  301
                        clus
vv                       TM9SF3 MUTATED TM9SF3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(1119) Variable = ATP2C1 MUTATION ANALYSIS
D1119V1, survival
                  sevent
clus2                0   1
  ATP2C1 MUTATED     7   5
  ATP2C1 WILD-TYPE 223 134
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
              12              357 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
               5              134 
$`ATP2C1 MUTATED`
TCGA-CG-4475 TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8363 
       22.98        26.70         6.97        34.68        31.10         0.26 
TCGA-BR-8487 TCGA-BR-A4IY TCGA-CD-A4MG TCGA-CG-4306 TCGA-VQ-A8P2 TCGA-VQ-AA64 
        1.12        12.89         6.58         1.02        38.14        18.41 

$`ATP2C1 WILD-TYPE`
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G 
       47.05        21.99        79.07        16.24         0.23        20.15 
TCGA-MX-A663 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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 

  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
            0.26             0.00 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
           38.14           122.30 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
           15.65            14.27 
[1] "0.3 - 38.1 (15.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.2"
D1119V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ATP2C1 MUTATED         0        0        1        0         3         3
  ATP2C1 WILD-TYPE       2       15       39       30        34        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP2C1 MUTATED           0          3          1          1        1
  ATP2C1 WILD-TYPE         3         67         52         31       37
D1119V3, multiclass
            clus
vv           ATP2C1 MUTATED ATP2C1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP2C1 MUTATED     0   1   7   5
  ATP2C1 WILD-TYPE  22  91 166  92
D1119V4, multiclass
    clus
vv   ATP2C1 MUTATED ATP2C1 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              7              166
  T4              5               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
  ATP2C1 MUTATED     7   3   3   0
  ATP2C1 WILD-TYPE 111 101  74  77
D1119V5, multiclass
    clus
vv   ATP2C1 MUTATED ATP2C1 WILD-TYPE
  N0              7              111
  N1              3              101
  N2              3               74
  N3              0               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"
D1119V6, binary
                  cls
clus                 0   1
  ATP2C1 MUTATED    11   1
  ATP2C1 WILD-TYPE 335  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED     11    1
  ATP2C1 WILD-TYPE  335   28
   clus
vv  ATP2C1 MUTATED ATP2C1 WILD-TYPE
  0             11              335
  1              1               28
[1] 2 2
[1] FALSE
D1119V7, binary
                  cls
clus                 0   1
  ATP2C1 MUTATED     6   7
  ATP2C1 WILD-TYPE 139 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED      6    7
  ATP2C1 WILD-TYPE  139  241
        clus
vv       ATP2C1 MUTATED ATP2C1 WILD-TYPE
  FEMALE              6              139
  MALE                7              241
[1] 2 2
[1] FALSE
D1119V8, binary
                  cls
clus                 0   1
  ATP2C1 MUTATED     9   2
  ATP2C1 WILD-TYPE 283  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED      9    2
  ATP2C1 WILD-TYPE  283   57
     clus
vv    ATP2C1 MUTATED ATP2C1 WILD-TYPE
  NO               9              283
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ATP2C1 MUTATED                                          0
  ATP2C1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ATP2C1 MUTATED                                       2
  ATP2C1 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATP2C1 MUTATED                                                        8
  ATP2C1 WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ATP2C1 MUTATED                                                   1
  ATP2C1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATP2C1 MUTATED                                                                   1
  ATP2C1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ATP2C1 MUTATED                                                    0
  ATP2C1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ATP2C1 MUTATED                                                  0
  ATP2C1 WILD-TYPE                                               61
D1119V9, multiclass
                                                                   clus
vv                                                                  ATP2C1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  ATP2C1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATP2C1 MUTATED     9   0   1   2
  ATP2C1 WILD-TYPE 302  14  14  22
D1119V10, multiclass
    clus
vv   ATP2C1 MUTATED ATP2C1 WILD-TYPE
  R0              9              302
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1119V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ATP2C1 MUTATED       2                         0
  ATP2C1 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATP2C1 MUTATED                                           0     9
  ATP2C1 WILD-TYPE                                         1   234
D1119V12, multiclass
                                           clus
vv                                          ATP2C1 MUTATED ATP2C1 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  9              234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1119V13, binary
                  cls
clus                 0   1
  ATP2C1 MUTATED     0   9
  ATP2C1 WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED      0    9
  ATP2C1 WILD-TYPE    4  301
                        clus
vv                       ATP2C1 MUTATED ATP2C1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(1120) Variable = STK36 MUTATION ANALYSIS
D1120V1, survival
                 sevent
clus2               0   1
  STK36 MUTATED     4   1
  STK36 WILD-TYPE 226 138
  STK36 MUTATED STK36 WILD-TYPE 
              5             364 
  STK36 MUTATED STK36 WILD-TYPE 
              1             138 
$`STK36 MUTATED`
TCGA-BR-6452 TCGA-BR-8680 TCGA-CD-A486 TCGA-CG-5721 TCGA-FP-8099 
       34.68        31.96         6.31         6.02        17.06 

$`STK36 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
       12.43        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-8209 TCGA-FP-8210 
        3.48        19.53        14.07        22.29        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 

  STK36 MUTATED STK36 WILD-TYPE 
           6.02            0.00 
  STK36 MUTATED STK36 WILD-TYPE 
          34.68          122.30 
  STK36 MUTATED STK36 WILD-TYPE 
          17.06           14.22 
[1] "6.0 - 34.7 (17.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2"  
D1120V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  STK36 MUTATED         0        0        1        0         3         1
  STK36 WILD-TYPE       2       15       39       30        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STK36 MUTATED           0          0          0          0        3
  STK36 WILD-TYPE         3         70         53         32       35
D1120V3, multiclass
            clus
vv           STK36 MUTATED STK36 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK36 MUTATED     0   1   3   4
  STK36 WILD-TYPE  22  91 170  93
D1120V4, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             3             170
  T4             4              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
  STK36 MUTATED     5   1   2   0
  STK36 WILD-TYPE 113 103  75  77
D1120V5, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  N0             5             113
  N1             1             103
  N2             2              75
  N3             0              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"
D1120V6, binary
                 cls
clus                0   1
  STK36 MUTATED     6   1
  STK36 WILD-TYPE 340  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED      6    1
  STK36 WILD-TYPE  340   28
   clus
vv  STK36 MUTATED STK36 WILD-TYPE
  0             6             340
  1             1              28
[1] 2 2
[1] FALSE
D1120V7, binary
                 cls
clus                0   1
  STK36 MUTATED     2   6
  STK36 WILD-TYPE 143 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED      2    6
  STK36 WILD-TYPE  143  242
        clus
vv       STK36 MUTATED STK36 WILD-TYPE
  FEMALE             2             143
  MALE               6             242
[1] 2 2
[1] FALSE
D1120V8, binary
                 cls
clus                0   1
  STK36 MUTATED     6   0
  STK36 WILD-TYPE 286  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED      6    0
  STK36 WILD-TYPE  286   59
     clus
vv    STK36 MUTATED STK36 WILD-TYPE
  NO              6             286
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  STK36 MUTATED                                          0
  STK36 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  STK36 MUTATED                                       0
  STK36 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  STK36 MUTATED                                                        4
  STK36 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  STK36 MUTATED                                                   0
  STK36 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  STK36 MUTATED                                                                   3
  STK36 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  STK36 MUTATED                                                    0
  STK36 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  STK36 MUTATED                                                  1
  STK36 WILD-TYPE                                               60
D1120V9, multiclass
                                                                   clus
vv                                                                  STK36 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  STK36 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STK36 MUTATED     6   0   0   1
  STK36 WILD-TYPE 305  14  15  23
D1120V10, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1120V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  STK36 MUTATED       2                         0
  STK36 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  STK36 MUTATED                                           0     4
  STK36 WILD-TYPE                                         1   239
D1120V12, multiclass
                                           clus
vv                                          STK36 MUTATED STK36 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1120V13, binary
                 cls
clus                0   1
  STK36 MUTATED     0   6
  STK36 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED      0    6
  STK36 WILD-TYPE    4  304
                        clus
vv                       STK36 MUTATED STK36 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(1121) Variable = ISM1 MUTATION ANALYSIS
D1121V1, survival
                sevent
clus2              0   1
  ISM1 MUTATED     7   5
  ISM1 WILD-TYPE 223 134
  ISM1 MUTATED ISM1 WILD-TYPE 
            12            357 
  ISM1 MUTATED ISM1 WILD-TYPE 
             5            134 
$`ISM1 MUTATED`
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8078 TCGA-BR-8487 TCGA-BR-8591 TCGA-CD-8527 
        9.34        34.68        29.59         1.12        28.14         7.17 
TCGA-CD-8536 TCGA-CG-5726 TCGA-CG-5733 TCGA-HU-8602 TCGA-HU-A4GH TCGA-RD-A7BT 
       12.43        28.96        21.07        22.32        11.77         8.61 

$`ISM1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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 

  ISM1 MUTATED ISM1 WILD-TYPE 
          1.12           0.00 
  ISM1 MUTATED ISM1 WILD-TYPE 
         34.68         122.30 
  ISM1 MUTATED ISM1 WILD-TYPE 
         16.75          14.27 
[1] "1.1 - 34.7 (16.8)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D1121V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ISM1 MUTATED         0        2        0        2         2         2
  ISM1 WILD-TYPE       2       13       40       28        35        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ISM1 MUTATED           0          1          0          1        1
  ISM1 WILD-TYPE         3         69         53         31       37
D1121V3, multiclass
            clus
vv           ISM1 MUTATED ISM1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              2             13
  STAGE IB              0             40
  STAGE II              2             28
  STAGE IIA             2             35
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ISM1 MUTATED     3   2   4   3
  ISM1 WILD-TYPE  19  90 169  94
D1121V4, multiclass
    clus
vv   ISM1 MUTATED ISM1 WILD-TYPE
  T1            3             19
  T2            2             90
  T3            4            169
  T4            3             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
  ISM1 MUTATED     7   2   1   2
  ISM1 WILD-TYPE 111 102  76  75
D1121V5, multiclass
    clus
vv   ISM1 MUTATED ISM1 WILD-TYPE
  N0            7            111
  N1            2            102
  N2            1             76
  N3            2             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"
D1121V6, binary
                cls
clus               0   1
  ISM1 MUTATED    13   0
  ISM1 WILD-TYPE 333  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  ISM1 MUTATED     13    0
  ISM1 WILD-TYPE  333   29
   clus
vv  ISM1 MUTATED ISM1 WILD-TYPE
  0           13            333
  1            0             29
[1] 2 2
[1] FALSE
D1121V7, binary
                cls
clus               0   1
  ISM1 MUTATED     7   6
  ISM1 WILD-TYPE 138 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  ISM1 MUTATED      7    6
  ISM1 WILD-TYPE  138  242
        clus
vv       ISM1 MUTATED ISM1 WILD-TYPE
  FEMALE            7            138
  MALE              6            242
[1] 2 2
[1] FALSE
D1121V8, binary
                cls
clus               0   1
  ISM1 MUTATED    11   0
  ISM1 WILD-TYPE 281  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  ISM1 MUTATED     11    0
  ISM1 WILD-TYPE  281   59
     clus
vv    ISM1 MUTATED ISM1 WILD-TYPE
  NO            11            281
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ISM1 MUTATED                                          0
  ISM1 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ISM1 MUTATED                                       1
  ISM1 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ISM1 MUTATED                                                        7
  ISM1 WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ISM1 MUTATED                                                   0
  ISM1 WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ISM1 MUTATED                                                                   4
  ISM1 WILD-TYPE                                                                64
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ISM1 MUTATED                                                    0
  ISM1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ISM1 MUTATED                                                  1
  ISM1 WILD-TYPE                                               60
D1121V9, multiclass
                                                                   clus
vv                                                                  ISM1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  ISM1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ISM1 MUTATED    10   0   1   2
  ISM1 WILD-TYPE 301  14  14  22
D1121V10, multiclass
    clus
vv   ISM1 MUTATED ISM1 WILD-TYPE
  R0           10            301
  R1            0             14
  R2            1             14
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1121V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  ISM1 MUTATED       4                         0
  ISM1 WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ISM1 MUTATED                                           1     6
  ISM1 WILD-TYPE                                         0   237
D1121V12, multiclass
                                           clus
vv                                          ISM1 MUTATED ISM1 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            1              0
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1121V13, binary
                cls
clus               0   1
  ISM1 MUTATED     0  11
  ISM1 WILD-TYPE   4 299
[1] "tbl2"
                cls
clus             [,1] [,2]
  ISM1 MUTATED      0   11
  ISM1 WILD-TYPE    4  299
                        clus
vv                       ISM1 MUTATED ISM1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           11            299
[1] 2 2
[1] FALSE

Clustering(1122) Variable = GLTPD1 MUTATION ANALYSIS
D1122V1, survival
                  sevent
clus2                0   1
  GLTPD1 MUTATED     2   2
  GLTPD1 WILD-TYPE 228 137
  GLTPD1 MUTATED GLTPD1 WILD-TYPE 
               4              365 
  GLTPD1 MUTATED GLTPD1 WILD-TYPE 
               2              137 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  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           14.270 
[1] "0.1 - 22.3 (13.5)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.8"
D1122V2, 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       2       15       40       30        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLTPD1 MUTATED           0          1          0          1        1
  GLTPD1 WILD-TYPE         3         69         53         31       37
D1122V3, multiclass
            clus
vv           GLTPD1 MUTATED GLTPD1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GLTPD1 MUTATED     0   1   0   3
  GLTPD1 WILD-TYPE  22  91 173  94
D1122V4, multiclass
    clus
vv   GLTPD1 MUTATED GLTPD1 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              0              173
  T4              3               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
  GLTPD1 MUTATED     1   1   2   0
  GLTPD1 WILD-TYPE 117 103  75  77
D1122V5, multiclass
    clus
vv   GLTPD1 MUTATED GLTPD1 WILD-TYPE
  N0              1              117
  N1              1              103
  N2              2               75
  N3              0               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"
D1122V6, binary
                  cls
clus                 0   1
  GLTPD1 MUTATED     4   0
  GLTPD1 WILD-TYPE 342  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD1 MUTATED      4    0
  GLTPD1 WILD-TYPE  342   29
   clus
vv  GLTPD1 MUTATED GLTPD1 WILD-TYPE
  0              4              342
  1              0               29
[1] 2 2
[1] FALSE
D1122V7, binary
                  cls
clus                 0   1
  GLTPD1 MUTATED     2   2
  GLTPD1 WILD-TYPE 143 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD1 MUTATED      2    2
  GLTPD1 WILD-TYPE  143  246
        clus
vv       GLTPD1 MUTATED GLTPD1 WILD-TYPE
  FEMALE              2              143
  MALE                2              246
[1] 2 2
[1] FALSE
D1122V8, binary
                  cls
clus                 0   1
  GLTPD1 MUTATED     4   0
  GLTPD1 WILD-TYPE 288  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD1 MUTATED      4    0
  GLTPD1 WILD-TYPE  288   59
     clus
vv    GLTPD1 MUTATED GLTPD1 WILD-TYPE
  NO               4              288
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GLTPD1 MUTATED                                          0
  GLTPD1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GLTPD1 MUTATED                                       1
  GLTPD1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GLTPD1 MUTATED                                                        0
  GLTPD1 WILD-TYPE                                                    158
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GLTPD1 MUTATED                                                   0
  GLTPD1 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GLTPD1 MUTATED                                                                   2
  GLTPD1 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GLTPD1 MUTATED                                                    0
  GLTPD1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GLTPD1 MUTATED                                                  1
  GLTPD1 WILD-TYPE                                               60
D1122V9, multiclass
                                                                   clus
vv                                                                  GLTPD1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         0
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  GLTPD1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         158
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GLTPD1 MUTATED     4   0   0   0
  GLTPD1 WILD-TYPE 307  14  15  24
D1122V10, multiclass
    clus
vv   GLTPD1 MUTATED GLTPD1 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1122V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GLTPD1 MUTATED       2                         0
  GLTPD1 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GLTPD1 MUTATED                                           0     0
  GLTPD1 WILD-TYPE                                         1   243
D1122V12, multiclass
[1] "Remove cluster labels:" "GLTPD1 MUTATED"        
clus
  GLTPD1 MUTATED GLTPD1 WILD-TYPE 
               2              338 
      TCGA-EQ-A4SO       TCGA-F1-6177       TCGA-FP-A8CX       TCGA-KB-A93G 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-MX-A663       TCGA-B7-5816       TCGA-B7-5818       TCGA-B7-A5TI 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-B7-A5TJ       TCGA-B7-A5TK       TCGA-B7-A5TN       TCGA-BR-4183 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-4184       TCGA-BR-4187       TCGA-BR-4188       TCGA-BR-4191 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-4201       TCGA-BR-4253       TCGA-BR-4255       TCGA-BR-4256 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-4257       TCGA-BR-4267       TCGA-BR-4279       TCGA-BR-4280 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-4292       TCGA-BR-4294       TCGA-BR-4357       TCGA-BR-4361 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-4362       TCGA-BR-4363       TCGA-BR-4366       TCGA-BR-4368 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-4369       TCGA-BR-4370       TCGA-BR-4371       TCGA-BR-6452 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-6453       TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-6457       TCGA-BR-6458       TCGA-BR-6563       TCGA-BR-6564 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-6565       TCGA-BR-6566       TCGA-BR-6705       TCGA-BR-6706 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-6707       TCGA-BR-6709       TCGA-BR-6710       TCGA-BR-6801 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-6802       TCGA-BR-6803       TCGA-BR-6852       TCGA-BR-7196 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-7197       TCGA-BR-7703       TCGA-BR-7704       TCGA-BR-7707 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-7715       TCGA-BR-7716       TCGA-BR-7717       TCGA-BR-7722 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-7723       TCGA-BR-7851       TCGA-BR-7901       TCGA-BR-7957 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-7958       TCGA-BR-7959       TCGA-BR-8058       TCGA-BR-8059 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8060       TCGA-BR-8077       TCGA-BR-8078       TCGA-BR-8080 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8081       TCGA-BR-8284       TCGA-BR-8285       TCGA-BR-8286 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8289       TCGA-BR-8291       TCGA-BR-8295       TCGA-BR-8297 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8360       TCGA-BR-8361       TCGA-BR-8363       TCGA-BR-8364 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8365       TCGA-BR-8366       TCGA-BR-8367       TCGA-BR-8368 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8369       TCGA-BR-8370       TCGA-BR-8371       TCGA-BR-8372 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8373       TCGA-BR-8380       TCGA-BR-8381       TCGA-BR-8382 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8384       TCGA-BR-8483       TCGA-BR-8484       TCGA-BR-8485 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8486       TCGA-BR-8487       TCGA-BR-8588       TCGA-BR-8589 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8590       TCGA-BR-8591       TCGA-BR-8592       TCGA-BR-8676 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8677       TCGA-BR-8678       TCGA-BR-8679       TCGA-BR-8680 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8682       TCGA-BR-8683       TCGA-BR-8686       TCGA-BR-8687 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-8690       TCGA-BR-A44T       TCGA-BR-A44U       TCGA-BR-A452 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-A453       TCGA-BR-A4CQ       TCGA-BR-A4CR       TCGA-BR-A4CS 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-A4IU       TCGA-BR-A4IV       TCGA-BR-A4IY       TCGA-BR-A4IZ 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-A4J1       TCGA-BR-A4J2       TCGA-BR-A4J4       TCGA-BR-A4J5 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-A4J6       TCGA-BR-A4J7       TCGA-BR-A4J8       TCGA-BR-A4PD 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-A4PE       TCGA-BR-A4PF       TCGA-BR-A4QI       TCGA-BR-A4QL 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-BR-A4QM       TCGA-CD-5798       TCGA-CD-5799       TCGA-CD-5800 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-CD-5801       TCGA-CD-5802       TCGA-CD-5803       TCGA-CD-5804 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-CD-5813       TCGA-CD-8524       TCGA-CD-8525       TCGA-CD-8526 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-CD-8527       TCGA-CD-8528       TCGA-CD-8529       TCGA-CD-8530 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-CD-8531       TCGA-CD-8532       TCGA-CD-8533       TCGA-CD-8534 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-CD-8535       TCGA-CD-8536       TCGA-CD-A486       TCGA-CD-A487 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-CD-A489       TCGA-CD-A48A       TCGA-CD-A48C       TCGA-CD-A4MG 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-CD-A4MH       TCGA-CD-A4MI       TCGA-CD-A4MJ       TCGA-D7-5577 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-5578       TCGA-D7-5579       TCGA-D7-6518       TCGA-D7-6519 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-6520       TCGA-D7-6521       TCGA-D7-6522       TCGA-D7-6524 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-6525       TCGA-D7-6526       TCGA-D7-6527       TCGA-D7-6528 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-6815       TCGA-D7-6817       TCGA-D7-6818       TCGA-D7-6820 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-6822       TCGA-D7-8570       TCGA-D7-8572       TCGA-D7-8573 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-8574       TCGA-D7-8575       TCGA-D7-8576       TCGA-D7-8578 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-8579       TCGA-D7-A4YT       TCGA-D7-A4YU       TCGA-D7-A4YV 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-A4YX       TCGA-D7-A4YY       TCGA-D7-A4Z0       TCGA-D7-A6ET 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-A6EV       TCGA-D7-A6EX       TCGA-D7-A6EY       TCGA-D7-A6EZ 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-A6F0       TCGA-D7-A6F2       TCGA-D7-A747       TCGA-D7-A748 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-D7-A74A       TCGA-D7-A74B       TCGA-EQ-5647       TCGA-EQ-8122 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-F1-6874       TCGA-F1-6875       TCGA-F1-A448       TCGA-F1-A72C 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-FP-7735       TCGA-FP-7829       TCGA-FP-7916       TCGA-FP-7998 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-FP-8099       TCGA-FP-8209       TCGA-FP-8210       TCGA-FP-8211 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-FP-8631       TCGA-FP-A4BE       TCGA-FP-A4BF       TCGA-FP-A9TM 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HJ-7597       TCGA-HU-8238       TCGA-HU-8243       TCGA-HU-8244 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-8249       TCGA-HU-8604       TCGA-HU-8608       TCGA-HU-8610 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-A4G2       TCGA-HU-A4G3       TCGA-HU-A4G6       TCGA-HU-A4G8 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-A4G9       TCGA-HU-A4GC       TCGA-HU-A4GD       TCGA-HU-A4GF 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-A4GH       TCGA-HU-A4GJ       TCGA-HU-A4GN       TCGA-HU-A4GP 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-A4GT       TCGA-HU-A4GU       TCGA-HU-A4GX       TCGA-HU-A4GY 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-A4H0       TCGA-HU-A4H2       TCGA-HU-A4H3       TCGA-HU-A4H4 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-A4H5       TCGA-HU-A4H6       TCGA-HU-A4H8       TCGA-HU-A4HB 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-HU-A4HD       TCGA-IN-7806       TCGA-IN-7808       TCGA-IN-8462 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-IN-8663       TCGA-IN-A6RI       TCGA-IN-A6RJ       TCGA-IN-A6RL 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-IN-A6RN       TCGA-IN-A6RO       TCGA-IN-A6RP       TCGA-IN-A6RR 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-IN-A6RS       TCGA-IN-A7NR       TCGA-IN-A7NT       TCGA-IN-A7NU 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-IN-AB1V       TCGA-IN-AB1X       TCGA-IP-7968       TCGA-KB-A93J 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-MX-A5UG       TCGA-MX-A5UJ       TCGA-MX-A666       TCGA-R5-A7O7 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-R5-A7ZE       TCGA-R5-A7ZF       TCGA-R5-A7ZI       TCGA-R5-A7ZR 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-R5-A804       TCGA-R5-A805       TCGA-RD-A7BS       TCGA-RD-A7BT 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-RD-A7BW       TCGA-RD-A7C1       TCGA-RD-A8MV       TCGA-RD-A8MW 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-RD-A8N0       TCGA-RD-A8N1       TCGA-RD-A8N2       TCGA-RD-A8N4 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-RD-A8N5       TCGA-RD-A8N6       TCGA-RD-A8N9       TCGA-SW-A7EA 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-SW-A7EB       TCGA-VQ-A8DL       TCGA-VQ-A8DU       TCGA-VQ-A8DV 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VQ-A8DZ       TCGA-VQ-A8E2       TCGA-VQ-A8E7       TCGA-VQ-A8P2 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VQ-A8P3       TCGA-VQ-A8PE       TCGA-VQ-A8PK       TCGA-VQ-A8PM 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VQ-A8PQ       TCGA-VQ-A91U       TCGA-VQ-A92D       TCGA-VQ-AA64 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VQ-AA68       TCGA-VQ-AA69       TCGA-VQ-AA6A       TCGA-VQ-AA6B 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VQ-AA6F       TCGA-VQ-AA6G       TCGA-VQ-AA6I       TCGA-VQ-AA6J 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
      TCGA-VQ-AA6K       TCGA-ZA-A8F6 
"GLTPD1 WILD-TYPE" "GLTPD1 WILD-TYPE" 
D1122V13, binary
                  cls
clus                 0   1
  GLTPD1 MUTATED     0   2
  GLTPD1 WILD-TYPE   4 308
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD1 MUTATED      0    2
  GLTPD1 WILD-TYPE    4  308
                        clus
vv                       GLTPD1 MUTATED GLTPD1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              2              308
[1] 2 2
[1] FALSE

Clustering(1123) Variable = CLDN5 MUTATION ANALYSIS
D1123V1, survival
                 sevent
clus2               0   1
  CLDN5 MUTATED     3   1
  CLDN5 WILD-TYPE 227 138
  CLDN5 MUTATED CLDN5 WILD-TYPE 
              4             365 
  CLDN5 MUTATED CLDN5 WILD-TYPE 
              1             138 
$`CLDN5 MUTATED`
TCGA-FP-A4BE TCGA-HF-7134 TCGA-HJ-7597 TCGA-R5-A7ZI 
       11.08        52.21        26.47        74.53 

$`CLDN5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-A5NB 
        0.56         5.52         6.21        77.29        63.06        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-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 

  CLDN5 MUTATED CLDN5 WILD-TYPE 
          11.08            0.00 
  CLDN5 MUTATED CLDN5 WILD-TYPE 
          74.53          122.30 
  CLDN5 MUTATED CLDN5 WILD-TYPE 
          39.34           14.17 
[1] "11.1 - 74.5 (39.3)" "0.0 - 122.3 (14.2)"
[1] "hr=" "2.7"
D1123V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CLDN5 MUTATED         0        1        1        0         1         0
  CLDN5 WILD-TYPE       2       14       39       30        36        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLDN5 MUTATED           0          0          0          0        1
  CLDN5 WILD-TYPE         3         70         53         32       37
D1123V3, multiclass
            clus
vv           CLDN5 MUTATED CLDN5 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CLDN5 MUTATED     1   1   1   1
  CLDN5 WILD-TYPE  21  91 172  96
D1123V4, multiclass
    clus
vv   CLDN5 MUTATED CLDN5 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             1             172
  T4             1              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
  CLDN5 MUTATED     3   1   0   0
  CLDN5 WILD-TYPE 115 103  77  77
D1123V5, multiclass
    clus
vv   CLDN5 MUTATED CLDN5 WILD-TYPE
  N0             3             115
  N1             1             103
  N2             0              77
  N3             0              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"
D1123V6, binary
                 cls
clus                0   1
  CLDN5 MUTATED     2   1
  CLDN5 WILD-TYPE 344  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN5 MUTATED      2    1
  CLDN5 WILD-TYPE  344   28
   clus
vv  CLDN5 MUTATED CLDN5 WILD-TYPE
  0             2             344
  1             1              28
[1] 2 2
[1] FALSE
D1123V7, binary
                 cls
clus                0   1
  CLDN5 MUTATED     2   2
  CLDN5 WILD-TYPE 143 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN5 MUTATED      2    2
  CLDN5 WILD-TYPE  143  246
        clus
vv       CLDN5 MUTATED CLDN5 WILD-TYPE
  FEMALE             2             143
  MALE               2             246
[1] 2 2
[1] FALSE
D1123V8, binary
                 cls
clus                0   1
  CLDN5 MUTATED     3   1
  CLDN5 WILD-TYPE 289  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN5 MUTATED      3    1
  CLDN5 WILD-TYPE  289   58
     clus
vv    CLDN5 MUTATED CLDN5 WILD-TYPE
  NO              3             289
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CLDN5 MUTATED                                          1
  CLDN5 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CLDN5 MUTATED                                       1
  CLDN5 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CLDN5 MUTATED                                                        1
  CLDN5 WILD-TYPE                                                    157
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CLDN5 MUTATED                                                   0
  CLDN5 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CLDN5 MUTATED                                                                   1
  CLDN5 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CLDN5 MUTATED                                                    0
  CLDN5 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CLDN5 MUTATED                                                  0
  CLDN5 WILD-TYPE                                               61
D1123V9, multiclass
                                                                   clus
vv                                                                  CLDN5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  CLDN5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CLDN5 MUTATED     4   0   0   0
  CLDN5 WILD-TYPE 307  14  15  24
D1123V10, multiclass
    clus
vv   CLDN5 MUTATED CLDN5 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1123V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  CLDN5 MUTATED       0                         1
  CLDN5 WILD-TYPE    87                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CLDN5 MUTATED                                           0     2
  CLDN5 WILD-TYPE                                         1   241
D1123V12, multiclass
                                           clus
vv                                          CLDN5 MUTATED CLDN5 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 2             241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1123V13, binary
                 cls
clus                0   1
  CLDN5 MUTATED     1   2
  CLDN5 WILD-TYPE   3 308
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLDN5 MUTATED      1    2
  CLDN5 WILD-TYPE    3  308
                        clus
vv                       CLDN5 MUTATED CLDN5 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             2             308
[1] 2 2
[1] FALSE

Clustering(1124) Variable = D4S234E MUTATION ANALYSIS
D1124V1, survival
                   sevent
clus2                 0   1
  D4S234E MUTATED     3   3
  D4S234E WILD-TYPE 227 136
  D4S234E MUTATED D4S234E WILD-TYPE 
                6               363 
  D4S234E MUTATED D4S234E WILD-TYPE 
                3               136 
$`D4S234E MUTATED`
TCGA-BR-4184 TCGA-BR-7717 TCGA-BR-8363 TCGA-BR-8366 TCGA-HF-7132 TCGA-MX-A5UJ 
        6.97        18.15         0.26         0.95        77.29        19.73 

$`D4S234E WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 
        6.18        31.10        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-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-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 

  D4S234E MUTATED D4S234E WILD-TYPE 
             0.26              0.00 
  D4S234E MUTATED D4S234E WILD-TYPE 
            77.29            122.30 
  D4S234E MUTATED D4S234E WILD-TYPE 
            12.56             14.27 
[1] "0.3 - 77.3 (12.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D1124V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  D4S234E MUTATED         0        0        1        1         1         0
  D4S234E WILD-TYPE       2       15       39       29        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  D4S234E MUTATED           0          2          0          0        2
  D4S234E WILD-TYPE         3         68         53         32       36
D1124V3, multiclass
            clus
vv           D4S234E MUTATED D4S234E WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 1                29
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               0                53
  STAGE IIIC               0                32
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  D4S234E MUTATED     0   2   3   2
  D4S234E WILD-TYPE  22  90 170  95
D1124V4, multiclass
    clus
vv   D4S234E MUTATED D4S234E WILD-TYPE
  T1               0                22
  T2               2                90
  T3               3               170
  T4               2                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
  D4S234E MUTATED     2   3   2   0
  D4S234E WILD-TYPE 116 101  75  77
D1124V5, multiclass
    clus
vv   D4S234E MUTATED D4S234E WILD-TYPE
  N0               2               116
  N1               3               101
  N2               2                75
  N3               0                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"
D1124V6, binary
                   cls
clus                  0   1
  D4S234E MUTATED     6   0
  D4S234E WILD-TYPE 340  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  D4S234E MUTATED      6    0
  D4S234E WILD-TYPE  340   29
   clus
vv  D4S234E MUTATED D4S234E WILD-TYPE
  0               6               340
  1               0                29
[1] 2 2
[1] FALSE
D1124V7, binary
                   cls
clus                  0   1
  D4S234E MUTATED     4   3
  D4S234E WILD-TYPE 141 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  D4S234E MUTATED      4    3
  D4S234E WILD-TYPE  141  245
        clus
vv       D4S234E MUTATED D4S234E WILD-TYPE
  FEMALE               4               141
  MALE                 3               245
[1] 2 2
[1] FALSE
D1124V8, binary
                   cls
clus                  0   1
  D4S234E MUTATED     5   1
  D4S234E WILD-TYPE 287  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  D4S234E MUTATED      5    1
  D4S234E WILD-TYPE  287   58
     clus
vv    D4S234E MUTATED D4S234E WILD-TYPE
  NO                5               287
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  D4S234E MUTATED                                          0
  D4S234E WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  D4S234E MUTATED                                       0
  D4S234E WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  D4S234E MUTATED                                                        5
  D4S234E WILD-TYPE                                                    153
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  D4S234E MUTATED                                                   1
  D4S234E WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  D4S234E MUTATED                                                                   0
  D4S234E WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  D4S234E MUTATED                                                    0
  D4S234E WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  D4S234E MUTATED                                                  1
  D4S234E WILD-TYPE                                               60
D1124V9, multiclass
                                                                   clus
vv                                                                  D4S234E MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  D4S234E WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  D4S234E MUTATED     5   0   0   2
  D4S234E WILD-TYPE 306  14  15  22
D1124V10, multiclass
    clus
vv   D4S234E MUTATED D4S234E WILD-TYPE
  R0               5               306
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1124V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  D4S234E MUTATED       0                         0
  D4S234E WILD-TYPE    87                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  D4S234E MUTATED                                           0     6
  D4S234E WILD-TYPE                                         1   237
D1124V12, multiclass
                                           clus
vv                                          D4S234E MUTATED D4S234E WILD-TYPE
  ASIAN                                                   0                87
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1124V13, binary
                   cls
clus                  0   1
  D4S234E MUTATED     0   6
  D4S234E WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  D4S234E MUTATED      0    6
  D4S234E WILD-TYPE    4  304
                        clus
vv                       D4S234E MUTATED D4S234E WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(1125) Variable = EGLN1 MUTATION ANALYSIS
D1125V1, survival
                 sevent
clus2               0   1
  EGLN1 MUTATED     3   1
  EGLN1 WILD-TYPE 227 138
  EGLN1 MUTATED EGLN1 WILD-TYPE 
              4             365 
  EGLN1 MUTATED EGLN1 WILD-TYPE 
              1             138 
$`EGLN1 MUTATED`
TCGA-BR-6452 TCGA-BR-8297 TCGA-BR-8487 TCGA-D7-A4YV 
       34.68         7.40         1.12         5.92 

$`EGLN1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  EGLN1 MUTATED EGLN1 WILD-TYPE 
           1.12            0.00 
  EGLN1 MUTATED EGLN1 WILD-TYPE 
          34.68          122.30 
  EGLN1 MUTATED EGLN1 WILD-TYPE 
           6.66           14.43 
[1] "1.1 - 34.7 (6.7)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "1.1"
D1125V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EGLN1 MUTATED         0        0        0        0         2         1
  EGLN1 WILD-TYPE       2       15       40       30        35        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EGLN1 MUTATED           0          0          0          1        1
  EGLN1 WILD-TYPE         3         70         53         31       37
D1125V3, multiclass
            clus
vv           EGLN1 MUTATED EGLN1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EGLN1 MUTATED     0   0   3   2
  EGLN1 WILD-TYPE  22  92 170  95
D1125V4, multiclass
    clus
vv   EGLN1 MUTATED EGLN1 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             3             170
  T4             2              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
  EGLN1 MUTATED     2   1   1   1
  EGLN1 WILD-TYPE 116 103  76  76
D1125V5, multiclass
    clus
vv   EGLN1 MUTATED EGLN1 WILD-TYPE
  N0             2             116
  N1             1             103
  N2             1              76
  N3             1              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"
D1125V6, binary
                 cls
clus                0   1
  EGLN1 MUTATED     5   0
  EGLN1 WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EGLN1 MUTATED      5    0
  EGLN1 WILD-TYPE  341   29
   clus
vv  EGLN1 MUTATED EGLN1 WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D1125V7, binary
                 cls
clus                0   1
  EGLN1 MUTATED     4   1
  EGLN1 WILD-TYPE 141 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EGLN1 MUTATED      4    1
  EGLN1 WILD-TYPE  141  247
        clus
vv       EGLN1 MUTATED EGLN1 WILD-TYPE
  FEMALE             4             141
  MALE               1             247
[1] 2 2
[1] FALSE
D1125V8, binary
                 cls
clus                0   1
  EGLN1 MUTATED     4   0
  EGLN1 WILD-TYPE 288  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EGLN1 MUTATED      4    0
  EGLN1 WILD-TYPE  288   59
     clus
vv    EGLN1 MUTATED EGLN1 WILD-TYPE
  NO              4             288
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EGLN1 MUTATED                                          0
  EGLN1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EGLN1 MUTATED                                       1
  EGLN1 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EGLN1 MUTATED                                                        3
  EGLN1 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EGLN1 MUTATED                                                   0
  EGLN1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EGLN1 MUTATED                                                                   0
  EGLN1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EGLN1 MUTATED                                                    0
  EGLN1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EGLN1 MUTATED                                                  1
  EGLN1 WILD-TYPE                                               60
D1125V9, multiclass
                                                                   clus
vv                                                                  EGLN1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  EGLN1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EGLN1 MUTATED     4   0   0   1
  EGLN1 WILD-TYPE 307  14  15  23
D1125V10, multiclass
    clus
vv   EGLN1 MUTATED EGLN1 WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1125V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EGLN1 MUTATED       0                         0
  EGLN1 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EGLN1 MUTATED                                           0     5
  EGLN1 WILD-TYPE                                         1   238
D1125V12, multiclass
                                           clus
vv                                          EGLN1 MUTATED EGLN1 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1125V13, binary
                 cls
clus                0   1
  EGLN1 MUTATED     0   5
  EGLN1 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EGLN1 MUTATED      0    5
  EGLN1 WILD-TYPE    4  305
                        clus
vv                       EGLN1 MUTATED EGLN1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(1126) Variable = C1ORF131 MUTATION ANALYSIS
D1126V1, survival
                    sevent
clus2                  0   1
  C1ORF131 MUTATED     4   0
  C1ORF131 WILD-TYPE 226 139
  C1ORF131 MUTATED C1ORF131 WILD-TYPE 
                 4                365 
  C1ORF131 MUTATED C1ORF131 WILD-TYPE 
                 0                139 
$`C1ORF131 MUTATED`
TCGA-BR-8078 TCGA-BR-8487 TCGA-HU-A4H8 TCGA-MX-A5UJ 
       29.59         1.12        14.07        19.73 

$`C1ORF131 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  C1ORF131 MUTATED C1ORF131 WILD-TYPE 
              1.12               0.00 
  C1ORF131 MUTATED C1ORF131 WILD-TYPE 
             29.59             122.30 
  C1ORF131 MUTATED C1ORF131 WILD-TYPE 
             16.90              14.27 
[1] "1.1 - 29.6 (16.9)"  "0.0 - 122.3 (14.3)"
[1] "hr="   "9e+06"
D1126V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  C1ORF131 MUTATED         0        0        1        0         1         1
  C1ORF131 WILD-TYPE       2       15       39       30        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF131 MUTATED           0          1          0          0        0
  C1ORF131 WILD-TYPE         3         69         53         32       38
D1126V3, multiclass
            clus
vv           C1ORF131 MUTATED C1ORF131 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                0                 53
  STAGE IIIC                0                 32
  STAGE IV                  0                 38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C1ORF131 MUTATED     1   0   2   1
  C1ORF131 WILD-TYPE  21  92 171  96
D1126V4, multiclass
    clus
vv   C1ORF131 MUTATED C1ORF131 WILD-TYPE
  T1                1                 21
  T2                0                 92
  T3                2                171
  T4                1                 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
  C1ORF131 MUTATED     2   2   1   0
  C1ORF131 WILD-TYPE 116 102  76  77
D1126V5, multiclass
    clus
vv   C1ORF131 MUTATED C1ORF131 WILD-TYPE
  N0                2                116
  N1                2                102
  N2                1                 76
  N3                0                 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"
D1126V6, binary
                    cls
clus                   0   1
  C1ORF131 MUTATED     5   0
  C1ORF131 WILD-TYPE 341  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF131 MUTATED      5    0
  C1ORF131 WILD-TYPE  341   29
   clus
vv  C1ORF131 MUTATED C1ORF131 WILD-TYPE
  0                5                341
  1                0                 29
[1] 2 2
[1] FALSE
D1126V7, binary
                    cls
clus                   0   1
  C1ORF131 MUTATED     4   1
  C1ORF131 WILD-TYPE 141 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF131 MUTATED      4    1
  C1ORF131 WILD-TYPE  141  247
        clus
vv       C1ORF131 MUTATED C1ORF131 WILD-TYPE
  FEMALE                4                141
  MALE                  1                247
[1] 2 2
[1] FALSE
D1126V8, binary
                    cls
clus                   0   1
  C1ORF131 MUTATED     4   0
  C1ORF131 WILD-TYPE 288  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF131 MUTATED      4    0
  C1ORF131 WILD-TYPE  288   59
     clus
vv    C1ORF131 MUTATED C1ORF131 WILD-TYPE
  NO                 4                288
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  C1ORF131 MUTATED                                          0
  C1ORF131 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  C1ORF131 MUTATED                                       0
  C1ORF131 WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C1ORF131 MUTATED                                                        3
  C1ORF131 WILD-TYPE                                                    155
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  C1ORF131 MUTATED                                                   0
  C1ORF131 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  C1ORF131 MUTATED                                                                   0
  C1ORF131 WILD-TYPE                                                                68
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  C1ORF131 MUTATED                                                    0
  C1ORF131 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  C1ORF131 MUTATED                                                  2
  C1ORF131 WILD-TYPE                                               59
D1126V9, multiclass
                                                                   clus
vv                                                                  C1ORF131 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  C1ORF131 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C1ORF131 MUTATED     4   0   0   1
  C1ORF131 WILD-TYPE 307  14  15  23
D1126V10, multiclass
    clus
vv   C1ORF131 MUTATED C1ORF131 WILD-TYPE
  R0                4                307
  R1                0                 14
  R2                0                 15
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1126V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  C1ORF131 MUTATED       1                         0
  C1ORF131 WILD-TYPE    86                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  C1ORF131 MUTATED                                           0     4
  C1ORF131 WILD-TYPE                                         1   239
D1126V12, multiclass
                                           clus
vv                                          C1ORF131 MUTATED C1ORF131 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    4                239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1126V13, binary
                    cls
clus                   0   1
  C1ORF131 MUTATED     0   5
  C1ORF131 WILD-TYPE   4 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF131 MUTATED      0    5
  C1ORF131 WILD-TYPE    4  305
                        clus
vv                       C1ORF131 MUTATED C1ORF131 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                5                305
[1] 2 2
[1] FALSE

Clustering(1127) Variable = CSF1 MUTATION ANALYSIS
D1127V1, survival
                sevent
clus2              0   1
  CSF1 MUTATED     2   3
  CSF1 WILD-TYPE 228 136
  CSF1 MUTATED CSF1 WILD-TYPE 
             5            364 
  CSF1 MUTATED CSF1 WILD-TYPE 
             3            136 
$`CSF1 MUTATED`
TCGA-BR-7707 TCGA-CD-A4MI TCGA-CG-4306 TCGA-HJ-7597 TCGA-VQ-A8P2 
       35.84        11.77         1.02        26.47        38.14 

$`CSF1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  CSF1 MUTATED CSF1 WILD-TYPE 
          1.02           0.00 
  CSF1 MUTATED CSF1 WILD-TYPE 
         38.14         122.30 
  CSF1 MUTATED CSF1 WILD-TYPE 
         26.47          14.22 
[1] "1.0 - 38.1 (26.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.3"
D1127V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CSF1 MUTATED         0        0        2        0         0         0
  CSF1 WILD-TYPE       2       15       38       30        37        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSF1 MUTATED           0          2          0          0        1
  CSF1 WILD-TYPE         3         68         53         32       37
D1127V3, multiclass
            clus
vv           CSF1 MUTATED CSF1 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             0             37
  STAGE IIB             0             52
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CSF1 MUTATED     0   2   2   1
  CSF1 WILD-TYPE  22  90 171  96
D1127V4, multiclass
    clus
vv   CSF1 MUTATED CSF1 WILD-TYPE
  T1            0             22
  T2            2             90
  T3            2            171
  T4            1             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
  CSF1 MUTATED     2   2   1   0
  CSF1 WILD-TYPE 116 102  76  77
D1127V5, multiclass
    clus
vv   CSF1 MUTATED CSF1 WILD-TYPE
  N0            2            116
  N1            2            102
  N2            1             76
  N3            0             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"
D1127V6, binary
                cls
clus               0   1
  CSF1 MUTATED     3   1
  CSF1 WILD-TYPE 343  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSF1 MUTATED      3    1
  CSF1 WILD-TYPE  343   28
   clus
vv  CSF1 MUTATED CSF1 WILD-TYPE
  0            3            343
  1            1             28
[1] 2 2
[1] FALSE
D1127V7, binary
                cls
clus               0   1
  CSF1 MUTATED     2   3
  CSF1 WILD-TYPE 143 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSF1 MUTATED      2    3
  CSF1 WILD-TYPE  143  245
        clus
vv       CSF1 MUTATED CSF1 WILD-TYPE
  FEMALE            2            143
  MALE              3            245
[1] 2 2
[1] FALSE
D1127V8, binary
                cls
clus               0   1
  CSF1 MUTATED     3   1
  CSF1 WILD-TYPE 289  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSF1 MUTATED      3    1
  CSF1 WILD-TYPE  289   58
     clus
vv    CSF1 MUTATED CSF1 WILD-TYPE
  NO             3            289
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CSF1 MUTATED                                          1
  CSF1 WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CSF1 MUTATED                                       0
  CSF1 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CSF1 MUTATED                                                        3
  CSF1 WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CSF1 MUTATED                                                   1
  CSF1 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CSF1 MUTATED                                                                   0
  CSF1 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CSF1 MUTATED                                                    0
  CSF1 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CSF1 MUTATED                                                  0
  CSF1 WILD-TYPE                                               61
D1127V9, multiclass
                                                                   clus
vv                                                                  CSF1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  CSF1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CSF1 MUTATED     3   0   1   0
  CSF1 WILD-TYPE 308  14  14  24
D1127V10, multiclass
    clus
vv   CSF1 MUTATED CSF1 WILD-TYPE
  R0            3            308
  R1            0             14
  R2            1             14
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1127V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CSF1 MUTATED       1                         0
  CSF1 WILD-TYPE    86                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CSF1 MUTATED                                           0     3
  CSF1 WILD-TYPE                                         1   240
D1127V12, multiclass
                                           clus
vv                                          CSF1 MUTATED CSF1 WILD-TYPE
  ASIAN                                                1             86
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1127V13, binary
                cls
clus               0   1
  CSF1 MUTATED     0   3
  CSF1 WILD-TYPE   4 307
[1] "tbl2"
                cls
clus             [,1] [,2]
  CSF1 MUTATED      0    3
  CSF1 WILD-TYPE    4  307
                        clus
vv                       CSF1 MUTATED CSF1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            3            307
[1] 2 2
[1] FALSE

Clustering(1128) Variable = TBC1D5 MUTATION ANALYSIS
D1128V1, survival
                  sevent
clus2                0   1
  TBC1D5 MUTATED     6   2
  TBC1D5 WILD-TYPE 224 137
  TBC1D5 MUTATED TBC1D5 WILD-TYPE 
               8              361 
  TBC1D5 MUTATED TBC1D5 WILD-TYPE 
               2              137 
$`TBC1D5 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8382 TCGA-BR-A4J5 TCGA-CG-4305 
       26.70        30.90        34.68        25.05        28.34        15.95 
TCGA-CG-5723 TCGA-CG-5728 
      105.07        65.10 

$`TBC1D5 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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 

  TBC1D5 MUTATED TBC1D5 WILD-TYPE 
           15.95             0.00 
  TBC1D5 MUTATED TBC1D5 WILD-TYPE 
          105.07           122.30 
  TBC1D5 MUTATED TBC1D5 WILD-TYPE 
           29.62            14.04 
[1] "15.9 - 105.1 (29.6)" "0.0 - 122.3 (14.0)" 
[1] "hr=" "2.8"
D1128V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TBC1D5 MUTATED         0        0        1        2         1         1
  TBC1D5 WILD-TYPE       2       15       39       28        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBC1D5 MUTATED           0          1          0          1        0
  TBC1D5 WILD-TYPE         3         69         53         31       38
D1128V3, multiclass
            clus
vv           TBC1D5 MUTATED TBC1D5 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TBC1D5 MUTATED     0   4   1   3
  TBC1D5 WILD-TYPE  22  88 172  94
D1128V4, multiclass
    clus
vv   TBC1D5 MUTATED TBC1D5 WILD-TYPE
  T1              0               22
  T2              4               88
  T3              1              172
  T4              3               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
  TBC1D5 MUTATED     3   4   0   1
  TBC1D5 WILD-TYPE 115 100  77  76
D1128V5, multiclass
    clus
vv   TBC1D5 MUTATED TBC1D5 WILD-TYPE
  N0              3              115
  N1              4              100
  N2              0               77
  N3              1               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"
D1128V6, binary
                  cls
clus                 0   1
  TBC1D5 MUTATED     9   0
  TBC1D5 WILD-TYPE 337  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TBC1D5 MUTATED      9    0
  TBC1D5 WILD-TYPE  337   29
   clus
vv  TBC1D5 MUTATED TBC1D5 WILD-TYPE
  0              9              337
  1              0               29
[1] 2 2
[1] FALSE
D1128V7, binary
                  cls
clus                 0   1
  TBC1D5 MUTATED     6   3
  TBC1D5 WILD-TYPE 139 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TBC1D5 MUTATED      6    3
  TBC1D5 WILD-TYPE  139  245
        clus
vv       TBC1D5 MUTATED TBC1D5 WILD-TYPE
  FEMALE              6              139
  MALE                3              245
[1] 2 2
[1] FALSE
D1128V8, binary
                  cls
clus                 0   1
  TBC1D5 MUTATED     7   0
  TBC1D5 WILD-TYPE 285  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TBC1D5 MUTATED      7    0
  TBC1D5 WILD-TYPE  285   59
     clus
vv    TBC1D5 MUTATED TBC1D5 WILD-TYPE
  NO               7              285
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TBC1D5 MUTATED                                          0
  TBC1D5 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TBC1D5 MUTATED                                       1
  TBC1D5 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TBC1D5 MUTATED                                                        6
  TBC1D5 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TBC1D5 MUTATED                                                   1
  TBC1D5 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TBC1D5 MUTATED                                                                   1
  TBC1D5 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TBC1D5 MUTATED                                                    0
  TBC1D5 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TBC1D5 MUTATED                                                  0
  TBC1D5 WILD-TYPE                                               61
D1128V9, multiclass
                                                                   clus
vv                                                                  TBC1D5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  TBC1D5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TBC1D5 MUTATED     7   0   0   2
  TBC1D5 WILD-TYPE 304  14  15  22
D1128V10, multiclass
    clus
vv   TBC1D5 MUTATED TBC1D5 WILD-TYPE
  R0              7              304
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1128V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TBC1D5 MUTATED       1                         0
  TBC1D5 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TBC1D5 MUTATED                                           0     5
  TBC1D5 WILD-TYPE                                         1   238
D1128V12, multiclass
                                           clus
vv                                          TBC1D5 MUTATED TBC1D5 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1128V13, binary
                  cls
clus                 0   1
  TBC1D5 MUTATED     0   6
  TBC1D5 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TBC1D5 MUTATED      0    6
  TBC1D5 WILD-TYPE    4  304
                        clus
vv                       TBC1D5 MUTATED TBC1D5 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(1129) Variable = ZNF428 MUTATION ANALYSIS
D1129V1, survival
                  sevent
clus2                0   1
  ZNF428 MUTATED     4   1
  ZNF428 WILD-TYPE 226 138
  ZNF428 MUTATED ZNF428 WILD-TYPE 
               5              364 
  ZNF428 MUTATED ZNF428 WILD-TYPE 
               1              138 
$`ZNF428 MUTATED`
TCGA-BR-8360 TCGA-BR-8487 TCGA-CG-5733 TCGA-FP-A4BE TCGA-VQ-A8P2 
        6.18         1.12        21.07        11.08        38.14 

$`ZNF428 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  ZNF428 MUTATED ZNF428 WILD-TYPE 
            1.12             0.00 
  ZNF428 MUTATED ZNF428 WILD-TYPE 
           38.14           122.30 
  ZNF428 MUTATED ZNF428 WILD-TYPE 
           11.08            14.35 
[1] "1.1 - 38.1 (11.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.6"
D1129V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF428 MUTATED         0        0        0        0         3         0
  ZNF428 WILD-TYPE       2       15       40       30        34        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF428 MUTATED           0          2          0          0        0
  ZNF428 WILD-TYPE         3         68         53         32       38
D1129V3, multiclass
            clus
vv           ZNF428 MUTATED ZNF428 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF428 MUTATED     0   1   3   1
  ZNF428 WILD-TYPE  22  91 170  96
D1129V4, multiclass
    clus
vv   ZNF428 MUTATED ZNF428 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              3              170
  T4              1               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
  ZNF428 MUTATED     3   1   1   0
  ZNF428 WILD-TYPE 115 103  76  77
D1129V5, multiclass
    clus
vv   ZNF428 MUTATED ZNF428 WILD-TYPE
  N0              3              115
  N1              1              103
  N2              1               76
  N3              0               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"
D1129V6, binary
                  cls
clus                 0   1
  ZNF428 MUTATED     5   0
  ZNF428 WILD-TYPE 341  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF428 MUTATED      5    0
  ZNF428 WILD-TYPE  341   29
   clus
vv  ZNF428 MUTATED ZNF428 WILD-TYPE
  0              5              341
  1              0               29
[1] 2 2
[1] FALSE
D1129V7, binary
                  cls
clus                 0   1
  ZNF428 MUTATED     2   3
  ZNF428 WILD-TYPE 143 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF428 MUTATED      2    3
  ZNF428 WILD-TYPE  143  245
        clus
vv       ZNF428 MUTATED ZNF428 WILD-TYPE
  FEMALE              2              143
  MALE                3              245
[1] 2 2
[1] FALSE
D1129V8, binary
                  cls
clus                 0   1
  ZNF428 MUTATED     3   2
  ZNF428 WILD-TYPE 289  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF428 MUTATED      3    2
  ZNF428 WILD-TYPE  289   57
     clus
vv    ZNF428 MUTATED ZNF428 WILD-TYPE
  NO               3              289
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF428 MUTATED                                          0
  ZNF428 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF428 MUTATED                                       0
  ZNF428 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF428 MUTATED                                                        2
  ZNF428 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF428 MUTATED                                                   1
  ZNF428 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF428 MUTATED                                                                   2
  ZNF428 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF428 MUTATED                                                    0
  ZNF428 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF428 MUTATED                                                  0
  ZNF428 WILD-TYPE                                               61
D1129V9, multiclass
                                                                   clus
vv                                                                  ZNF428 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  ZNF428 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF428 MUTATED     5   0   0   0
  ZNF428 WILD-TYPE 306  14  15  24
D1129V10, multiclass
    clus
vv   ZNF428 MUTATED ZNF428 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1129V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF428 MUTATED       0                         1
  ZNF428 WILD-TYPE    87                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF428 MUTATED                                           0     3
  ZNF428 WILD-TYPE                                         1   240
D1129V12, multiclass
                                           clus
vv                                          ZNF428 MUTATED ZNF428 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1129V13, binary
                  cls
clus                 0   1
  ZNF428 MUTATED     0   3
  ZNF428 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF428 MUTATED      0    3
  ZNF428 WILD-TYPE    4  307
                        clus
vv                       ZNF428 MUTATED ZNF428 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(1130) Variable = SLC38A1 MUTATION ANALYSIS
D1130V1, survival
                   sevent
clus2                 0   1
  SLC38A1 MUTATED     4   3
  SLC38A1 WILD-TYPE 226 136
  SLC38A1 MUTATED SLC38A1 WILD-TYPE 
                7               362 
  SLC38A1 MUTATED SLC38A1 WILD-TYPE 
                3               136 
$`SLC38A1 MUTATED`
TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-6802 TCGA-CG-4300 TCGA-HF-A5NB TCGA-HU-A4GT 
        6.97        30.90        30.90        20.02        30.51         6.51 
TCGA-VQ-A8P2 
       38.14 

$`SLC38A1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-4301 TCGA-CG-4304 TCGA-CG-4305 
       12.20        11.77        12.62         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 

  SLC38A1 MUTATED SLC38A1 WILD-TYPE 
             6.51              0.00 
  SLC38A1 MUTATED SLC38A1 WILD-TYPE 
            38.14            122.30 
  SLC38A1 MUTATED SLC38A1 WILD-TYPE 
            30.51             14.12 
[1] "6.5 - 38.1 (30.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.2"
D1130V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC38A1 MUTATED         0        0        0        0         1         0
  SLC38A1 WILD-TYPE       2       15       40       30        36        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC38A1 MUTATED           0          3          1          1        0
  SLC38A1 WILD-TYPE         3         67         52         31       38
D1130V3, multiclass
            clus
vv           SLC38A1 MUTATED SLC38A1 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                0                52
  STAGE III                0                 3
  STAGE IIIA               3                67
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 0                38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC38A1 MUTATED     0   1   4   2
  SLC38A1 WILD-TYPE  22  91 169  95
D1130V4, multiclass
    clus
vv   SLC38A1 MUTATED SLC38A1 WILD-TYPE
  T1               0                22
  T2               1                91
  T3               4               169
  T4               2                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
  SLC38A1 MUTATED     1   2   2   1
  SLC38A1 WILD-TYPE 117 102  75  76
D1130V5, multiclass
    clus
vv   SLC38A1 MUTATED SLC38A1 WILD-TYPE
  N0               1               117
  N1               2               102
  N2               2                75
  N3               1                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"
D1130V6, binary
                   cls
clus                  0   1
  SLC38A1 MUTATED     6   0
  SLC38A1 WILD-TYPE 340  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A1 MUTATED      6    0
  SLC38A1 WILD-TYPE  340   29
   clus
vv  SLC38A1 MUTATED SLC38A1 WILD-TYPE
  0               6               340
  1               0                29
[1] 2 2
[1] FALSE
D1130V7, binary
                   cls
clus                  0   1
  SLC38A1 MUTATED     3   4
  SLC38A1 WILD-TYPE 142 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A1 MUTATED      3    4
  SLC38A1 WILD-TYPE  142  244
        clus
vv       SLC38A1 MUTATED SLC38A1 WILD-TYPE
  FEMALE               3               142
  MALE                 4               244
[1] 2 2
[1] FALSE
D1130V8, binary
                   cls
clus                  0   1
  SLC38A1 MUTATED     4   2
  SLC38A1 WILD-TYPE 288  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A1 MUTATED      4    2
  SLC38A1 WILD-TYPE  288   57
     clus
vv    SLC38A1 MUTATED SLC38A1 WILD-TYPE
  NO                4               288
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC38A1 MUTATED                                          0
  SLC38A1 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC38A1 MUTATED                                       0
  SLC38A1 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC38A1 MUTATED                                                        4
  SLC38A1 WILD-TYPE                                                    154
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC38A1 MUTATED                                                   2
  SLC38A1 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC38A1 MUTATED                                                                   0
  SLC38A1 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC38A1 MUTATED                                                    0
  SLC38A1 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC38A1 MUTATED                                                  1
  SLC38A1 WILD-TYPE                                               60
D1130V9, multiclass
                                                                   clus
vv                                                                  SLC38A1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  SLC38A1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC38A1 MUTATED     4   1   0   2
  SLC38A1 WILD-TYPE 307  13  15  22
D1130V10, multiclass
    clus
vv   SLC38A1 MUTATED SLC38A1 WILD-TYPE
  R0               4               307
  R1               1                13
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1130V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC38A1 MUTATED       1                         0
  SLC38A1 WILD-TYPE    86                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC38A1 MUTATED                                           0     4
  SLC38A1 WILD-TYPE                                         1   239
D1130V12, multiclass
                                           clus
vv                                          SLC38A1 MUTATED SLC38A1 WILD-TYPE
  ASIAN                                                   1                86
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1130V13, binary
                   cls
clus                  0   1
  SLC38A1 MUTATED     0   4
  SLC38A1 WILD-TYPE   4 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A1 MUTATED      0    4
  SLC38A1 WILD-TYPE    4  306
                        clus
vv                       SLC38A1 MUTATED SLC38A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4               306
[1] 2 2
[1] FALSE

Clustering(1131) Variable = ZNF570 MUTATION ANALYSIS
D1131V1, survival
                  sevent
clus2                0   1
  ZNF570 MUTATED     7   3
  ZNF570 WILD-TYPE 223 136
  ZNF570 MUTATED ZNF570 WILD-TYPE 
              10              359 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
               3              136 
$`ZNF570 MUTATED`
TCGA-BR-4184 TCGA-BR-8078 TCGA-BR-8363 TCGA-BR-8680 TCGA-BR-A4J5 TCGA-CG-5723 
        6.97        29.59         0.26        31.96        28.34       105.07 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-IN-A7NT TCGA-VQ-AA6I 
        8.98         6.58        10.62        16.14 

$`ZNF570 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         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-A7NU 
       19.53         6.44         6.74        12.59         6.51        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-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       54.12        26.04        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 
           13.38            14.27 
[1] "0.3 - 105.1 (13.4)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D1131V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ZNF570 MUTATED         0        1        1        1         1         3
  ZNF570 WILD-TYPE       2       14       39       29        36        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF570 MUTATED           0          2          1          0        1
  ZNF570 WILD-TYPE         3         68         52         32       37
D1131V3, multiclass
            clus
vv           ZNF570 MUTATED ZNF570 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF570 MUTATED     1   3   4   3
  ZNF570 WILD-TYPE  21  89 169  94
D1131V4, multiclass
    clus
vv   ZNF570 MUTATED ZNF570 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              4              169
  T4              3               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
  ZNF570 MUTATED     3   6   1   1
  ZNF570 WILD-TYPE 115  98  76  76
D1131V5, multiclass
    clus
vv   ZNF570 MUTATED ZNF570 WILD-TYPE
  N0              3              115
  N1              6               98
  N2              1               76
  N3              1               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"
D1131V6, binary
                  cls
clus                 0   1
  ZNF570 MUTATED    10   1
  ZNF570 WILD-TYPE 336  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED     10    1
  ZNF570 WILD-TYPE  336   28
   clus
vv  ZNF570 MUTATED ZNF570 WILD-TYPE
  0             10              336
  1              1               28
[1] 2 2
[1] FALSE
D1131V7, binary
                  cls
clus                 0   1
  ZNF570 MUTATED     5   7
  ZNF570 WILD-TYPE 140 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED      5    7
  ZNF570 WILD-TYPE  140  241
        clus
vv       ZNF570 MUTATED ZNF570 WILD-TYPE
  FEMALE              5              140
  MALE                7              241
[1] 2 2
[1] FALSE
D1131V8, binary
                  cls
clus                 0   1
  ZNF570 MUTATED    10   1
  ZNF570 WILD-TYPE 282  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED     10    1
  ZNF570 WILD-TYPE  282   58
     clus
vv    ZNF570 MUTATED ZNF570 WILD-TYPE
  NO              10              282
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ZNF570 MUTATED                                          0
  ZNF570 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ZNF570 MUTATED                                       2
  ZNF570 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF570 MUTATED                                                        7
  ZNF570 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ZNF570 MUTATED                                                   1
  ZNF570 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ZNF570 MUTATED                                                                   1
  ZNF570 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ZNF570 MUTATED                                                    0
  ZNF570 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ZNF570 MUTATED                                                  1
  ZNF570 WILD-TYPE                                               60
D1131V9, multiclass
                                                                   clus
vv                                                                  ZNF570 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ZNF570 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF570 MUTATED    10   0   0   2
  ZNF570 WILD-TYPE 301  14  15  22
D1131V10, multiclass
    clus
vv   ZNF570 MUTATED ZNF570 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1131V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ZNF570 MUTATED       5                         0
  ZNF570 WILD-TYPE    82                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ZNF570 MUTATED                                           0     6
  ZNF570 WILD-TYPE                                         1   237
D1131V12, multiclass
                                           clus
vv                                          ZNF570 MUTATED ZNF570 WILD-TYPE
  ASIAN                                                  5               82
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1131V13, binary
                  cls
clus                 0   1
  ZNF570 MUTATED     0  10
  ZNF570 WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED      0   10
  ZNF570 WILD-TYPE    4  300
                        clus
vv                       ZNF570 MUTATED ZNF570 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(1132) Variable = GPR115 MUTATION ANALYSIS
D1132V1, survival
                  sevent
clus2                0   1
  GPR115 MUTATED     2   0
  GPR115 WILD-TYPE 228 139
  GPR115 MUTATED GPR115 WILD-TYPE 
               2              367 
  GPR115 MUTATED GPR115 WILD-TYPE 
               0              139 
$`GPR115 MUTATED`
TCGA-HF-7132 TCGA-SW-A7EA 
       77.29        19.04 

$`GPR115 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  GPR115 MUTATED GPR115 WILD-TYPE 
           19.04             0.00 
  GPR115 MUTATED GPR115 WILD-TYPE 
           77.29           122.30 
  GPR115 MUTATED GPR115 WILD-TYPE 
          48.165           14.170 
[1] "19.0 - 77.3 (48.2)" "0.0 - 122.3 (14.2)"
[1] "Remove cluster labels:" "GPR115 MUTATED"        
D1132V2, 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       1       15       38       29        37        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR115 MUTATED           0          1          0          0        0
  GPR115 WILD-TYPE         3         69         53         32       38
D1132V3, multiclass
            clus
vv           GPR115 MUTATED GPR115 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               0               37
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR115 MUTATED     1   3   0   1
  GPR115 WILD-TYPE  21  89 173  96
D1132V4, multiclass
    clus
vv   GPR115 MUTATED GPR115 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              0              173
  T4              1               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
  GPR115 MUTATED     3   2   0   0
  GPR115 WILD-TYPE 115 102  77  77
D1132V5, multiclass
    clus
vv   GPR115 MUTATED GPR115 WILD-TYPE
  N0              3              115
  N1              2              102
  N2              0               77
  N3              0               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"
D1132V6, binary
                  cls
clus                 0   1
  GPR115 MUTATED     4   0
  GPR115 WILD-TYPE 342  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED      4    0
  GPR115 WILD-TYPE  342   29
   clus
vv  GPR115 MUTATED GPR115 WILD-TYPE
  0              4              342
  1              0               29
[1] 2 2
[1] FALSE
D1132V7, binary
                  cls
clus                 0   1
  GPR115 MUTATED     2   3
  GPR115 WILD-TYPE 143 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED      2    3
  GPR115 WILD-TYPE  143  245
        clus
vv       GPR115 MUTATED GPR115 WILD-TYPE
  FEMALE              2              143
  MALE                3              245
[1] 2 2
[1] FALSE
D1132V8, binary
                  cls
clus                 0   1
  GPR115 MUTATED     2   1
  GPR115 WILD-TYPE 290  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED      2    1
  GPR115 WILD-TYPE  290   58
     clus
vv    GPR115 MUTATED GPR115 WILD-TYPE
  NO               2              290
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GPR115 MUTATED                                          0
  GPR115 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GPR115 MUTATED                                       1
  GPR115 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR115 MUTATED                                                        2
  GPR115 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GPR115 MUTATED                                                   1
  GPR115 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GPR115 MUTATED                                                                   1
  GPR115 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GPR115 MUTATED                                                    0
  GPR115 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GPR115 MUTATED                                                  0
  GPR115 WILD-TYPE                                               61
D1132V9, multiclass
                                                                   clus
vv                                                                  GPR115 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  GPR115 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR115 MUTATED     4   0   0   1
  GPR115 WILD-TYPE 307  14  15  23
D1132V10, multiclass
    clus
vv   GPR115 MUTATED GPR115 WILD-TYPE
  R0              4              307
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1132V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GPR115 MUTATED       0                         1
  GPR115 WILD-TYPE    87                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GPR115 MUTATED                                           0     2
  GPR115 WILD-TYPE                                         1   241
D1132V12, multiclass
                                           clus
vv                                          GPR115 MUTATED GPR115 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  2              241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1132V13, binary
                  cls
clus                 0   1
  GPR115 MUTATED     0   3
  GPR115 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED      0    3
  GPR115 WILD-TYPE    4  307
                        clus
vv                       GPR115 MUTATED GPR115 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(1133) Variable = SLC45A4 MUTATION ANALYSIS
D1133V1, survival
                   sevent
clus2                 0   1
  SLC45A4 MUTATED    13   3
  SLC45A4 WILD-TYPE 217 136
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
               16               353 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
                3               136 
$`SLC45A4 MUTATED`
TCGA-BR-6452 TCGA-BR-8284 TCGA-BR-8372 TCGA-BR-8382 TCGA-CD-8536 TCGA-CD-A4MJ 
       34.68         8.05        31.27        25.05        12.43        12.62 
TCGA-CG-4449 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5728 TCGA-F1-A448 TCGA-FP-A4BE 
       19.07         6.02       105.07        65.10        21.27        11.08 
TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GU TCGA-RD-A7BW 
       22.32        24.20         6.58         5.13 

$`SLC45A4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
             5.13              0.00 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
           105.07            122.30 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
            20.17             14.17 
[1] "5.1 - 105.1 (20.2)" "0.0 - 122.3 (14.2)"
[1] "hr=" "2.4"
D1133V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC45A4 MUTATED         1        1        3        3         2         2
  SLC45A4 WILD-TYPE       1       14       37       27        35        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC45A4 MUTATED           0          1          1          3        1
  SLC45A4 WILD-TYPE         3         69         52         29       37
D1133V3, multiclass
            clus
vv           SLC45A4 MUTATED SLC45A4 WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 1                14
  STAGE IB                 3                37
  STAGE II                 3                27
  STAGE IIA                2                35
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               1                69
  STAGE IIIB               1                52
  STAGE IIIC               3                29
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC45A4 MUTATED     2   5   5   6
  SLC45A4 WILD-TYPE  20  87 168  91
D1133V4, multiclass
    clus
vv   SLC45A4 MUTATED SLC45A4 WILD-TYPE
  T1               2                20
  T2               5                87
  T3               5               168
  T4               6                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
  SLC45A4 MUTATED     9   5   0   4
  SLC45A4 WILD-TYPE 109  99  77  73
D1133V5, multiclass
    clus
vv   SLC45A4 MUTATED SLC45A4 WILD-TYPE
  N0               9               109
  N1               5                99
  N2               0                77
  N3               4                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"
D1133V6, binary
                   cls
clus                  0   1
  SLC45A4 MUTATED    18   0
  SLC45A4 WILD-TYPE 328  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED     18    0
  SLC45A4 WILD-TYPE  328   29
   clus
vv  SLC45A4 MUTATED SLC45A4 WILD-TYPE
  0              18               328
  1               0                29
[1] 2 2
[1] FALSE
D1133V7, binary
                   cls
clus                  0   1
  SLC45A4 MUTATED     9  10
  SLC45A4 WILD-TYPE 136 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED      9   10
  SLC45A4 WILD-TYPE  136  238
        clus
vv       SLC45A4 MUTATED SLC45A4 WILD-TYPE
  FEMALE               9               136
  MALE                10               238
[1] 2 2
[1] FALSE
D1133V8, binary
                   cls
clus                  0   1
  SLC45A4 MUTATED    13   3
  SLC45A4 WILD-TYPE 279  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED     13    3
  SLC45A4 WILD-TYPE  279   56
     clus
vv    SLC45A4 MUTATED SLC45A4 WILD-TYPE
  NO               13               279
  YES               3                56
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC45A4 MUTATED                                          0
  SLC45A4 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC45A4 MUTATED                                       3
  SLC45A4 WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC45A4 MUTATED                                                       10
  SLC45A4 WILD-TYPE                                                    148
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC45A4 MUTATED                                                   2
  SLC45A4 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC45A4 MUTATED                                                                   3
  SLC45A4 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC45A4 MUTATED                                                    0
  SLC45A4 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC45A4 MUTATED                                                  1
  SLC45A4 WILD-TYPE                                               60
D1133V9, multiclass
                                                                   clus
vv                                                                  SLC45A4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  SLC45A4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC45A4 MUTATED    16   0   0   2
  SLC45A4 WILD-TYPE 295  14  15  22
D1133V10, multiclass
    clus
vv   SLC45A4 MUTATED SLC45A4 WILD-TYPE
  R0              16               295
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1133V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC45A4 MUTATED       5                         2
  SLC45A4 WILD-TYPE    82                         7
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC45A4 MUTATED                                           0     8
  SLC45A4 WILD-TYPE                                         1   235
D1133V12, multiclass
                                           clus
vv                                          SLC45A4 MUTATED SLC45A4 WILD-TYPE
  ASIAN                                                   5                82
  BLACK OR AFRICAN AMERICAN                               2                 7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1133V13, binary
                   cls
clus                  0   1
  SLC45A4 MUTATED     1  14
  SLC45A4 WILD-TYPE   3 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED      1   14
  SLC45A4 WILD-TYPE    3  296
                        clus
vv                       SLC45A4 MUTATED SLC45A4 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              14               296
[1] 2 2
[1] FALSE

Clustering(1134) Variable = NKX2-3 MUTATION ANALYSIS
D1134V1, survival
                  sevent
clus2                0   1
  NKX2-3 MUTATED     2   4
  NKX2-3 WILD-TYPE 228 135
  NKX2-3 MUTATED NKX2-3 WILD-TYPE 
               6              363 
  NKX2-3 MUTATED NKX2-3 WILD-TYPE 
               4              135 
$`NKX2-3 MUTATED`
TCGA-BR-A4QL TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H8 TCGA-RD-A7C1 TCGA-VQ-A91U 
       16.14         0.10         6.51        14.07        16.67         1.71 

$`NKX2-3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  NKX2-3 MUTATED NKX2-3 WILD-TYPE 
             0.1              0.0 
  NKX2-3 MUTATED NKX2-3 WILD-TYPE 
           16.67           122.30 
  NKX2-3 MUTATED NKX2-3 WILD-TYPE 
           10.29            14.43 
[1] "0.1 - 16.7 (10.3)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "3.3"
D1134V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  NKX2-3 MUTATED         0        0        2        0         1         0
  NKX2-3 WILD-TYPE       2       15       38       30        36        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NKX2-3 MUTATED           0          1          1          1        1
  NKX2-3 WILD-TYPE         3         69         52         31       37
D1134V3, multiclass
            clus
vv           NKX2-3 MUTATED NKX2-3 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NKX2-3 MUTATED     1   1   3   2
  NKX2-3 WILD-TYPE  21  91 170  95
D1134V4, multiclass
    clus
vv   NKX2-3 MUTATED NKX2-3 WILD-TYPE
  T1              1               21
  T2              1               91
  T3              3              170
  T4              2               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
  NKX2-3 MUTATED     2   3   2   1
  NKX2-3 WILD-TYPE 116 101  75  76
D1134V5, multiclass
    clus
vv   NKX2-3 MUTATED NKX2-3 WILD-TYPE
  N0              2              116
  N1              3              101
  N2              2               75
  N3              1               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"
D1134V6, binary
                  cls
clus                 0   1
  NKX2-3 MUTATED     8   0
  NKX2-3 WILD-TYPE 338  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NKX2-3 MUTATED      8    0
  NKX2-3 WILD-TYPE  338   29
   clus
vv  NKX2-3 MUTATED NKX2-3 WILD-TYPE
  0              8              338
  1              0               29
[1] 2 2
[1] FALSE
D1134V7, binary
                  cls
clus                 0   1
  NKX2-3 MUTATED     4   4
  NKX2-3 WILD-TYPE 141 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NKX2-3 MUTATED      4    4
  NKX2-3 WILD-TYPE  141  244
        clus
vv       NKX2-3 MUTATED NKX2-3 WILD-TYPE
  FEMALE              4              141
  MALE                4              244
[1] 2 2
[1] FALSE
D1134V8, binary
                  cls
clus                 0   1
  NKX2-3 MUTATED     6   0
  NKX2-3 WILD-TYPE 286  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NKX2-3 MUTATED      6    0
  NKX2-3 WILD-TYPE  286   59
     clus
vv    NKX2-3 MUTATED NKX2-3 WILD-TYPE
  NO               6              286
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  NKX2-3 MUTATED                                          0
  NKX2-3 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  NKX2-3 MUTATED                                       1
  NKX2-3 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NKX2-3 MUTATED                                                        3
  NKX2-3 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  NKX2-3 MUTATED                                                   0
  NKX2-3 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  NKX2-3 MUTATED                                                                   1
  NKX2-3 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  NKX2-3 MUTATED                                                    0
  NKX2-3 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  NKX2-3 MUTATED                                                  3
  NKX2-3 WILD-TYPE                                               58
D1134V9, multiclass
                                                                   clus
vv                                                                  NKX2-3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  NKX2-3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NKX2-3 MUTATED     6   0   0   2
  NKX2-3 WILD-TYPE 305  14  15  22
D1134V10, multiclass
    clus
vv   NKX2-3 MUTATED NKX2-3 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1134V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  NKX2-3 MUTATED       4                         0
  NKX2-3 WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  NKX2-3 MUTATED                                           0     4
  NKX2-3 WILD-TYPE                                         1   239
D1134V12, multiclass
                                           clus
vv                                          NKX2-3 MUTATED NKX2-3 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1134V13, binary
                  cls
clus                 0   1
  NKX2-3 MUTATED     0   7
  NKX2-3 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NKX2-3 MUTATED      0    7
  NKX2-3 WILD-TYPE    4  303
                        clus
vv                       NKX2-3 MUTATED NKX2-3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(1135) Variable = EPHA3 MUTATION ANALYSIS
D1135V1, survival
                 sevent
clus2               0   1
  EPHA3 MUTATED    20   8
  EPHA3 WILD-TYPE 210 131
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             28             341 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
              8             131 
$`EPHA3 MUTATED`
TCGA-CG-4444 TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-8372 
       47.05         6.97         9.34        34.68        30.90        31.27 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A4QM 
        1.12        27.12        28.14        31.96        10.68         5.13 
TCGA-CD-5801 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4436 TCGA-CG-5723 TCGA-CG-5728 
       13.18        12.43        11.61         7.99       105.07        65.10 
TCGA-D7-6527 TCGA-D7-6820 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-A9TM TCGA-HU-A4H4 
       10.26        11.31        72.23        21.27         6.21        23.84 
TCGA-HU-A4H5 TCGA-IN-A6RR TCGA-VQ-A8DU TCGA-VQ-A8P2 
       23.80         6.74         5.46        38.14 

$`EPHA3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-8590 
        5.39        25.18         9.21        20.22        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-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       20.88         8.22        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-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-A4MG 
       12.82        12.43         6.31        12.30        11.31         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-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-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-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        15.22        15.98        12.79        12.36 
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-A72C 
       19.96         7.13         0.62         7.99        14.47        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-7132 
        5.03        13.58         0.56        11.08         5.52        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-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-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-A8DV TCGA-VQ-A8DZ 
       19.04         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-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 

  EPHA3 MUTATED EPHA3 WILD-TYPE 
           1.12            0.00 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
         105.07          122.30 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
         17.225          14.270 
[1] "1.1 - 105.1 (17.2)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.6"
D1135V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPHA3 MUTATED         0        1        3        2         3         3
  EPHA3 WILD-TYPE       2       14       37       28        34        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPHA3 MUTATED           0          8          3          2        1
  EPHA3 WILD-TYPE         3         62         50         30       37
D1135V3, multiclass
            clus
vv           EPHA3 MUTATED EPHA3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               2              28
  STAGE IIA              3              34
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             8              62
  STAGE IIIB             3              50
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHA3 MUTATED     1   9  12   5
  EPHA3 WILD-TYPE  21  83 161  92
D1135V4, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  T1             1              21
  T2             9              83
  T3            12             161
  T4             5              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
  EPHA3 MUTATED     7  11   6   4
  EPHA3 WILD-TYPE 111  93  71  73
D1135V5, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  N0             7             111
  N1            11              93
  N2             6              71
  N3             4              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"
D1135V6, binary
                 cls
clus                0   1
  EPHA3 MUTATED    26   1
  EPHA3 WILD-TYPE 320  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     26    1
  EPHA3 WILD-TYPE  320   28
   clus
vv  EPHA3 MUTATED EPHA3 WILD-TYPE
  0            26             320
  1             1              28
[1] 2 2
[1] FALSE
D1135V7, binary
                 cls
clus                0   1
  EPHA3 MUTATED     6  22
  EPHA3 WILD-TYPE 139 226
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED      6   22
  EPHA3 WILD-TYPE  139  226
        clus
vv       EPHA3 MUTATED EPHA3 WILD-TYPE
  FEMALE             6             139
  MALE              22             226
[1] 2 2
[1] FALSE
D1135V8, binary
                 cls
clus                0   1
  EPHA3 MUTATED    21   6
  EPHA3 WILD-TYPE 271  53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     21    6
  EPHA3 WILD-TYPE  271   53
     clus
vv    EPHA3 MUTATED EPHA3 WILD-TYPE
  NO             21             271
  YES             6              53
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EPHA3 MUTATED                                          0
  EPHA3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EPHA3 MUTATED                                       1
  EPHA3 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPHA3 MUTATED                                                       17
  EPHA3 WILD-TYPE                                                    141
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EPHA3 MUTATED                                                   2
  EPHA3 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPHA3 MUTATED                                                                   2
  EPHA3 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EPHA3 MUTATED                                                    2
  EPHA3 WILD-TYPE                                                  3
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EPHA3 MUTATED                                                  4
  EPHA3 WILD-TYPE                                               57
D1135V9, multiclass
                                                                   clus
vv                                                                  EPHA3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       17
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  EPHA3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        141
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EPHA3 MUTATED    24   0   0   2
  EPHA3 WILD-TYPE 287  14  15  22
D1135V10, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  R0            24             287
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1135V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  EPHA3 MUTATED       6                         1
  EPHA3 WILD-TYPE    81                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPHA3 MUTATED                                           0    17
  EPHA3 WILD-TYPE                                         1   226
D1135V12, multiclass
                                           clus
vv                                          EPHA3 MUTATED EPHA3 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                17             226
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1135V13, binary
                 cls
clus                0   1
  EPHA3 MUTATED     1  21
  EPHA3 WILD-TYPE   3 289
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED      1   21
  EPHA3 WILD-TYPE    3  289
                        clus
vv                       EPHA3 MUTATED EPHA3 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            21             289
[1] 2 2
[1] FALSE

Clustering(1136) Variable = GABRG3 MUTATION ANALYSIS
D1136V1, survival
                  sevent
clus2                0   1
  GABRG3 MUTATED     7   2
  GABRG3 WILD-TYPE 223 137
  GABRG3 MUTATED GABRG3 WILD-TYPE 
               9              360 
  GABRG3 MUTATED GABRG3 WILD-TYPE 
               2              137 
$`GABRG3 MUTATED`
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-8381 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CG-5728 
        9.34        34.68         7.36        31.96         6.58        65.10 
TCGA-HU-8604 TCGA-MX-A5UJ TCGA-VQ-A8P3 
       22.82        19.73        37.22 

$`GABRG3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  GABRG3 MUTATED GABRG3 WILD-TYPE 
            6.58             0.00 
  GABRG3 MUTATED GABRG3 WILD-TYPE 
            65.1            122.3 
  GABRG3 MUTATED GABRG3 WILD-TYPE 
           22.82            14.12 
[1] "6.6 - 65.1 (22.8)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.2"
D1136V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  GABRG3 MUTATED         0        0        1        0         3         1
  GABRG3 WILD-TYPE       2       15       39       30        34        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GABRG3 MUTATED           0          2          0          0        1
  GABRG3 WILD-TYPE         3         68         53         32       37
D1136V3, multiclass
            clus
vv           GABRG3 MUTATED GABRG3 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                0               30
  STAGE IIA               3               34
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GABRG3 MUTATED     0   1   5   2
  GABRG3 WILD-TYPE  22  91 168  95
D1136V4, multiclass
    clus
vv   GABRG3 MUTATED GABRG3 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              5              168
  T4              2               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
  GABRG3 MUTATED     4   3   2   0
  GABRG3 WILD-TYPE 114 101  75  77
D1136V5, multiclass
    clus
vv   GABRG3 MUTATED GABRG3 WILD-TYPE
  N0              4              114
  N1              3              101
  N2              2               75
  N3              0               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"
D1136V6, binary
                  cls
clus                 0   1
  GABRG3 MUTATED     8   1
  GABRG3 WILD-TYPE 338  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRG3 MUTATED      8    1
  GABRG3 WILD-TYPE  338   28
   clus
vv  GABRG3 MUTATED GABRG3 WILD-TYPE
  0              8              338
  1              1               28
[1] 2 2
[1] FALSE
D1136V7, binary
                  cls
clus                 0   1
  GABRG3 MUTATED     4   5
  GABRG3 WILD-TYPE 141 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRG3 MUTATED      4    5
  GABRG3 WILD-TYPE  141  243
        clus
vv       GABRG3 MUTATED GABRG3 WILD-TYPE
  FEMALE              4              141
  MALE                5              243
[1] 2 2
[1] FALSE
D1136V8, binary
                  cls
clus                 0   1
  GABRG3 MUTATED     7   1
  GABRG3 WILD-TYPE 285  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRG3 MUTATED      7    1
  GABRG3 WILD-TYPE  285   58
     clus
vv    GABRG3 MUTATED GABRG3 WILD-TYPE
  NO               7              285
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  GABRG3 MUTATED                                          0
  GABRG3 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  GABRG3 MUTATED                                       1
  GABRG3 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GABRG3 MUTATED                                                        3
  GABRG3 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  GABRG3 MUTATED                                                   0
  GABRG3 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  GABRG3 MUTATED                                                                   1
  GABRG3 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  GABRG3 MUTATED                                                    0
  GABRG3 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  GABRG3 MUTATED                                                  4
  GABRG3 WILD-TYPE                                               57
D1136V9, multiclass
                                                                   clus
vv                                                                  GABRG3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  GABRG3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GABRG3 MUTATED     7   0   0   1
  GABRG3 WILD-TYPE 304  14  15  23
D1136V10, multiclass
    clus
vv   GABRG3 MUTATED GABRG3 WILD-TYPE
  R0              7              304
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1136V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  GABRG3 MUTATED       3                         0
  GABRG3 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  GABRG3 MUTATED                                           0     5
  GABRG3 WILD-TYPE                                         1   238
D1136V12, multiclass
                                           clus
vv                                          GABRG3 MUTATED GABRG3 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  5              238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1136V13, binary
                  cls
clus                 0   1
  GABRG3 MUTATED     0   7
  GABRG3 WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRG3 MUTATED      0    7
  GABRG3 WILD-TYPE    4  303
                        clus
vv                       GABRG3 MUTATED GABRG3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(1137) Variable = EPHA10 MUTATION ANALYSIS
D1137V1, survival
                  sevent
clus2                0   1
  EPHA10 MUTATED    12   2
  EPHA10 WILD-TYPE 218 137
  EPHA10 MUTATED EPHA10 WILD-TYPE 
              14              355 
  EPHA10 MUTATED EPHA10 WILD-TYPE 
               2              137 
$`EPHA10 MUTATED`
TCGA-B7-5816 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8591 TCGA-CG-4437 
       26.70        14.43        29.59        32.25        28.14         8.05 
TCGA-CG-5721 TCGA-CG-5733 TCGA-D7-A4YT TCGA-F1-6874 TCGA-HF-7132 TCGA-HU-8602 
        6.02        21.07        14.27        14.47        77.29        22.32 
TCGA-HU-A4G8 TCGA-VQ-A8P2 
       22.68        38.14 

$`EPHA10 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-D7-6518 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-F1-6875 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-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-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 

  EPHA10 MUTATED EPHA10 WILD-TYPE 
            6.02             0.00 
  EPHA10 MUTATED EPHA10 WILD-TYPE 
           77.29           122.30 
  EPHA10 MUTATED EPHA10 WILD-TYPE 
           22.50            14.04 
[1] "6.0 - 77.3 (22.5)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "3.8"
D1137V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  EPHA10 MUTATED         0        0        1        2         0         5
  EPHA10 WILD-TYPE       2       15       39       28        37        47
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPHA10 MUTATED           1          4          0          1        1
  EPHA10 WILD-TYPE         2         66         53         31       37
D1137V3, multiclass
            clus
vv           EPHA10 MUTATED EPHA10 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               0               37
  STAGE IIB               5               47
  STAGE III               1                2
  STAGE IIIA              4               66
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EPHA10 MUTATED     0   5   1   9
  EPHA10 WILD-TYPE  22  87 172  88
D1137V4, multiclass
    clus
vv   EPHA10 MUTATED EPHA10 WILD-TYPE
  T1              0               22
  T2              5               87
  T3              1              172
  T4              9               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
  EPHA10 MUTATED     6   7   1   2
  EPHA10 WILD-TYPE 112  97  76  75
D1137V5, multiclass
    clus
vv   EPHA10 MUTATED EPHA10 WILD-TYPE
  N0              6              112
  N1              7               97
  N2              1               76
  N3              2               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"
D1137V6, binary
                  cls
clus                 0   1
  EPHA10 MUTATED    17   0
  EPHA10 WILD-TYPE 329  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPHA10 MUTATED     17    0
  EPHA10 WILD-TYPE  329   29
   clus
vv  EPHA10 MUTATED EPHA10 WILD-TYPE
  0             17              329
  1              0               29
[1] 2 2
[1] FALSE
D1137V7, binary
                  cls
clus                 0   1
  EPHA10 MUTATED     9   8
  EPHA10 WILD-TYPE 136 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPHA10 MUTATED      9    8
  EPHA10 WILD-TYPE  136  240
        clus
vv       EPHA10 MUTATED EPHA10 WILD-TYPE
  FEMALE              9              136
  MALE                8              240
[1] 2 2
[1] FALSE
D1137V8, binary
                  cls
clus                 0   1
  EPHA10 MUTATED    12   2
  EPHA10 WILD-TYPE 280  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPHA10 MUTATED     12    2
  EPHA10 WILD-TYPE  280   57
     clus
vv    EPHA10 MUTATED EPHA10 WILD-TYPE
  NO              12              280
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  EPHA10 MUTATED                                          0
  EPHA10 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  EPHA10 MUTATED                                       3
  EPHA10 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPHA10 MUTATED                                                        6
  EPHA10 WILD-TYPE                                                    152
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  EPHA10 MUTATED                                                   2
  EPHA10 WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  EPHA10 MUTATED                                                                   5
  EPHA10 WILD-TYPE                                                                63
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  EPHA10 MUTATED                                                    0
  EPHA10 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  EPHA10 MUTATED                                                  1
  EPHA10 WILD-TYPE                                               60
D1137V9, multiclass
                                                                   clus
vv                                                                  EPHA10 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  EPHA10 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EPHA10 MUTATED    13   0   0   3
  EPHA10 WILD-TYPE 298  14  15  21
D1137V10, multiclass
    clus
vv   EPHA10 MUTATED EPHA10 WILD-TYPE
  R0             13              298
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1137V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  EPHA10 MUTATED       2                         0
  EPHA10 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  EPHA10 MUTATED                                           0    11
  EPHA10 WILD-TYPE                                         1   232
D1137V12, multiclass
                                           clus
vv                                          EPHA10 MUTATED EPHA10 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 11              232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1137V13, binary
                  cls
clus                 0   1
  EPHA10 MUTATED     0  12
  EPHA10 WILD-TYPE   4 298
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPHA10 MUTATED      0   12
  EPHA10 WILD-TYPE    4  298
                        clus
vv                       EPHA10 MUTATED EPHA10 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             12              298
[1] 2 2
[1] FALSE

Clustering(1138) Variable = SLC44A4 MUTATION ANALYSIS
D1138V1, survival
                   sevent
clus2                 0   1
  SLC44A4 MUTATED     9   4
  SLC44A4 WILD-TYPE 221 135
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
               13               356 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
                4               135 
$`SLC44A4 MUTATED`
TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-8078 TCGA-BR-A4J8 TCGA-CG-4465 
       11.01         6.97        30.90        29.59        13.51         9.01 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4GQ TCGA-IN-A7NR TCGA-KB-A6F7 TCGA-MX-A5UJ 
       22.32        22.82         0.10         6.51        63.62        19.73 
TCGA-R5-A7ZI 
       74.53 

$`SLC44A4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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-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-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 

  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
              0.1               0.0 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
            74.53            122.30 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
            19.73             14.22 
[1] "0.1 - 74.5 (19.7)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.5"
D1138V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SLC44A4 MUTATED         0        0        2        0         1         3
  SLC44A4 WILD-TYPE       2       15       38       30        36        49
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC44A4 MUTATED           0          2          1          1        3
  SLC44A4 WILD-TYPE         3         68         52         31       35
D1138V3, multiclass
            clus
vv           SLC44A4 MUTATED SLC44A4 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 2                38
  STAGE II                 0                30
  STAGE IIA                1                36
  STAGE IIB                3                49
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 3                35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC44A4 MUTATED     2   2   5   6
  SLC44A4 WILD-TYPE  20  90 168  91
D1138V4, multiclass
    clus
vv   SLC44A4 MUTATED SLC44A4 WILD-TYPE
  T1               2                20
  T2               2                90
  T3               5               168
  T4               6                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
  SLC44A4 MUTATED     4   3   2   3
  SLC44A4 WILD-TYPE 114 101  75  74
D1138V5, multiclass
    clus
vv   SLC44A4 MUTATED SLC44A4 WILD-TYPE
  N0               4               114
  N1               3               101
  N2               2                75
  N3               3                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"
D1138V6, binary
                   cls
clus                  0   1
  SLC44A4 MUTATED    11   3
  SLC44A4 WILD-TYPE 335  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED     11    3
  SLC44A4 WILD-TYPE  335   26
   clus
vv  SLC44A4 MUTATED SLC44A4 WILD-TYPE
  0              11               335
  1               3                26
[1] 2 2
[1] FALSE
D1138V7, binary
                   cls
clus                  0   1
  SLC44A4 MUTATED    11   4
  SLC44A4 WILD-TYPE 134 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED     11    4
  SLC44A4 WILD-TYPE  134  244
        clus
vv       SLC44A4 MUTATED SLC44A4 WILD-TYPE
  FEMALE              11               134
  MALE                 4               244
[1] 2 2
[1] FALSE
D1138V8, binary
                   cls
clus                  0   1
  SLC44A4 MUTATED    11   1
  SLC44A4 WILD-TYPE 281  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED     11    1
  SLC44A4 WILD-TYPE  281   58
     clus
vv    SLC44A4 MUTATED SLC44A4 WILD-TYPE
  NO               11               281
  YES               1                58
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SLC44A4 MUTATED                                          0
  SLC44A4 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SLC44A4 MUTATED                                       3
  SLC44A4 WILD-TYPE                                    67
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC44A4 MUTATED                                                        6
  SLC44A4 WILD-TYPE                                                    152
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SLC44A4 MUTATED                                                   0
  SLC44A4 WILD-TYPE                                                21
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SLC44A4 MUTATED                                                                   3
  SLC44A4 WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SLC44A4 MUTATED                                                    0
  SLC44A4 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SLC44A4 MUTATED                                                  3
  SLC44A4 WILD-TYPE                                               58
D1138V9, multiclass
                                                                   clus
vv                                                                  SLC44A4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  SLC44A4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          152
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC44A4 MUTATED    10   0   1   3
  SLC44A4 WILD-TYPE 301  14  14  21
D1138V10, multiclass
    clus
vv   SLC44A4 MUTATED SLC44A4 WILD-TYPE
  R0              10               301
  R1               0                14
  R2               1                14
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1138V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  SLC44A4 MUTATED       3                         0
  SLC44A4 WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SLC44A4 MUTATED                                           0     9
  SLC44A4 WILD-TYPE                                         1   234
D1138V12, multiclass
                                           clus
vv                                          SLC44A4 MUTATED SLC44A4 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1138V13, binary
                   cls
clus                  0   1
  SLC44A4 MUTATED     1  11
  SLC44A4 WILD-TYPE   3 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED      1   11
  SLC44A4 WILD-TYPE    3  299
                        clus
vv                       SLC44A4 MUTATED SLC44A4 WILD-TYPE
  HISPANIC OR LATINO                   1                 3
  NOT HISPANIC OR LATINO              11               299
[1] 2 2
[1] FALSE

Clustering(1139) Variable = PPL MUTATION ANALYSIS
D1139V1, survival
               sevent
clus2             0   1
  PPL MUTATED    13   3
  PPL WILD-TYPE 217 136
  PPL MUTATED PPL WILD-TYPE 
           16           353 
  PPL MUTATED PPL WILD-TYPE 
            3           136 
$`PPL MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-8372 TCGA-BR-8589 
       26.70        34.68        32.78        44.94        31.27        27.12 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5732 TCGA-D7-A6F2 
        6.58         6.02       105.07        28.96        69.04        15.65 
TCGA-HU-A4GT TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-VQ-A8P2 
        6.51        23.84        14.07        38.14 

$`PPL WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-5724 TCGA-CG-5725 
       36.00         1.02         0.99         0.99        12.03        15.02 
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-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-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 

  PPL MUTATED PPL WILD-TYPE 
         6.02          0.00 
  PPL MUTATED PPL WILD-TYPE 
       105.07        122.30 
  PPL MUTATED PPL WILD-TYPE 
        28.04         14.04 
[1] "6.0 - 105.1 (28.0)" "0.0 - 122.3 (14.0)"
[1] "hr=" "3.2"
D1139V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PPL MUTATED         0        1        2        1         5         2
  PPL WILD-TYPE       2       14       38       29        32        50
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPL MUTATED           0          2          1          1        2
  PPL WILD-TYPE         3         68         52         31       36
D1139V3, multiclass
            clus
vv           PPL MUTATED PPL WILD-TYPE
  STAGE I              0             2
  STAGE IA             1            14
  STAGE IB             2            38
  STAGE II             1            29
  STAGE IIA            5            32
  STAGE IIB            2            50
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           1            52
  STAGE IIIC           1            31
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  PPL MUTATED     3   4   5   6
  PPL WILD-TYPE  19  88 168  91
D1139V4, multiclass
    clus
vv   PPL MUTATED PPL WILD-TYPE
  T1           3            19
  T2           4            88
  T3           5           168
  T4           6            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
  PPL MUTATED     9   5   1   2
  PPL WILD-TYPE 109  99  76  75
D1139V5, multiclass
    clus
vv   PPL MUTATED PPL WILD-TYPE
  N0           9           109
  N1           5            99
  N2           1            76
  N3           2            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"
D1139V6, binary
               cls
clus              0   1
  PPL MUTATED    18   0
  PPL WILD-TYPE 328  29
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED     18    0
  PPL WILD-TYPE  328   29
   clus
vv  PPL MUTATED PPL WILD-TYPE
  0          18           328
  1           0            29
[1] 2 2
[1] FALSE
D1139V7, binary
               cls
clus              0   1
  PPL MUTATED     8  10
  PPL WILD-TYPE 137 238
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED      8   10
  PPL WILD-TYPE  137  238
        clus
vv       PPL MUTATED PPL WILD-TYPE
  FEMALE           8           137
  MALE            10           238
[1] 2 2
[1] FALSE
D1139V8, binary
               cls
clus              0   1
  PPL MUTATED    14   1
  PPL WILD-TYPE 278  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED     14    1
  PPL WILD-TYPE  278   58
     clus
vv    PPL MUTATED PPL WILD-TYPE
  NO           14           278
  YES           1            58
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PPL MUTATED                                          0
  PPL WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PPL MUTATED                                       2
  PPL WILD-TYPE                                    68
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPL MUTATED                                                        8
  PPL WILD-TYPE                                                    150
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PPL MUTATED                                                   1
  PPL WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PPL MUTATED                                                                   3
  PPL WILD-TYPE                                                                65
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PPL MUTATED                                                    0
  PPL WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PPL MUTATED                                                  4
  PPL WILD-TYPE                                               57
D1139V9, multiclass
                                                                   clus
vv                                                                  PPL MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            4
                                                                   clus
vv                                                                  PPL WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  PPL MUTATED    15   0   0   2
  PPL WILD-TYPE 296  14  15  22
D1139V10, multiclass
    clus
vv   PPL MUTATED PPL WILD-TYPE
  R0          15           296
  R1           0            14
  R2           0            15
  RX           2            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1139V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  PPL MUTATED       4                         0
  PPL WILD-TYPE    83                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PPL MUTATED                                           0    10
  PPL WILD-TYPE                                         1   233
D1139V12, multiclass
                                           clus
vv                                          PPL MUTATED PPL WILD-TYPE
  ASIAN                                               4            83
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                              10           233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1139V13, binary
               cls
clus              0   1
  PPL MUTATED     0  13
  PPL WILD-TYPE   4 297
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED      0   13
  PPL WILD-TYPE    4  297
                        clus
vv                       PPL MUTATED PPL WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          13           297
[1] 2 2
[1] FALSE

Clustering(1140) Variable = TMEM63A MUTATION ANALYSIS
D1140V1, survival
                   sevent
clus2                 0   1
  TMEM63A MUTATED     6   4
  TMEM63A WILD-TYPE 224 135
  TMEM63A MUTATED TMEM63A WILD-TYPE 
               10               359 
  TMEM63A MUTATED TMEM63A WILD-TYPE 
                4               135 
$`TMEM63A MUTATED`
TCGA-BR-8078 TCGA-BR-8382 TCGA-BR-8591 TCGA-CD-8536 TCGA-CG-4305 TCGA-CG-5723 
       29.59        25.05        28.14        12.43        15.95       105.07 
TCGA-CG-5733 TCGA-HU-A4GQ TCGA-VQ-A8P2 TCGA-VQ-AA64 
       21.07         0.10        38.14        18.41 

$`TMEM63A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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 

  TMEM63A MUTATED TMEM63A WILD-TYPE 
              0.1               0.0 
  TMEM63A MUTATED TMEM63A WILD-TYPE 
           105.07            122.30 
  TMEM63A MUTATED TMEM63A WILD-TYPE 
            23.06             14.07 
[1] "0.1 - 105.1 (23.1)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.3"
D1140V2, 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       2       15       40       27        37        50
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM63A MUTATED           0          2          1          3        1
  TMEM63A WILD-TYPE         3         68         52         29       37
D1140V3, multiclass
            clus
vv           TMEM63A MUTATED TMEM63A WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 0                40
  STAGE II                 3                27
  STAGE IIA                0                37
  STAGE IIB                2                50
  STAGE III                0                 3
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               3                29
  STAGE IV                 1                37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM63A MUTATED     0   3   2   7
  TMEM63A WILD-TYPE  22  89 171  90
D1140V4, multiclass
    clus
vv   TMEM63A MUTATED TMEM63A WILD-TYPE
  T1               0                22
  T2               3                89
  T3               2               171
  T4               7                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
  TMEM63A MUTATED     3   4   4   2
  TMEM63A WILD-TYPE 115 100  73  75
D1140V5, multiclass
    clus
vv   TMEM63A MUTATED TMEM63A WILD-TYPE
  N0               3               115
  N1               4               100
  N2               4                73
  N3               2                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"
D1140V6, binary
                   cls
clus                  0   1
  TMEM63A MUTATED    13   0
  TMEM63A WILD-TYPE 333  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM63A MUTATED     13    0
  TMEM63A WILD-TYPE  333   29
   clus
vv  TMEM63A MUTATED TMEM63A WILD-TYPE
  0              13               333
  1               0                29
[1] 2 2
[1] FALSE
D1140V7, binary
                   cls
clus                  0   1
  TMEM63A MUTATED     5   8
  TMEM63A WILD-TYPE 140 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM63A MUTATED      5    8
  TMEM63A WILD-TYPE  140  240
        clus
vv       TMEM63A MUTATED TMEM63A WILD-TYPE
  FEMALE               5               140
  MALE                 8               240
[1] 2 2
[1] FALSE
D1140V8, binary
                   cls
clus                  0   1
  TMEM63A MUTATED     9   2
  TMEM63A WILD-TYPE 283  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM63A MUTATED      9    2
  TMEM63A WILD-TYPE  283   57
     clus
vv    TMEM63A MUTATED TMEM63A WILD-TYPE
  NO                9               283
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TMEM63A MUTATED                                          0
  TMEM63A WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TMEM63A MUTATED                                       0
  TMEM63A WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM63A MUTATED                                                        8
  TMEM63A WILD-TYPE                                                    150
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TMEM63A MUTATED                                                   1
  TMEM63A WILD-TYPE                                                20
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMEM63A MUTATED                                                                   3
  TMEM63A WILD-TYPE                                                                65
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TMEM63A MUTATED                                                    0
  TMEM63A WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TMEM63A MUTATED                                                  1
  TMEM63A WILD-TYPE                                               60
D1140V9, multiclass
                                                                   clus
vv                                                                  TMEM63A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                1
                                                                   clus
vv                                                                  TMEM63A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM63A MUTATED    11   0   0   2
  TMEM63A WILD-TYPE 300  14  15  22
D1140V10, multiclass
    clus
vv   TMEM63A MUTATED TMEM63A WILD-TYPE
  R0              11               300
  R1               0                14
  R2               0                15
  RX               2                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1140V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  TMEM63A MUTATED       2                         0
  TMEM63A WILD-TYPE    85                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMEM63A MUTATED                                           0     8
  TMEM63A WILD-TYPE                                         1   235
D1140V12, multiclass
                                           clus
vv                                          TMEM63A MUTATED TMEM63A WILD-TYPE
  ASIAN                                                   2                85
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   8               235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1140V13, binary
                   cls
clus                  0   1
  TMEM63A MUTATED     0   8
  TMEM63A WILD-TYPE   4 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM63A MUTATED      0    8
  TMEM63A WILD-TYPE    4  302
                        clus
vv                       TMEM63A MUTATED TMEM63A WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               302
[1] 2 2
[1] FALSE

Clustering(1141) Variable = ANKRD42 MUTATION ANALYSIS
D1141V1, survival
                   sevent
clus2                 0   1
  ANKRD42 MUTATED     4   3
  ANKRD42 WILD-TYPE 226 136
  ANKRD42 MUTATED ANKRD42 WILD-TYPE 
                7               362 
  ANKRD42 MUTATED ANKRD42 WILD-TYPE 
                3               136 
$`ANKRD42 MUTATED`
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-8680 TCGA-BR-8686 TCGA-HF-A5NB TCGA-HU-A4H8 
        6.97         6.61        31.96        20.88        30.51        14.07 
TCGA-VQ-A8P2 
       38.14 

$`ANKRD42 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  ANKRD42 MUTATED ANKRD42 WILD-TYPE 
             6.61              0.00 
  ANKRD42 MUTATED ANKRD42 WILD-TYPE 
            38.14            122.30 
  ANKRD42 MUTATED ANKRD42 WILD-TYPE 
            20.88             14.22 
[1] "6.6 - 38.1 (20.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D1141V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ANKRD42 MUTATED         0        0        1        0         0         0
  ANKRD42 WILD-TYPE       2       15       39       30        37        52
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD42 MUTATED           1          2          1          1        2
  ANKRD42 WILD-TYPE         2         68         52         31       36
D1141V3, multiclass
            clus
vv           ANKRD42 MUTATED ANKRD42 WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                15
  STAGE IB                 1                39
  STAGE II                 0                30
  STAGE IIA                0                37
  STAGE IIB                0                52
  STAGE III                1                 2
  STAGE IIIA               2                68
  STAGE IIIB               1                52
  STAGE IIIC               1                31
  STAGE IV                 2                36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD42 MUTATED     1   1   1   5
  ANKRD42 WILD-TYPE  21  91 172  92
D1141V4, multiclass
    clus
vv   ANKRD42 MUTATED ANKRD42 WILD-TYPE
  T1               1                21
  T2               1                91
  T3               1               172
  T4               5                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
  ANKRD42 MUTATED     0   5   2   1
  ANKRD42 WILD-TYPE 118  99  75  76
D1141V5, multiclass
    clus
vv   ANKRD42 MUTATED ANKRD42 WILD-TYPE
  N0               0               118
  N1               5                99
  N2               2                75
  N3               1                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"
D1141V6, binary
                   cls
clus                  0   1
  ANKRD42 MUTATED     6   1
  ANKRD42 WILD-TYPE 340  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD42 MUTATED      6    1
  ANKRD42 WILD-TYPE  340   28
   clus
vv  ANKRD42 MUTATED ANKRD42 WILD-TYPE
  0               6               340
  1               1                28
[1] 2 2
[1] FALSE
D1141V7, binary
                   cls
clus                  0   1
  ANKRD42 MUTATED     3   5
  ANKRD42 WILD-TYPE 142 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD42 MUTATED      3    5
  ANKRD42 WILD-TYPE  142  243
        clus
vv       ANKRD42 MUTATED ANKRD42 WILD-TYPE
  FEMALE               3               142
  MALE                 5               243
[1] 2 2
[1] FALSE
D1141V8, binary
                   cls
clus                  0   1
  ANKRD42 MUTATED     5   2
  ANKRD42 WILD-TYPE 287  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD42 MUTATED      5    2
  ANKRD42 WILD-TYPE  287   57
     clus
vv    ANKRD42 MUTATED ANKRD42 WILD-TYPE
  NO                5               287
  YES               2                57
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ANKRD42 MUTATED                                          0
  ANKRD42 WILD-TYPE                                        8
                   vv
clus                STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ANKRD42 MUTATED                                       0
  ANKRD42 WILD-TYPE                                    70
                   vv
clus                STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANKRD42 MUTATED                                                        3
  ANKRD42 WILD-TYPE                                                    155
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ANKRD42 MUTATED                                                   2
  ANKRD42 WILD-TYPE                                                19
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ANKRD42 MUTATED                                                                   0
  ANKRD42 WILD-TYPE                                                                68
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ANKRD42 MUTATED                                                    0
  ANKRD42 WILD-TYPE                                                  5
                   vv
clus                STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ANKRD42 MUTATED                                                  3
  ANKRD42 WILD-TYPE                                               58
D1141V9, multiclass
                                                                   clus
vv                                                                  ANKRD42 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                3
                                                                   clus
vv                                                                  ANKRD42 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                          8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ANKRD42 MUTATED     4   1   0   3
  ANKRD42 WILD-TYPE 307  13  15  21
D1141V10, multiclass
    clus
vv   ANKRD42 MUTATED ANKRD42 WILD-TYPE
  R0               4               307
  R1               1                13
  R2               0                15
  RX               3                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1141V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  ANKRD42 MUTATED       3                         0
  ANKRD42 WILD-TYPE    84                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ANKRD42 MUTATED                                           0     4
  ANKRD42 WILD-TYPE                                         1   239
D1141V12, multiclass
                                           clus
vv                                          ANKRD42 MUTATED ANKRD42 WILD-TYPE
  ASIAN                                                   3                84
  BLACK OR AFRICAN AMERICAN                               0                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1141V13, binary
                   cls
clus                  0   1
  ANKRD42 MUTATED     0   6
  ANKRD42 WILD-TYPE   4 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD42 MUTATED      0    6
  ANKRD42 WILD-TYPE    4  304
                        clus
vv                       ANKRD42 MUTATED ANKRD42 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               304
[1] 2 2
[1] FALSE

Clustering(1142) Variable = AVPR1A MUTATION ANALYSIS
D1142V1, survival
                  sevent
clus2                0   1
  AVPR1A MUTATED     8   6
  AVPR1A WILD-TYPE 222 133
  AVPR1A MUTATED AVPR1A WILD-TYPE 
              14              355 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
               6              133 
$`AVPR1A MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8591 TCGA-BR-A4QL 
       21.99         6.97        30.90        44.94        28.14        16.14 
TCGA-CD-A4MG TCGA-CG-5721 TCGA-EQ-8122 TCGA-HF-7132 TCGA-HU-A4GQ TCGA-IN-A7NR 
        6.58         6.02         7.99        77.29         0.10         6.51 
TCGA-VQ-A8P2 TCGA-VQ-AA6J 
       38.14        27.55 

$`AVPR1A WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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-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-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-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 
       12.59        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-AA6K 
       38.93        32.94        54.12        26.04        16.14        12.43 
TCGA-ZA-A8F6 
       17.26 

  AVPR1A MUTATED AVPR1A WILD-TYPE 
             0.1              0.0 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
           77.29           122.30 
  AVPR1A MUTATED AVPR1A WILD-TYPE 
          19.065           14.170 
[1] "0.1 - 77.3 (19.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1"  
D1142V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AVPR1A MUTATED         1        0        0        1         2         1
  AVPR1A WILD-TYPE       1       15       40       29        35        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AVPR1A MUTATED           0          3          2          2        3
  AVPR1A WILD-TYPE         3         67         51         30       35
D1142V3, multiclass
            clus
vv           AVPR1A MUTATED AVPR1A WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              2               51
  STAGE IIIC              2               30
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AVPR1A MUTATED     1   1   7   6
  AVPR1A WILD-TYPE  21  91 166  91
D1142V4, multiclass
    clus
vv   AVPR1A MUTATED AVPR1A WILD-TYPE
  T1              1               21
  T2              1               91
  T3              7              166
  T4              6               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
  AVPR1A MUTATED     2   7   3   3
  AVPR1A WILD-TYPE 116  97  74  74
D1142V5, multiclass
    clus
vv   AVPR1A MUTATED AVPR1A WILD-TYPE
  N0              2              116
  N1              7               97
  N2              3               74
  N3              3               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"
D1142V6, binary
                  cls
clus                 0   1
  AVPR1A MUTATED    10   2
  AVPR1A WILD-TYPE 336  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AVPR1A MUTATED     10    2
  AVPR1A WILD-TYPE  336   27
   clus
vv  AVPR1A MUTATED AVPR1A WILD-TYPE
  0             10              336
  1              2               27
[1] 2 2
[1] FALSE
D1142V7, binary
                  cls
clus                 0   1
  AVPR1A MUTATED     5  10
  AVPR1A WILD-TYPE 140 238
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AVPR1A MUTATED      5   10
  AVPR1A WILD-TYPE  140  238
        clus
vv       AVPR1A MUTATED AVPR1A WILD-TYPE
  FEMALE              5              140
  MALE               10              238
[1] 2 2
[1] FALSE
D1142V8, binary
                  cls
clus                 0   1
  AVPR1A MUTATED    12   3
  AVPR1A WILD-TYPE 280  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AVPR1A MUTATED     12    3
  AVPR1A WILD-TYPE  280   56
     clus
vv    AVPR1A MUTATED AVPR1A WILD-TYPE
  NO              12              280
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AVPR1A MUTATED                                          0
  AVPR1A WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AVPR1A MUTATED                                       1
  AVPR1A WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AVPR1A MUTATED                                                        7
  AVPR1A WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AVPR1A MUTATED                                                   2
  AVPR1A WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AVPR1A MUTATED                                                                   4
  AVPR1A WILD-TYPE                                                                64
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AVPR1A MUTATED                                                    0
  AVPR1A WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AVPR1A MUTATED                                                  1
  AVPR1A WILD-TYPE                                               60
D1142V9, multiclass
                                                                   clus
vv                                                                  AVPR1A MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  AVPR1A WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  AVPR1A MUTATED    11   0   1   1
  AVPR1A WILD-TYPE 300  14  14  23
D1142V10, multiclass
    clus
vv   AVPR1A MUTATED AVPR1A WILD-TYPE
  R0             11              300
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1142V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  AVPR1A MUTATED       2                         2
  AVPR1A WILD-TYPE    85                         7
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AVPR1A MUTATED                                           0     8
  AVPR1A WILD-TYPE                                         1   235
D1142V12, multiclass
                                           clus
vv                                          AVPR1A MUTATED AVPR1A WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              2                7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1142V13, binary
                  cls
clus                 0   1
  AVPR1A MUTATED     0  10
  AVPR1A WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AVPR1A MUTATED      0   10
  AVPR1A WILD-TYPE    4  300
                        clus
vv                       AVPR1A MUTATED AVPR1A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(1143) Variable = VILL MUTATION ANALYSIS
D1143V1, survival
                sevent
clus2              0   1
  VILL MUTATED     8   2
  VILL WILD-TYPE 222 137
  VILL MUTATED VILL WILD-TYPE 
            10            359 
  VILL MUTATED VILL WILD-TYPE 
             2            137 
$`VILL MUTATED`
TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-8078 TCGA-BR-8286 TCGA-BR-8363 TCGA-BR-8382 
       34.68        36.16        29.59        29.42         0.26        25.05 
TCGA-BR-A4PD TCGA-CG-4305 TCGA-CG-5721 TCGA-CG-5728 
       20.65        15.95         6.02        65.10 

$`VILL WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  VILL MUTATED VILL WILD-TYPE 
          0.26           0.00 
  VILL MUTATED VILL WILD-TYPE 
          65.1          122.3 
  VILL MUTATED VILL WILD-TYPE 
        27.235         14.070 
[1] "0.3 - 65.1 (27.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.6"
D1143V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  VILL MUTATED         0        1        2        2         1         2
  VILL WILD-TYPE       2       14       38       28        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VILL MUTATED           0          1          0          1        1
  VILL WILD-TYPE         3         69         53         31       37
D1143V3, multiclass
            clus
vv           VILL MUTATED VILL WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              2             38
  STAGE II              2             28
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  VILL MUTATED     1   3   2   5
  VILL WILD-TYPE  21  89 171  92
D1143V4, multiclass
    clus
vv   VILL MUTATED VILL WILD-TYPE
  T1            1             21
  T2            3             89
  T3            2            171
  T4            5             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
  VILL MUTATED     8   2   0   1
  VILL WILD-TYPE 110 102  77  76
D1143V5, multiclass
    clus
vv   VILL MUTATED VILL WILD-TYPE
  N0            8            110
  N1            2            102
  N2            0             77
  N3            1             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"
D1143V6, binary
                cls
clus               0   1
  VILL MUTATED    11   0
  VILL WILD-TYPE 335  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  VILL MUTATED     11    0
  VILL WILD-TYPE  335   29
   clus
vv  VILL MUTATED VILL WILD-TYPE
  0           11            335
  1            0             29
[1] 2 2
[1] FALSE
D1143V7, binary
                cls
clus               0   1
  VILL MUTATED     7   4
  VILL WILD-TYPE 138 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  VILL MUTATED      7    4
  VILL WILD-TYPE  138  244
        clus
vv       VILL MUTATED VILL WILD-TYPE
  FEMALE            7            138
  MALE              4            244
[1] 2 2
[1] FALSE
D1143V8, binary
                cls
clus               0   1
  VILL MUTATED     9   0
  VILL WILD-TYPE 283  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  VILL MUTATED      9    0
  VILL WILD-TYPE  283   59
     clus
vv    VILL MUTATED VILL WILD-TYPE
  NO             9            283
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  VILL MUTATED                                          0
  VILL WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  VILL MUTATED                                       0
  VILL WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  VILL MUTATED                                                        8
  VILL WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  VILL MUTATED                                                   0
  VILL WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  VILL MUTATED                                                                   2
  VILL WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  VILL MUTATED                                                    1
  VILL WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  VILL MUTATED                                                  0
  VILL WILD-TYPE                                               61
D1143V9, multiclass
                                                                   clus
vv                                                                  VILL MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  VILL WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  VILL MUTATED    10   0   0   1
  VILL WILD-TYPE 301  14  15  23
D1143V10, multiclass
    clus
vv   VILL MUTATED VILL WILD-TYPE
  R0           10            301
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1143V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  VILL MUTATED       0                         0
  VILL WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  VILL MUTATED                                           0     8
  VILL WILD-TYPE                                         1   235
D1143V12, multiclass
                                           clus
vv                                          VILL MUTATED VILL WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                8            235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1143V13, binary
                cls
clus               0   1
  VILL MUTATED     0   8
  VILL WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  VILL MUTATED      0    8
  VILL WILD-TYPE    4  302
                        clus
vv                       VILL MUTATED VILL WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(1144) Variable = ARRDC5 MUTATION ANALYSIS
D1144V1, survival
                  sevent
clus2                0   1
  ARRDC5 MUTATED     1   2
  ARRDC5 WILD-TYPE 229 137
  ARRDC5 MUTATED ARRDC5 WILD-TYPE 
               3              366 
  ARRDC5 MUTATED ARRDC5 WILD-TYPE 
               2              137 
$`ARRDC5 MUTATED`
TCGA-BR-6706 TCGA-HU-A4GQ TCGA-VQ-A8P2 
       18.05         0.10        38.14 

$`ARRDC5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  ARRDC5 MUTATED ARRDC5 WILD-TYPE 
             0.1              0.0 
  ARRDC5 MUTATED ARRDC5 WILD-TYPE 
           38.14           122.30 
  ARRDC5 MUTATED ARRDC5 WILD-TYPE 
           18.05            14.22 
[1] "0.1 - 38.1 (18.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.8"
D1144V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ARRDC5 MUTATED         0        0        0        0         0         0
  ARRDC5 WILD-TYPE       2       15       40       30        37        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARRDC5 MUTATED           0          2          0          1        0
  ARRDC5 WILD-TYPE         3         68         53         31       38
D1144V3, multiclass
            clus
vv           ARRDC5 MUTATED ARRDC5 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               0               37
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARRDC5 MUTATED     0   0   1   2
  ARRDC5 WILD-TYPE  22  92 172  95
D1144V4, multiclass
    clus
vv   ARRDC5 MUTATED ARRDC5 WILD-TYPE
  T1              0               22
  T2              0               92
  T3              1              172
  T4              2               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
  ARRDC5 MUTATED     0   2   1   0
  ARRDC5 WILD-TYPE 118 102  76  77
D1144V5, multiclass
    clus
vv   ARRDC5 MUTATED ARRDC5 WILD-TYPE
  N0              0              118
  N1              2              102
  N2              1               76
  N3              0               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"
D1144V6, binary
                  cls
clus                 0   1
  ARRDC5 MUTATED     4   0
  ARRDC5 WILD-TYPE 342  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARRDC5 MUTATED      4    0
  ARRDC5 WILD-TYPE  342   29
   clus
vv  ARRDC5 MUTATED ARRDC5 WILD-TYPE
  0              4              342
  1              0               29
[1] 2 2
[1] FALSE
D1144V7, binary
                  cls
clus                 0   1
  ARRDC5 MUTATED     1   3
  ARRDC5 WILD-TYPE 144 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARRDC5 MUTATED      1    3
  ARRDC5 WILD-TYPE  144  245
        clus
vv       ARRDC5 MUTATED ARRDC5 WILD-TYPE
  FEMALE              1              144
  MALE                3              245
[1] 2 2
[1] FALSE
D1144V8, binary
                  cls
clus                 0   1
  ARRDC5 MUTATED     2   1
  ARRDC5 WILD-TYPE 290  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARRDC5 MUTATED      2    1
  ARRDC5 WILD-TYPE  290   58
     clus
vv    ARRDC5 MUTATED ARRDC5 WILD-TYPE
  NO               2              290
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ARRDC5 MUTATED                                          0
  ARRDC5 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ARRDC5 MUTATED                                       0
  ARRDC5 WILD-TYPE                                    70
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARRDC5 MUTATED                                                        2
  ARRDC5 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ARRDC5 MUTATED                                                   1
  ARRDC5 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ARRDC5 MUTATED                                                                   0
  ARRDC5 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ARRDC5 MUTATED                                                    0
  ARRDC5 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ARRDC5 MUTATED                                                  1
  ARRDC5 WILD-TYPE                                               60
D1144V9, multiclass
                                                                   clus
vv                                                                  ARRDC5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  ARRDC5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARRDC5 MUTATED     3   0   0   1
  ARRDC5 WILD-TYPE 308  14  15  23
D1144V10, multiclass
    clus
vv   ARRDC5 MUTATED ARRDC5 WILD-TYPE
  R0              3              308
  R1              0               14
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1144V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  ARRDC5 MUTATED       1                         0
  ARRDC5 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ARRDC5 MUTATED                                           0     3
  ARRDC5 WILD-TYPE                                         1   240
D1144V12, multiclass
                                           clus
vv                                          ARRDC5 MUTATED ARRDC5 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1144V13, binary
                  cls
clus                 0   1
  ARRDC5 MUTATED     0   3
  ARRDC5 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARRDC5 MUTATED      0    3
  ARRDC5 WILD-TYPE    4  307
                        clus
vv                       ARRDC5 MUTATED ARRDC5 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(1145) Variable = P2RY12 MUTATION ANALYSIS
D1145V1, survival
                  sevent
clus2                0   1
  P2RY12 MUTATED     4   4
  P2RY12 WILD-TYPE 226 135
  P2RY12 MUTATED P2RY12 WILD-TYPE 
               8              361 
  P2RY12 MUTATED P2RY12 WILD-TYPE 
               4              135 
$`P2RY12 MUTATED`
TCGA-BR-4253 TCGA-BR-6452 TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-5724 TCGA-CG-5733 
        4.08        34.68         6.58        15.95        12.03        21.07 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       38.14        37.22 

$`P2RY12 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        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-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-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 

  P2RY12 MUTATED P2RY12 WILD-TYPE 
            4.08             0.00 
  P2RY12 MUTATED P2RY12 WILD-TYPE 
           38.14           122.30 
  P2RY12 MUTATED P2RY12 WILD-TYPE 
           18.51            14.17 
[1] "4.1 - 38.1 (18.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D1145V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  P2RY12 MUTATED         0        0        1        1         2         0
  P2RY12 WILD-TYPE       2       15       39       29        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  P2RY12 MUTATED           0          4          0          0        1
  P2RY12 WILD-TYPE         3         66         53         32       37
D1145V3, multiclass
            clus
vv           P2RY12 MUTATED P2RY12 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              4               66
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  P2RY12 MUTATED     0   3   4   2
  P2RY12 WILD-TYPE  22  89 169  95
D1145V4, multiclass
    clus
vv   P2RY12 MUTATED P2RY12 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              4              169
  T4              2               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
  P2RY12 MUTATED     3   4   1   1
  P2RY12 WILD-TYPE 115 100  76  76
D1145V5, multiclass
    clus
vv   P2RY12 MUTATED P2RY12 WILD-TYPE
  N0              3              115
  N1              4              100
  N2              1               76
  N3              1               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"
D1145V6, binary
                  cls
clus                 0   1
  P2RY12 MUTATED     8   1
  P2RY12 WILD-TYPE 338  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY12 MUTATED      8    1
  P2RY12 WILD-TYPE  338   28
   clus
vv  P2RY12 MUTATED P2RY12 WILD-TYPE
  0              8              338
  1              1               28
[1] 2 2
[1] FALSE
D1145V7, binary
                  cls
clus                 0   1
  P2RY12 MUTATED     3   6
  P2RY12 WILD-TYPE 142 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY12 MUTATED      3    6
  P2RY12 WILD-TYPE  142  242
        clus
vv       P2RY12 MUTATED P2RY12 WILD-TYPE
  FEMALE              3              142
  MALE                6              242
[1] 2 2
[1] FALSE
D1145V8, binary
                  cls
clus                 0   1
  P2RY12 MUTATED     6   2
  P2RY12 WILD-TYPE 286  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY12 MUTATED      6    2
  P2RY12 WILD-TYPE  286   57
     clus
vv    P2RY12 MUTATED P2RY12 WILD-TYPE
  NO               6              286
  YES              2               57
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  P2RY12 MUTATED                                          0
  P2RY12 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  P2RY12 MUTATED                                       2
  P2RY12 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  P2RY12 MUTATED                                                        3
  P2RY12 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  P2RY12 MUTATED                                                   1
  P2RY12 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  P2RY12 MUTATED                                                                   2
  P2RY12 WILD-TYPE                                                                66
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  P2RY12 MUTATED                                                    0
  P2RY12 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  P2RY12 MUTATED                                                  1
  P2RY12 WILD-TYPE                                               60
D1145V9, multiclass
                                                                   clus
vv                                                                  P2RY12 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  P2RY12 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  P2RY12 MUTATED     6   0   1   1
  P2RY12 WILD-TYPE 305  14  14  23
D1145V10, multiclass
    clus
vv   P2RY12 MUTATED P2RY12 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              1               14
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1145V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  P2RY12 MUTATED       1                         0
  P2RY12 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  P2RY12 MUTATED                                           0     4
  P2RY12 WILD-TYPE                                         1   239
D1145V12, multiclass
                                           clus
vv                                          P2RY12 MUTATED P2RY12 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1145V13, binary
                  cls
clus                 0   1
  P2RY12 MUTATED     0   3
  P2RY12 WILD-TYPE   4 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY12 MUTATED      0    3
  P2RY12 WILD-TYPE    4  307
                        clus
vv                       P2RY12 MUTATED P2RY12 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              307
[1] 2 2
[1] FALSE

Clustering(1146) Variable = KIAA1217 MUTATION ANALYSIS
D1146V1, survival
                    sevent
clus2                  0   1
  KIAA1217 MUTATED    19   8
  KIAA1217 WILD-TYPE 211 131
  KIAA1217 MUTATED KIAA1217 WILD-TYPE 
                27                342 
  KIAA1217 MUTATED KIAA1217 WILD-TYPE 
                 8                131 
$`KIAA1217 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-8372 
        6.97        34.68        32.78        35.24        35.84        31.27 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8687 TCGA-BR-A4CQ TCGA-CD-8527 TCGA-CD-A4MI 
       28.14         7.53         8.22        34.98         7.17        11.77 
TCGA-CG-4306 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-A4YY TCGA-FP-A4BE TCGA-FP-A4BF 
        1.02       105.07        65.10        13.78        11.08         5.52 
TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GT TCGA-HU-A4GU TCGA-IN-A6RS TCGA-R5-A7ZE 
       26.47        22.32         6.51         6.58        12.59        18.21 
TCGA-R5-A7ZI TCGA-VQ-A8P2 TCGA-VQ-AA6A 
       74.53        38.14        38.93 

$`KIAA1217 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-7715 TCGA-BR-7716 
       44.94        21.90         9.21        36.16        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-8677 TCGA-BR-8678 TCGA-BR-8680 
       27.12         9.34         6.28        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-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-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-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-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-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-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-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-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-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-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-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-AA6B 
       66.81        11.24        18.41        43.66        28.41        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 

  KIAA1217 MUTATED KIAA1217 WILD-TYPE 
              1.02               0.00 
  KIAA1217 MUTATED KIAA1217 WILD-TYPE 
            105.07             122.30 
  KIAA1217 MUTATED KIAA1217 WILD-TYPE 
             22.32              14.12 
[1] "1.0 - 105.1 (22.3)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.7"
D1146V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA1217 MUTATED         0        1        3        3         4         2
  KIAA1217 WILD-TYPE       2       14       37       27        33        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1217 MUTATED           0          6          2          4        2
  KIAA1217 WILD-TYPE         3         64         51         28       36
D1146V3, multiclass
            clus
vv           KIAA1217 MUTATED KIAA1217 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  3                 37
  STAGE II                  3                 27
  STAGE IIA                 4                 33
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                6                 64
  STAGE IIIB                2                 51
  STAGE IIIC                4                 28
  STAGE IV                  2                 36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1217 MUTATED     1   5  13   8
  KIAA1217 WILD-TYPE  21  87 160  89
D1146V4, multiclass
    clus
vv   KIAA1217 MUTATED KIAA1217 WILD-TYPE
  T1                1                 21
  T2                5                 87
  T3               13                160
  T4                8                 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
  KIAA1217 MUTATED    10   8   4   5
  KIAA1217 WILD-TYPE 108  96  73  72
D1146V5, multiclass
    clus
vv   KIAA1217 MUTATED KIAA1217 WILD-TYPE
  N0               10                108
  N1                8                 96
  N2                4                 73
  N3                5                 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"
D1146V6, binary
                    cls
clus                   0   1
  KIAA1217 MUTATED    23   2
  KIAA1217 WILD-TYPE 323  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1217 MUTATED     23    2
  KIAA1217 WILD-TYPE  323   27
   clus
vv  KIAA1217 MUTATED KIAA1217 WILD-TYPE
  0               23                323
  1                2                 27
[1] 2 2
[1] FALSE
D1146V7, binary
                    cls
clus                   0   1
  KIAA1217 MUTATED    12  15
  KIAA1217 WILD-TYPE 133 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1217 MUTATED     12   15
  KIAA1217 WILD-TYPE  133  233
        clus
vv       KIAA1217 MUTATED KIAA1217 WILD-TYPE
  FEMALE               12                133
  MALE                 15                233
[1] 2 2
[1] FALSE
D1146V8, binary
                    cls
clus                   0   1
  KIAA1217 MUTATED    21   4
  KIAA1217 WILD-TYPE 271  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1217 MUTATED     21    4
  KIAA1217 WILD-TYPE  271   55
     clus
vv    KIAA1217 MUTATED KIAA1217 WILD-TYPE
  NO                21                271
  YES                4                 55
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA1217 MUTATED                                          2
  KIAA1217 WILD-TYPE                                        6
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA1217 MUTATED                                       3
  KIAA1217 WILD-TYPE                                    67
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1217 MUTATED                                                       14
  KIAA1217 WILD-TYPE                                                    144
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA1217 MUTATED                                                   1
  KIAA1217 WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA1217 MUTATED                                                                   5
  KIAA1217 WILD-TYPE                                                                63
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA1217 MUTATED                                                    0
  KIAA1217 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA1217 MUTATED                                                  2
  KIAA1217 WILD-TYPE                                               59
D1146V9, multiclass
                                                                   clus
vv                                                                  KIAA1217 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                          14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 2
                                                                   clus
vv                                                                  KIAA1217 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1217 MUTATED    21   2   1   1
  KIAA1217 WILD-TYPE 290  12  14  23
D1146V10, multiclass
    clus
vv   KIAA1217 MUTATED KIAA1217 WILD-TYPE
  R0               21                290
  R1                2                 12
  R2                1                 14
  RX                1                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1146V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA1217 MUTATED       5                         1
  KIAA1217 WILD-TYPE    82                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA1217 MUTATED                                           0    18
  KIAA1217 WILD-TYPE                                         1   225
D1146V12, multiclass
                                           clus
vv                                          KIAA1217 MUTATED KIAA1217 WILD-TYPE
  ASIAN                                                    5                 82
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   18                225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1146V13, binary
                    cls
clus                   0   1
  KIAA1217 MUTATED     1  21
  KIAA1217 WILD-TYPE   3 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1217 MUTATED      1   21
  KIAA1217 WILD-TYPE    3  289
                        clus
vv                       KIAA1217 MUTATED KIAA1217 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO               21                289
[1] 2 2
[1] FALSE

Clustering(1147) Variable = MEPCE MUTATION ANALYSIS
D1147V1, survival
                 sevent
clus2               0   1
  MEPCE MUTATED     5   1
  MEPCE WILD-TYPE 225 138
  MEPCE MUTATED MEPCE WILD-TYPE 
              6             363 
  MEPCE MUTATED MEPCE WILD-TYPE 
              1             138 
$`MEPCE MUTATED`
TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-8078 TCGA-CD-A4MG TCGA-VQ-A8P2 
       34.68        44.94        36.16        29.59         6.58        38.14 

$`MEPCE WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  MEPCE MUTATED MEPCE WILD-TYPE 
           6.58            0.00 
  MEPCE MUTATED MEPCE WILD-TYPE 
          44.94          122.30 
  MEPCE MUTATED MEPCE WILD-TYPE 
          35.42           14.07 
[1] "6.6 - 44.9 (35.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.7"
D1147V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MEPCE MUTATED         1        1        0        0         3         1
  MEPCE WILD-TYPE       1       14       40       30        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MEPCE MUTATED           0          1          0          0        0
  MEPCE WILD-TYPE         3         69         53         32       38
D1147V3, multiclass
            clus
vv           MEPCE MUTATED MEPCE WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MEPCE MUTATED     2   0   3   2
  MEPCE WILD-TYPE  20  92 170  95
D1147V4, multiclass
    clus
vv   MEPCE MUTATED MEPCE WILD-TYPE
  T1             2              20
  T2             0              92
  T3             3             170
  T4             2              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
  MEPCE MUTATED     5   3   0   0
  MEPCE WILD-TYPE 113 101  77  77
D1147V5, multiclass
    clus
vv   MEPCE MUTATED MEPCE WILD-TYPE
  N0             5             113
  N1             3             101
  N2             0              77
  N3             0              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"
D1147V6, binary
                 cls
clus                0   1
  MEPCE MUTATED     7   0
  MEPCE WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEPCE MUTATED      7    0
  MEPCE WILD-TYPE  339   29
   clus
vv  MEPCE MUTATED MEPCE WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D1147V7, binary
                 cls
clus                0   1
  MEPCE MUTATED     4   4
  MEPCE WILD-TYPE 141 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEPCE MUTATED      4    4
  MEPCE WILD-TYPE  141  244
        clus
vv       MEPCE MUTATED MEPCE WILD-TYPE
  FEMALE             4             141
  MALE               4             244
[1] 2 2
[1] FALSE
D1147V8, binary
                 cls
clus                0   1
  MEPCE MUTATED     6   1
  MEPCE WILD-TYPE 286  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEPCE MUTATED      6    1
  MEPCE WILD-TYPE  286   58
     clus
vv    MEPCE MUTATED MEPCE WILD-TYPE
  NO              6             286
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MEPCE MUTATED                                          0
  MEPCE WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MEPCE MUTATED                                       1
  MEPCE WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MEPCE MUTATED                                                        5
  MEPCE WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MEPCE MUTATED                                                   1
  MEPCE WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MEPCE MUTATED                                                                   0
  MEPCE WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MEPCE MUTATED                                                    1
  MEPCE WILD-TYPE                                                  4
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MEPCE MUTATED                                                  0
  MEPCE WILD-TYPE                                               61
D1147V9, multiclass
                                                                   clus
vv                                                                  MEPCE MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  MEPCE WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MEPCE MUTATED     6   0   0   1
  MEPCE WILD-TYPE 305  14  15  23
D1147V10, multiclass
    clus
vv   MEPCE MUTATED MEPCE WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1147V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MEPCE MUTATED       1                         1
  MEPCE WILD-TYPE    86                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MEPCE MUTATED                                           0     6
  MEPCE WILD-TYPE                                         1   237
D1147V12, multiclass
                                           clus
vv                                          MEPCE MUTATED MEPCE WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1147V13, binary
                 cls
clus                0   1
  MEPCE MUTATED     0   7
  MEPCE WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEPCE MUTATED      0    7
  MEPCE WILD-TYPE    4  303
                        clus
vv                       MEPCE MUTATED MEPCE WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(1148) Variable = TRIM27 MUTATION ANALYSIS
D1148V1, survival
                  sevent
clus2                0   1
  TRIM27 MUTATED     4   0
  TRIM27 WILD-TYPE 226 139
  TRIM27 MUTATED TRIM27 WILD-TYPE 
               4              365 
  TRIM27 MUTATED TRIM27 WILD-TYPE 
               0              139 
$`TRIM27 MUTATED`
TCGA-B7-5816 TCGA-BR-7707 TCGA-CG-4305 TCGA-F1-6874 
       26.70        35.84        15.95        14.47 

$`TRIM27 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-F1-6875 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-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 

  TRIM27 MUTATED TRIM27 WILD-TYPE 
           14.47             0.00 
  TRIM27 MUTATED TRIM27 WILD-TYPE 
           35.84           122.30 
  TRIM27 MUTATED TRIM27 WILD-TYPE 
          21.325           14.070 
[1] "14.5 - 35.8 (21.3)" "0.0 - 122.3 (14.1)"
[1] "hr="     "9100000"
D1148V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIM27 MUTATED         1        0        2        1         0         1
  TRIM27 WILD-TYPE       1       15       38       29        37        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM27 MUTATED           0          0          0          0        0
  TRIM27 WILD-TYPE         3         70         53         32       38
D1148V3, multiclass
            clus
vv           TRIM27 MUTATED TRIM27 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               0               37
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              0               70
  STAGE IIIB              0               53
  STAGE IIIC              0               32
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM27 MUTATED     1   3   0   1
  TRIM27 WILD-TYPE  21  89 173  96
D1148V4, multiclass
    clus
vv   TRIM27 MUTATED TRIM27 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              0              173
  T4              1               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
  TRIM27 MUTATED     3   2   0   0
  TRIM27 WILD-TYPE 115 102  77  77
D1148V5, multiclass
    clus
vv   TRIM27 MUTATED TRIM27 WILD-TYPE
  N0              3              115
  N1              2              102
  N2              0               77
  N3              0               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"
D1148V6, binary
                  cls
clus                 0   1
  TRIM27 MUTATED     4   0
  TRIM27 WILD-TYPE 342  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM27 MUTATED      4    0
  TRIM27 WILD-TYPE  342   29
   clus
vv  TRIM27 MUTATED TRIM27 WILD-TYPE
  0              4              342
  1              0               29
[1] 2 2
[1] FALSE
D1148V7, binary
                  cls
clus                 0   1
  TRIM27 MUTATED     2   3
  TRIM27 WILD-TYPE 143 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM27 MUTATED      2    3
  TRIM27 WILD-TYPE  143  245
        clus
vv       TRIM27 MUTATED TRIM27 WILD-TYPE
  FEMALE              2              143
  MALE                3              245
[1] 2 2
[1] FALSE
D1148V8, binary
                  cls
clus                 0   1
  TRIM27 MUTATED     5   0
  TRIM27 WILD-TYPE 287  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM27 MUTATED      5    0
  TRIM27 WILD-TYPE  287   59
     clus
vv    TRIM27 MUTATED TRIM27 WILD-TYPE
  NO               5              287
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TRIM27 MUTATED                                          0
  TRIM27 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TRIM27 MUTATED                                       1
  TRIM27 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRIM27 MUTATED                                                        3
  TRIM27 WILD-TYPE                                                    155
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TRIM27 MUTATED                                                   0
  TRIM27 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRIM27 MUTATED                                                                   1
  TRIM27 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TRIM27 MUTATED                                                    0
  TRIM27 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TRIM27 MUTATED                                                  0
  TRIM27 WILD-TYPE                                               61
D1148V9, multiclass
                                                                   clus
vv                                                                  TRIM27 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  TRIM27 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIM27 MUTATED     5   0   0   0
  TRIM27 WILD-TYPE 306  14  15  24
D1148V10, multiclass
    clus
vv   TRIM27 MUTATED TRIM27 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1148V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  TRIM27 MUTATED       0                         1
  TRIM27 WILD-TYPE    87                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRIM27 MUTATED                                           0     3
  TRIM27 WILD-TYPE                                         1   240
D1148V12, multiclass
                                           clus
vv                                          TRIM27 MUTATED TRIM27 WILD-TYPE
  ASIAN                                                  0               87
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  3              240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1148V13, binary
                  cls
clus                 0   1
  TRIM27 MUTATED     0   4
  TRIM27 WILD-TYPE   4 306
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM27 MUTATED      0    4
  TRIM27 WILD-TYPE    4  306
                        clus
vv                       TRIM27 MUTATED TRIM27 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              306
[1] 2 2
[1] FALSE

Clustering(1149) Variable = PTPN12 MUTATION ANALYSIS
D1149V1, survival
                  sevent
clus2                0   1
  PTPN12 MUTATED     8   2
  PTPN12 WILD-TYPE 222 137
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              10              359 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
               2              137 
$`PTPN12 MUTATED`
TCGA-BR-8368 TCGA-BR-8591 TCGA-BR-8680 TCGA-CG-5723 TCGA-D7-A4YY TCGA-D7-A6EY 
        4.31        28.14        31.96       105.07        13.78        11.44 
TCGA-EQ-5647 TCGA-HU-A4G3 TCGA-HU-A4GX TCGA-MX-A666 
        0.62         5.59        20.25        14.04 

$`PTPN12 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A4Z0 
       20.91        14.27        16.44         5.92        36.43        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-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-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-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZI 
        3.72        19.73        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 

  PTPN12 MUTATED PTPN12 WILD-TYPE 
            0.62             0.00 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
          105.07           122.30 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
           13.91            14.43 
[1] "0.6 - 105.1 (13.9)" "0.0 - 122.3 (14.4)"
[1] "hr=" "2"  
D1149V2, 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       2       15       39       29        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN12 MUTATED           0          1          2          2        2
  PTPN12 WILD-TYPE         3         69         51         30       36
D1149V3, multiclass
            clus
vv           PTPN12 MUTATED PTPN12 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              2               51
  STAGE IIIC              2               30
  STAGE IV                2               36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTPN12 MUTATED     0   4   2   5
  PTPN12 WILD-TYPE  22  88 171  92
D1149V4, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  T1              0               22
  T2              4               88
  T3              2              171
  T4              5               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
  PTPN12 MUTATED     2   1   3   4
  PTPN12 WILD-TYPE 116 103  74  73
D1149V5, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  N0              2              116
  N1              1              103
  N2              3               74
  N3              4               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"
D1149V6, binary
                  cls
clus                 0   1
  PTPN12 MUTATED     9   2
  PTPN12 WILD-TYPE 337  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED      9    2
  PTPN12 WILD-TYPE  337   27
   clus
vv  PTPN12 MUTATED PTPN12 WILD-TYPE
  0              9              337
  1              2               27
[1] 2 2
[1] FALSE
D1149V7, binary
                  cls
clus                 0   1
  PTPN12 MUTATED     5   7
  PTPN12 WILD-TYPE 140 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED      5    7
  PTPN12 WILD-TYPE  140  241
        clus
vv       PTPN12 MUTATED PTPN12 WILD-TYPE
  FEMALE              5              140
  MALE                7              241
[1] 2 2
[1] FALSE
D1149V8, binary
                  cls
clus                 0   1
  PTPN12 MUTATED     9   1
  PTPN12 WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED      9    1
  PTPN12 WILD-TYPE  283   58
     clus
vv    PTPN12 MUTATED PTPN12 WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PTPN12 MUTATED                                          0
  PTPN12 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PTPN12 MUTATED                                       1
  PTPN12 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTPN12 MUTATED                                                        8
  PTPN12 WILD-TYPE                                                    150
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PTPN12 MUTATED                                                   0
  PTPN12 WILD-TYPE                                                21
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTPN12 MUTATED                                                                   0
  PTPN12 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PTPN12 MUTATED                                                    0
  PTPN12 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PTPN12 MUTATED                                                  3
  PTPN12 WILD-TYPE                                               58
D1149V9, multiclass
                                                                   clus
vv                                                                  PTPN12 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               3
                                                                   clus
vv                                                                  PTPN12 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PTPN12 MUTATED     8   0   1   2
  PTPN12 WILD-TYPE 303  14  14  22
D1149V10, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  R0              8              303
  R1              0               14
  R2              1               14
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1149V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PTPN12 MUTATED       3                         0
  PTPN12 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPN12 MUTATED                                           0     8
  PTPN12 WILD-TYPE                                         1   235
D1149V12, multiclass
                                           clus
vv                                          PTPN12 MUTATED PTPN12 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1149V13, binary
                  cls
clus                 0   1
  PTPN12 MUTATED     0  11
  PTPN12 WILD-TYPE   4 299
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED      0   11
  PTPN12 WILD-TYPE    4  299
                        clus
vv                       PTPN12 MUTATED PTPN12 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              299
[1] 2 2
[1] FALSE

Clustering(1150) Variable = ITGAV MUTATION ANALYSIS
D1150V1, survival
                 sevent
clus2               0   1
  ITGAV MUTATED    13   3
  ITGAV WILD-TYPE 217 136
  ITGAV MUTATED ITGAV WILD-TYPE 
             16             353 
  ITGAV MUTATED ITGAV WILD-TYPE 
              3             136 
$`ITGAV MUTATED`
TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7722 TCGA-BR-8078 TCGA-BR-8487 TCGA-CG-4305 
       19.33         9.21        15.32        29.59         1.12        15.95 
TCGA-CG-5730 TCGA-D7-6528 TCGA-HU-8602 TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4H8 
        4.01        15.22        22.32        25.81         6.51        14.07 
TCGA-KB-A93J TCGA-VQ-A8P2 TCGA-VQ-AA6K TCGA-ZA-A8F6 
       36.95        38.14        12.43        17.26 

$`ITGAV WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
          38.14          122.30 
  ITGAV MUTATED ITGAV WILD-TYPE 
         15.635          14.070 
[1] "1.1 - 38.1 (15.6)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.1"
D1150V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ITGAV MUTATED         0        1        3        3         3         4
  ITGAV WILD-TYPE       2       14       37       27        34        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ITGAV MUTATED           0          1          0          1        2
  ITGAV WILD-TYPE         3         69         53         31       36
D1150V3, multiclass
            clus
vv           ITGAV MUTATED ITGAV WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               3              37
  STAGE II               3              27
  STAGE IIA              3              34
  STAGE IIB              4              48
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGAV MUTATED     2   5   6   5
  ITGAV WILD-TYPE  20  87 167  92
D1150V4, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  T1             2              20
  T2             5              87
  T3             6             167
  T4             5              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
  ITGAV MUTATED     9   7   1   1
  ITGAV WILD-TYPE 109  97  76  76
D1150V5, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  N0             9             109
  N1             7              97
  N2             1              76
  N3             1              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"
D1150V6, binary
                 cls
clus                0   1
  ITGAV MUTATED    16   1
  ITGAV WILD-TYPE 330  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED     16    1
  ITGAV WILD-TYPE  330   28
   clus
vv  ITGAV MUTATED ITGAV WILD-TYPE
  0            16             330
  1             1              28
[1] 2 2
[1] FALSE
D1150V7, binary
                 cls
clus                0   1
  ITGAV MUTATED     8  10
  ITGAV WILD-TYPE 137 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED      8   10
  ITGAV WILD-TYPE  137  238
        clus
vv       ITGAV MUTATED ITGAV WILD-TYPE
  FEMALE             8             137
  MALE              10             238
[1] 2 2
[1] FALSE
D1150V8, binary
                 cls
clus                0   1
  ITGAV MUTATED    12   4
  ITGAV WILD-TYPE 280  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED     12    4
  ITGAV WILD-TYPE  280   55
     clus
vv    ITGAV MUTATED ITGAV WILD-TYPE
  NO             12             280
  YES             4              55
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ITGAV MUTATED                                          1
  ITGAV WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ITGAV MUTATED                                       2
  ITGAV WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ITGAV MUTATED                                                        8
  ITGAV WILD-TYPE                                                    150
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ITGAV MUTATED                                                   1
  ITGAV WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ITGAV MUTATED                                                                   2
  ITGAV WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ITGAV MUTATED                                                    0
  ITGAV WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ITGAV MUTATED                                                  4
  ITGAV WILD-TYPE                                               57
D1150V9, multiclass
                                                                   clus
vv                                                                  ITGAV MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  ITGAV WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ITGAV MUTATED    15   1   1   1
  ITGAV WILD-TYPE 296  13  14  23
D1150V10, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  R0            15             296
  R1             1              13
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1150V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ITGAV MUTATED       5                         0
  ITGAV WILD-TYPE    82                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ITGAV MUTATED                                           0    11
  ITGAV WILD-TYPE                                         1   232
D1150V12, multiclass
                                           clus
vv                                          ITGAV MUTATED ITGAV WILD-TYPE
  ASIAN                                                 5              82
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                11             232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1150V13, binary
                 cls
clus                0   1
  ITGAV MUTATED     0  13
  ITGAV WILD-TYPE   4 297
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED      0   13
  ITGAV WILD-TYPE    4  297
                        clus
vv                       ITGAV MUTATED ITGAV WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            13             297
[1] 2 2
[1] FALSE

Clustering(1151) Variable = PATL1 MUTATION ANALYSIS
D1151V1, survival
                 sevent
clus2               0   1
  PATL1 MUTATED     4   2
  PATL1 WILD-TYPE 226 137
  PATL1 MUTATED PATL1 WILD-TYPE 
              6             363 
  PATL1 MUTATED PATL1 WILD-TYPE 
              2             137 
$`PATL1 MUTATED`
TCGA-BR-8589 TCGA-BR-A453 TCGA-CG-5721 TCGA-D7-A4YV TCGA-HU-A4GT TCGA-HU-A4H8 
       27.12         6.08         6.02         5.92         6.51        14.07 

$`PATL1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       34.13        13.87         7.53        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-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-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 

  PATL1 MUTATED PATL1 WILD-TYPE 
           5.92            0.00 
  PATL1 MUTATED PATL1 WILD-TYPE 
          27.12          122.30 
  PATL1 MUTATED PATL1 WILD-TYPE 
          6.295          14.470 
[1] "5.9 - 27.1 (6.3)"   "0.0 - 122.3 (14.5)"
[1] "hr=" "1.5"
D1151V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PATL1 MUTATED         0        0        1        0         1         1
  PATL1 WILD-TYPE       2       15       39       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PATL1 MUTATED           0          1          1          0        2
  PATL1 WILD-TYPE         3         69         52         32       36
D1151V3, multiclass
            clus
vv           PATL1 MUTATED PATL1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PATL1 MUTATED     1   0   2   4
  PATL1 WILD-TYPE  21  92 171  93
D1151V4, multiclass
    clus
vv   PATL1 MUTATED PATL1 WILD-TYPE
  T1             1              21
  T2             0              92
  T3             2             171
  T4             4              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
  PATL1 MUTATED     2   4   0   1
  PATL1 WILD-TYPE 116 100  77  76
D1151V5, multiclass
    clus
vv   PATL1 MUTATED PATL1 WILD-TYPE
  N0             2             116
  N1             4             100
  N2             0              77
  N3             1              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"
D1151V6, binary
                 cls
clus                0   1
  PATL1 MUTATED     6   1
  PATL1 WILD-TYPE 340  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PATL1 MUTATED      6    1
  PATL1 WILD-TYPE  340   28
   clus
vv  PATL1 MUTATED PATL1 WILD-TYPE
  0             6             340
  1             1              28
[1] 2 2
[1] FALSE
D1151V7, binary
                 cls
clus                0   1
  PATL1 MUTATED     3   4
  PATL1 WILD-TYPE 142 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PATL1 MUTATED      3    4
  PATL1 WILD-TYPE  142  244
        clus
vv       PATL1 MUTATED PATL1 WILD-TYPE
  FEMALE             3             142
  MALE               4             244
[1] 2 2
[1] FALSE
D1151V8, binary
                 cls
clus                0   1
  PATL1 MUTATED     6   0
  PATL1 WILD-TYPE 286  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PATL1 MUTATED      6    0
  PATL1 WILD-TYPE  286   59
     clus
vv    PATL1 MUTATED PATL1 WILD-TYPE
  NO              6             286
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PATL1 MUTATED                                          1
  PATL1 WILD-TYPE                                        7
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PATL1 MUTATED                                       0
  PATL1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PATL1 MUTATED                                                        2
  PATL1 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PATL1 MUTATED                                                   0
  PATL1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PATL1 MUTATED                                                                   1
  PATL1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PATL1 MUTATED                                                    0
  PATL1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PATL1 MUTATED                                                  3
  PATL1 WILD-TYPE                                               58
D1151V9, multiclass
                                                                   clus
vv                                                                  PATL1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  PATL1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PATL1 MUTATED     6   0   0   1
  PATL1 WILD-TYPE 305  14  15  23
D1151V10, multiclass
    clus
vv   PATL1 MUTATED PATL1 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1151V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PATL1 MUTATED       3                         0
  PATL1 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PATL1 MUTATED                                           0     3
  PATL1 WILD-TYPE                                         1   240
D1151V12, multiclass
                                           clus
vv                                          PATL1 MUTATED PATL1 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1151V13, binary
                 cls
clus                0   1
  PATL1 MUTATED     0   6
  PATL1 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PATL1 MUTATED      0    6
  PATL1 WILD-TYPE    4  304
                        clus
vv                       PATL1 MUTATED PATL1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(1152) Variable = KCNE1 MUTATION ANALYSIS
D1152V1, survival
                 sevent
clus2               0   1
  KCNE1 MUTATED     3   1
  KCNE1 WILD-TYPE 227 138
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              4             365 
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              1             138 
$`KCNE1 MUTATED`
TCGA-B7-A5TI TCGA-BR-8372 TCGA-BR-8484 TCGA-HU-8602 
       19.56        31.27        25.18        22.32 

$`KCNE1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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 

  KCNE1 MUTATED KCNE1 WILD-TYPE 
          19.56            0.00 
  KCNE1 MUTATED KCNE1 WILD-TYPE 
          31.27          122.30 
  KCNE1 MUTATED KCNE1 WILD-TYPE 
          23.75           14.07 
[1] "19.6 - 31.3 (23.8)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.2"
D1152V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KCNE1 MUTATED         0        0        0        0         0         1
  KCNE1 WILD-TYPE       2       15       40       30        37        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCNE1 MUTATED           0          1          0          2        0
  KCNE1 WILD-TYPE         3         69         53         30       38
D1152V3, multiclass
            clus
vv           KCNE1 MUTATED KCNE1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              0              37
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNE1 MUTATED     0   0   0   4
  KCNE1 WILD-TYPE  22  92 173  93
D1152V4, multiclass
    clus
vv   KCNE1 MUTATED KCNE1 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             0             173
  T4             4              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
  KCNE1 MUTATED     1   1   0   2
  KCNE1 WILD-TYPE 117 103  77  75
D1152V5, multiclass
    clus
vv   KCNE1 MUTATED KCNE1 WILD-TYPE
  N0             1             117
  N1             1             103
  N2             0              77
  N3             2              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"
D1152V6, binary
                 cls
clus                0   1
  KCNE1 MUTATED     4   0
  KCNE1 WILD-TYPE 342  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNE1 MUTATED      4    0
  KCNE1 WILD-TYPE  342   29
   clus
vv  KCNE1 MUTATED KCNE1 WILD-TYPE
  0             4             342
  1             0              29
[1] 2 2
[1] FALSE
D1152V7, binary
                 cls
clus                0   1
  KCNE1 MUTATED     1   3
  KCNE1 WILD-TYPE 144 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNE1 MUTATED      1    3
  KCNE1 WILD-TYPE  144  245
        clus
vv       KCNE1 MUTATED KCNE1 WILD-TYPE
  FEMALE             1             144
  MALE               3             245
[1] 2 2
[1] FALSE
D1152V8, binary
                 cls
clus                0   1
  KCNE1 MUTATED     4   0
  KCNE1 WILD-TYPE 288  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNE1 MUTATED      4    0
  KCNE1 WILD-TYPE  288   59
     clus
vv    KCNE1 MUTATED KCNE1 WILD-TYPE
  NO              4             288
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KCNE1 MUTATED                                          0
  KCNE1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KCNE1 MUTATED                                       2
  KCNE1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNE1 MUTATED                                                        2
  KCNE1 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KCNE1 MUTATED                                                   0
  KCNE1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KCNE1 MUTATED                                                                   0
  KCNE1 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KCNE1 MUTATED                                                    0
  KCNE1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KCNE1 MUTATED                                                  0
  KCNE1 WILD-TYPE                                               61
D1152V9, multiclass
                                                                   clus
vv                                                                  KCNE1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  KCNE1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCNE1 MUTATED     3   0   0   0
  KCNE1 WILD-TYPE 308  14  15  24
D1152V10, multiclass
    clus
vv   KCNE1 MUTATED KCNE1 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1152V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  KCNE1 MUTATED       1                         0
  KCNE1 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KCNE1 MUTATED                                           0     3
  KCNE1 WILD-TYPE                                         1   240
D1152V12, multiclass
                                           clus
vv                                          KCNE1 MUTATED KCNE1 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1152V13, binary
                 cls
clus                0   1
  KCNE1 MUTATED     0   4
  KCNE1 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNE1 MUTATED      0    4
  KCNE1 WILD-TYPE    4  306
                        clus
vv                       KCNE1 MUTATED KCNE1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(1153) Variable = TLR4 MUTATION ANALYSIS
D1153V1, survival
                sevent
clus2              0   1
  TLR4 MUTATED    17   7
  TLR4 WILD-TYPE 213 132
  TLR4 MUTATED TLR4 WILD-TYPE 
            24            345 
  TLR4 MUTATED TLR4 WILD-TYPE 
             7            132 
$`TLR4 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6706 TCGA-BR-7723 TCGA-BR-8297 
        6.97        34.68        15.95        18.05        28.73         7.40 
TCGA-BR-8487 TCGA-BR-8690 TCGA-CD-8524 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5724 
        1.12        10.68        12.76        18.97         7.07        12.03 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6822 TCGA-F1-6875 TCGA-F1-A448 TCGA-HF-A5NB 
       17.19        10.26        12.33        72.23        21.27        30.51 
TCGA-HU-A4H4 TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1X TCGA-RD-A8N1 TCGA-VQ-AA6J 
       23.84         6.51        11.70        13.51       115.69        27.55 

$`TLR4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-A44T 
       31.96        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-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-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-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-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-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       13.35        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-D7-8578 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-A72C TCGA-FP-7735 
        7.13         0.62         7.99        14.47        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-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       13.35        19.53         6.44         6.74        12.59        10.62 
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-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-AA6K TCGA-ZA-A8F6 
       16.14        12.43        17.26 

  TLR4 MUTATED TLR4 WILD-TYPE 
          1.12           0.00 
  TLR4 MUTATED TLR4 WILD-TYPE 
        115.69         122.30 
  TLR4 MUTATED TLR4 WILD-TYPE 
         14.73          14.27 
[1] "1.1 - 115.7 (14.7)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D1153V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TLR4 MUTATED         0        1        3        2         4         2
  TLR4 WILD-TYPE       2       14       37       28        33        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TLR4 MUTATED           0          3          6          2        3
  TLR4 WILD-TYPE         3         67         47         30       35
D1153V3, multiclass
            clus
vv           TLR4 MUTATED TLR4 WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              3             37
  STAGE II              2             28
  STAGE IIA             4             33
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            6             47
  STAGE IIIC            2             30
  STAGE IV              3             35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TLR4 MUTATED     0   7  15   4
  TLR4 WILD-TYPE  22  85 158  93
D1153V4, multiclass
    clus
vv   TLR4 MUTATED TLR4 WILD-TYPE
  T1            0             22
  T2            7             85
  T3           15            158
  T4            4             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
  TLR4 MUTATED     9   4   4   9
  TLR4 WILD-TYPE 109 100  73  68
D1153V5, multiclass
    clus
vv   TLR4 MUTATED TLR4 WILD-TYPE
  N0            9            109
  N1            4            100
  N2            4             73
  N3            9             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"
D1153V6, binary
                cls
clus               0   1
  TLR4 MUTATED    24   2
  TLR4 WILD-TYPE 322  27
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR4 MUTATED     24    2
  TLR4 WILD-TYPE  322   27
   clus
vv  TLR4 MUTATED TLR4 WILD-TYPE
  0           24            322
  1            2             27
[1] 2 2
[1] FALSE
D1153V7, binary
                cls
clus               0   1
  TLR4 MUTATED    11  16
  TLR4 WILD-TYPE 134 232
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR4 MUTATED     11   16
  TLR4 WILD-TYPE  134  232
        clus
vv       TLR4 MUTATED TLR4 WILD-TYPE
  FEMALE           11            134
  MALE             16            232
[1] 2 2
[1] FALSE
D1153V8, binary
                cls
clus               0   1
  TLR4 MUTATED    21   4
  TLR4 WILD-TYPE 271  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR4 MUTATED     21    4
  TLR4 WILD-TYPE  271   55
     clus
vv    TLR4 MUTATED TLR4 WILD-TYPE
  NO            21            271
  YES            4             55
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TLR4 MUTATED                                          0
  TLR4 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TLR4 MUTATED                                       3
  TLR4 WILD-TYPE                                    67
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TLR4 MUTATED                                                       13
  TLR4 WILD-TYPE                                                    145
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TLR4 MUTATED                                                   2
  TLR4 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TLR4 MUTATED                                                                   5
  TLR4 WILD-TYPE                                                                63
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TLR4 MUTATED                                                    1
  TLR4 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TLR4 MUTATED                                                  3
  TLR4 WILD-TYPE                                               58
D1153V9, multiclass
                                                                   clus
vv                                                                  TLR4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      13
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  TLR4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       145
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TLR4 MUTATED    21   3   1   2
  TLR4 WILD-TYPE 290  11  14  22
D1153V10, multiclass
    clus
vv   TLR4 MUTATED TLR4 WILD-TYPE
  R0           21            290
  R1            3             11
  R2            1             14
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1153V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TLR4 MUTATED       2                         2
  TLR4 WILD-TYPE    85                         7
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TLR4 MUTATED                                           0    19
  TLR4 WILD-TYPE                                         1   224
D1153V12, multiclass
                                           clus
vv                                          TLR4 MUTATED TLR4 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            2              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               19            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1153V13, binary
                cls
clus               0   1
  TLR4 MUTATED     1  21
  TLR4 WILD-TYPE   3 289
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR4 MUTATED      1   21
  TLR4 WILD-TYPE    3  289
                        clus
vv                       TLR4 MUTATED TLR4 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           21            289
[1] 2 2
[1] FALSE

Clustering(1154) Variable = XRCC2 MUTATION ANALYSIS
D1154V1, survival
                 sevent
clus2               0   1
  XRCC2 MUTATED     3   1
  XRCC2 WILD-TYPE 227 138
  XRCC2 MUTATED XRCC2 WILD-TYPE 
              4             365 
  XRCC2 MUTATED XRCC2 WILD-TYPE 
              1             138 
$`XRCC2 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-HU-A4GN TCGA-HU-A4GT 
       21.99        34.68        29.98         6.51 

$`XRCC2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-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-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 

  XRCC2 MUTATED XRCC2 WILD-TYPE 
           6.51            0.00 
  XRCC2 MUTATED XRCC2 WILD-TYPE 
          34.68          122.30 
  XRCC2 MUTATED XRCC2 WILD-TYPE 
         25.985          14.170 
[1] "6.5 - 34.7 (26.0)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "2"  
D1154V2, 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       2       15       40       30        34        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XRCC2 MUTATED           0          1          0          0        1
  XRCC2 WILD-TYPE         3         69         53         32       37
D1154V3, multiclass
            clus
vv           XRCC2 MUTATED XRCC2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              3              34
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  XRCC2 MUTATED     0   1   2   2
  XRCC2 WILD-TYPE  22  91 171  95
D1154V4, multiclass
    clus
vv   XRCC2 MUTATED XRCC2 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             2             171
  T4             2              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
  XRCC2 MUTATED     3   3   0   0
  XRCC2 WILD-TYPE 115 101  77  77
D1154V5, multiclass
    clus
vv   XRCC2 MUTATED XRCC2 WILD-TYPE
  N0             3             115
  N1             3             101
  N2             0              77
  N3             0              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"
D1154V6, binary
                 cls
clus                0   1
  XRCC2 MUTATED     5   1
  XRCC2 WILD-TYPE 341  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC2 MUTATED      5    1
  XRCC2 WILD-TYPE  341   28
   clus
vv  XRCC2 MUTATED XRCC2 WILD-TYPE
  0             5             341
  1             1              28
[1] 2 2
[1] FALSE
D1154V7, binary
                 cls
clus                0   1
  XRCC2 MUTATED     5   1
  XRCC2 WILD-TYPE 140 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC2 MUTATED      5    1
  XRCC2 WILD-TYPE  140  247
        clus
vv       XRCC2 MUTATED XRCC2 WILD-TYPE
  FEMALE             5             140
  MALE               1             247
[1] 2 2
[1] FALSE
D1154V8, binary
                 cls
clus                0   1
  XRCC2 MUTATED     4   0
  XRCC2 WILD-TYPE 288  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC2 MUTATED      4    0
  XRCC2 WILD-TYPE  288   59
     clus
vv    XRCC2 MUTATED XRCC2 WILD-TYPE
  NO              4             288
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  XRCC2 MUTATED                                          0
  XRCC2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  XRCC2 MUTATED                                       0
  XRCC2 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XRCC2 MUTATED                                                        3
  XRCC2 WILD-TYPE                                                    155
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  XRCC2 MUTATED                                                   0
  XRCC2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XRCC2 MUTATED                                                                   1
  XRCC2 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  XRCC2 MUTATED                                                    0
  XRCC2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  XRCC2 MUTATED                                                  2
  XRCC2 WILD-TYPE                                               59
D1154V9, multiclass
                                                                   clus
vv                                                                  XRCC2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  XRCC2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  XRCC2 MUTATED     3   0   1   2
  XRCC2 WILD-TYPE 308  14  14  22
D1154V10, multiclass
    clus
vv   XRCC2 MUTATED XRCC2 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             1              14
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1154V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  XRCC2 MUTATED       2                         0
  XRCC2 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XRCC2 MUTATED                                           0     3
  XRCC2 WILD-TYPE                                         1   240
D1154V12, multiclass
                                           clus
vv                                          XRCC2 MUTATED XRCC2 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1154V13, binary
                 cls
clus                0   1
  XRCC2 MUTATED     0   5
  XRCC2 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC2 MUTATED      0    5
  XRCC2 WILD-TYPE    4  305
                        clus
vv                       XRCC2 MUTATED XRCC2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(1155) Variable = CRYBB1 MUTATION ANALYSIS
D1155V1, survival
                  sevent
clus2                0   1
  CRYBB1 MUTATED     6   2
  CRYBB1 WILD-TYPE 224 137
  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
               8              361 
  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
               2              137 
$`CRYBB1 MUTATED`
TCGA-BR-4201 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-A4QL TCGA-D7-A6F2 TCGA-HU-A4GU 
       30.90        44.94        35.24        16.14        15.65         6.58 
TCGA-HU-A4H5 TCGA-VQ-A8P2 
       23.80        38.14 

$`CRYBB1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-7707 
       30.90        31.20        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-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-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-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-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-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 

  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
            6.58             0.00 
  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
           44.94           122.30 
  CRYBB1 MUTATED CRYBB1 WILD-TYPE 
           27.35            14.07 
[1] "6.6 - 44.9 (27.4)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.1"
D1155V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CRYBB1 MUTATED         0        0        2        1         1         1
  CRYBB1 WILD-TYPE       2       15       38       29        36        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CRYBB1 MUTATED           0          1          1          0        1
  CRYBB1 WILD-TYPE         3         69         52         32       37
D1155V3, multiclass
            clus
vv           CRYBB1 MUTATED CRYBB1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                2               38
  STAGE II                1               29
  STAGE IIA               1               36
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CRYBB1 MUTATED     1   3   4   2
  CRYBB1 WILD-TYPE  21  89 169  95
D1155V4, multiclass
    clus
vv   CRYBB1 MUTATED CRYBB1 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              4              169
  T4              2               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
  CRYBB1 MUTATED     4   2   1   1
  CRYBB1 WILD-TYPE 114 102  76  76
D1155V5, multiclass
    clus
vv   CRYBB1 MUTATED CRYBB1 WILD-TYPE
  N0              4              114
  N1              2              102
  N2              1               76
  N3              1               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"
D1155V6, binary
                  cls
clus                 0   1
  CRYBB1 MUTATED    10   0
  CRYBB1 WILD-TYPE 336  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBB1 MUTATED     10    0
  CRYBB1 WILD-TYPE  336   29
   clus
vv  CRYBB1 MUTATED CRYBB1 WILD-TYPE
  0             10              336
  1              0               29
[1] 2 2
[1] FALSE
D1155V7, binary
                  cls
clus                 0   1
  CRYBB1 MUTATED     6   4
  CRYBB1 WILD-TYPE 139 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBB1 MUTATED      6    4
  CRYBB1 WILD-TYPE  139  244
        clus
vv       CRYBB1 MUTATED CRYBB1 WILD-TYPE
  FEMALE              6              139
  MALE                4              244
[1] 2 2
[1] FALSE
D1155V8, binary
                  cls
clus                 0   1
  CRYBB1 MUTATED     7   1
  CRYBB1 WILD-TYPE 285  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBB1 MUTATED      7    1
  CRYBB1 WILD-TYPE  285   58
     clus
vv    CRYBB1 MUTATED CRYBB1 WILD-TYPE
  NO               7              285
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CRYBB1 MUTATED                                          0
  CRYBB1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CRYBB1 MUTATED                                       1
  CRYBB1 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CRYBB1 MUTATED                                                        5
  CRYBB1 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CRYBB1 MUTATED                                                   1
  CRYBB1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CRYBB1 MUTATED                                                                   1
  CRYBB1 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CRYBB1 MUTATED                                                    1
  CRYBB1 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CRYBB1 MUTATED                                                  1
  CRYBB1 WILD-TYPE                                               60
D1155V9, multiclass
                                                                   clus
vv                                                                  CRYBB1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  CRYBB1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CRYBB1 MUTATED     7   0   0   3
  CRYBB1 WILD-TYPE 304  14  15  21
D1155V10, multiclass
    clus
vv   CRYBB1 MUTATED CRYBB1 WILD-TYPE
  R0              7              304
  R1              0               14
  R2              0               15
  RX              3               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1155V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CRYBB1 MUTATED       2                         0
  CRYBB1 WILD-TYPE    85                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CRYBB1 MUTATED                                           0     8
  CRYBB1 WILD-TYPE                                         1   235
D1155V12, multiclass
                                           clus
vv                                          CRYBB1 MUTATED CRYBB1 WILD-TYPE
  ASIAN                                                  2               85
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1155V13, binary
                  cls
clus                 0   1
  CRYBB1 MUTATED     0   9
  CRYBB1 WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRYBB1 MUTATED      0    9
  CRYBB1 WILD-TYPE    4  301
                        clus
vv                       CRYBB1 MUTATED CRYBB1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(1156) Variable = MED23 MUTATION ANALYSIS
D1156V1, survival
                 sevent
clus2               0   1
  MED23 MUTATED    12   5
  MED23 WILD-TYPE 218 134
  MED23 MUTATED MED23 WILD-TYPE 
             17             352 
  MED23 MUTATED MED23 WILD-TYPE 
              5             134 
$`MED23 MUTATED`
TCGA-CG-4460 TCGA-BR-4184 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-8363 TCGA-BR-8591 
       21.99         6.97         6.18        34.68         0.26        28.14 
TCGA-BR-8680 TCGA-CG-4305 TCGA-CG-4437 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-A6EY 
       31.96        15.95         8.05         6.02       105.07        11.44 
TCGA-F1-6874 TCGA-HU-A4GT TCGA-IN-8462 TCGA-IN-A6RN TCGA-KB-A6F5 
       14.47         6.51        18.81        19.53         5.56 

$`MED23 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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 
          14.47           14.22 
[1] "0.3 - 105.1 (14.5)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.2"
D1156V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  MED23 MUTATED         0        0        3        3         3         1
  MED23 WILD-TYPE       2       15       37       27        34        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MED23 MUTATED           0          2          1          1        3
  MED23 WILD-TYPE         3         68         52         31       35
D1156V3, multiclass
            clus
vv           MED23 MUTATED MED23 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               3              37
  STAGE II               3              27
  STAGE IIA              3              34
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             1              31
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MED23 MUTATED     1   7   6   4
  MED23 WILD-TYPE  21  85 167  93
D1156V4, multiclass
    clus
vv   MED23 MUTATED MED23 WILD-TYPE
  T1             1              21
  T2             7              85
  T3             6             167
  T4             4              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
  MED23 MUTATED     5   7   3   2
  MED23 WILD-TYPE 113  97  74  75
D1156V5, multiclass
    clus
vv   MED23 MUTATED MED23 WILD-TYPE
  N0             5             113
  N1             7              97
  N2             3              74
  N3             2              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"
D1156V6, binary
                 cls
clus                0   1
  MED23 MUTATED    14   2
  MED23 WILD-TYPE 332  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED23 MUTATED     14    2
  MED23 WILD-TYPE  332   27
   clus
vv  MED23 MUTATED MED23 WILD-TYPE
  0            14             332
  1             2              27
[1] 2 2
[1] FALSE
D1156V7, binary
                 cls
clus                0   1
  MED23 MUTATED     7  11
  MED23 WILD-TYPE 138 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED23 MUTATED      7   11
  MED23 WILD-TYPE  138  237
        clus
vv       MED23 MUTATED MED23 WILD-TYPE
  FEMALE             7             138
  MALE              11             237
[1] 2 2
[1] FALSE
D1156V8, binary
                 cls
clus                0   1
  MED23 MUTATED    17   0
  MED23 WILD-TYPE 275  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED23 MUTATED     17    0
  MED23 WILD-TYPE  275   59
     clus
vv    MED23 MUTATED MED23 WILD-TYPE
  NO             17             275
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  MED23 MUTATED                                          0
  MED23 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  MED23 MUTATED                                       0
  MED23 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MED23 MUTATED                                                       10
  MED23 WILD-TYPE                                                    148
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  MED23 MUTATED                                                   0
  MED23 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  MED23 MUTATED                                                                   5
  MED23 WILD-TYPE                                                                63
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  MED23 MUTATED                                                    0
  MED23 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  MED23 MUTATED                                                  3
  MED23 WILD-TYPE                                               58
D1156V9, multiclass
                                                                   clus
vv                                                                  MED23 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  MED23 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        148
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MED23 MUTATED    14   0   1   3
  MED23 WILD-TYPE 297  14  14  21
D1156V10, multiclass
    clus
vv   MED23 MUTATED MED23 WILD-TYPE
  R0            14             297
  R1             0              14
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1156V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  MED23 MUTATED       2                         0
  MED23 WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  MED23 MUTATED                                           0    10
  MED23 WILD-TYPE                                         1   233
D1156V12, multiclass
                                           clus
vv                                          MED23 MUTATED MED23 WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                10             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1156V13, binary
                 cls
clus                0   1
  MED23 MUTATED     0  12
  MED23 WILD-TYPE   4 298
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED23 MUTATED      0   12
  MED23 WILD-TYPE    4  298
                        clus
vv                       MED23 MUTATED MED23 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             298
[1] 2 2
[1] FALSE

Clustering(1157) Variable = SFRS2 MUTATION ANALYSIS
D1157V1, survival
                 sevent
clus2               0   1
  SFRS2 MUTATED     1   2
  SFRS2 WILD-TYPE 229 137
  SFRS2 MUTATED SFRS2 WILD-TYPE 
              3             366 
  SFRS2 MUTATED SFRS2 WILD-TYPE 
              2             137 
$`SFRS2 MUTATED`
TCGA-BR-6452 TCGA-CD-A4MI TCGA-D7-A6EY 
       34.68        11.77        11.44 

$`SFRS2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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 

  SFRS2 MUTATED SFRS2 WILD-TYPE 
          11.44            0.00 
  SFRS2 MUTATED SFRS2 WILD-TYPE 
          34.68          122.30 
  SFRS2 MUTATED SFRS2 WILD-TYPE 
          11.77           14.35 
[1] "11.4 - 34.7 (11.8)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.7"
D1157V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SFRS2 MUTATED         0        0        0        0         1         1
  SFRS2 WILD-TYPE       2       15       40       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFRS2 MUTATED           0          1          1          0        0
  SFRS2 WILD-TYPE         3         69         52         32       38
D1157V3, multiclass
            clus
vv           SFRS2 MUTATED SFRS2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SFRS2 MUTATED     0   0   3   1
  SFRS2 WILD-TYPE  22  92 170  96
D1157V4, multiclass
    clus
vv   SFRS2 MUTATED SFRS2 WILD-TYPE
  T1             0              22
  T2             0              92
  T3             3             170
  T4             1              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
  SFRS2 MUTATED     2   1   0   1
  SFRS2 WILD-TYPE 116 103  77  76
D1157V5, multiclass
    clus
vv   SFRS2 MUTATED SFRS2 WILD-TYPE
  N0             2             116
  N1             1             103
  N2             0              77
  N3             1              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"
D1157V6, binary
                 cls
clus                0   1
  SFRS2 MUTATED     4   0
  SFRS2 WILD-TYPE 342  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRS2 MUTATED      4    0
  SFRS2 WILD-TYPE  342   29
   clus
vv  SFRS2 MUTATED SFRS2 WILD-TYPE
  0             4             342
  1             0              29
[1] 2 2
[1] FALSE
D1157V7, binary
                 cls
clus                0   1
  SFRS2 MUTATED     2   2
  SFRS2 WILD-TYPE 143 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRS2 MUTATED      2    2
  SFRS2 WILD-TYPE  143  246
        clus
vv       SFRS2 MUTATED SFRS2 WILD-TYPE
  FEMALE             2             143
  MALE               2             246
[1] 2 2
[1] FALSE
D1157V8, binary
                 cls
clus                0   1
  SFRS2 MUTATED     4   0
  SFRS2 WILD-TYPE 288  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRS2 MUTATED      4    0
  SFRS2 WILD-TYPE  288   59
     clus
vv    SFRS2 MUTATED SFRS2 WILD-TYPE
  NO              4             288
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SFRS2 MUTATED                                          0
  SFRS2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SFRS2 MUTATED                                       0
  SFRS2 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SFRS2 MUTATED                                                        2
  SFRS2 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SFRS2 MUTATED                                                   0
  SFRS2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SFRS2 MUTATED                                                                   1
  SFRS2 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SFRS2 MUTATED                                                    0
  SFRS2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SFRS2 MUTATED                                                  1
  SFRS2 WILD-TYPE                                               60
D1157V9, multiclass
                                                                   clus
vv                                                                  SFRS2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  SFRS2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SFRS2 MUTATED     3   0   0   0
  SFRS2 WILD-TYPE 308  14  15  24
D1157V10, multiclass
    clus
vv   SFRS2 MUTATED SFRS2 WILD-TYPE
  R0             3             308
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1157V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  SFRS2 MUTATED       1                         0
  SFRS2 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SFRS2 MUTATED                                           0     3
  SFRS2 WILD-TYPE                                         1   240
D1157V12, multiclass
                                           clus
vv                                          SFRS2 MUTATED SFRS2 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1157V13, binary
                 cls
clus                0   1
  SFRS2 MUTATED     0   4
  SFRS2 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRS2 MUTATED      0    4
  SFRS2 WILD-TYPE    4  306
                        clus
vv                       SFRS2 MUTATED SFRS2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(1158) Variable = SGK196 MUTATION ANALYSIS
D1158V1, survival
                  sevent
clus2                0   1
  SGK196 MUTATED     4   3
  SGK196 WILD-TYPE 226 136
  SGK196 MUTATED SGK196 WILD-TYPE 
               7              362 
  SGK196 MUTATED SGK196 WILD-TYPE 
               3              136 
$`SGK196 MUTATED`
TCGA-BR-4184 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6453 TCGA-HU-A4GQ TCGA-R5-A7ZI 
        6.97         9.34        34.68        15.95         0.10        74.53 
TCGA-VQ-A8P2 
       38.14 

$`SGK196 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  SGK196 MUTATED SGK196 WILD-TYPE 
             0.1              0.0 
  SGK196 MUTATED SGK196 WILD-TYPE 
           74.53           122.30 
  SGK196 MUTATED SGK196 WILD-TYPE 
           15.95            14.22 
[1] "0.1 - 74.5 (15.9)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D1158V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SGK196 MUTATED         0        0        0        0         2         0
  SGK196 WILD-TYPE       2       15       40       30        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SGK196 MUTATED           0          2          0          1        1
  SGK196 WILD-TYPE         3         68         53         31       37
D1158V3, multiclass
            clus
vv           SGK196 MUTATED SGK196 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SGK196 MUTATED     0   1   2   3
  SGK196 WILD-TYPE  22  91 171  94
D1158V4, multiclass
    clus
vv   SGK196 MUTATED SGK196 WILD-TYPE
  T1              0               22
  T2              1               91
  T3              2              171
  T4              3               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
  SGK196 MUTATED     1   5   1   0
  SGK196 WILD-TYPE 117  99  76  77
D1158V5, multiclass
    clus
vv   SGK196 MUTATED SGK196 WILD-TYPE
  N0              1              117
  N1              5               99
  N2              1               76
  N3              0               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"
D1158V6, binary
                  cls
clus                 0   1
  SGK196 MUTATED     5   1
  SGK196 WILD-TYPE 341  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK196 MUTATED      5    1
  SGK196 WILD-TYPE  341   28
   clus
vv  SGK196 MUTATED SGK196 WILD-TYPE
  0              5              341
  1              1               28
[1] 2 2
[1] FALSE
D1158V7, binary
                  cls
clus                 0   1
  SGK196 MUTATED     2   5
  SGK196 WILD-TYPE 143 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK196 MUTATED      2    5
  SGK196 WILD-TYPE  143  243
        clus
vv       SGK196 MUTATED SGK196 WILD-TYPE
  FEMALE              2              143
  MALE                5              243
[1] 2 2
[1] FALSE
D1158V8, binary
                  cls
clus                 0   1
  SGK196 MUTATED     6   1
  SGK196 WILD-TYPE 286  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK196 MUTATED      6    1
  SGK196 WILD-TYPE  286   58
     clus
vv    SGK196 MUTATED SGK196 WILD-TYPE
  NO               6              286
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SGK196 MUTATED                                          0
  SGK196 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SGK196 MUTATED                                       1
  SGK196 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SGK196 MUTATED                                                        4
  SGK196 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SGK196 MUTATED                                                   1
  SGK196 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SGK196 MUTATED                                                                   0
  SGK196 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SGK196 MUTATED                                                    0
  SGK196 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SGK196 MUTATED                                                  1
  SGK196 WILD-TYPE                                               60
D1158V9, multiclass
                                                                   clus
vv                                                                  SGK196 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  SGK196 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SGK196 MUTATED     5   0   0   2
  SGK196 WILD-TYPE 306  14  15  22
D1158V10, multiclass
    clus
vv   SGK196 MUTATED SGK196 WILD-TYPE
  R0              5              306
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1158V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SGK196 MUTATED       1                         0
  SGK196 WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SGK196 MUTATED                                           0     6
  SGK196 WILD-TYPE                                         1   237
D1158V12, multiclass
                                           clus
vv                                          SGK196 MUTATED SGK196 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1158V13, binary
                  cls
clus                 0   1
  SGK196 MUTATED     1   5
  SGK196 WILD-TYPE   3 305
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK196 MUTATED      1    5
  SGK196 WILD-TYPE    3  305
                        clus
vv                       SGK196 MUTATED SGK196 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              5              305
[1] 2 2
[1] FALSE

Clustering(1159) Variable = TDG MUTATION ANALYSIS
D1159V1, survival
               sevent
clus2             0   1
  TDG MUTATED     4   2
  TDG WILD-TYPE 226 137
  TDG MUTATED TDG WILD-TYPE 
            6           363 
  TDG MUTATED TDG WILD-TYPE 
            2           137 
$`TDG MUTATED`
TCGA-BR-6452 TCGA-CG-5721 TCGA-CG-5732 TCGA-HU-A4GQ TCGA-VQ-A8P2 TCGA-VQ-AA69 
       34.68         6.02        69.04         0.10        38.14        28.41 

$`TDG WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-5733 TCGA-CG-5734 
       15.02        28.96        65.10         4.01        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-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-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        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 

  TDG MUTATED TDG WILD-TYPE 
          0.1           0.0 
  TDG MUTATED TDG WILD-TYPE 
        69.04        122.30 
  TDG MUTATED TDG WILD-TYPE 
       31.545        14.170 
[1] "0.1 - 69.0 (31.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D1159V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TDG MUTATED         0        0        0        0         1         0
  TDG WILD-TYPE       2       15       40       30        36        52
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TDG MUTATED           0          2          0          1        2
  TDG WILD-TYPE         3         68         53         31       36
D1159V3, multiclass
            clus
vv           TDG MUTATED TDG WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             0            40
  STAGE II             0            30
  STAGE IIA            1            36
  STAGE IIB            0            52
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           0            53
  STAGE IIIC           1            31
  STAGE IV             2            36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  TDG MUTATED     0   1   2   3
  TDG WILD-TYPE  22  91 171  94
D1159V4, multiclass
    clus
vv   TDG MUTATED TDG WILD-TYPE
  T1           0            22
  T2           1            91
  T3           2           171
  T4           3            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
  TDG MUTATED     1   2   2   1
  TDG WILD-TYPE 117 102  75  76
D1159V5, multiclass
    clus
vv   TDG MUTATED TDG WILD-TYPE
  N0           1           117
  N1           2           102
  N2           2            75
  N3           1            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"
D1159V6, binary
               cls
clus              0   1
  TDG MUTATED     6   0
  TDG WILD-TYPE 340  29
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      6    0
  TDG WILD-TYPE  340   29
   clus
vv  TDG MUTATED TDG WILD-TYPE
  0           6           340
  1           0            29
[1] 2 2
[1] FALSE
D1159V7, binary
               cls
clus              0   1
  TDG MUTATED     1   5
  TDG WILD-TYPE 144 243
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      1    5
  TDG WILD-TYPE  144  243
        clus
vv       TDG MUTATED TDG WILD-TYPE
  FEMALE           1           144
  MALE             5           243
[1] 2 2
[1] FALSE
D1159V8, binary
               cls
clus              0   1
  TDG MUTATED     4   2
  TDG WILD-TYPE 288  57
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      4    2
  TDG WILD-TYPE  288   57
     clus
vv    TDG MUTATED TDG WILD-TYPE
  NO            4           288
  YES           2            57
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TDG MUTATED                                          0
  TDG WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TDG MUTATED                                       0
  TDG WILD-TYPE                                    70
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TDG MUTATED                                                        1
  TDG WILD-TYPE                                                    157
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TDG MUTATED                                                   1
  TDG WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TDG MUTATED                                                                   3
  TDG WILD-TYPE                                                                65
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TDG MUTATED                                                    0
  TDG WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TDG MUTATED                                                  1
  TDG WILD-TYPE                                               60
D1159V9, multiclass
                                                                   clus
vv                                                                  TDG MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            1
                                                                   clus
vv                                                                  TDG WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  TDG MUTATED     6   0   0   0
  TDG WILD-TYPE 305  14  15  24
D1159V10, multiclass
    clus
vv   TDG MUTATED TDG WILD-TYPE
  R0           6           305
  R1           0            14
  R2           0            15
  RX           0            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1159V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  TDG MUTATED       1                         0
  TDG WILD-TYPE    86                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TDG MUTATED                                           0     3
  TDG WILD-TYPE                                         1   240
D1159V12, multiclass
                                           clus
vv                                          TDG MUTATED TDG WILD-TYPE
  ASIAN                                               1            86
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               3           240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1159V13, binary
               cls
clus              0   1
  TDG MUTATED     0   2
  TDG WILD-TYPE   4 308
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      0    2
  TDG WILD-TYPE    4  308
                        clus
vv                       TDG MUTATED TDG WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           2           308
[1] 2 2
[1] FALSE

Clustering(1160) Variable = KIAA0408 MUTATION ANALYSIS
D1160V1, survival
                    sevent
clus2                  0   1
  KIAA0408 MUTATED     8   3
  KIAA0408 WILD-TYPE 222 136
  KIAA0408 MUTATED KIAA0408 WILD-TYPE 
                11                358 
  KIAA0408 MUTATED KIAA0408 WILD-TYPE 
                 3                136 
$`KIAA0408 MUTATED`
TCGA-BR-4256 TCGA-BR-8289 TCGA-BR-8372 TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-A4J8 
        9.34         2.66        31.27        27.12        31.96        13.51 
TCGA-CG-5721 TCGA-D7-A4Z0 TCGA-FP-A9TM TCGA-RD-A7C1 TCGA-VQ-A8P2 
        6.02        14.76         6.21        16.67        38.14 

$`KIAA0408 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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-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 

  KIAA0408 MUTATED KIAA0408 WILD-TYPE 
              2.66               0.00 
  KIAA0408 MUTATED KIAA0408 WILD-TYPE 
             38.14             122.30 
  KIAA0408 MUTATED KIAA0408 WILD-TYPE 
             14.76              14.22 
[1] "2.7 - 38.1 (14.8)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D1160V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  KIAA0408 MUTATED         1        0        1        0         0         2
  KIAA0408 WILD-TYPE       1       15       39       30        37        50
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0408 MUTATED           0          1          2          1        3
  KIAA0408 WILD-TYPE         3         69         51         31       35
D1160V3, multiclass
            clus
vv           KIAA0408 MUTATED KIAA0408 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  0                 15
  STAGE IB                  1                 39
  STAGE II                  0                 30
  STAGE IIA                 0                 37
  STAGE IIB                 2                 50
  STAGE III                 0                  3
  STAGE IIIA                1                 69
  STAGE IIIB                2                 51
  STAGE IIIC                1                 31
  STAGE IV                  3                 35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0408 MUTATED     2   2   1   7
  KIAA0408 WILD-TYPE  20  90 172  90
D1160V4, multiclass
    clus
vv   KIAA0408 MUTATED KIAA0408 WILD-TYPE
  T1                2                 20
  T2                2                 90
  T3                1                172
  T4                7                 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
  KIAA0408 MUTATED     2   6   2   3
  KIAA0408 WILD-TYPE 116  98  75  74
D1160V5, multiclass
    clus
vv   KIAA0408 MUTATED KIAA0408 WILD-TYPE
  N0                2                116
  N1                6                 98
  N2                2                 75
  N3                3                 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"
D1160V6, binary
                    cls
clus                   0   1
  KIAA0408 MUTATED    11   2
  KIAA0408 WILD-TYPE 335  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0408 MUTATED     11    2
  KIAA0408 WILD-TYPE  335   27
   clus
vv  KIAA0408 MUTATED KIAA0408 WILD-TYPE
  0               11                335
  1                2                 27
[1] 2 2
[1] FALSE
D1160V7, binary
                    cls
clus                   0   1
  KIAA0408 MUTATED     2  12
  KIAA0408 WILD-TYPE 143 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0408 MUTATED      2   12
  KIAA0408 WILD-TYPE  143  236
        clus
vv       KIAA0408 MUTATED KIAA0408 WILD-TYPE
  FEMALE                2                143
  MALE                 12                236
[1] 2 2
[1] FALSE
D1160V8, binary
                    cls
clus                   0   1
  KIAA0408 MUTATED    10   3
  KIAA0408 WILD-TYPE 282  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0408 MUTATED     10    3
  KIAA0408 WILD-TYPE  282   56
     clus
vv    KIAA0408 MUTATED KIAA0408 WILD-TYPE
  NO                10                282
  YES                3                 56
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  KIAA0408 MUTATED                                          0
  KIAA0408 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  KIAA0408 MUTATED                                       1
  KIAA0408 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0408 MUTATED                                                        7
  KIAA0408 WILD-TYPE                                                    151
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  KIAA0408 MUTATED                                                   2
  KIAA0408 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  KIAA0408 MUTATED                                                                   3
  KIAA0408 WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  KIAA0408 MUTATED                                                    0
  KIAA0408 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  KIAA0408 MUTATED                                                  1
  KIAA0408 WILD-TYPE                                               60
D1160V9, multiclass
                                                                   clus
vv                                                                  KIAA0408 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  KIAA0408 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0408 MUTATED    12   0   0   2
  KIAA0408 WILD-TYPE 299  14  15  22
D1160V10, multiclass
    clus
vv   KIAA0408 MUTATED KIAA0408 WILD-TYPE
  R0               12                299
  R1                0                 14
  R2                0                 15
  RX                2                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1160V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  KIAA0408 MUTATED       1                         1
  KIAA0408 WILD-TYPE    86                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  KIAA0408 MUTATED                                           0    11
  KIAA0408 WILD-TYPE                                         1   232
D1160V12, multiclass
                                           clus
vv                                          KIAA0408 MUTATED KIAA0408 WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   11                232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1160V13, binary
                    cls
clus                   0   1
  KIAA0408 MUTATED     0  12
  KIAA0408 WILD-TYPE   4 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0408 MUTATED      0   12
  KIAA0408 WILD-TYPE    4  298
                        clus
vv                       KIAA0408 MUTATED KIAA0408 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               12                298
[1] 2 2
[1] FALSE

Clustering(1161) Variable = PIAS1 MUTATION ANALYSIS
D1161V1, survival
                 sevent
clus2               0   1
  PIAS1 MUTATED     6   2
  PIAS1 WILD-TYPE 224 137
  PIAS1 MUTATED PIAS1 WILD-TYPE 
              8             361 
  PIAS1 MUTATED PIAS1 WILD-TYPE 
              2             137 
$`PIAS1 MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-8361 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8487 
        6.97        34.68        31.10        14.79        25.05         1.12 
TCGA-CG-5721 TCGA-CG-5723 
        6.02       105.07 

$`PIAS1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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 
          19.92           14.17 
[1] "1.1 - 105.1 (19.9)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.8"
D1161V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PIAS1 MUTATED         1        0        0        1         2         0
  PIAS1 WILD-TYPE       1       15       40       29        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIAS1 MUTATED           0          2          0          2        1
  PIAS1 WILD-TYPE         3         68         53         30       37
D1161V3, multiclass
            clus
vv           PIAS1 MUTATED PIAS1 WILD-TYPE
  STAGE I                1               1
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             2              30
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PIAS1 MUTATED     1   1   3   4
  PIAS1 WILD-TYPE  21  91 170  93
D1161V4, multiclass
    clus
vv   PIAS1 MUTATED PIAS1 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             3             170
  T4             4              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
  PIAS1 MUTATED     2   5   1   1
  PIAS1 WILD-TYPE 116  99  76  76
D1161V5, multiclass
    clus
vv   PIAS1 MUTATED PIAS1 WILD-TYPE
  N0             2             116
  N1             5              99
  N2             1              76
  N3             1              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"
D1161V6, binary
                 cls
clus                0   1
  PIAS1 MUTATED     7   0
  PIAS1 WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED      7    0
  PIAS1 WILD-TYPE  339   29
   clus
vv  PIAS1 MUTATED PIAS1 WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D1161V7, binary
                 cls
clus                0   1
  PIAS1 MUTATED     5   4
  PIAS1 WILD-TYPE 140 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED      5    4
  PIAS1 WILD-TYPE  140  244
        clus
vv       PIAS1 MUTATED PIAS1 WILD-TYPE
  FEMALE             5             140
  MALE               4             244
[1] 2 2
[1] FALSE
D1161V8, binary
                 cls
clus                0   1
  PIAS1 MUTATED     9   0
  PIAS1 WILD-TYPE 283  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED      9    0
  PIAS1 WILD-TYPE  283   59
     clus
vv    PIAS1 MUTATED PIAS1 WILD-TYPE
  NO              9             283
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PIAS1 MUTATED                                          0
  PIAS1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PIAS1 MUTATED                                       0
  PIAS1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIAS1 MUTATED                                                        7
  PIAS1 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PIAS1 MUTATED                                                   0
  PIAS1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PIAS1 MUTATED                                                                   2
  PIAS1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PIAS1 MUTATED                                                    0
  PIAS1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PIAS1 MUTATED                                                  0
  PIAS1 WILD-TYPE                                               61
D1161V9, multiclass
                                                                   clus
vv                                                                  PIAS1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  PIAS1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PIAS1 MUTATED     8   0   0   1
  PIAS1 WILD-TYPE 303  14  15  23
D1161V10, multiclass
    clus
vv   PIAS1 MUTATED PIAS1 WILD-TYPE
  R0             8             303
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1161V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  PIAS1 MUTATED       0                         1
  PIAS1 WILD-TYPE    87                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PIAS1 MUTATED                                           0     6
  PIAS1 WILD-TYPE                                         1   237
D1161V12, multiclass
                                           clus
vv                                          PIAS1 MUTATED PIAS1 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1161V13, binary
                 cls
clus                0   1
  PIAS1 MUTATED     0   7
  PIAS1 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS1 MUTATED      0    7
  PIAS1 WILD-TYPE    4  303
                        clus
vv                       PIAS1 MUTATED PIAS1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(1162) Variable = FLJ10357 MUTATION ANALYSIS
D1162V1, survival
                    sevent
clus2                  0   1
  FLJ10357 MUTATED    10   5
  FLJ10357 WILD-TYPE 220 134
  FLJ10357 MUTATED FLJ10357 WILD-TYPE 
                15                354 
  FLJ10357 MUTATED FLJ10357 WILD-TYPE 
                 5                134 
$`FLJ10357 MUTATED`
TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8284 TCGA-BR-8487 TCGA-BR-8591 
        9.34        34.68        44.94         8.05         1.12        28.14 
TCGA-BR-8680 TCGA-D7-A6EY TCGA-F1-6874 TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-8602 
       31.96        11.44        14.47        77.29        26.47        22.32 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-VQ-A8P2 
       29.98         0.10        38.14 

$`FLJ10357 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-F1-6875 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-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-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-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 

  FLJ10357 MUTATED FLJ10357 WILD-TYPE 
               0.1                0.0 
  FLJ10357 MUTATED FLJ10357 WILD-TYPE 
             77.29             122.30 
  FLJ10357 MUTATED FLJ10357 WILD-TYPE 
             26.47              14.07 
[1] "0.1 - 77.3 (26.5)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D1162V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FLJ10357 MUTATED         1        0        3        1         4         1
  FLJ10357 WILD-TYPE       1       15       37       29        33        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FLJ10357 MUTATED           0          2          1          3        1
  FLJ10357 WILD-TYPE         3         68         52         29       37
D1162V3, multiclass
            clus
vv           FLJ10357 MUTATED FLJ10357 WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  0                 15
  STAGE IB                  3                 37
  STAGE II                  1                 29
  STAGE IIA                 4                 33
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                2                 68
  STAGE IIIB                1                 52
  STAGE IIIC                3                 29
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  FLJ10357 MUTATED     1   5   5   7
  FLJ10357 WILD-TYPE  21  87 168  90
D1162V4, multiclass
    clus
vv   FLJ10357 MUTATED FLJ10357 WILD-TYPE
  T1                1                 21
  T2                5                 87
  T3                5                168
  T4                7                 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
  FLJ10357 MUTATED     8   6   2   3
  FLJ10357 WILD-TYPE 110  98  75  74
D1162V5, multiclass
    clus
vv   FLJ10357 MUTATED FLJ10357 WILD-TYPE
  N0                8                110
  N1                6                 98
  N2                2                 75
  N3                3                 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"
D1162V6, binary
                    cls
clus                   0   1
  FLJ10357 MUTATED    16   1
  FLJ10357 WILD-TYPE 330  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FLJ10357 MUTATED     16    1
  FLJ10357 WILD-TYPE  330   28
   clus
vv  FLJ10357 MUTATED FLJ10357 WILD-TYPE
  0               16                330
  1                1                 28
[1] 2 2
[1] FALSE
D1162V7, binary
                    cls
clus                   0   1
  FLJ10357 MUTATED    10  10
  FLJ10357 WILD-TYPE 135 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FLJ10357 MUTATED     10   10
  FLJ10357 WILD-TYPE  135  238
        clus
vv       FLJ10357 MUTATED FLJ10357 WILD-TYPE
  FEMALE               10                135
  MALE                 10                238
[1] 2 2
[1] FALSE
D1162V8, binary
                    cls
clus                   0   1
  FLJ10357 MUTATED    14   2
  FLJ10357 WILD-TYPE 278  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FLJ10357 MUTATED     14    2
  FLJ10357 WILD-TYPE  278   57
     clus
vv    FLJ10357 MUTATED FLJ10357 WILD-TYPE
  NO                14                278
  YES                2                 57
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FLJ10357 MUTATED                                          1
  FLJ10357 WILD-TYPE                                        7
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FLJ10357 MUTATED                                       1
  FLJ10357 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FLJ10357 MUTATED                                                        9
  FLJ10357 WILD-TYPE                                                    149
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FLJ10357 MUTATED                                                   2
  FLJ10357 WILD-TYPE                                                19
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FLJ10357 MUTATED                                                                   3
  FLJ10357 WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FLJ10357 MUTATED                                                    0
  FLJ10357 WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FLJ10357 MUTATED                                                  4
  FLJ10357 WILD-TYPE                                               57
D1162V9, multiclass
                                                                   clus
vv                                                                  FLJ10357 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 4
                                                                   clus
vv                                                                  FLJ10357 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           149
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  FLJ10357 MUTATED    16   0   0   4
  FLJ10357 WILD-TYPE 295  14  15  20
D1162V10, multiclass
    clus
vv   FLJ10357 MUTATED FLJ10357 WILD-TYPE
  R0               16                295
  R1                0                 14
  R2                0                 15
  RX                4                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1162V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  FLJ10357 MUTATED       4                         1
  FLJ10357 WILD-TYPE    83                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FLJ10357 MUTATED                                           0    13
  FLJ10357 WILD-TYPE                                         1   230
D1162V12, multiclass
                                           clus
vv                                          FLJ10357 MUTATED FLJ10357 WILD-TYPE
  ASIAN                                                    4                 83
  BLACK OR AFRICAN AMERICAN                                1                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   13                230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1162V13, binary
                    cls
clus                   0   1
  FLJ10357 MUTATED     0  17
  FLJ10357 WILD-TYPE   4 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FLJ10357 MUTATED      0   17
  FLJ10357 WILD-TYPE    4  293
                        clus
vv                       FLJ10357 MUTATED FLJ10357 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               17                293
[1] 2 2
[1] FALSE

Clustering(1163) Variable = SMC5 MUTATION ANALYSIS
D1163V1, survival
                sevent
clus2              0   1
  SMC5 MUTATED     6   4
  SMC5 WILD-TYPE 224 135
  SMC5 MUTATED SMC5 WILD-TYPE 
            10            359 
  SMC5 MUTATED SMC5 WILD-TYPE 
             4            135 
$`SMC5 MUTATED`
TCGA-BR-4184 TCGA-BR-4257 TCGA-BR-8059 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8591 
        6.97         9.67        14.43         0.26         4.31        28.14 
TCGA-BR-8680 TCGA-HF-7133 TCGA-HU-A4GT TCGA-VQ-A8P2 
       31.96        63.06         6.51        38.14 

$`SMC5 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-7134 TCGA-HF-A5NB 
       11.08         5.52         6.21        77.29        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-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 

  SMC5 MUTATED SMC5 WILD-TYPE 
          0.26           0.00 
  SMC5 MUTATED SMC5 WILD-TYPE 
         63.06         122.30 
  SMC5 MUTATED SMC5 WILD-TYPE 
         12.05          14.27 
[1] "0.3 - 63.1 (12.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.1"
D1163V2, 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       2       15       38       30        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMC5 MUTATED           1          2          0          1        2
  SMC5 WILD-TYPE         2         68         53         31       36
D1163V3, multiclass
            clus
vv           SMC5 MUTATED SMC5 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              2             38
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             0             52
  STAGE III             1              2
  STAGE IIIA            2             68
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SMC5 MUTATED     0   3   2   4
  SMC5 WILD-TYPE  22  89 171  93
D1163V4, multiclass
    clus
vv   SMC5 MUTATED SMC5 WILD-TYPE
  T1            0             22
  T2            3             89
  T3            2            171
  T4            4             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
  SMC5 MUTATED     3   3   1   2
  SMC5 WILD-TYPE 115 101  76  75
D1163V5, multiclass
    clus
vv   SMC5 MUTATED SMC5 WILD-TYPE
  N0            3            115
  N1            3            101
  N2            1             76
  N3            2             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"
D1163V6, binary
                cls
clus               0   1
  SMC5 MUTATED     8   1
  SMC5 WILD-TYPE 338  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC5 MUTATED      8    1
  SMC5 WILD-TYPE  338   28
   clus
vv  SMC5 MUTATED SMC5 WILD-TYPE
  0            8            338
  1            1             28
[1] 2 2
[1] FALSE
D1163V7, binary
                cls
clus               0   1
  SMC5 MUTATED     5   5
  SMC5 WILD-TYPE 140 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC5 MUTATED      5    5
  SMC5 WILD-TYPE  140  243
        clus
vv       SMC5 MUTATED SMC5 WILD-TYPE
  FEMALE            5            140
  MALE              5            243
[1] 2 2
[1] FALSE
D1163V8, binary
                cls
clus               0   1
  SMC5 MUTATED     8   2
  SMC5 WILD-TYPE 284  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC5 MUTATED      8    2
  SMC5 WILD-TYPE  284   57
     clus
vv    SMC5 MUTATED SMC5 WILD-TYPE
  NO             8            284
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SMC5 MUTATED                                          0
  SMC5 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SMC5 MUTATED                                       0
  SMC5 WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMC5 MUTATED                                                        5
  SMC5 WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SMC5 MUTATED                                                   2
  SMC5 WILD-TYPE                                                19
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SMC5 MUTATED                                                                   1
  SMC5 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SMC5 MUTATED                                                    0
  SMC5 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SMC5 MUTATED                                                  2
  SMC5 WILD-TYPE                                               59
D1163V9, multiclass
                                                                   clus
vv                                                                  SMC5 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  SMC5 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SMC5 MUTATED     7   1   0   2
  SMC5 WILD-TYPE 304  13  15  22
D1163V10, multiclass
    clus
vv   SMC5 MUTATED SMC5 WILD-TYPE
  R0            7            304
  R1            1             13
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1163V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SMC5 MUTATED       2                         0
  SMC5 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SMC5 MUTATED                                           0     7
  SMC5 WILD-TYPE                                         1   236
D1163V12, multiclass
                                           clus
vv                                          SMC5 MUTATED SMC5 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1163V13, binary
                cls
clus               0   1
  SMC5 MUTATED     0   8
  SMC5 WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC5 MUTATED      0    8
  SMC5 WILD-TYPE    4  302
                        clus
vv                       SMC5 MUTATED SMC5 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(1164) Variable = ATOH1 MUTATION ANALYSIS
D1164V1, survival
                 sevent
clus2               0   1
  ATOH1 MUTATED     3   3
  ATOH1 WILD-TYPE 227 136
  ATOH1 MUTATED ATOH1 WILD-TYPE 
              6             363 
  ATOH1 MUTATED ATOH1 WILD-TYPE 
              3             136 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-F1-6874 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 

  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           14.17 
[1] "6.0 - 44.9 (22.6)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D1164V2, 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       2       14       40       30        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATOH1 MUTATED           1          0          1          0        1
  ATOH1 WILD-TYPE         2         70         52         32       37
D1164V3, multiclass
            clus
vv           ATOH1 MUTATED ATOH1 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              1               2
  STAGE IIIA             0              70
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATOH1 MUTATED     1   1   2   2
  ATOH1 WILD-TYPE  21  91 171  95
D1164V4, multiclass
    clus
vv   ATOH1 MUTATED ATOH1 WILD-TYPE
  T1             1              21
  T2             1              91
  T3             2             171
  T4             2              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
  ATOH1 MUTATED     3   2   0   1
  ATOH1 WILD-TYPE 115 102  77  76
D1164V5, multiclass
    clus
vv   ATOH1 MUTATED ATOH1 WILD-TYPE
  N0             3             115
  N1             2             102
  N2             0              77
  N3             1              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"
D1164V6, binary
                 cls
clus                0   1
  ATOH1 MUTATED     6   0
  ATOH1 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATOH1 MUTATED      6    0
  ATOH1 WILD-TYPE  340   29
   clus
vv  ATOH1 MUTATED ATOH1 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D1164V7, binary
                 cls
clus                0   1
  ATOH1 MUTATED     4   2
  ATOH1 WILD-TYPE 141 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATOH1 MUTATED      4    2
  ATOH1 WILD-TYPE  141  246
        clus
vv       ATOH1 MUTATED ATOH1 WILD-TYPE
  FEMALE             4             141
  MALE               2             246
[1] 2 2
[1] FALSE
D1164V8, binary
                 cls
clus                0   1
  ATOH1 MUTATED     5   0
  ATOH1 WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATOH1 MUTATED      5    0
  ATOH1 WILD-TYPE  287   59
     clus
vv    ATOH1 MUTATED ATOH1 WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ATOH1 MUTATED                                          0
  ATOH1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ATOH1 MUTATED                                       0
  ATOH1 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATOH1 MUTATED                                                        4
  ATOH1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ATOH1 MUTATED                                                   0
  ATOH1 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ATOH1 MUTATED                                                                   2
  ATOH1 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ATOH1 MUTATED                                                    0
  ATOH1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ATOH1 MUTATED                                                  0
  ATOH1 WILD-TYPE                                               61
D1164V9, multiclass
                                                                   clus
vv                                                                  ATOH1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  ATOH1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ATOH1 MUTATED     5   0   0   1
  ATOH1 WILD-TYPE 306  14  15  23
D1164V10, multiclass
    clus
vv   ATOH1 MUTATED ATOH1 WILD-TYPE
  R0             5             306
  R1             0              14
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1164V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ATOH1 MUTATED       0                         0
  ATOH1 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ATOH1 MUTATED                                           0     4
  ATOH1 WILD-TYPE                                         1   239
D1164V12, multiclass
                                           clus
vv                                          ATOH1 MUTATED ATOH1 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1164V13, binary
                 cls
clus                0   1
  ATOH1 MUTATED     0   4
  ATOH1 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATOH1 MUTATED      0    4
  ATOH1 WILD-TYPE    4  306
                        clus
vv                       ATOH1 MUTATED ATOH1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(1165) Variable = AAMP MUTATION ANALYSIS
D1165V1, survival
                sevent
clus2              0   1
  AAMP MUTATED     2   1
  AAMP WILD-TYPE 228 138
  AAMP MUTATED AAMP WILD-TYPE 
             3            366 
  AAMP MUTATED AAMP WILD-TYPE 
             1            138 
$`AAMP MUTATED`
TCGA-BR-4257 TCGA-BR-6566 TCGA-BR-7707 
        9.67        32.78        35.84 

$`AAMP WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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 

  AAMP MUTATED AAMP WILD-TYPE 
          9.67           0.00 
  AAMP MUTATED AAMP WILD-TYPE 
         35.84         122.30 
  AAMP MUTATED AAMP WILD-TYPE 
         32.78          14.22 
[1] "9.7 - 35.8 (32.8)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.6"
D1165V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  AAMP MUTATED         0        0        1        0         1         0
  AAMP WILD-TYPE       2       15       39       30        36        52
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AAMP MUTATED           0          0          0          0        0
  AAMP WILD-TYPE         3         70         53         32       38
D1165V3, multiclass
[1] "Remove cluster labels:" "AAMP MUTATED"          
clus
  AAMP MUTATED AAMP WILD-TYPE 
             2            370 
    TCGA-CG-4444     TCGA-CG-4460     TCGA-CG-4475     TCGA-CG-4476 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5716     TCGA-CG-5727     TCGA-EQ-A4SO     TCGA-F1-6177 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-A8CX     TCGA-HF-7131     TCGA-KB-A93G     TCGA-MX-A663 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-B7-5816     TCGA-B7-5818     TCGA-B7-A5TI     TCGA-B7-A5TJ 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-B7-A5TK     TCGA-B7-A5TN     TCGA-BR-4183     TCGA-BR-4184 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-4253     TCGA-BR-4255     TCGA-BR-4267     TCGA-BR-4279 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-4280     TCGA-BR-4361     TCGA-BR-4368     TCGA-BR-6452 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6453     TCGA-BR-6454     TCGA-BR-6455     TCGA-BR-6456 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6457     TCGA-BR-6458     TCGA-BR-6563     TCGA-BR-6564 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6565     TCGA-BR-6705     TCGA-BR-6706     TCGA-BR-6707 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6709     TCGA-BR-6710     TCGA-BR-6801     TCGA-BR-6802 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6803     TCGA-BR-6852     TCGA-BR-7196     TCGA-BR-7197 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-7703     TCGA-BR-7704     TCGA-BR-7715     TCGA-BR-7716 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-7717     TCGA-BR-7722     TCGA-BR-7723     TCGA-BR-7851 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-7901     TCGA-BR-7957     TCGA-BR-7958     TCGA-BR-7959 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8058     TCGA-BR-8059     TCGA-BR-8060     TCGA-BR-8077 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8078     TCGA-BR-8080     TCGA-BR-8081     TCGA-BR-8284 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8285     TCGA-BR-8286     TCGA-BR-8289     TCGA-BR-8291 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8295     TCGA-BR-8297     TCGA-BR-8360     TCGA-BR-8361 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8363     TCGA-BR-8364     TCGA-BR-8365     TCGA-BR-8366 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8367     TCGA-BR-8368     TCGA-BR-8369     TCGA-BR-8370 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8371     TCGA-BR-8372     TCGA-BR-8373     TCGA-BR-8380 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8381     TCGA-BR-8382     TCGA-BR-8384     TCGA-BR-8483 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8484     TCGA-BR-8485     TCGA-BR-8486     TCGA-BR-8487 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8588     TCGA-BR-8589     TCGA-BR-8590     TCGA-BR-8591 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8592     TCGA-BR-8676     TCGA-BR-8677     TCGA-BR-8678 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8679     TCGA-BR-8680     TCGA-BR-8682     TCGA-BR-8683 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8686     TCGA-BR-8687     TCGA-BR-8690     TCGA-BR-A44T 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A44U     TCGA-BR-A452     TCGA-BR-A453     TCGA-BR-A4CQ 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4CR     TCGA-BR-A4CS     TCGA-BR-A4IU     TCGA-BR-A4IV 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4IY     TCGA-BR-A4IZ     TCGA-BR-A4J1     TCGA-BR-A4J2 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4J4     TCGA-BR-A4J5     TCGA-BR-A4J6     TCGA-BR-A4J7 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4J8     TCGA-BR-A4PD     TCGA-BR-A4PE     TCGA-BR-A4PF 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4QI     TCGA-BR-A4QL     TCGA-BR-A4QM     TCGA-CD-5798 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-5799     TCGA-CD-5800     TCGA-CD-5801     TCGA-CD-5802 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-5803     TCGA-CD-5813     TCGA-CD-8524     TCGA-CD-8525 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-8526     TCGA-CD-8527     TCGA-CD-8528     TCGA-CD-8529 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-8530     TCGA-CD-8531     TCGA-CD-8532     TCGA-CD-8533 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-8534     TCGA-CD-8535     TCGA-CD-8536     TCGA-CD-A486 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-A487     TCGA-CD-A489     TCGA-CD-A48A     TCGA-CD-A48C 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-A4MG     TCGA-CD-A4MH     TCGA-CD-A4MI     TCGA-CD-A4MJ 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4300     TCGA-CG-4301     TCGA-CG-4304     TCGA-CG-4305 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4306     TCGA-CG-4436     TCGA-CG-4437     TCGA-CG-4438 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4440     TCGA-CG-4441     TCGA-CG-4442     TCGA-CG-4443 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4449     TCGA-CG-4455     TCGA-CG-4462     TCGA-CG-4465 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4466     TCGA-CG-4469     TCGA-CG-4474     TCGA-CG-4477 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5717     TCGA-CG-5718     TCGA-CG-5719     TCGA-CG-5720 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5721     TCGA-CG-5722     TCGA-CG-5723     TCGA-CG-5724 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5725     TCGA-CG-5726     TCGA-CG-5728     TCGA-CG-5730 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5732     TCGA-CG-5733     TCGA-CG-5734     TCGA-D7-5577 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-5578     TCGA-D7-5579     TCGA-D7-6518     TCGA-D7-6520 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-6522     TCGA-D7-6524     TCGA-D7-6525     TCGA-D7-6526 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-6527     TCGA-D7-6528     TCGA-D7-6815     TCGA-D7-6817 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-6818     TCGA-D7-6820     TCGA-D7-6822     TCGA-D7-8570 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-8572     TCGA-D7-8573     TCGA-D7-8574     TCGA-D7-8575 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-8576     TCGA-D7-8578     TCGA-D7-8579     TCGA-D7-A4YT 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A4YU     TCGA-D7-A4YV     TCGA-D7-A4YX     TCGA-D7-A4YY 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A4Z0     TCGA-D7-A6ET     TCGA-D7-A6EV     TCGA-D7-A6EX 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A6EY     TCGA-D7-A6EZ     TCGA-D7-A6F0     TCGA-D7-A6F2 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A747     TCGA-D7-A748     TCGA-D7-A74A     TCGA-D7-A74B 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-EQ-5647     TCGA-EQ-8122     TCGA-F1-6874     TCGA-F1-6875 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-F1-A448     TCGA-F1-A72C     TCGA-FP-7735     TCGA-FP-7829 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-7916     TCGA-FP-7998     TCGA-FP-8099     TCGA-FP-8209 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-8210     TCGA-FP-8211     TCGA-FP-8631     TCGA-FP-A4BE 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-A4BF     TCGA-HF-7132     TCGA-HF-7133     TCGA-HF-7134 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HF-7136     TCGA-HF-A5NB     TCGA-HJ-7597     TCGA-HU-8243 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-8244     TCGA-HU-8249     TCGA-HU-8602     TCGA-HU-8604 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-8608     TCGA-HU-8610     TCGA-HU-A4G2     TCGA-HU-A4G3 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4G6     TCGA-HU-A4G8     TCGA-HU-A4G9     TCGA-HU-A4GC 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4GD     TCGA-HU-A4GF     TCGA-HU-A4GH     TCGA-HU-A4GJ 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4GN     TCGA-HU-A4GP     TCGA-HU-A4GQ     TCGA-HU-A4GT 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4GU     TCGA-HU-A4GX     TCGA-HU-A4GY     TCGA-HU-A4H0 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4H2     TCGA-HU-A4H3     TCGA-HU-A4H4     TCGA-HU-A4H5 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4H6     TCGA-HU-A4H8     TCGA-HU-A4HB     TCGA-HU-A4HD 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-7806     TCGA-IN-8462     TCGA-IN-8663     TCGA-IN-A6RI 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-A6RJ     TCGA-IN-A6RL     TCGA-IN-A6RN     TCGA-IN-A6RO 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-A6RP     TCGA-IN-A6RR     TCGA-IN-A6RS     TCGA-IN-A7NR 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-A7NT     TCGA-IN-A7NU     TCGA-IN-AB1V     TCGA-IN-AB1X 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IP-7968     TCGA-KB-A6F5     TCGA-KB-A6F7     TCGA-KB-A93J 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-MX-A5UG     TCGA-MX-A5UJ     TCGA-MX-A666     TCGA-R5-A7O7 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-R5-A7ZE     TCGA-R5-A7ZF     TCGA-R5-A7ZI     TCGA-R5-A7ZR 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-R5-A804     TCGA-R5-A805     TCGA-RD-A7BS     TCGA-RD-A7BT 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-RD-A7BW     TCGA-RD-A7C1     TCGA-RD-A8MV     TCGA-RD-A8MW 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-RD-A8N0     TCGA-RD-A8N1     TCGA-RD-A8N2     TCGA-RD-A8N4 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-RD-A8N5     TCGA-RD-A8N6     TCGA-RD-A8N9     TCGA-SW-A7EA 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-SW-A7EB     TCGA-VQ-A8DL     TCGA-VQ-A8DT     TCGA-VQ-A8DU 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A8DV     TCGA-VQ-A8DZ     TCGA-VQ-A8E2     TCGA-VQ-A8E7 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A8P2     TCGA-VQ-A8P3     TCGA-VQ-A8PE     TCGA-VQ-A8PK 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A8PM     TCGA-VQ-A8PQ     TCGA-VQ-A91Q     TCGA-VQ-A91U 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A91V     TCGA-VQ-A92D     TCGA-VQ-A94T     TCGA-VQ-AA64 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-AA68     TCGA-VQ-AA69     TCGA-VQ-AA6A     TCGA-VQ-AA6B 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-AA6F     TCGA-VQ-AA6G     TCGA-VQ-AA6I     TCGA-VQ-AA6J 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-AA6K     TCGA-ZA-A8F6 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" 
                vv
clus              T1  T2  T3  T4
  AAMP MUTATED     0   1   1   0
  AAMP WILD-TYPE  22  91 172  97
D1165V4, multiclass
[1] "Remove cluster labels:" "AAMP MUTATED"          
clus
  AAMP MUTATED AAMP WILD-TYPE 
             2            382 
    TCGA-CG-4444     TCGA-CG-4460     TCGA-CG-4475     TCGA-CG-4476 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5716     TCGA-CG-5727     TCGA-EQ-A4SO     TCGA-F1-6177 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-A8CX     TCGA-HF-7131     TCGA-KB-A93G     TCGA-MX-A663 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-B7-5816     TCGA-B7-5818     TCGA-B7-A5TI     TCGA-B7-A5TJ 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-B7-A5TK     TCGA-B7-A5TN     TCGA-BR-4183     TCGA-BR-4184 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-4201     TCGA-BR-4253     TCGA-BR-4255     TCGA-BR-4267 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-4279     TCGA-BR-4280     TCGA-BR-4292     TCGA-BR-4294 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-4357     TCGA-BR-4361     TCGA-BR-4363     TCGA-BR-4368 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-4371     TCGA-BR-6452     TCGA-BR-6453     TCGA-BR-6454 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6455     TCGA-BR-6456     TCGA-BR-6457     TCGA-BR-6458 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6563     TCGA-BR-6564     TCGA-BR-6565     TCGA-BR-6705 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6706     TCGA-BR-6707     TCGA-BR-6709     TCGA-BR-6710 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6801     TCGA-BR-6802     TCGA-BR-6803     TCGA-BR-6852 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-7196     TCGA-BR-7197     TCGA-BR-7703     TCGA-BR-7704 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-7715     TCGA-BR-7716     TCGA-BR-7717     TCGA-BR-7722 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-7723     TCGA-BR-7851     TCGA-BR-7901     TCGA-BR-7957 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-7958     TCGA-BR-7959     TCGA-BR-8058     TCGA-BR-8059 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8060     TCGA-BR-8077     TCGA-BR-8078     TCGA-BR-8080 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8081     TCGA-BR-8284     TCGA-BR-8285     TCGA-BR-8286 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8289     TCGA-BR-8291     TCGA-BR-8295     TCGA-BR-8297 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8360     TCGA-BR-8361     TCGA-BR-8363     TCGA-BR-8364 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8365     TCGA-BR-8366     TCGA-BR-8367     TCGA-BR-8368 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8369     TCGA-BR-8370     TCGA-BR-8371     TCGA-BR-8372 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8373     TCGA-BR-8380     TCGA-BR-8381     TCGA-BR-8382 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8384     TCGA-BR-8483     TCGA-BR-8484     TCGA-BR-8485 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8486     TCGA-BR-8487     TCGA-BR-8588     TCGA-BR-8589 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8590     TCGA-BR-8591     TCGA-BR-8592     TCGA-BR-8676 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8677     TCGA-BR-8678     TCGA-BR-8679     TCGA-BR-8680 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8682     TCGA-BR-8683     TCGA-BR-8686     TCGA-BR-8687 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8690     TCGA-BR-A44T     TCGA-BR-A44U     TCGA-BR-A452 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A453     TCGA-BR-A4CQ     TCGA-BR-A4CR     TCGA-BR-A4CS 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4IU     TCGA-BR-A4IV     TCGA-BR-A4IY     TCGA-BR-A4IZ 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4J1     TCGA-BR-A4J2     TCGA-BR-A4J4     TCGA-BR-A4J5 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4J6     TCGA-BR-A4J7     TCGA-BR-A4J8     TCGA-BR-A4PD 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4PE     TCGA-BR-A4PF     TCGA-BR-A4QI     TCGA-BR-A4QL 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4QM     TCGA-CD-5798     TCGA-CD-5799     TCGA-CD-5800 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-5801     TCGA-CD-5802     TCGA-CD-5803     TCGA-CD-5804 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-5813     TCGA-CD-8524     TCGA-CD-8525     TCGA-CD-8526 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-8527     TCGA-CD-8528     TCGA-CD-8529     TCGA-CD-8530 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-8531     TCGA-CD-8532     TCGA-CD-8533     TCGA-CD-8534 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-8535     TCGA-CD-8536     TCGA-CD-A486     TCGA-CD-A487 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-A489     TCGA-CD-A48A     TCGA-CD-A48C     TCGA-CD-A4MG 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-A4MH     TCGA-CD-A4MI     TCGA-CD-A4MJ     TCGA-CG-4300 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4301     TCGA-CG-4304     TCGA-CG-4305     TCGA-CG-4306 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4436     TCGA-CG-4437     TCGA-CG-4438     TCGA-CG-4440 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4441     TCGA-CG-4442     TCGA-CG-4443     TCGA-CG-4449 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4455     TCGA-CG-4462     TCGA-CG-4465     TCGA-CG-4466 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4469     TCGA-CG-4474     TCGA-CG-4477     TCGA-CG-5717 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5718     TCGA-CG-5719     TCGA-CG-5720     TCGA-CG-5721 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5722     TCGA-CG-5723     TCGA-CG-5724     TCGA-CG-5725 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5726     TCGA-CG-5728     TCGA-CG-5730     TCGA-CG-5732 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5733     TCGA-CG-5734     TCGA-D7-5577     TCGA-D7-5578 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-5579     TCGA-D7-6518     TCGA-D7-6519     TCGA-D7-6520 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-6521     TCGA-D7-6522     TCGA-D7-6524     TCGA-D7-6525 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-6526     TCGA-D7-6527     TCGA-D7-6528     TCGA-D7-6815 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-6817     TCGA-D7-6818     TCGA-D7-6820     TCGA-D7-6822 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-8570     TCGA-D7-8572     TCGA-D7-8573     TCGA-D7-8574 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-8575     TCGA-D7-8576     TCGA-D7-8578     TCGA-D7-8579 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A4YT     TCGA-D7-A4YU     TCGA-D7-A4YV     TCGA-D7-A4YX 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A4YY     TCGA-D7-A4Z0     TCGA-D7-A6ET     TCGA-D7-A6EV 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A6EX     TCGA-D7-A6EY     TCGA-D7-A6EZ     TCGA-D7-A6F0 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A6F2     TCGA-D7-A747     TCGA-D7-A748     TCGA-D7-A74A 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A74B     TCGA-EQ-5647     TCGA-EQ-8122     TCGA-F1-6874 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-F1-6875     TCGA-F1-A448     TCGA-F1-A72C     TCGA-FP-7735 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-7829     TCGA-FP-7916     TCGA-FP-7998     TCGA-FP-8099 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-8209     TCGA-FP-8210     TCGA-FP-8211     TCGA-FP-8631 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-A4BE     TCGA-FP-A4BF     TCGA-FP-A9TM     TCGA-HF-7132 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HF-7133     TCGA-HF-7134     TCGA-HF-7136     TCGA-HF-A5NB 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HJ-7597     TCGA-HU-8238     TCGA-HU-8243     TCGA-HU-8244 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-8249     TCGA-HU-8602     TCGA-HU-8604     TCGA-HU-8608 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-8610     TCGA-HU-A4G2     TCGA-HU-A4G3     TCGA-HU-A4G6 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4G8     TCGA-HU-A4G9     TCGA-HU-A4GC     TCGA-HU-A4GD 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4GF     TCGA-HU-A4GH     TCGA-HU-A4GJ     TCGA-HU-A4GN 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4GP     TCGA-HU-A4GQ     TCGA-HU-A4GT     TCGA-HU-A4GU 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4GX     TCGA-HU-A4GY     TCGA-HU-A4H0     TCGA-HU-A4H2 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4H3     TCGA-HU-A4H4     TCGA-HU-A4H5     TCGA-HU-A4H6 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4H8     TCGA-HU-A4HB     TCGA-HU-A4HD     TCGA-IN-7806 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-7808     TCGA-IN-8462     TCGA-IN-8663     TCGA-IN-A6RI 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-A6RJ     TCGA-IN-A6RL     TCGA-IN-A6RN     TCGA-IN-A6RO 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-A6RP     TCGA-IN-A6RR     TCGA-IN-A6RS     TCGA-IN-A7NR 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-A7NT     TCGA-IN-A7NU     TCGA-IN-AB1V     TCGA-IN-AB1X 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IP-7968     TCGA-KB-A6F5     TCGA-KB-A6F7     TCGA-KB-A93J 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-MX-A5UG     TCGA-MX-A5UJ     TCGA-MX-A666     TCGA-R5-A7O7 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-R5-A7ZE     TCGA-R5-A7ZF     TCGA-R5-A7ZI     TCGA-R5-A7ZR 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-R5-A804     TCGA-R5-A805     TCGA-RD-A7BS     TCGA-RD-A7BT 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-RD-A7BW     TCGA-RD-A7C1     TCGA-RD-A8MV     TCGA-RD-A8MW 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-RD-A8N0     TCGA-RD-A8N1     TCGA-RD-A8N2     TCGA-RD-A8N4 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-RD-A8N5     TCGA-RD-A8N6     TCGA-RD-A8N9     TCGA-SW-A7EA 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-SW-A7EB     TCGA-VQ-A8DL     TCGA-VQ-A8DT     TCGA-VQ-A8DU 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A8DV     TCGA-VQ-A8DZ     TCGA-VQ-A8E2     TCGA-VQ-A8E7 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A8P2     TCGA-VQ-A8P3     TCGA-VQ-A8PE     TCGA-VQ-A8PK 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A8PM     TCGA-VQ-A8PQ     TCGA-VQ-A91Q     TCGA-VQ-A91U 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A91V     TCGA-VQ-A92D     TCGA-VQ-A94T     TCGA-VQ-AA64 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-AA68     TCGA-VQ-AA69     TCGA-VQ-AA6A     TCGA-VQ-AA6B 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-AA6F     TCGA-VQ-AA6G     TCGA-VQ-AA6I     TCGA-VQ-AA6J 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-AA6K     TCGA-ZA-A8F6 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" 
                vv
clus              N0  N1  N2  N3
  AAMP MUTATED     2   0   0   0
  AAMP WILD-TYPE 116 104  77  77
D1165V5, multiclass
[1] "Remove cluster labels:" "AAMP MUTATED"          
clus
  AAMP MUTATED AAMP WILD-TYPE 
             2            374 
    TCGA-CG-4444     TCGA-CG-4460     TCGA-CG-4475     TCGA-CG-4476 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5716     TCGA-CG-5727     TCGA-EQ-A4SO     TCGA-F1-6177 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-A8CX     TCGA-HF-7131     TCGA-KB-A93G     TCGA-MX-A663 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-B7-5816     TCGA-B7-5818     TCGA-B7-A5TI     TCGA-BR-4183 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-4184     TCGA-BR-4188     TCGA-BR-4191     TCGA-BR-4253 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-4255     TCGA-BR-4256     TCGA-BR-4267     TCGA-BR-4279 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-4280     TCGA-BR-4361     TCGA-BR-4362     TCGA-BR-4368 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6452     TCGA-BR-6453     TCGA-BR-6454     TCGA-BR-6455 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6456     TCGA-BR-6457     TCGA-BR-6458     TCGA-BR-6563 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6564     TCGA-BR-6565     TCGA-BR-6705     TCGA-BR-6706 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6707     TCGA-BR-6709     TCGA-BR-6710     TCGA-BR-6801 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6802     TCGA-BR-6803     TCGA-BR-6852     TCGA-BR-7196 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-7197     TCGA-BR-7703     TCGA-BR-7704     TCGA-BR-7715 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-7716     TCGA-BR-7717     TCGA-BR-7722     TCGA-BR-7723 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-7851     TCGA-BR-7901     TCGA-BR-7957     TCGA-BR-7958 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-7959     TCGA-BR-8058     TCGA-BR-8059     TCGA-BR-8060 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8077     TCGA-BR-8078     TCGA-BR-8080     TCGA-BR-8081 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8284     TCGA-BR-8285     TCGA-BR-8286     TCGA-BR-8289 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8291     TCGA-BR-8295     TCGA-BR-8297     TCGA-BR-8360 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8361     TCGA-BR-8363     TCGA-BR-8364     TCGA-BR-8365 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8366     TCGA-BR-8367     TCGA-BR-8368     TCGA-BR-8369 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8370     TCGA-BR-8371     TCGA-BR-8372     TCGA-BR-8373 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8380     TCGA-BR-8381     TCGA-BR-8382     TCGA-BR-8384 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8483     TCGA-BR-8484     TCGA-BR-8485     TCGA-BR-8486 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8487     TCGA-BR-8588     TCGA-BR-8589     TCGA-BR-8590 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8591     TCGA-BR-8592     TCGA-BR-8676     TCGA-BR-8677 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8678     TCGA-BR-8679     TCGA-BR-8680     TCGA-BR-8682 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8683     TCGA-BR-8686     TCGA-BR-8687     TCGA-BR-8690 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A44T     TCGA-BR-A44U     TCGA-BR-A452     TCGA-BR-A453 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4CQ     TCGA-BR-A4CR     TCGA-BR-A4CS     TCGA-BR-A4IU 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4IV     TCGA-BR-A4IY     TCGA-BR-A4IZ     TCGA-BR-A4J1 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4J2     TCGA-BR-A4J4     TCGA-BR-A4J5     TCGA-BR-A4J6 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4J8     TCGA-BR-A4PD     TCGA-BR-A4PE     TCGA-BR-A4PF 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4QI     TCGA-BR-A4QL     TCGA-BR-A4QM     TCGA-CD-5798 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-5799     TCGA-CD-5800     TCGA-CD-5801     TCGA-CD-5802 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-5803     TCGA-CD-5804     TCGA-CD-5813     TCGA-CD-8524 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-8525     TCGA-CD-8526     TCGA-CD-8527     TCGA-CD-8528 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-8529     TCGA-CD-8530     TCGA-CD-8531     TCGA-CD-8532 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-8533     TCGA-CD-8534     TCGA-CD-8535     TCGA-CD-8536 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-A486     TCGA-CD-A487     TCGA-CD-A489     TCGA-CD-A48A 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-A48C     TCGA-CD-A4MG     TCGA-CD-A4MH     TCGA-CD-A4MI 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-A4MJ     TCGA-CG-4300     TCGA-CG-4301     TCGA-CG-4304 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4305     TCGA-CG-4306     TCGA-CG-4436     TCGA-CG-4437 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4438     TCGA-CG-4440     TCGA-CG-4441     TCGA-CG-4442 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4443     TCGA-CG-4449     TCGA-CG-4455     TCGA-CG-4462 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4465     TCGA-CG-4466     TCGA-CG-4469     TCGA-CG-4474 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4477     TCGA-CG-5717     TCGA-CG-5718     TCGA-CG-5719 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5720     TCGA-CG-5721     TCGA-CG-5722     TCGA-CG-5723 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5724     TCGA-CG-5725     TCGA-CG-5726     TCGA-CG-5728 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5730     TCGA-CG-5732     TCGA-CG-5733     TCGA-CG-5734 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-5577     TCGA-D7-5578     TCGA-D7-5579     TCGA-D7-6518 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-6519     TCGA-D7-6520     TCGA-D7-6521     TCGA-D7-6522 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-6524     TCGA-D7-6525     TCGA-D7-6526     TCGA-D7-6527 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-6528     TCGA-D7-6815     TCGA-D7-6817     TCGA-D7-6818 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-6820     TCGA-D7-6822     TCGA-D7-8570     TCGA-D7-8572 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-8573     TCGA-D7-8574     TCGA-D7-8575     TCGA-D7-8576 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-8578     TCGA-D7-8579     TCGA-D7-A4YT     TCGA-D7-A4YU 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A4YV     TCGA-D7-A4YX     TCGA-D7-A4YY     TCGA-D7-A4Z0 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A6ET     TCGA-D7-A6EV     TCGA-D7-A6EX     TCGA-D7-A6EY 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A6EZ     TCGA-D7-A6F0     TCGA-D7-A6F2     TCGA-D7-A747 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A748     TCGA-D7-A74A     TCGA-D7-A74B     TCGA-EQ-5647 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-EQ-8122     TCGA-F1-6874     TCGA-F1-6875     TCGA-F1-A448 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-F1-A72C     TCGA-FP-7735     TCGA-FP-7829     TCGA-FP-7916 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-7998     TCGA-FP-8099     TCGA-FP-8209     TCGA-FP-8210 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-8211     TCGA-FP-8631     TCGA-FP-A4BE     TCGA-FP-A4BF 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-A9TM     TCGA-HF-7132     TCGA-HF-7133     TCGA-HF-7134 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HF-7136     TCGA-HF-A5NB     TCGA-HJ-7597     TCGA-HU-8238 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-8243     TCGA-HU-8244     TCGA-HU-8249     TCGA-HU-8602 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-8604     TCGA-HU-8608     TCGA-HU-8610     TCGA-HU-A4G2 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4G3     TCGA-HU-A4G6     TCGA-HU-A4G8     TCGA-HU-A4G9 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4GC     TCGA-HU-A4GD     TCGA-HU-A4GF     TCGA-HU-A4GH 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4GJ     TCGA-HU-A4GN     TCGA-HU-A4GP     TCGA-HU-A4GQ 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4GT     TCGA-HU-A4GU     TCGA-HU-A4GX     TCGA-HU-A4GY 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4H0     TCGA-HU-A4H2     TCGA-HU-A4H3     TCGA-HU-A4H4 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4H5     TCGA-HU-A4H6     TCGA-HU-A4H8     TCGA-HU-A4HB 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4HD     TCGA-IN-7806     TCGA-IN-7808     TCGA-IN-8462 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-8663     TCGA-IN-A6RI     TCGA-IN-A6RJ     TCGA-IN-A6RL 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-A6RN     TCGA-IN-A6RO     TCGA-IN-A6RP     TCGA-IN-A6RR 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-A6RS     TCGA-IN-A7NR     TCGA-IN-A7NT     TCGA-IN-A7NU 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-AB1V     TCGA-IN-AB1X     TCGA-IP-7968     TCGA-KB-A6F5 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-KB-A6F7     TCGA-KB-A93J     TCGA-MX-A5UG     TCGA-MX-A5UJ 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-R5-A7O7     TCGA-R5-A7ZE     TCGA-R5-A7ZF     TCGA-R5-A7ZI 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-R5-A804     TCGA-R5-A805     TCGA-RD-A7BS     TCGA-RD-A7BT 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-RD-A7BW     TCGA-RD-A7C1     TCGA-RD-A8MV     TCGA-RD-A8MW 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-RD-A8N0     TCGA-RD-A8N1     TCGA-RD-A8N2     TCGA-RD-A8N4 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-RD-A8N5     TCGA-RD-A8N6     TCGA-RD-A8N9     TCGA-SW-A7EA 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-SW-A7EB     TCGA-VQ-A8DL     TCGA-VQ-A8DT     TCGA-VQ-A8DU 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A8DV     TCGA-VQ-A8DZ     TCGA-VQ-A8E2     TCGA-VQ-A8E7 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A8P2     TCGA-VQ-A8P3     TCGA-VQ-A8PE     TCGA-VQ-A8PK 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A8PM     TCGA-VQ-A8PQ     TCGA-VQ-A91Q     TCGA-VQ-A91U 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A91V     TCGA-VQ-A92D     TCGA-VQ-A94T     TCGA-VQ-AA64 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-AA68     TCGA-VQ-AA69     TCGA-VQ-AA6A     TCGA-VQ-AA6B 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-AA6F     TCGA-VQ-AA6G     TCGA-VQ-AA6I     TCGA-VQ-AA6J 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-AA6K     TCGA-ZA-A8F6 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" 
D1165V6, binary
                cls
clus               0   1
  AAMP MUTATED     3   0
  AAMP WILD-TYPE 343  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      3    0
  AAMP WILD-TYPE  343   29
   clus
vv  AAMP MUTATED AAMP WILD-TYPE
  0            3            343
  1            0             29
[1] 2 2
[1] FALSE
D1165V7, binary
                cls
clus               0   1
  AAMP MUTATED     3   0
  AAMP WILD-TYPE 142 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      3    0
  AAMP WILD-TYPE  142  248
        clus
vv       AAMP MUTATED AAMP WILD-TYPE
  FEMALE            3            142
  MALE              0            248
[1] 2 2
[1] FALSE
D1165V8, binary
                cls
clus               0   1
  AAMP MUTATED     3   0
  AAMP WILD-TYPE 289  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      3    0
  AAMP WILD-TYPE  289   59
     clus
vv    AAMP MUTATED AAMP WILD-TYPE
  NO             3            289
  YES            0             59
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  AAMP MUTATED                                          0
  AAMP WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  AAMP MUTATED                                       0
  AAMP WILD-TYPE                                    70
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AAMP MUTATED                                                        3
  AAMP WILD-TYPE                                                    155
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  AAMP MUTATED                                                   0
  AAMP WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  AAMP MUTATED                                                                   0
  AAMP WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  AAMP MUTATED                                                    0
  AAMP WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  AAMP MUTATED                                                  0
  AAMP WILD-TYPE                                               61
D1165V9, multiclass
                                                                   clus
vv                                                                  AAMP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  AAMP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       155
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AAMP MUTATED     2   0   0   1
  AAMP WILD-TYPE 309  14  15  23
D1165V10, multiclass
    clus
vv   AAMP MUTATED AAMP WILD-TYPE
  R0            2            309
  R1            0             14
  R2            0             15
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1165V11, continuous
[1] "Remove cluster labels:" "AAMP MUTATED"          
clus
  AAMP MUTATED AAMP WILD-TYPE 
             2            341 
    TCGA-CG-4444     TCGA-CG-4460     TCGA-CG-4475     TCGA-CG-4476 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5727     TCGA-EQ-A4SO     TCGA-F1-6177     TCGA-FP-A8CX 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HF-7131     TCGA-KB-A93G     TCGA-MX-A663     TCGA-B7-5816 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-B7-A5TI     TCGA-BR-4183     TCGA-BR-4184     TCGA-BR-4188 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-4191     TCGA-BR-4253     TCGA-BR-4255     TCGA-BR-4256 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-4267     TCGA-BR-4279     TCGA-BR-4280     TCGA-BR-4361 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-4362     TCGA-BR-4368     TCGA-BR-6452     TCGA-BR-6453 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6454     TCGA-BR-6455     TCGA-BR-6456     TCGA-BR-6457 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6458     TCGA-BR-6563     TCGA-BR-6564     TCGA-BR-6565 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6705     TCGA-BR-6706     TCGA-BR-6707     TCGA-BR-6709 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6710     TCGA-BR-6801     TCGA-BR-6802     TCGA-BR-6803 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-6852     TCGA-BR-7196     TCGA-BR-7197     TCGA-BR-7703 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-7704     TCGA-BR-7715     TCGA-BR-7716     TCGA-BR-7717 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-7722     TCGA-BR-7723     TCGA-BR-7851     TCGA-BR-7901 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-7957     TCGA-BR-7958     TCGA-BR-7959     TCGA-BR-8058 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8059     TCGA-BR-8060     TCGA-BR-8077     TCGA-BR-8078 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8080     TCGA-BR-8081     TCGA-BR-8284     TCGA-BR-8285 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8286     TCGA-BR-8289     TCGA-BR-8291     TCGA-BR-8295 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8297     TCGA-BR-8360     TCGA-BR-8361     TCGA-BR-8363 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8364     TCGA-BR-8365     TCGA-BR-8366     TCGA-BR-8367 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8368     TCGA-BR-8369     TCGA-BR-8370     TCGA-BR-8371 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8372     TCGA-BR-8373     TCGA-BR-8380     TCGA-BR-8381 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8382     TCGA-BR-8384     TCGA-BR-8483     TCGA-BR-8484 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8485     TCGA-BR-8486     TCGA-BR-8487     TCGA-BR-8588 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8589     TCGA-BR-8590     TCGA-BR-8591     TCGA-BR-8592 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8676     TCGA-BR-8677     TCGA-BR-8678     TCGA-BR-8679 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8680     TCGA-BR-8682     TCGA-BR-8683     TCGA-BR-8686 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-8687     TCGA-BR-8690     TCGA-BR-A44T     TCGA-BR-A44U 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A452     TCGA-BR-A453     TCGA-BR-A4CQ     TCGA-BR-A4CR 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4CS     TCGA-BR-A4IU     TCGA-BR-A4IV     TCGA-BR-A4IY 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4IZ     TCGA-BR-A4J1     TCGA-BR-A4J2     TCGA-BR-A4J4 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4J5     TCGA-BR-A4J6     TCGA-BR-A4J8     TCGA-BR-A4PD 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4PE     TCGA-BR-A4PF     TCGA-BR-A4QI     TCGA-BR-A4QL 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-BR-A4QM     TCGA-CD-5804     TCGA-CD-8525     TCGA-CD-8526 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CD-8531     TCGA-CD-8535     TCGA-CD-A487     TCGA-CG-4301 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4304     TCGA-CG-4305     TCGA-CG-4436     TCGA-CG-4437 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4438     TCGA-CG-4440     TCGA-CG-4441     TCGA-CG-4442 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4443     TCGA-CG-4449     TCGA-CG-4455     TCGA-CG-4462 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4465     TCGA-CG-4466     TCGA-CG-4469     TCGA-CG-4474 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-4477     TCGA-CG-5717     TCGA-CG-5718     TCGA-CG-5719 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5720     TCGA-CG-5721     TCGA-CG-5722     TCGA-CG-5723 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5724     TCGA-CG-5725     TCGA-CG-5726     TCGA-CG-5728 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-CG-5730     TCGA-CG-5732     TCGA-CG-5733     TCGA-CG-5734 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-5577     TCGA-D7-5578     TCGA-D7-5579     TCGA-D7-6518 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-6519     TCGA-D7-6520     TCGA-D7-6521     TCGA-D7-6522 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-6524     TCGA-D7-6525     TCGA-D7-6526     TCGA-D7-6527 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-6528     TCGA-D7-6815     TCGA-D7-6817     TCGA-D7-6818 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-6820     TCGA-D7-6822     TCGA-D7-8570     TCGA-D7-8572 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-8573     TCGA-D7-8574     TCGA-D7-8575     TCGA-D7-8576 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-8578     TCGA-D7-8579     TCGA-D7-A4YT     TCGA-D7-A4YU 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A4YV     TCGA-D7-A4YX     TCGA-D7-A4YY     TCGA-D7-A4Z0 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A6ET     TCGA-D7-A6EV     TCGA-D7-A6EX     TCGA-D7-A6EY 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A6EZ     TCGA-D7-A6F0     TCGA-D7-A6F2     TCGA-D7-A747 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-D7-A748     TCGA-D7-A74A     TCGA-D7-A74B     TCGA-EQ-5647 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-EQ-8122     TCGA-F1-6874     TCGA-F1-6875     TCGA-F1-A448 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-F1-A72C     TCGA-FP-7735     TCGA-FP-7829     TCGA-FP-7916 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-7998     TCGA-FP-8099     TCGA-FP-8209     TCGA-FP-8210 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-8211     TCGA-FP-8631     TCGA-FP-A4BE     TCGA-FP-A4BF 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FP-A9TM     TCGA-HF-7132     TCGA-HF-7133     TCGA-HF-7134 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HF-7136     TCGA-HF-A5NB     TCGA-HJ-7597     TCGA-HU-8238 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-8243     TCGA-HU-8244     TCGA-HU-8249     TCGA-HU-8602 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-8604     TCGA-HU-8608     TCGA-HU-8610     TCGA-HU-A4G2 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4G3     TCGA-HU-A4G6     TCGA-HU-A4G8     TCGA-HU-A4G9 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4GC     TCGA-HU-A4GD     TCGA-HU-A4GF     TCGA-HU-A4GH 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4GJ     TCGA-HU-A4GN     TCGA-HU-A4GP     TCGA-HU-A4GQ 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4GT     TCGA-HU-A4GU     TCGA-HU-A4GX     TCGA-HU-A4GY 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4H0     TCGA-HU-A4H2     TCGA-HU-A4H3     TCGA-HU-A4H4 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4H5     TCGA-HU-A4H6     TCGA-HU-A4H8     TCGA-HU-A4HB 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HU-A4HD     TCGA-IN-7806     TCGA-IN-7808     TCGA-IN-8462 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-8663     TCGA-IN-A6RI     TCGA-IN-A6RJ     TCGA-IN-A6RL 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-A6RN     TCGA-IN-A6RO     TCGA-IN-A6RP     TCGA-IN-A6RR 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-A6RS     TCGA-IN-A7NR     TCGA-IN-A7NT     TCGA-IN-A7NU 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IN-AB1V     TCGA-IN-AB1X     TCGA-IP-7968     TCGA-KB-A6F5 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-KB-A6F7     TCGA-KB-A93J     TCGA-MX-A5UG     TCGA-MX-A5UJ 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-R5-A7ZI     TCGA-RD-A7BS     TCGA-RD-A7BT     TCGA-RD-A7BW 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-RD-A7C1     TCGA-RD-A8MV     TCGA-RD-A8MW     TCGA-RD-A8N0 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-RD-A8N1     TCGA-RD-A8N2     TCGA-RD-A8N4     TCGA-RD-A8N5 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-RD-A8N6     TCGA-RD-A8N9     TCGA-SW-A7EA     TCGA-SW-A7EB 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A8DL     TCGA-VQ-A8DT     TCGA-VQ-A8DU     TCGA-VQ-A8DV 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A8DZ     TCGA-VQ-A8E2     TCGA-VQ-A8E7     TCGA-VQ-A8P2 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A8P3     TCGA-VQ-A8PE     TCGA-VQ-A8PK     TCGA-VQ-A8PM 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A8PQ     TCGA-VQ-A91Q     TCGA-VQ-A91U     TCGA-VQ-A91V 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-A92D     TCGA-VQ-A94T     TCGA-VQ-AA64     TCGA-VQ-AA68 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-AA69     TCGA-VQ-AA6A     TCGA-VQ-AA6B     TCGA-VQ-AA6F 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-VQ-AA6G     TCGA-VQ-AA6I     TCGA-VQ-AA6J     TCGA-VQ-AA6K 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-ZA-A8F6 
"AAMP WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  AAMP MUTATED       0                         0
  AAMP WILD-TYPE    87                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AAMP MUTATED                                           0     3
  AAMP WILD-TYPE                                         1   240
D1165V12, multiclass
                                           clus
vv                                          AAMP MUTATED AAMP WILD-TYPE
  ASIAN                                                0             87
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                3            240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1165V13, binary
                cls
clus               0   1
  AAMP MUTATED     0   3
  AAMP WILD-TYPE   4 307
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      0    3
  AAMP WILD-TYPE    4  307
                        clus
vv                       AAMP MUTATED AAMP WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            3            307
[1] 2 2
[1] FALSE

Clustering(1166) Variable = SYBU MUTATION ANALYSIS
D1166V1, survival
                sevent
clus2              0   1
  SYBU MUTATED    10   4
  SYBU WILD-TYPE 220 135
  SYBU MUTATED SYBU WILD-TYPE 
            14            355 
  SYBU MUTATED SYBU WILD-TYPE 
             4            135 
$`SYBU MUTATED`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-8680 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-5723 
       26.70        34.68        31.96         6.58        12.62       105.07 
TCGA-F1-6874 TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4H2 TCGA-IN-8663 
       14.47        11.08        22.32         0.10        12.95         3.39 
TCGA-MX-A5UJ TCGA-RD-A7BS 
       19.73        11.05 

$`SYBU WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-F1-6875 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-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        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-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 

  SYBU MUTATED SYBU WILD-TYPE 
           0.1            0.0 
  SYBU MUTATED SYBU WILD-TYPE 
        105.07         122.30 
  SYBU MUTATED SYBU WILD-TYPE 
         13.71          14.27 
[1] "0.1 - 105.1 (13.7)" "0.0 - 122.3 (14.3)"
[1] "hr=" "1.4"
D1166V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SYBU MUTATED         0        0        3        1         3         3
  SYBU WILD-TYPE       2       15       37       29        34        49
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYBU MUTATED           0          2          1          1        1
  SYBU WILD-TYPE         3         68         52         31       37
D1166V3, multiclass
            clus
vv           SYBU MUTATED SYBU WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              3             37
  STAGE II              1             29
  STAGE IIA             3             34
  STAGE IIB             3             49
  STAGE III             0              3
  STAGE IIIA            2             68
  STAGE IIIB            1             52
  STAGE IIIC            1             31
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SYBU MUTATED     0   5   6   4
  SYBU WILD-TYPE  22  87 167  93
D1166V4, multiclass
    clus
vv   SYBU MUTATED SYBU WILD-TYPE
  T1            0             22
  T2            5             87
  T3            6            167
  T4            4             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
  SYBU MUTATED     8   2   4   1
  SYBU WILD-TYPE 110 102  73  76
D1166V5, multiclass
    clus
vv   SYBU MUTATED SYBU WILD-TYPE
  N0            8            110
  N1            2            102
  N2            4             73
  N3            1             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"
D1166V6, binary
                cls
clus               0   1
  SYBU MUTATED    14   1
  SYBU WILD-TYPE 332  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYBU MUTATED     14    1
  SYBU WILD-TYPE  332   28
   clus
vv  SYBU MUTATED SYBU WILD-TYPE
  0           14            332
  1            1             28
[1] 2 2
[1] FALSE
D1166V7, binary
                cls
clus               0   1
  SYBU MUTATED     5  10
  SYBU WILD-TYPE 140 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYBU MUTATED      5   10
  SYBU WILD-TYPE  140  238
        clus
vv       SYBU MUTATED SYBU WILD-TYPE
  FEMALE            5            140
  MALE             10            238
[1] 2 2
[1] FALSE
D1166V8, binary
                cls
clus               0   1
  SYBU MUTATED    12   2
  SYBU WILD-TYPE 280  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYBU MUTATED     12    2
  SYBU WILD-TYPE  280   57
     clus
vv    SYBU MUTATED SYBU WILD-TYPE
  NO            12            280
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SYBU MUTATED                                          0
  SYBU WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SYBU MUTATED                                       4
  SYBU WILD-TYPE                                    66
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SYBU MUTATED                                                        5
  SYBU WILD-TYPE                                                    153
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SYBU MUTATED                                                   0
  SYBU WILD-TYPE                                                21
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SYBU MUTATED                                                                   2
  SYBU WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SYBU MUTATED                                                    0
  SYBU WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SYBU MUTATED                                                  4
  SYBU WILD-TYPE                                               57
D1166V9, multiclass
                                                                   clus
vv                                                                  SYBU MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        4
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  SYBU WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         66
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SYBU MUTATED    13   0   0   0
  SYBU WILD-TYPE 298  14  15  24
D1166V10, multiclass
    clus
vv   SYBU MUTATED SYBU WILD-TYPE
  R0           13            298
  R1            0             14
  R2            0             15
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1166V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  SYBU MUTATED       6                         1
  SYBU WILD-TYPE    81                         8
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SYBU MUTATED                                           0     6
  SYBU WILD-TYPE                                         1   237
D1166V12, multiclass
                                           clus
vv                                          SYBU MUTATED SYBU WILD-TYPE
  ASIAN                                                6             81
  BLACK OR AFRICAN AMERICAN                            1              8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                6            237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1166V13, binary
                cls
clus               0   1
  SYBU MUTATED     0  13
  SYBU WILD-TYPE   4 297
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYBU MUTATED      0   13
  SYBU WILD-TYPE    4  297
                        clus
vv                       SYBU MUTATED SYBU WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           13            297
[1] 2 2
[1] FALSE

Clustering(1167) Variable = CPT2 MUTATION ANALYSIS
D1167V1, survival
                sevent
clus2              0   1
  CPT2 MUTATED     5   1
  CPT2 WILD-TYPE 225 138
  CPT2 MUTATED CPT2 WILD-TYPE 
             6            363 
  CPT2 MUTATED CPT2 WILD-TYPE 
             1            138 
$`CPT2 MUTATED`
TCGA-CG-4460 TCGA-BR-6452 TCGA-CG-5721 TCGA-HF-A5NB TCGA-HU-A4G2 TCGA-HU-A4GN 
       21.99        34.68         6.02        30.51        24.30        29.98 

$`CPT2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
        9.86        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-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-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         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 

  CPT2 MUTATED CPT2 WILD-TYPE 
          6.02           0.00 
  CPT2 MUTATED CPT2 WILD-TYPE 
         34.68         122.30 
  CPT2 MUTATED CPT2 WILD-TYPE 
         27.14          14.07 
[1] "6.0 - 34.7 (27.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3.2"
D1167V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CPT2 MUTATED         0        0        0        0         2         1
  CPT2 WILD-TYPE       2       15       40       30        35        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CPT2 MUTATED           0          0          0          1        2
  CPT2 WILD-TYPE         3         70         53         31       36
D1167V3, multiclass
            clus
vv           CPT2 MUTATED CPT2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              0             40
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            0             70
  STAGE IIIB            0             53
  STAGE IIIC            1             31
  STAGE IV              2             36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CPT2 MUTATED     0   1   2   3
  CPT2 WILD-TYPE  22  91 171  94
D1167V4, multiclass
    clus
vv   CPT2 MUTATED CPT2 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            2            171
  T4            3             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
  CPT2 MUTATED     1   4   0   1
  CPT2 WILD-TYPE 117 100  77  76
D1167V5, multiclass
    clus
vv   CPT2 MUTATED CPT2 WILD-TYPE
  N0            1            117
  N1            4            100
  N2            0             77
  N3            1             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"
D1167V6, binary
                cls
clus               0   1
  CPT2 MUTATED     5   1
  CPT2 WILD-TYPE 341  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPT2 MUTATED      5    1
  CPT2 WILD-TYPE  341   28
   clus
vv  CPT2 MUTATED CPT2 WILD-TYPE
  0            5            341
  1            1             28
[1] 2 2
[1] FALSE
D1167V7, binary
                cls
clus               0   1
  CPT2 MUTATED     3   3
  CPT2 WILD-TYPE 142 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPT2 MUTATED      3    3
  CPT2 WILD-TYPE  142  245
        clus
vv       CPT2 MUTATED CPT2 WILD-TYPE
  FEMALE            3            142
  MALE              3            245
[1] 2 2
[1] FALSE
D1167V8, binary
                cls
clus               0   1
  CPT2 MUTATED     5   1
  CPT2 WILD-TYPE 287  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPT2 MUTATED      5    1
  CPT2 WILD-TYPE  287   58
     clus
vv    CPT2 MUTATED CPT2 WILD-TYPE
  NO             5            287
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CPT2 MUTATED                                          0
  CPT2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CPT2 MUTATED                                       1
  CPT2 WILD-TYPE                                    69
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CPT2 MUTATED                                                        1
  CPT2 WILD-TYPE                                                    157
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CPT2 MUTATED                                                   1
  CPT2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CPT2 MUTATED                                                                   2
  CPT2 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CPT2 MUTATED                                                    0
  CPT2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CPT2 MUTATED                                                  1
  CPT2 WILD-TYPE                                               60
D1167V9, multiclass
                                                                   clus
vv                                                                  CPT2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             1
                                                                   clus
vv                                                                  CPT2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CPT2 MUTATED     4   1   1   0
  CPT2 WILD-TYPE 307  13  14  24
D1167V10, multiclass
    clus
vv   CPT2 MUTATED CPT2 WILD-TYPE
  R0            4            307
  R1            1             13
  R2            1             14
  RX            0             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1167V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  CPT2 MUTATED       2                         0
  CPT2 WILD-TYPE    85                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CPT2 MUTATED                                           0     1
  CPT2 WILD-TYPE                                         1   242
D1167V12, multiclass
                                           clus
vv                                          CPT2 MUTATED CPT2 WILD-TYPE
  ASIAN                                                2             85
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                1            242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1167V13, binary
                cls
clus               0   1
  CPT2 MUTATED     0   3
  CPT2 WILD-TYPE   4 307
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPT2 MUTATED      0    3
  CPT2 WILD-TYPE    4  307
                        clus
vv                       CPT2 MUTATED CPT2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            3            307
[1] 2 2
[1] FALSE

Clustering(1168) Variable = SCNN1D MUTATION ANALYSIS
D1168V1, survival
                  sevent
clus2                0   1
  SCNN1D MUTATED     8   2
  SCNN1D WILD-TYPE 222 137
  SCNN1D MUTATED SCNN1D WILD-TYPE 
              10              359 
  SCNN1D MUTATED SCNN1D WILD-TYPE 
               2              137 
$`SCNN1D MUTATED`
TCGA-CG-5727 TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-7703 TCGA-BR-7957 TCGA-BR-8487 
       79.07        19.56         9.47        36.16         9.07         1.12 
TCGA-CG-5733 TCGA-F1-6874 TCGA-HF-7132 TCGA-HU-A4GN 
       21.07        14.47        77.29        29.98 

$`SCNN1D WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
        9.86        26.70        11.70        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-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-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-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-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-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-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 

  SCNN1D MUTATED SCNN1D WILD-TYPE 
            1.12             0.00 
  SCNN1D MUTATED SCNN1D WILD-TYPE 
           79.07           122.30 
  SCNN1D MUTATED SCNN1D WILD-TYPE 
          20.315           14.070 
[1] "1.1 - 79.1 (20.3)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.7"
D1168V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SCNN1D MUTATED         0        1        1        2         2         0
  SCNN1D WILD-TYPE       2       14       39       28        35        52
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SCNN1D MUTATED           0          2          0          1        1
  SCNN1D WILD-TYPE         3         68         53         31       37
D1168V3, multiclass
            clus
vv           SCNN1D MUTATED SCNN1D WILD-TYPE
  STAGE I                 0                2
  STAGE IA                1               14
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               2               35
  STAGE IIB               0               52
  STAGE III               0                3
  STAGE IIIA              2               68
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SCNN1D MUTATED     1   4   3   2
  SCNN1D WILD-TYPE  21  88 170  95
D1168V4, multiclass
    clus
vv   SCNN1D MUTATED SCNN1D WILD-TYPE
  T1              1               21
  T2              4               88
  T3              3              170
  T4              2               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
  SCNN1D MUTATED     4   2   1   2
  SCNN1D WILD-TYPE 114 102  76  75
D1168V5, multiclass
    clus
vv   SCNN1D MUTATED SCNN1D WILD-TYPE
  N0              4              114
  N1              2              102
  N2              1               76
  N3              2               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"
D1168V6, binary
                  cls
clus                 0   1
  SCNN1D MUTATED     9   1
  SCNN1D WILD-TYPE 337  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCNN1D MUTATED      9    1
  SCNN1D WILD-TYPE  337   28
   clus
vv  SCNN1D MUTATED SCNN1D WILD-TYPE
  0              9              337
  1              1               28
[1] 2 2
[1] FALSE
D1168V7, binary
                  cls
clus                 0   1
  SCNN1D MUTATED     3   7
  SCNN1D WILD-TYPE 142 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCNN1D MUTATED      3    7
  SCNN1D WILD-TYPE  142  241
        clus
vv       SCNN1D MUTATED SCNN1D WILD-TYPE
  FEMALE              3              142
  MALE                7              241
[1] 2 2
[1] FALSE
D1168V8, binary
                  cls
clus                 0   1
  SCNN1D MUTATED     9   1
  SCNN1D WILD-TYPE 283  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCNN1D MUTATED      9    1
  SCNN1D WILD-TYPE  283   58
     clus
vv    SCNN1D MUTATED SCNN1D WILD-TYPE
  NO               9              283
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SCNN1D MUTATED                                          0
  SCNN1D WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SCNN1D MUTATED                                       1
  SCNN1D WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SCNN1D MUTATED                                                        1
  SCNN1D WILD-TYPE                                                    157
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SCNN1D MUTATED                                                   1
  SCNN1D WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SCNN1D MUTATED                                                                   5
  SCNN1D WILD-TYPE                                                                63
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SCNN1D MUTATED                                                    1
  SCNN1D WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SCNN1D MUTATED                                                  1
  SCNN1D WILD-TYPE                                               60
D1168V9, multiclass
                                                                   clus
vv                                                                  SCNN1D MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               1
                                                                   clus
vv                                                                  SCNN1D WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SCNN1D MUTATED     8   0   0   0
  SCNN1D WILD-TYPE 303  14  15  24
D1168V10, multiclass
    clus
vv   SCNN1D MUTATED SCNN1D WILD-TYPE
  R0              8              303
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1168V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SCNN1D MUTATED       1                         0
  SCNN1D WILD-TYPE    86                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SCNN1D MUTATED                                           0     6
  SCNN1D WILD-TYPE                                         1   237
D1168V12, multiclass
                                           clus
vv                                          SCNN1D MUTATED SCNN1D WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1168V13, binary
                  cls
clus                 0   1
  SCNN1D MUTATED     0   7
  SCNN1D WILD-TYPE   4 303
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCNN1D MUTATED      0    7
  SCNN1D WILD-TYPE    4  303
                        clus
vv                       SCNN1D MUTATED SCNN1D WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              303
[1] 2 2
[1] FALSE

Clustering(1169) Variable = OLFM3 MUTATION ANALYSIS
D1169V1, survival
                 sevent
clus2               0   1
  OLFM3 MUTATED     5   3
  OLFM3 WILD-TYPE 225 136
  OLFM3 MUTATED OLFM3 WILD-TYPE 
              8             361 
  OLFM3 MUTATED OLFM3 WILD-TYPE 
              3             136 
$`OLFM3 MUTATED`
TCGA-B7-A5TJ TCGA-BR-6452 TCGA-CD-A4MG TCGA-D7-A4YU TCGA-D7-A747 TCGA-IN-8663 
       11.01        34.68         6.58        16.44         8.38         3.39 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       38.14        37.22 

$`OLFM3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TK 
       20.15         9.86        26.70        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-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-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-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-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-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-F1-6874 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-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-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 

  OLFM3 MUTATED OLFM3 WILD-TYPE 
           3.39            0.00 
  OLFM3 MUTATED OLFM3 WILD-TYPE 
          38.14          122.30 
  OLFM3 MUTATED OLFM3 WILD-TYPE 
         13.725          14.270 
[1] "3.4 - 38.1 (13.7)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1"  
D1169V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OLFM3 MUTATED         0        0        0        0         2         3
  OLFM3 WILD-TYPE       2       15       40       30        35        49
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OLFM3 MUTATED           0          2          1          0        0
  OLFM3 WILD-TYPE         3         68         52         32       38
D1169V3, multiclass
            clus
vv           OLFM3 MUTATED OLFM3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              3              49
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             1              52
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OLFM3 MUTATED     0   1   4   3
  OLFM3 WILD-TYPE  22  91 169  94
D1169V4, multiclass
    clus
vv   OLFM3 MUTATED OLFM3 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             4             169
  T4             3              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
  OLFM3 MUTATED     2   3   1   1
  OLFM3 WILD-TYPE 116 101  76  76
D1169V5, multiclass
    clus
vv   OLFM3 MUTATED OLFM3 WILD-TYPE
  N0             2             116
  N1             3             101
  N2             1              76
  N3             1              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"
D1169V6, binary
                 cls
clus                0   1
  OLFM3 MUTATED     8   0
  OLFM3 WILD-TYPE 338  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLFM3 MUTATED      8    0
  OLFM3 WILD-TYPE  338   29
   clus
vv  OLFM3 MUTATED OLFM3 WILD-TYPE
  0             8             338
  1             0              29
[1] 2 2
[1] FALSE
D1169V7, binary
                 cls
clus                0   1
  OLFM3 MUTATED     1   7
  OLFM3 WILD-TYPE 144 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLFM3 MUTATED      1    7
  OLFM3 WILD-TYPE  144  241
        clus
vv       OLFM3 MUTATED OLFM3 WILD-TYPE
  FEMALE             1             144
  MALE               7             241
[1] 2 2
[1] FALSE
D1169V8, binary
                 cls
clus                0   1
  OLFM3 MUTATED     6   2
  OLFM3 WILD-TYPE 286  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLFM3 MUTATED      6    2
  OLFM3 WILD-TYPE  286   57
     clus
vv    OLFM3 MUTATED OLFM3 WILD-TYPE
  NO              6             286
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OLFM3 MUTATED                                          0
  OLFM3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OLFM3 MUTATED                                       2
  OLFM3 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OLFM3 MUTATED                                                        2
  OLFM3 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OLFM3 MUTATED                                                   1
  OLFM3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OLFM3 MUTATED                                                                   1
  OLFM3 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OLFM3 MUTATED                                                    0
  OLFM3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OLFM3 MUTATED                                                  2
  OLFM3 WILD-TYPE                                               59
D1169V9, multiclass
                                                                   clus
vv                                                                  OLFM3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  OLFM3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OLFM3 MUTATED     6   0   0   0
  OLFM3 WILD-TYPE 305  14  15  24
D1169V10, multiclass
    clus
vv   OLFM3 MUTATED OLFM3 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1169V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OLFM3 MUTATED       1                         0
  OLFM3 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OLFM3 MUTATED                                           0     7
  OLFM3 WILD-TYPE                                         1   236
D1169V12, multiclass
                                           clus
vv                                          OLFM3 MUTATED OLFM3 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 7             236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1169V13, binary
                 cls
clus                0   1
  OLFM3 MUTATED     0   6
  OLFM3 WILD-TYPE   4 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLFM3 MUTATED      0    6
  OLFM3 WILD-TYPE    4  304
                        clus
vv                       OLFM3 MUTATED OLFM3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(1170) Variable = LRRC43 MUTATION ANALYSIS
D1170V1, survival
                  sevent
clus2                0   1
  LRRC43 MUTATED     8   2
  LRRC43 WILD-TYPE 222 137
  LRRC43 MUTATED LRRC43 WILD-TYPE 
              10              359 
  LRRC43 MUTATED LRRC43 WILD-TYPE 
               2              137 
$`LRRC43 MUTATED`
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-7707 TCGA-BR-8487 TCGA-CD-8529 
       26.70        30.90        34.68        35.84         1.12        12.30 
TCGA-FP-A4BE TCGA-HF-7132 TCGA-RD-A8MW TCGA-VQ-A8P2 
       11.08        77.29        37.91        38.14 

$`LRRC43 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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-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-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-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 

  LRRC43 MUTATED LRRC43 WILD-TYPE 
            1.12             0.00 
  LRRC43 MUTATED LRRC43 WILD-TYPE 
           77.29           122.30 
  LRRC43 MUTATED LRRC43 WILD-TYPE 
           32.79            14.07 
[1] "1.1 - 77.3 (32.8)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "3"  
D1170V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  LRRC43 MUTATED         1        0        1        1         3         1
  LRRC43 WILD-TYPE       1       15       39       29        34        51
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC43 MUTATED           0          1          1          0        1
  LRRC43 WILD-TYPE         3         69         52         32       37
D1170V3, multiclass
            clus
vv           LRRC43 MUTATED LRRC43 WILD-TYPE
  STAGE I                 1                1
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                1               29
  STAGE IIA               3               34
  STAGE IIB               1               51
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              1               52
  STAGE IIIC              0               32
  STAGE IV                1               37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LRRC43 MUTATED     1   3   5   3
  LRRC43 WILD-TYPE  21  89 168  94
D1170V4, multiclass
    clus
vv   LRRC43 MUTATED LRRC43 WILD-TYPE
  T1              1               21
  T2              3               89
  T3              5              168
  T4              3               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
  LRRC43 MUTATED     6   3   1   0
  LRRC43 WILD-TYPE 112 101  76  77
D1170V5, multiclass
    clus
vv   LRRC43 MUTATED LRRC43 WILD-TYPE
  N0              6              112
  N1              3              101
  N2              1               76
  N3              0               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"
D1170V6, binary
                  cls
clus                 0   1
  LRRC43 MUTATED     9   1
  LRRC43 WILD-TYPE 337  28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC43 MUTATED      9    1
  LRRC43 WILD-TYPE  337   28
   clus
vv  LRRC43 MUTATED LRRC43 WILD-TYPE
  0              9              337
  1              1               28
[1] 2 2
[1] FALSE
D1170V7, binary
                  cls
clus                 0   1
  LRRC43 MUTATED     6   6
  LRRC43 WILD-TYPE 139 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC43 MUTATED      6    6
  LRRC43 WILD-TYPE  139  242
        clus
vv       LRRC43 MUTATED LRRC43 WILD-TYPE
  FEMALE              6              139
  MALE                6              242
[1] 2 2
[1] FALSE
D1170V8, binary
                  cls
clus                 0   1
  LRRC43 MUTATED     6   5
  LRRC43 WILD-TYPE 286  54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC43 MUTATED      6    5
  LRRC43 WILD-TYPE  286   54
     clus
vv    LRRC43 MUTATED LRRC43 WILD-TYPE
  NO               6              286
  YES              5               54
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LRRC43 MUTATED                                          0
  LRRC43 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LRRC43 MUTATED                                       1
  LRRC43 WILD-TYPE                                    69
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LRRC43 MUTATED                                                        7
  LRRC43 WILD-TYPE                                                    151
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LRRC43 MUTATED                                                   3
  LRRC43 WILD-TYPE                                                18
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LRRC43 MUTATED                                                                   1
  LRRC43 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LRRC43 MUTATED                                                    0
  LRRC43 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LRRC43 MUTATED                                                  0
  LRRC43 WILD-TYPE                                               61
D1170V9, multiclass
                                                                   clus
vv                                                                  LRRC43 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  LRRC43 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LRRC43 MUTATED    10   0   0   2
  LRRC43 WILD-TYPE 301  14  15  22
D1170V10, multiclass
    clus
vv   LRRC43 MUTATED LRRC43 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1170V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  LRRC43 MUTATED       1                         2
  LRRC43 WILD-TYPE    86                         7
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LRRC43 MUTATED                                           0     8
  LRRC43 WILD-TYPE                                         1   235
D1170V12, multiclass
                                           clus
vv                                          LRRC43 MUTATED LRRC43 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              2                7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  8              235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1170V13, binary
                  cls
clus                 0   1
  LRRC43 MUTATED     0  10
  LRRC43 WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC43 MUTATED      0   10
  LRRC43 WILD-TYPE    4  300
                        clus
vv                       LRRC43 MUTATED LRRC43 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(1171) Variable = TMC2 MUTATION ANALYSIS
D1171V1, survival
                sevent
clus2              0   1
  TMC2 MUTATED    11   4
  TMC2 WILD-TYPE 219 135
  TMC2 MUTATED TMC2 WILD-TYPE 
            15            354 
  TMC2 MUTATED TMC2 WILD-TYPE 
             4            135 
$`TMC2 MUTATED`
TCGA-BR-4184 TCGA-BR-7703 TCGA-BR-8370 TCGA-BR-8680 TCGA-CG-4462 TCGA-CG-4465 
        6.97        36.16         3.32        31.96         0.00         9.01 
TCGA-CG-5721 TCGA-FP-8631 TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GU 
        6.02         0.56        22.32        29.98         0.10         6.58 
TCGA-HU-A4H2 TCGA-IN-AB1V TCGA-VQ-A8P2 
       12.95        15.75        38.14 

$`TMC2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-4466 TCGA-CG-4469 TCGA-CG-4477 
       29.98        19.07        12.03        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-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-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-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        8.98         6.51        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-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
       10.62        11.70        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 

  TMC2 MUTATED TMC2 WILD-TYPE 
          0.00           0.23 
  TMC2 MUTATED TMC2 WILD-TYPE 
         38.14         122.30 
  TMC2 MUTATED TMC2 WILD-TYPE 
          9.01          14.45 
[1] "0.0 - 38.1 (9.0)"   "0.2 - 122.3 (14.4)"
[1] "hr=" "1.1"
D1171V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TMC2 MUTATED         0        2        1        0         1         2
  TMC2 WILD-TYPE       2       13       39       30        36        50
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMC2 MUTATED           0          3          2          1        4
  TMC2 WILD-TYPE         3         67         51         31       34
D1171V3, multiclass
            clus
vv           TMC2 MUTATED TMC2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              2             13
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             1             36
  STAGE IIB             2             50
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            2             51
  STAGE IIIC            1             31
  STAGE IV              4             34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TMC2 MUTATED     2   2   7   6
  TMC2 WILD-TYPE  20  90 166  91
D1171V4, multiclass
    clus
vv   TMC2 MUTATED TMC2 WILD-TYPE
  T1            2             20
  T2            2             90
  T3            7            166
  T4            6             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
  TMC2 MUTATED     4   5   3   4
  TMC2 WILD-TYPE 114  99  74  73
D1171V5, multiclass
    clus
vv   TMC2 MUTATED TMC2 WILD-TYPE
  N0            4            114
  N1            5             99
  N2            3             74
  N3            4             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"
D1171V6, binary
                cls
clus               0   1
  TMC2 MUTATED    10   3
  TMC2 WILD-TYPE 336  26
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC2 MUTATED     10    3
  TMC2 WILD-TYPE  336   26
   clus
vv  TMC2 MUTATED TMC2 WILD-TYPE
  0           10            336
  1            3             26
[1] 2 2
[1] FALSE
D1171V7, binary
                cls
clus               0   1
  TMC2 MUTATED     5  12
  TMC2 WILD-TYPE 140 236
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC2 MUTATED      5   12
  TMC2 WILD-TYPE  140  236
        clus
vv       TMC2 MUTATED TMC2 WILD-TYPE
  FEMALE            5            140
  MALE             12            236
[1] 2 2
[1] FALSE
D1171V8, binary
                cls
clus               0   1
  TMC2 MUTATED    11   2
  TMC2 WILD-TYPE 281  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC2 MUTATED     11    2
  TMC2 WILD-TYPE  281   57
     clus
vv    TMC2 MUTATED TMC2 WILD-TYPE
  NO            11            281
  YES            2             57
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TMC2 MUTATED                                          0
  TMC2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TMC2 MUTATED                                       5
  TMC2 WILD-TYPE                                    65
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMC2 MUTATED                                                        4
  TMC2 WILD-TYPE                                                    154
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TMC2 MUTATED                                                   1
  TMC2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TMC2 MUTATED                                                                   2
  TMC2 WILD-TYPE                                                                66
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TMC2 MUTATED                                                    1
  TMC2 WILD-TYPE                                                  4
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TMC2 MUTATED                                                  4
  TMC2 WILD-TYPE                                               57
D1171V9, multiclass
                                                                   clus
vv                                                                  TMC2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             4
                                                                   clus
vv                                                                  TMC2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         65
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TMC2 MUTATED    13   0   2   2
  TMC2 WILD-TYPE 298  14  13  22
D1171V10, multiclass
    clus
vv   TMC2 MUTATED TMC2 WILD-TYPE
  R0           13            298
  R1            0             14
  R2            2             13
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1171V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TMC2 MUTATED       6                         0
  TMC2 WILD-TYPE    81                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TMC2 MUTATED                                           0     7
  TMC2 WILD-TYPE                                         1   236
D1171V12, multiclass
                                           clus
vv                                          TMC2 MUTATED TMC2 WILD-TYPE
  ASIAN                                                6             81
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                7            236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1171V13, binary
                cls
clus               0   1
  TMC2 MUTATED     0  12
  TMC2 WILD-TYPE   4 298
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC2 MUTATED      0   12
  TMC2 WILD-TYPE    4  298
                        clus
vv                       TMC2 MUTATED TMC2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           12            298
[1] 2 2
[1] FALSE

Clustering(1172) Variable = USP30 MUTATION ANALYSIS
D1172V1, survival
                 sevent
clus2               0   1
  USP30 MUTATED     7   1
  USP30 WILD-TYPE 223 138
  USP30 MUTATED USP30 WILD-TYPE 
              8             361 
  USP30 MUTATED USP30 WILD-TYPE 
              1             138 
$`USP30 MUTATED`
TCGA-BR-6452 TCGA-BR-8591 TCGA-CG-4440 TCGA-CG-5721 TCGA-FP-A4BE TCGA-HF-7132 
       34.68        28.14         4.01         6.02        11.08        77.29 
TCGA-HU-A4H8 TCGA-VQ-A8P2 
       14.07        38.14 

$`USP30 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  USP30 MUTATED USP30 WILD-TYPE 
           4.01            0.00 
  USP30 MUTATED USP30 WILD-TYPE 
          77.29          122.30 
  USP30 MUTATED USP30 WILD-TYPE 
         21.105          14.270 
[1] "4.0 - 77.3 (21.1)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "3.9"
D1172V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  USP30 MUTATED         0        0        1        1         2         0
  USP30 WILD-TYPE       2       15       39       29        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  USP30 MUTATED           0          1          0          1        2
  USP30 WILD-TYPE         3         69         53         31       36
D1172V3, multiclass
            clus
vv           USP30 MUTATED USP30 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP30 MUTATED     2   1   3   3
  USP30 WILD-TYPE  20  91 170  94
D1172V4, multiclass
    clus
vv   USP30 MUTATED USP30 WILD-TYPE
  T1             2              20
  T2             1              91
  T3             3             170
  T4             3              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
  USP30 MUTATED     2   4   0   2
  USP30 WILD-TYPE 116 100  77  75
D1172V5, multiclass
    clus
vv   USP30 MUTATED USP30 WILD-TYPE
  N0             2             116
  N1             4             100
  N2             0              77
  N3             2              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"
D1172V6, binary
                 cls
clus                0   1
  USP30 MUTATED     8   1
  USP30 WILD-TYPE 338  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP30 MUTATED      8    1
  USP30 WILD-TYPE  338   28
   clus
vv  USP30 MUTATED USP30 WILD-TYPE
  0             8             338
  1             1              28
[1] 2 2
[1] FALSE
D1172V7, binary
                 cls
clus                0   1
  USP30 MUTATED     3   6
  USP30 WILD-TYPE 142 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP30 MUTATED      3    6
  USP30 WILD-TYPE  142  242
        clus
vv       USP30 MUTATED USP30 WILD-TYPE
  FEMALE             3             142
  MALE               6             242
[1] 2 2
[1] FALSE
D1172V8, binary
                 cls
clus                0   1
  USP30 MUTATED     4   3
  USP30 WILD-TYPE 288  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP30 MUTATED      4    3
  USP30 WILD-TYPE  288   56
     clus
vv    USP30 MUTATED USP30 WILD-TYPE
  NO              4             288
  YES             3              56
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  USP30 MUTATED                                          0
  USP30 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  USP30 MUTATED                                       0
  USP30 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  USP30 MUTATED                                                        4
  USP30 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  USP30 MUTATED                                                   2
  USP30 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  USP30 MUTATED                                                                   2
  USP30 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  USP30 MUTATED                                                    0
  USP30 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  USP30 MUTATED                                                  1
  USP30 WILD-TYPE                                               60
D1172V9, multiclass
                                                                   clus
vv                                                                  USP30 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  USP30 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP30 MUTATED     7   0   1   1
  USP30 WILD-TYPE 304  14  14  23
D1172V10, multiclass
    clus
vv   USP30 MUTATED USP30 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1172V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  USP30 MUTATED       1                         1
  USP30 WILD-TYPE    86                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  USP30 MUTATED                                           0     4
  USP30 WILD-TYPE                                         1   239
D1172V12, multiclass
                                           clus
vv                                          USP30 MUTATED USP30 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1172V13, binary
                 cls
clus                0   1
  USP30 MUTATED     0   5
  USP30 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP30 MUTATED      0    5
  USP30 WILD-TYPE    4  305
                        clus
vv                       USP30 MUTATED USP30 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(1173) Variable = TRIP6 MUTATION ANALYSIS
D1173V1, survival
                 sevent
clus2               0   1
  TRIP6 MUTATED     5   2
  TRIP6 WILD-TYPE 225 137
  TRIP6 MUTATED TRIP6 WILD-TYPE 
              7             362 
  TRIP6 MUTATED TRIP6 WILD-TYPE 
              2             137 
$`TRIP6 MUTATED`
TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-8059 TCGA-BR-8487 TCGA-CG-5723 TCGA-HU-A4GT 
       30.90        34.68        14.43         1.12       105.07         6.51 
TCGA-R5-A7ZI 
       74.53 

$`TRIP6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  TRIP6 MUTATED TRIP6 WILD-TYPE 
           1.12            0.00 
  TRIP6 MUTATED TRIP6 WILD-TYPE 
         105.07          122.30 
  TRIP6 MUTATED TRIP6 WILD-TYPE 
          30.90           14.12 
[1] "1.1 - 105.1 (30.9)" "0.0 - 122.3 (14.1)"
[1] "hr=" "2.1"
D1173V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TRIP6 MUTATED         0        0        0        1         3         0
  TRIP6 WILD-TYPE       2       15       40       29        34        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIP6 MUTATED           1          0          0          0        1
  TRIP6 WILD-TYPE         2         70         53         32       37
D1173V3, multiclass
            clus
vv           TRIP6 MUTATED TRIP6 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              3              34
  STAGE IIB              0              52
  STAGE III              1               2
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRIP6 MUTATED     1   2   3   2
  TRIP6 WILD-TYPE  21  90 170  95
D1173V4, multiclass
    clus
vv   TRIP6 MUTATED TRIP6 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             3             170
  T4             2              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
  TRIP6 MUTATED     3   3   0   0
  TRIP6 WILD-TYPE 115 101  77  77
D1173V5, multiclass
    clus
vv   TRIP6 MUTATED TRIP6 WILD-TYPE
  N0             3             115
  N1             3             101
  N2             0              77
  N3             0              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"
D1173V6, binary
                 cls
clus                0   1
  TRIP6 MUTATED     7   1
  TRIP6 WILD-TYPE 339  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP6 MUTATED      7    1
  TRIP6 WILD-TYPE  339   28
   clus
vv  TRIP6 MUTATED TRIP6 WILD-TYPE
  0             7             339
  1             1              28
[1] 2 2
[1] FALSE
D1173V7, binary
                 cls
clus                0   1
  TRIP6 MUTATED     6   2
  TRIP6 WILD-TYPE 139 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP6 MUTATED      6    2
  TRIP6 WILD-TYPE  139  246
        clus
vv       TRIP6 MUTATED TRIP6 WILD-TYPE
  FEMALE             6             139
  MALE               2             246
[1] 2 2
[1] FALSE
D1173V8, binary
                 cls
clus                0   1
  TRIP6 MUTATED     7   0
  TRIP6 WILD-TYPE 285  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP6 MUTATED      7    0
  TRIP6 WILD-TYPE  285   59
     clus
vv    TRIP6 MUTATED TRIP6 WILD-TYPE
  NO              7             285
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TRIP6 MUTATED                                          0
  TRIP6 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TRIP6 MUTATED                                       1
  TRIP6 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRIP6 MUTATED                                                        5
  TRIP6 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TRIP6 MUTATED                                                   0
  TRIP6 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TRIP6 MUTATED                                                                   1
  TRIP6 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TRIP6 MUTATED                                                    0
  TRIP6 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TRIP6 MUTATED                                                  1
  TRIP6 WILD-TYPE                                               60
D1173V9, multiclass
                                                                   clus
vv                                                                  TRIP6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  TRIP6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRIP6 MUTATED     6   0   0   2
  TRIP6 WILD-TYPE 305  14  15  22
D1173V10, multiclass
    clus
vv   TRIP6 MUTATED TRIP6 WILD-TYPE
  R0             6             305
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1173V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TRIP6 MUTATED       1                         0
  TRIP6 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TRIP6 MUTATED                                           0     6
  TRIP6 WILD-TYPE                                         1   237
D1173V12, multiclass
                                           clus
vv                                          TRIP6 MUTATED TRIP6 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 6             237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1173V13, binary
                 cls
clus                0   1
  TRIP6 MUTATED     1   6
  TRIP6 WILD-TYPE   3 304
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP6 MUTATED      1    6
  TRIP6 WILD-TYPE    3  304
                        clus
vv                       TRIP6 MUTATED TRIP6 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             6             304
[1] 2 2
[1] FALSE

Clustering(1174) Variable = PBX2 MUTATION ANALYSIS
D1174V1, survival
                sevent
clus2              0   1
  PBX2 MUTATED     3   6
  PBX2 WILD-TYPE 227 133
  PBX2 MUTATED PBX2 WILD-TYPE 
             9            360 
  PBX2 MUTATED PBX2 WILD-TYPE 
             6            133 
$`PBX2 MUTATED`
TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-8363 TCGA-BR-A4CS TCGA-CD-A4MG TCGA-CD-A4MI 
       34.68        19.33         0.26         1.48         6.58        11.77 
TCGA-CG-4306 TCGA-HF-A5NB TCGA-HU-A4GY 
        1.02        30.51         0.26 

$`PBX2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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 

  PBX2 MUTATED PBX2 WILD-TYPE 
          0.26           0.00 
  PBX2 MUTATED PBX2 WILD-TYPE 
         34.68         122.30 
  PBX2 MUTATED PBX2 WILD-TYPE 
          6.58          14.45 
[1] "0.3 - 34.7 (6.6)"   "0.0 - 122.3 (14.4)"
[1] "hr=" "2.8"
D1174V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PBX2 MUTATED         0        0        1        0         2         1
  PBX2 WILD-TYPE       2       15       39       30        35        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PBX2 MUTATED           0          3          0          2        1
  PBX2 WILD-TYPE         3         67         53         30       37
D1174V3, multiclass
            clus
vv           PBX2 MUTATED PBX2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              0             30
  STAGE IIA             2             35
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            3             67
  STAGE IIIB            0             53
  STAGE IIIC            2             30
  STAGE IV              1             37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PBX2 MUTATED     0   1   5   4
  PBX2 WILD-TYPE  22  91 168  93
D1174V4, multiclass
    clus
vv   PBX2 MUTATED PBX2 WILD-TYPE
  T1            0             22
  T2            1             91
  T3            5            168
  T4            4             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
  PBX2 MUTATED     4   3   1   2
  PBX2 WILD-TYPE 114 101  76  75
D1174V5, multiclass
    clus
vv   PBX2 MUTATED PBX2 WILD-TYPE
  N0            4            114
  N1            3            101
  N2            1             76
  N3            2             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"
D1174V6, binary
                cls
clus               0   1
  PBX2 MUTATED     9   1
  PBX2 WILD-TYPE 337  28
[1] "tbl2"
                cls
clus             [,1] [,2]
  PBX2 MUTATED      9    1
  PBX2 WILD-TYPE  337   28
   clus
vv  PBX2 MUTATED PBX2 WILD-TYPE
  0            9            337
  1            1             28
[1] 2 2
[1] FALSE
D1174V7, binary
                cls
clus               0   1
  PBX2 MUTATED     6   4
  PBX2 WILD-TYPE 139 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  PBX2 MUTATED      6    4
  PBX2 WILD-TYPE  139  244
        clus
vv       PBX2 MUTATED PBX2 WILD-TYPE
  FEMALE            6            139
  MALE              4            244
[1] 2 2
[1] FALSE
D1174V8, binary
                cls
clus               0   1
  PBX2 MUTATED     7   1
  PBX2 WILD-TYPE 285  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  PBX2 MUTATED      7    1
  PBX2 WILD-TYPE  285   58
     clus
vv    PBX2 MUTATED PBX2 WILD-TYPE
  NO             7            285
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PBX2 MUTATED                                          0
  PBX2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PBX2 MUTATED                                       2
  PBX2 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PBX2 MUTATED                                                        7
  PBX2 WILD-TYPE                                                    151
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PBX2 MUTATED                                                   1
  PBX2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PBX2 MUTATED                                                                   0
  PBX2 WILD-TYPE                                                                68
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PBX2 MUTATED                                                    0
  PBX2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PBX2 MUTATED                                                  0
  PBX2 WILD-TYPE                                               61
D1174V9, multiclass
                                                                   clus
vv                                                                  PBX2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             0
                                                                   clus
vv                                                                  PBX2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PBX2 MUTATED     5   1   1   1
  PBX2 WILD-TYPE 306  13  14  23
D1174V10, multiclass
    clus
vv   PBX2 MUTATED PBX2 WILD-TYPE
  R0            5            306
  R1            1             13
  R2            1             14
  RX            1             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1174V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  PBX2 MUTATED       3                         0
  PBX2 WILD-TYPE    84                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PBX2 MUTATED                                           0     5
  PBX2 WILD-TYPE                                         1   238
D1174V12, multiclass
                                           clus
vv                                          PBX2 MUTATED PBX2 WILD-TYPE
  ASIAN                                                3             84
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                5            238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1174V13, binary
                cls
clus               0   1
  PBX2 MUTATED     0   8
  PBX2 WILD-TYPE   4 302
[1] "tbl2"
                cls
clus             [,1] [,2]
  PBX2 MUTATED      0    8
  PBX2 WILD-TYPE    4  302
                        clus
vv                       PBX2 MUTATED PBX2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            302
[1] 2 2
[1] FALSE

Clustering(1175) Variable = TNNT3 MUTATION ANALYSIS
D1175V1, survival
                 sevent
clus2               0   1
  TNNT3 MUTATED     5   2
  TNNT3 WILD-TYPE 225 137
  TNNT3 MUTATED TNNT3 WILD-TYPE 
              7             362 
  TNNT3 MUTATED TNNT3 WILD-TYPE 
              2             137 
$`TNNT3 MUTATED`
TCGA-BR-8487 TCGA-CG-5721 TCGA-IN-AB1X TCGA-MX-A5UJ TCGA-VQ-A8DV TCGA-VQ-A8P2 
        1.12         6.02        13.51        19.73        13.25        38.14 
TCGA-VQ-A91U 
        1.71 

$`TNNT3 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-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-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-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 

  TNNT3 MUTATED TNNT3 WILD-TYPE 
           1.12            0.00 
  TNNT3 MUTATED TNNT3 WILD-TYPE 
          38.14          122.30 
  TNNT3 MUTATED TNNT3 WILD-TYPE 
          13.25           14.45 
[1] "1.1 - 38.1 (13.2)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1"  
D1175V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TNNT3 MUTATED         0        0        1        0         2         0
  TNNT3 WILD-TYPE       2       15       39       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNNT3 MUTATED           0          3          0          0        1
  TNNT3 WILD-TYPE         3         67         53         32       37
D1175V3, multiclass
            clus
vv           TNNT3 MUTATED TNNT3 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               1              39
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TNNT3 MUTATED     0   1   4   2
  TNNT3 WILD-TYPE  22  91 169  95
D1175V4, multiclass
    clus
vv   TNNT3 MUTATED TNNT3 WILD-TYPE
  T1             0              22
  T2             1              91
  T3             4             169
  T4             2              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
  TNNT3 MUTATED     3   3   1   0
  TNNT3 WILD-TYPE 115 101  76  77
D1175V5, multiclass
    clus
vv   TNNT3 MUTATED TNNT3 WILD-TYPE
  N0             3             115
  N1             3             101
  N2             1              76
  N3             0              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"
D1175V6, binary
                 cls
clus                0   1
  TNNT3 MUTATED     7   0
  TNNT3 WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNNT3 MUTATED      7    0
  TNNT3 WILD-TYPE  339   29
   clus
vv  TNNT3 MUTATED TNNT3 WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D1175V7, binary
                 cls
clus                0   1
  TNNT3 MUTATED     3   4
  TNNT3 WILD-TYPE 142 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNNT3 MUTATED      3    4
  TNNT3 WILD-TYPE  142  244
        clus
vv       TNNT3 MUTATED TNNT3 WILD-TYPE
  FEMALE             3             142
  MALE               4             244
[1] 2 2
[1] FALSE
D1175V8, binary
                 cls
clus                0   1
  TNNT3 MUTATED     6   1
  TNNT3 WILD-TYPE 286  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNNT3 MUTATED      6    1
  TNNT3 WILD-TYPE  286   58
     clus
vv    TNNT3 MUTATED TNNT3 WILD-TYPE
  NO              6             286
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TNNT3 MUTATED                                          0
  TNNT3 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TNNT3 MUTATED                                       0
  TNNT3 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNNT3 MUTATED                                                        2
  TNNT3 WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TNNT3 MUTATED                                                   1
  TNNT3 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TNNT3 MUTATED                                                                   3
  TNNT3 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TNNT3 MUTATED                                                    0
  TNNT3 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TNNT3 MUTATED                                                  1
  TNNT3 WILD-TYPE                                               60
D1175V9, multiclass
                                                                   clus
vv                                                                  TNNT3 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  TNNT3 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TNNT3 MUTATED     7   0   0   0
  TNNT3 WILD-TYPE 304  14  15  24
D1175V10, multiclass
    clus
vv   TNNT3 MUTATED TNNT3 WILD-TYPE
  R0             7             304
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1175V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TNNT3 MUTATED       1                         0
  TNNT3 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TNNT3 MUTATED                                           0     5
  TNNT3 WILD-TYPE                                         1   238
D1175V12, multiclass
                                           clus
vv                                          TNNT3 MUTATED TNNT3 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 5             238
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1175V13, binary
                 cls
clus                0   1
  TNNT3 MUTATED     0   3
  TNNT3 WILD-TYPE   4 307
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNNT3 MUTATED      0    3
  TNNT3 WILD-TYPE    4  307
                        clus
vv                       TNNT3 MUTATED TNNT3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             307
[1] 2 2
[1] FALSE

Clustering(1176) Variable = OSTALPHA MUTATION ANALYSIS
D1176V1, survival
                    sevent
clus2                  0   1
  OSTALPHA MUTATED     3   0
  OSTALPHA WILD-TYPE 227 139
  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
                 3                366 
  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
                 0                139 
$`OSTALPHA MUTATED`
TCGA-BR-8487 TCGA-BR-8680 TCGA-HF-A5NB 
        1.12        31.96        30.51 

$`OSTALPHA WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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 

  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
              1.12               0.00 
  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
             31.96             122.30 
  OSTALPHA MUTATED OSTALPHA WILD-TYPE 
             30.51              14.22 
[1] "1.1 - 32.0 (30.5)"  "0.0 - 122.3 (14.2)"
[1] "hr="     "3300000"
D1176V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OSTALPHA MUTATED         0        0        0        0         1         1
  OSTALPHA WILD-TYPE       2       15       40       30        36        51
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSTALPHA MUTATED           0          0          0          1        1
  OSTALPHA WILD-TYPE         3         70         53         31       37
D1176V3, multiclass
            clus
vv           OSTALPHA MUTATED OSTALPHA WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 15
  STAGE IB                  0                 40
  STAGE II                  0                 30
  STAGE IIA                 1                 36
  STAGE IIB                 1                 51
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                0                 53
  STAGE IIIC                1                 31
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  OSTALPHA MUTATED     0   0   1   3
  OSTALPHA WILD-TYPE  22  92 172  94
D1176V4, multiclass
    clus
vv   OSTALPHA MUTATED OSTALPHA WILD-TYPE
  T1                0                 22
  T2                0                 92
  T3                1                172
  T4                3                 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
  OSTALPHA MUTATED     2   0   1   1
  OSTALPHA WILD-TYPE 116 104  76  76
D1176V5, multiclass
    clus
vv   OSTALPHA MUTATED OSTALPHA WILD-TYPE
  N0                2                116
  N1                0                104
  N2                1                 76
  N3                1                 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"
D1176V6, binary
                    cls
clus                   0   1
  OSTALPHA MUTATED     3   1
  OSTALPHA WILD-TYPE 343  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  OSTALPHA MUTATED      3    1
  OSTALPHA WILD-TYPE  343   28
   clus
vv  OSTALPHA MUTATED OSTALPHA WILD-TYPE
  0                3                343
  1                1                 28
[1] 2 2
[1] FALSE
D1176V7, binary
                    cls
clus                   0   1
  OSTALPHA MUTATED     2   2
  OSTALPHA WILD-TYPE 143 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  OSTALPHA MUTATED      2    2
  OSTALPHA WILD-TYPE  143  246
        clus
vv       OSTALPHA MUTATED OSTALPHA WILD-TYPE
  FEMALE                2                143
  MALE                  2                246
[1] 2 2
[1] FALSE
D1176V8, binary
                    cls
clus                   0   1
  OSTALPHA MUTATED     3   1
  OSTALPHA WILD-TYPE 289  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  OSTALPHA MUTATED      3    1
  OSTALPHA WILD-TYPE  289   58
     clus
vv    OSTALPHA MUTATED OSTALPHA WILD-TYPE
  NO                 3                289
  YES                1                 58
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OSTALPHA MUTATED                                          0
  OSTALPHA WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OSTALPHA MUTATED                                       0
  OSTALPHA WILD-TYPE                                    70
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OSTALPHA MUTATED                                                        1
  OSTALPHA WILD-TYPE                                                    157
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OSTALPHA MUTATED                                                   1
  OSTALPHA WILD-TYPE                                                20
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OSTALPHA MUTATED                                                                   1
  OSTALPHA WILD-TYPE                                                                67
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OSTALPHA MUTATED                                                    0
  OSTALPHA WILD-TYPE                                                  5
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OSTALPHA MUTATED                                                  1
  OSTALPHA WILD-TYPE                                               60
D1176V9, multiclass
                                                                   clus
vv                                                                  OSTALPHA MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  OSTALPHA WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           157
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  OSTALPHA MUTATED     3   1   0   0
  OSTALPHA WILD-TYPE 308  13  15  24
D1176V10, multiclass
    clus
vv   OSTALPHA MUTATED OSTALPHA WILD-TYPE
  R0                3                308
  R1                1                 13
  R2                0                 15
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1176V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  OSTALPHA MUTATED       1                         0
  OSTALPHA WILD-TYPE    86                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OSTALPHA MUTATED                                           0     2
  OSTALPHA WILD-TYPE                                         1   241
D1176V12, multiclass
                                           clus
vv                                          OSTALPHA MUTATED OSTALPHA WILD-TYPE
  ASIAN                                                    1                 86
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    2                241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1176V13, binary
                    cls
clus                   0   1
  OSTALPHA MUTATED     0   3
  OSTALPHA WILD-TYPE   4 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  OSTALPHA MUTATED      0    3
  OSTALPHA WILD-TYPE    4  307
                        clus
vv                       OSTALPHA MUTATED OSTALPHA WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                3                307
[1] 2 2
[1] FALSE

Clustering(1177) Variable = OXCT2 MUTATION ANALYSIS
D1177V1, survival
                 sevent
clus2               0   1
  OXCT2 MUTATED     4   1
  OXCT2 WILD-TYPE 226 138
  OXCT2 MUTATED OXCT2 WILD-TYPE 
              5             364 
  OXCT2 MUTATED OXCT2 WILD-TYPE 
              1             138 
$`OXCT2 MUTATED`
TCGA-BR-7707 TCGA-BR-8363 TCGA-BR-A4J6 TCGA-HU-A4GN TCGA-IN-A6RS 
       35.84         0.26         0.66        29.98        12.59 

$`OXCT2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       28.34        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-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-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 

  OXCT2 MUTATED OXCT2 WILD-TYPE 
           0.26            0.00 
  OXCT2 MUTATED OXCT2 WILD-TYPE 
          35.84          122.30 
  OXCT2 MUTATED OXCT2 WILD-TYPE 
          12.59           14.35 
[1] "0.3 - 35.8 (12.6)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.7"
D1177V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  OXCT2 MUTATED         0        1        2        0         2         0
  OXCT2 WILD-TYPE       2       14       38       30        35        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OXCT2 MUTATED           0          0          0          0        0
  OXCT2 WILD-TYPE         3         70         53         32       38
D1177V3, multiclass
            clus
vv           OXCT2 MUTATED OXCT2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               2              38
  STAGE II               0              30
  STAGE IIA              2              35
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             0              70
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OXCT2 MUTATED     1   3   1   0
  OXCT2 WILD-TYPE  21  89 172  97
D1177V4, multiclass
    clus
vv   OXCT2 MUTATED OXCT2 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             1             172
  T4             0              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
  OXCT2 MUTATED     4   1   0   0
  OXCT2 WILD-TYPE 114 103  77  77
D1177V5, multiclass
    clus
vv   OXCT2 MUTATED OXCT2 WILD-TYPE
  N0             4             114
  N1             1             103
  N2             0              77
  N3             0              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"
D1177V6, binary
                 cls
clus                0   1
  OXCT2 MUTATED     5   0
  OXCT2 WILD-TYPE 341  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXCT2 MUTATED      5    0
  OXCT2 WILD-TYPE  341   29
   clus
vv  OXCT2 MUTATED OXCT2 WILD-TYPE
  0             5             341
  1             0              29
[1] 2 2
[1] FALSE
D1177V7, binary
                 cls
clus                0   1
  OXCT2 MUTATED     3   2
  OXCT2 WILD-TYPE 142 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXCT2 MUTATED      3    2
  OXCT2 WILD-TYPE  142  246
        clus
vv       OXCT2 MUTATED OXCT2 WILD-TYPE
  FEMALE             3             142
  MALE               2             246
[1] 2 2
[1] FALSE
D1177V8, binary
                 cls
clus                0   1
  OXCT2 MUTATED     5   0
  OXCT2 WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXCT2 MUTATED      5    0
  OXCT2 WILD-TYPE  287   59
     clus
vv    OXCT2 MUTATED OXCT2 WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  OXCT2 MUTATED                                          0
  OXCT2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  OXCT2 MUTATED                                       0
  OXCT2 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OXCT2 MUTATED                                                        4
  OXCT2 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  OXCT2 MUTATED                                                   0
  OXCT2 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  OXCT2 MUTATED                                                                   0
  OXCT2 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  OXCT2 MUTATED                                                    0
  OXCT2 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  OXCT2 MUTATED                                                  1
  OXCT2 WILD-TYPE                                               60
D1177V9, multiclass
                                                                   clus
vv                                                                  OXCT2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  OXCT2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OXCT2 MUTATED     5   0   0   0
  OXCT2 WILD-TYPE 306  14  15  24
D1177V10, multiclass
    clus
vv   OXCT2 MUTATED OXCT2 WILD-TYPE
  R0             5             306
  R1             0              14
  R2             0              15
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1177V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  OXCT2 MUTATED       1                         0
  OXCT2 WILD-TYPE    86                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  OXCT2 MUTATED                                           0     4
  OXCT2 WILD-TYPE                                         1   239
D1177V12, multiclass
                                           clus
vv                                          OXCT2 MUTATED OXCT2 WILD-TYPE
  ASIAN                                                 1              86
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1177V13, binary
                 cls
clus                0   1
  OXCT2 MUTATED     0   5
  OXCT2 WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OXCT2 MUTATED      0    5
  OXCT2 WILD-TYPE    4  305
                        clus
vv                       OXCT2 MUTATED OXCT2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(1178) Variable = XIRP2 MUTATION ANALYSIS
D1178V1, survival
                 sevent
clus2               0   1
  XIRP2 MUTATED    36  13
  XIRP2 WILD-TYPE 194 126
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             49             320 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
             13             126 
$`XIRP2 MUTATED`
TCGA-B7-A5TI TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6452 
       19.56         6.97        30.90         9.67         6.61        34.68 
TCGA-BR-6706 TCGA-BR-7703 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8297 
       18.05        36.16        14.43        29.59        32.25         7.40 
TCGA-BR-8360 TCGA-BR-8680 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5800 TCGA-CD-5801 
        6.18        31.96        20.65        20.42        13.15        13.18 
TCGA-CD-8525 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CG-4436 TCGA-CG-4449 TCGA-CG-4465 
       12.59        12.30         6.58         7.99        19.07         9.01 
TCGA-CG-4466 TCGA-CG-5721 TCGA-CG-5728 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 
       18.97         6.02        65.10        12.66        20.91        18.84 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-EQ-5647 
       17.19        15.22        14.76        11.44        20.32         0.62 
TCGA-F1-6874 TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4G8 TCGA-HU-A4GP TCGA-HU-A4GU 
       14.47        77.29        22.32        22.68         8.98         6.58 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-IN-A6RL TCGA-SW-A7EA TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       12.95        23.84        13.35        19.04        38.14        37.22 
TCGA-VQ-AA69 
       28.41 

$`XIRP2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-6453 TCGA-BR-6455 
        4.08         9.34         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-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-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-8060 
        3.45         9.07        29.56        33.21        37.25        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-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       19.96         2.20        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-A4PF TCGA-BR-A4QI 
       28.34         0.66        32.52        13.51         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 
       16.14         5.13        13.41        13.02        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-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-4304 
       12.20        11.77        12.62        20.02         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-4455 TCGA-CG-4462 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5717 
       29.98        12.03         0.00         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-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       25.71        19.13        20.55        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       13.35        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-A6F0 
       36.43        13.78        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-8122 
       15.65         8.38         4.34        19.96         7.13         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-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-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        0.10         6.51        20.25         0.26         2.10        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-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-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-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-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 

  XIRP2 MUTATED XIRP2 WILD-TYPE 
           0.62            0.00 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
          77.29          122.30 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
          17.19           14.04 
[1] "0.6 - 77.3 (17.2)"  "0.0 - 122.3 (14.0)"
[1] "hr=" "1.6"
D1178V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XIRP2 MUTATED         0        1        9        3         5         9
  XIRP2 WILD-TYPE       2       14       31       27        32        43
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XIRP2 MUTATED           2         14          2          2        4
  XIRP2 WILD-TYPE         1         56         51         30       34
D1178V3, multiclass
            clus
vv           XIRP2 MUTATED XIRP2 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               9              31
  STAGE II               3              27
  STAGE IIA              5              32
  STAGE IIB              9              43
  STAGE III              2               1
  STAGE IIIA            14              56
  STAGE IIIB             2              51
  STAGE IIIC             2              30
  STAGE IV               4              34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  XIRP2 MUTATED     1  18  21  14
  XIRP2 WILD-TYPE  21  74 152  83
D1178V4, multiclass
    clus
vv   XIRP2 MUTATED XIRP2 WILD-TYPE
  T1             1              21
  T2            18              74
  T3            21             152
  T4            14              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  XIRP2 MUTATED   20 17  9  6
  XIRP2 WILD-TYPE 98 87 68 71
D1178V5, multiclass
    clus
vv   XIRP2 MUTATED XIRP2 WILD-TYPE
  N0            20              98
  N1            17              87
  N2             9              68
  N3             6              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"
D1178V6, binary
                 cls
clus                0   1
  XIRP2 MUTATED    50   3
  XIRP2 WILD-TYPE 296  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED     50    3
  XIRP2 WILD-TYPE  296   26
   clus
vv  XIRP2 MUTATED XIRP2 WILD-TYPE
  0            50             296
  1             3              26
[1] 2 2
[1] FALSE
D1178V7, binary
                 cls
clus                0   1
  XIRP2 MUTATED    28  28
  XIRP2 WILD-TYPE 117 220
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED     28   28
  XIRP2 WILD-TYPE  117  220
        clus
vv       XIRP2 MUTATED XIRP2 WILD-TYPE
  FEMALE            28             117
  MALE              28             220
[1] 2 2
[1] FALSE
D1178V8, binary
                 cls
clus                0   1
  XIRP2 MUTATED    42   6
  XIRP2 WILD-TYPE 250  53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED     42    6
  XIRP2 WILD-TYPE  250   53
     clus
vv    XIRP2 MUTATED XIRP2 WILD-TYPE
  NO             42             250
  YES             6              53
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  XIRP2 MUTATED                                          0
  XIRP2 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  XIRP2 MUTATED                                      10
  XIRP2 WILD-TYPE                                    60
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XIRP2 MUTATED                                                       19
  XIRP2 WILD-TYPE                                                    139
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  XIRP2 MUTATED                                                   6
  XIRP2 WILD-TYPE                                                15
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  XIRP2 MUTATED                                                                  10
  XIRP2 WILD-TYPE                                                                58
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  XIRP2 MUTATED                                                    2
  XIRP2 WILD-TYPE                                                  3
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  XIRP2 MUTATED                                                  9
  XIRP2 WILD-TYPE                                               52
D1178V9, multiclass
                                                                   clus
vv                                                                  XIRP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        10
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       19
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            10
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              9
                                                                   clus
vv                                                                  XIRP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          60
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        139
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              15
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              58
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               52
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  XIRP2 MUTATED    42   1   2   8
  XIRP2 WILD-TYPE 269  13  13  16
D1178V10, multiclass
    clus
vv   XIRP2 MUTATED XIRP2 WILD-TYPE
  R0            42             269
  R1             1              13
  R2             2              13
  RX             8              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1178V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  XIRP2 MUTATED      12                         0
  XIRP2 WILD-TYPE    75                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XIRP2 MUTATED                                           0    36
  XIRP2 WILD-TYPE                                         1   207
D1178V12, multiclass
                                           clus
vv                                          XIRP2 MUTATED XIRP2 WILD-TYPE
  ASIAN                                                12              75
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                36             207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1178V13, binary
                 cls
clus                0   1
  XIRP2 MUTATED     0  45
  XIRP2 WILD-TYPE   4 265
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED      0   45
  XIRP2 WILD-TYPE    4  265
                        clus
vv                       XIRP2 MUTATED XIRP2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            45             265
[1] 2 2
[1] FALSE

Clustering(1179) Variable = CREBBP MUTATION ANALYSIS
D1179V1, survival
                  sevent
clus2                0   1
  CREBBP MUTATED    20  13
  CREBBP WILD-TYPE 210 126
  CREBBP MUTATED CREBBP WILD-TYPE 
              33              336 
  CREBBP MUTATED CREBBP WILD-TYPE 
              13              126 
$`CREBBP MUTATED`
TCGA-CG-4460 TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-4256 TCGA-BR-6452 TCGA-BR-6566 
       21.99        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-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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
        9.86        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-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-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-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-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-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-D7-6818 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-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19        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-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-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-A4GY TCGA-HU-A4H2 
       21.37         8.98         0.10         6.51         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-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-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-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 
       32.94        54.12        26.04        27.55        12.43        17.26 

  CREBBP MUTATED CREBBP WILD-TYPE 
            0.26             0.00 
  CREBBP MUTATED CREBBP WILD-TYPE 
           77.29           122.30 
  CREBBP MUTATED CREBBP WILD-TYPE 
          18.210           14.055 
[1] "0.3 - 77.3 (18.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1"  
D1179V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CREBBP MUTATED         0        0        5        1         6         5
  CREBBP WILD-TYPE       2       15       35       29        31        47
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CREBBP MUTATED           0          6          4          4        3
  CREBBP WILD-TYPE         3         64         49         28       35
D1179V3, multiclass
            clus
vv           CREBBP MUTATED CREBBP WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                5               35
  STAGE II                1               29
  STAGE IIA               6               31
  STAGE IIB               5               47
  STAGE III               0                3
  STAGE IIIA              6               64
  STAGE IIIB              4               49
  STAGE IIIC              4               28
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CREBBP MUTATED     0  10  14  11
  CREBBP WILD-TYPE  22  82 159  86
D1179V4, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  T1              0               22
  T2             10               82
  T3             14              159
  T4             11               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
  CREBBP MUTATED    14   7   6   8
  CREBBP WILD-TYPE 104  97  71  69
D1179V5, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  N0             14              104
  N1              7               97
  N2              6               71
  N3              8               69
[1] 4 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
  CREBBP MUTATED    33   2
  CREBBP WILD-TYPE 313  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     33    2
  CREBBP WILD-TYPE  313   27
   clus
vv  CREBBP MUTATED CREBBP WILD-TYPE
  0             33              313
  1              2               27
[1] 2 2
[1] FALSE
D1179V7, binary
                  cls
clus                 0   1
  CREBBP MUTATED    21  15
  CREBBP WILD-TYPE 124 233
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     21   15
  CREBBP WILD-TYPE  124  233
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  FEMALE             21              124
  MALE               15              233
[1] 2 2
[1] FALSE
D1179V8, binary
                  cls
clus                 0   1
  CREBBP MUTATED    30   4
  CREBBP WILD-TYPE 262  55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     30    4
  CREBBP WILD-TYPE  262   55
     clus
vv    CREBBP MUTATED CREBBP WILD-TYPE
  NO              30              262
  YES              4               55
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CREBBP MUTATED                                          1
  CREBBP WILD-TYPE                                        7
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CREBBP MUTATED                                       6
  CREBBP WILD-TYPE                                    64
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CREBBP MUTATED                                                       16
  CREBBP WILD-TYPE                                                    142
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CREBBP MUTATED                                                   2
  CREBBP WILD-TYPE                                                19
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CREBBP MUTATED                                                                   5
  CREBBP WILD-TYPE                                                                63
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CREBBP MUTATED                                                    0
  CREBBP WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CREBBP MUTATED                                                  6
  CREBBP WILD-TYPE                                               55
D1179V9, multiclass
                                                                   clus
vv                                                                  CREBBP MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          6
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        16
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               6
                                                                   clus
vv                                                                  CREBBP WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           64
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         142
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               63
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                55
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CREBBP MUTATED    27   1   1   4
  CREBBP WILD-TYPE 284  13  14  20
D1179V10, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  R0             27              284
  R1              1               13
  R2              1               14
  RX              4               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1179V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  CREBBP MUTATED       8                         1
  CREBBP WILD-TYPE    79                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CREBBP MUTATED                                           0    23
  CREBBP WILD-TYPE                                         1   220
D1179V12, multiclass
                                           clus
vv                                          CREBBP MUTATED CREBBP WILD-TYPE
  ASIAN                                                  8               79
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                 23              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1179V13, binary
                  cls
clus                 0   1
  CREBBP MUTATED     0  31
  CREBBP WILD-TYPE   4 279
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      0   31
  CREBBP WILD-TYPE    4  279
                        clus
vv                       CREBBP MUTATED CREBBP WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             31              279
[1] 2 2
[1] FALSE

Clustering(1180) Variable = TJP2 MUTATION ANALYSIS
D1180V1, survival
                sevent
clus2              0   1
  TJP2 MUTATED     9   3
  TJP2 WILD-TYPE 221 136
  TJP2 MUTATED TJP2 WILD-TYPE 
            12            357 
  TJP2 MUTATED TJP2 WILD-TYPE 
             3            136 
$`TJP2 MUTATED`
TCGA-BR-4256 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6852 TCGA-BR-8373 TCGA-BR-8487 
        9.34         9.67        34.68        44.94        14.79         1.12 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-D7-8573 TCGA-HF-7132 TCGA-HU-8602 TCGA-HU-A4H8 
       12.43         6.58        19.50        77.29        22.32        14.07 

$`TJP2 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-D7-6526 
       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-D7-8575 TCGA-D7-8576 
       12.33        24.72        16.80        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-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-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 

  TJP2 MUTATED TJP2 WILD-TYPE 
          1.12           0.00 
  TJP2 MUTATED TJP2 WILD-TYPE 
         77.29         122.30 
  TJP2 MUTATED TJP2 WILD-TYPE 
         14.43          14.27 
[1] "1.1 - 77.3 (14.4)"  "0.0 - 122.3 (14.3)"
[1] "hr=" "1.7"
D1180V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  TJP2 MUTATED         0        0        1        2         5         1
  TJP2 WILD-TYPE       2       15       39       28        32        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TJP2 MUTATED           0          1          0          0        0
  TJP2 WILD-TYPE         3         69         53         32       38
D1180V3, multiclass
            clus
vv           TJP2 MUTATED TJP2 WILD-TYPE
  STAGE I               0              2
  STAGE IA              0             15
  STAGE IB              1             39
  STAGE II              2             28
  STAGE IIA             5             32
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            1             69
  STAGE IIIB            0             53
  STAGE IIIC            0             32
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TJP2 MUTATED     1   1   6   2
  TJP2 WILD-TYPE  21  91 167  95
D1180V4, multiclass
    clus
vv   TJP2 MUTATED TJP2 WILD-TYPE
  T1            1             21
  T2            1             91
  T3            6            167
  T4            2             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
  TJP2 MUTATED     7   5   0   0
  TJP2 WILD-TYPE 111  99  77  77
D1180V5, multiclass
    clus
vv   TJP2 MUTATED TJP2 WILD-TYPE
  N0            7            111
  N1            5             99
  N2            0             77
  N3            0             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"
D1180V6, binary
                cls
clus               0   1
  TJP2 MUTATED    14   0
  TJP2 WILD-TYPE 332  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  TJP2 MUTATED     14    0
  TJP2 WILD-TYPE  332   29
   clus
vv  TJP2 MUTATED TJP2 WILD-TYPE
  0           14            332
  1            0             29
[1] 2 2
[1] FALSE
D1180V7, binary
                cls
clus               0   1
  TJP2 MUTATED     8   6
  TJP2 WILD-TYPE 137 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  TJP2 MUTATED      8    6
  TJP2 WILD-TYPE  137  242
        clus
vv       TJP2 MUTATED TJP2 WILD-TYPE
  FEMALE            8            137
  MALE              6            242
[1] 2 2
[1] FALSE
D1180V8, binary
                cls
clus               0   1
  TJP2 MUTATED    11   1
  TJP2 WILD-TYPE 281  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  TJP2 MUTATED     11    1
  TJP2 WILD-TYPE  281   58
     clus
vv    TJP2 MUTATED TJP2 WILD-TYPE
  NO            11            281
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TJP2 MUTATED                                          0
  TJP2 WILD-TYPE                                        8
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TJP2 MUTATED                                       2
  TJP2 WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TJP2 MUTATED                                                        8
  TJP2 WILD-TYPE                                                    150
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TJP2 MUTATED                                                   1
  TJP2 WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TJP2 MUTATED                                                                   1
  TJP2 WILD-TYPE                                                                67
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TJP2 MUTATED                                                    0
  TJP2 WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TJP2 MUTATED                                                  2
  TJP2 WILD-TYPE                                               59
D1180V9, multiclass
                                                                   clus
vv                                                                  TJP2 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       8
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             2
                                                                   clus
vv                                                                  TJP2 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       150
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TJP2 MUTATED     9   0   0   4
  TJP2 WILD-TYPE 302  14  15  20
D1180V10, multiclass
    clus
vv   TJP2 MUTATED TJP2 WILD-TYPE
  R0            9            302
  R1            0             14
  R2            0             15
  RX            4             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1180V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  TJP2 MUTATED       4                         0
  TJP2 WILD-TYPE    83                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TJP2 MUTATED                                           0     9
  TJP2 WILD-TYPE                                         1   234
D1180V12, multiclass
                                           clus
vv                                          TJP2 MUTATED TJP2 WILD-TYPE
  ASIAN                                                4             83
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                                9            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1180V13, binary
                cls
clus               0   1
  TJP2 MUTATED     0  13
  TJP2 WILD-TYPE   4 297
[1] "tbl2"
                cls
clus             [,1] [,2]
  TJP2 MUTATED      0   13
  TJP2 WILD-TYPE    4  297
                        clus
vv                       TJP2 MUTATED TJP2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           13            297
[1] 2 2
[1] FALSE

Clustering(1181) Variable = PTPN11 MUTATION ANALYSIS
D1181V1, survival
                  sevent
clus2                0   1
  PTPN11 MUTATED     5   2
  PTPN11 WILD-TYPE 225 137
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               7              362 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               2              137 
$`PTPN11 MUTATED`
TCGA-B7-5816 TCGA-BR-8487 TCGA-BR-8680 TCGA-CG-5733 TCGA-D7-6820 TCGA-HF-A5NB 
       26.70         1.12        31.96        21.07        11.31        30.51 
TCGA-R5-A804 
        4.60 

$`PTPN11 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-D7-6822 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-F1-6875 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-A805 
       45.67        18.21         8.52        74.53         6.08         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 

  PTPN11 MUTATED PTPN11 WILD-TYPE 
            1.12             0.00 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
           31.96           122.30 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
           21.07            14.22 
[1] "1.1 - 32.0 (21.1)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D1181V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  PTPN11 MUTATED         0        0        0        0         1         2
  PTPN11 WILD-TYPE       2       15       40       30        36        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN11 MUTATED           0          1          0          1        3
  PTPN11 WILD-TYPE         3         69         53         31       35
D1181V3, multiclass
            clus
vv           PTPN11 MUTATED PTPN11 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               1               36
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              1               69
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                3               35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTPN11 MUTATED     0   2   2   4
  PTPN11 WILD-TYPE  22  90 171  93
D1181V4, multiclass
    clus
vv   PTPN11 MUTATED PTPN11 WILD-TYPE
  T1              0               22
  T2              2               90
  T3              2              171
  T4              4               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
  PTPN11 MUTATED     2   1   4   1
  PTPN11 WILD-TYPE 116 103  73  76
D1181V5, multiclass
    clus
vv   PTPN11 MUTATED PTPN11 WILD-TYPE
  N0              2              116
  N1              1              103
  N2              4               73
  N3              1               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"
D1181V6, binary
                  cls
clus                 0   1
  PTPN11 MUTATED     6   2
  PTPN11 WILD-TYPE 340  27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED      6    2
  PTPN11 WILD-TYPE  340   27
   clus
vv  PTPN11 MUTATED PTPN11 WILD-TYPE
  0              6              340
  1              2               27
[1] 2 2
[1] FALSE
D1181V7, binary
                  cls
clus                 0   1
  PTPN11 MUTATED     5   3
  PTPN11 WILD-TYPE 140 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED      5    3
  PTPN11 WILD-TYPE  140  245
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  FEMALE              5              140
  MALE                3              245
[1] 2 2
[1] FALSE
D1181V8, binary
                  cls
clus                 0   1
  PTPN11 MUTATED     6   1
  PTPN11 WILD-TYPE 286  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED      6    1
  PTPN11 WILD-TYPE  286   58
     clus
vv    PTPN11 MUTATED PTPN11 WILD-TYPE
  NO               6              286
  YES              1               58
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  PTPN11 MUTATED                                          0
  PTPN11 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  PTPN11 MUTATED                                       2
  PTPN11 WILD-TYPE                                    68
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTPN11 MUTATED                                                        2
  PTPN11 WILD-TYPE                                                    156
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  PTPN11 MUTATED                                                   1
  PTPN11 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  PTPN11 MUTATED                                                                   1
  PTPN11 WILD-TYPE                                                                67
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  PTPN11 MUTATED                                                    0
  PTPN11 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  PTPN11 MUTATED                                                  2
  PTPN11 WILD-TYPE                                               59
D1181V9, multiclass
                                                                   clus
vv                                                                  PTPN11 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               2
                                                                   clus
vv                                                                  PTPN11 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PTPN11 MUTATED     5   1   0   1
  PTPN11 WILD-TYPE 306  13  15  23
D1181V10, multiclass
    clus
vv   PTPN11 MUTATED PTPN11 WILD-TYPE
  R0              5              306
  R1              1               13
  R2              0               15
  RX              1               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1181V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  PTPN11 MUTATED       1                         1
  PTPN11 WILD-TYPE    86                         8
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  PTPN11 MUTATED                                           0     4
  PTPN11 WILD-TYPE                                         1   239
D1181V12, multiclass
                                           clus
vv                                          PTPN11 MUTATED PTPN11 WILD-TYPE
  ASIAN                                                  1               86
  BLACK OR AFRICAN AMERICAN                              1                8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  4              239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1181V13, binary
                  cls
clus                 0   1
  PTPN11 MUTATED     0   6
  PTPN11 WILD-TYPE   4 304
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED      0    6
  PTPN11 WILD-TYPE    4  304
                        clus
vv                       PTPN11 MUTATED PTPN11 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              304
[1] 2 2
[1] FALSE

Clustering(1182) Variable = ASCL4 MUTATION ANALYSIS
D1182V1, survival
                 sevent
clus2               0   1
  ASCL4 MUTATED     2   5
  ASCL4 WILD-TYPE 228 134
  ASCL4 MUTATED ASCL4 WILD-TYPE 
              7             362 
  ASCL4 MUTATED ASCL4 WILD-TYPE 
              5             134 
$`ASCL4 MUTATED`
TCGA-BR-4184 TCGA-BR-8078 TCGA-BR-8363 TCGA-CG-4305 TCGA-CG-4469 TCGA-CG-5726 
        6.97        29.59         0.26        15.95         7.07        28.96 
TCGA-D7-A4YV 
        5.92 

$`ASCL4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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 

  ASCL4 MUTATED ASCL4 WILD-TYPE 
           0.26            0.00 
  ASCL4 MUTATED ASCL4 WILD-TYPE 
          29.59          122.30 
  ASCL4 MUTATED ASCL4 WILD-TYPE 
           7.07           14.35 
[1] "0.3 - 29.6 (7.1)"   "0.0 - 122.3 (14.3)"
[1] "hr=" "2.5"
D1182V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ASCL4 MUTATED         0        1        1        1         0         2
  ASCL4 WILD-TYPE       2       14       39       29        37        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ASCL4 MUTATED           0          1          0          0        1
  ASCL4 WILD-TYPE         3         69         53         32       37
D1182V3, multiclass
            clus
vv           ASCL4 MUTATED ASCL4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               1              39
  STAGE II               1              29
  STAGE IIA              0              37
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ASCL4 MUTATED     1   2   3   1
  ASCL4 WILD-TYPE  21  90 170  96
D1182V4, multiclass
    clus
vv   ASCL4 MUTATED ASCL4 WILD-TYPE
  T1             1              21
  T2             2              90
  T3             3             170
  T4             1              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
  ASCL4 MUTATED     3   3   0   1
  ASCL4 WILD-TYPE 115 101  77  76
D1182V5, multiclass
    clus
vv   ASCL4 MUTATED ASCL4 WILD-TYPE
  N0             3             115
  N1             3             101
  N2             0              77
  N3             1              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"
D1182V6, binary
                 cls
clus                0   1
  ASCL4 MUTATED     6   0
  ASCL4 WILD-TYPE 340  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL4 MUTATED      6    0
  ASCL4 WILD-TYPE  340   29
   clus
vv  ASCL4 MUTATED ASCL4 WILD-TYPE
  0             6             340
  1             0              29
[1] 2 2
[1] FALSE
D1182V7, binary
                 cls
clus                0   1
  ASCL4 MUTATED     3   4
  ASCL4 WILD-TYPE 142 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL4 MUTATED      3    4
  ASCL4 WILD-TYPE  142  244
        clus
vv       ASCL4 MUTATED ASCL4 WILD-TYPE
  FEMALE             3             142
  MALE               4             244
[1] 2 2
[1] FALSE
D1182V8, binary
                 cls
clus                0   1
  ASCL4 MUTATED     5   0
  ASCL4 WILD-TYPE 287  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL4 MUTATED      5    0
  ASCL4 WILD-TYPE  287   59
     clus
vv    ASCL4 MUTATED ASCL4 WILD-TYPE
  NO              5             287
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ASCL4 MUTATED                                          0
  ASCL4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ASCL4 MUTATED                                       0
  ASCL4 WILD-TYPE                                    70
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ASCL4 MUTATED                                                        4
  ASCL4 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ASCL4 MUTATED                                                   0
  ASCL4 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ASCL4 MUTATED                                                                   2
  ASCL4 WILD-TYPE                                                                66
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ASCL4 MUTATED                                                    0
  ASCL4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ASCL4 MUTATED                                                  1
  ASCL4 WILD-TYPE                                               60
D1182V9, multiclass
                                                                   clus
vv                                                                  ASCL4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         0
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  ASCL4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          70
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ASCL4 MUTATED     5   1   0   1
  ASCL4 WILD-TYPE 306  13  15  23
D1182V10, multiclass
    clus
vv   ASCL4 MUTATED ASCL4 WILD-TYPE
  R0             5             306
  R1             1              13
  R2             0              15
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1182V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ASCL4 MUTATED       0                         0
  ASCL4 WILD-TYPE    87                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ASCL4 MUTATED                                           0     4
  ASCL4 WILD-TYPE                                         1   239
D1182V12, multiclass
                                           clus
vv                                          ASCL4 MUTATED ASCL4 WILD-TYPE
  ASIAN                                                 0              87
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1182V13, binary
                 cls
clus                0   1
  ASCL4 MUTATED     0   4
  ASCL4 WILD-TYPE   4 306
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL4 MUTATED      0    4
  ASCL4 WILD-TYPE    4  306
                        clus
vv                       ASCL4 MUTATED ASCL4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             306
[1] 2 2
[1] FALSE

Clustering(1183) Variable = TESK1 MUTATION ANALYSIS
D1183V1, survival
                 sevent
clus2               0   1
  TESK1 MUTATED     6   5
  TESK1 WILD-TYPE 224 134
  TESK1 MUTATED TESK1 WILD-TYPE 
             11             358 
  TESK1 MUTATED TESK1 WILD-TYPE 
              5             134 
$`TESK1 MUTATED`
TCGA-BR-6452 TCGA-BR-8487 TCGA-CD-A4MG TCGA-CG-4465 TCGA-CG-5723 TCGA-CG-5733 
       34.68         1.12         6.58         9.01       105.07        21.07 
TCGA-D7-A6EY TCGA-F1-A448 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GQ 
       11.44        21.27        24.20        29.98         0.10 

$`TESK1 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-F1-6874 
        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-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-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 

  TESK1 MUTATED TESK1 WILD-TYPE 
            0.1             0.0 
  TESK1 MUTATED TESK1 WILD-TYPE 
         105.07          122.30 
  TESK1 MUTATED TESK1 WILD-TYPE 
          21.07           14.22 
[1] "0.1 - 105.1 (21.1)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.1"
D1183V2, 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       1       14       40       29        33        52
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TESK1 MUTATED           0          1          2          1        1
  TESK1 WILD-TYPE         3         69         51         31       37
D1183V3, multiclass
            clus
vv           TESK1 MUTATED TESK1 WILD-TYPE
  STAGE I                1               1
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              4              33
  STAGE IIB              0              52
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             2              51
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TESK1 MUTATED     2   3   5   2
  TESK1 WILD-TYPE  20  89 168  95
D1183V4, multiclass
    clus
vv   TESK1 MUTATED TESK1 WILD-TYPE
  T1             2              20
  T2             3              89
  T3             5             168
  T4             2              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
  TESK1 MUTATED     4   3   2   3
  TESK1 WILD-TYPE 114 101  75  74
D1183V5, multiclass
    clus
vv   TESK1 MUTATED TESK1 WILD-TYPE
  N0             4             114
  N1             3             101
  N2             2              75
  N3             3              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"
D1183V6, binary
                 cls
clus                0   1
  TESK1 MUTATED    10   1
  TESK1 WILD-TYPE 336  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TESK1 MUTATED     10    1
  TESK1 WILD-TYPE  336   28
   clus
vv  TESK1 MUTATED TESK1 WILD-TYPE
  0            10             336
  1             1              28
[1] 2 2
[1] FALSE
D1183V7, binary
                 cls
clus                0   1
  TESK1 MUTATED     6   6
  TESK1 WILD-TYPE 139 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TESK1 MUTATED      6    6
  TESK1 WILD-TYPE  139  242
        clus
vv       TESK1 MUTATED TESK1 WILD-TYPE
  FEMALE             6             139
  MALE               6             242
[1] 2 2
[1] FALSE
D1183V8, binary
                 cls
clus                0   1
  TESK1 MUTATED    10   1
  TESK1 WILD-TYPE 282  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TESK1 MUTATED     10    1
  TESK1 WILD-TYPE  282   58
     clus
vv    TESK1 MUTATED TESK1 WILD-TYPE
  NO             10             282
  YES             1              58
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  TESK1 MUTATED                                          0
  TESK1 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  TESK1 MUTATED                                       2
  TESK1 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TESK1 MUTATED                                                        4
  TESK1 WILD-TYPE                                                    154
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  TESK1 MUTATED                                                   1
  TESK1 WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  TESK1 MUTATED                                                                   1
  TESK1 WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  TESK1 MUTATED                                                    0
  TESK1 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  TESK1 MUTATED                                                  4
  TESK1 WILD-TYPE                                               57
D1183V9, multiclass
                                                                   clus
vv                                                                  TESK1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              4
                                                                   clus
vv                                                                  TESK1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TESK1 MUTATED    10   0   1   0
  TESK1 WILD-TYPE 301  14  14  24
D1183V10, multiclass
    clus
vv   TESK1 MUTATED TESK1 WILD-TYPE
  R0            10             301
  R1             0              14
  R2             1              14
  RX             0              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1183V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  TESK1 MUTATED       4                         1
  TESK1 WILD-TYPE    83                         8
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  TESK1 MUTATED                                           0     4
  TESK1 WILD-TYPE                                         1   239
D1183V12, multiclass
                                           clus
vv                                          TESK1 MUTATED TESK1 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             1               8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1183V13, binary
                 cls
clus                0   1
  TESK1 MUTATED     1   8
  TESK1 WILD-TYPE   3 302
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TESK1 MUTATED      1    8
  TESK1 WILD-TYPE    3  302
                        clus
vv                       TESK1 MUTATED TESK1 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             8             302
[1] 2 2
[1] FALSE

Clustering(1184) Variable = ORC2L MUTATION ANALYSIS
D1184V1, survival
                 sevent
clus2               0   1
  ORC2L MUTATED     4   2
  ORC2L WILD-TYPE 226 137
  ORC2L MUTATED ORC2L WILD-TYPE 
              6             363 
  ORC2L MUTATED ORC2L WILD-TYPE 
              2             137 
$`ORC2L MUTATED`
TCGA-BR-4201 TCGA-BR-7704 TCGA-CD-A4MG TCGA-HU-A4H4 TCGA-VQ-A8P2 TCGA-VQ-A91V 
       30.90        35.24         6.58        23.84        38.14        42.64 

$`ORC2L WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-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-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       20.81         1.71        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 

  ORC2L MUTATED ORC2L WILD-TYPE 
           6.58            0.00 
  ORC2L MUTATED ORC2L WILD-TYPE 
          42.64          122.30 
  ORC2L MUTATED ORC2L WILD-TYPE 
          33.07           14.07 
[1] "6.6 - 42.6 (33.1)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.8"
D1184V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  ORC2L MUTATED         0        0        0        1         1         1
  ORC2L WILD-TYPE       2       15       40       29        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ORC2L MUTATED           0          2          0          0        0
  ORC2L WILD-TYPE         3         68         53         32       38
D1184V3, multiclass
            clus
vv           ORC2L MUTATED ORC2L WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               1              29
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             2              68
  STAGE IIIB             0              53
  STAGE IIIC             0              32
  STAGE IV               0              38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ORC2L MUTATED     1   2   3   1
  ORC2L WILD-TYPE  21  90 170  96
D1184V4, multiclass
    clus
vv   ORC2L MUTATED ORC2L WILD-TYPE
  T1             1              21
  T2             2              90
  T3             3             170
  T4             1              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
  ORC2L MUTATED     2   1   2   0
  ORC2L WILD-TYPE 116 103  75  77
D1184V5, multiclass
    clus
vv   ORC2L MUTATED ORC2L WILD-TYPE
  N0             2             116
  N1             1             103
  N2             2              75
  N3             0              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"
D1184V6, binary
                 cls
clus                0   1
  ORC2L MUTATED     7   0
  ORC2L WILD-TYPE 339  29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC2L MUTATED      7    0
  ORC2L WILD-TYPE  339   29
   clus
vv  ORC2L MUTATED ORC2L WILD-TYPE
  0             7             339
  1             0              29
[1] 2 2
[1] FALSE
D1184V7, binary
                 cls
clus                0   1
  ORC2L MUTATED     4   3
  ORC2L WILD-TYPE 141 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC2L MUTATED      4    3
  ORC2L WILD-TYPE  141  245
        clus
vv       ORC2L MUTATED ORC2L WILD-TYPE
  FEMALE             4             141
  MALE               3             245
[1] 2 2
[1] FALSE
D1184V8, binary
                 cls
clus                0   1
  ORC2L MUTATED     4   2
  ORC2L WILD-TYPE 288  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC2L MUTATED      4    2
  ORC2L WILD-TYPE  288   57
     clus
vv    ORC2L MUTATED ORC2L WILD-TYPE
  NO              4             288
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  ORC2L MUTATED                                          0
  ORC2L WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  ORC2L MUTATED                                       1
  ORC2L WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ORC2L MUTATED                                                        2
  ORC2L WILD-TYPE                                                    156
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  ORC2L MUTATED                                                   1
  ORC2L WILD-TYPE                                                20
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  ORC2L MUTATED                                                                   1
  ORC2L WILD-TYPE                                                                67
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  ORC2L MUTATED                                                    0
  ORC2L WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  ORC2L MUTATED                                                  2
  ORC2L WILD-TYPE                                               59
D1184V9, multiclass
                                                                   clus
vv                                                                  ORC2L MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              2
                                                                   clus
vv                                                                  ORC2L WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               59
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ORC2L MUTATED     4   0   0   2
  ORC2L WILD-TYPE 307  14  15  22
D1184V10, multiclass
    clus
vv   ORC2L MUTATED ORC2L WILD-TYPE
  R0             4             307
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1184V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  ORC2L MUTATED       2                         0
  ORC2L WILD-TYPE    85                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  ORC2L MUTATED                                           0     4
  ORC2L WILD-TYPE                                         1   239
D1184V12, multiclass
                                           clus
vv                                          ORC2L MUTATED ORC2L WILD-TYPE
  ASIAN                                                 2              85
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 4             239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1184V13, binary
                 cls
clus                0   1
  ORC2L MUTATED     0   5
  ORC2L WILD-TYPE   4 305
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC2L MUTATED      0    5
  ORC2L WILD-TYPE    4  305
                        clus
vv                       ORC2L MUTATED ORC2L WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             305
[1] 2 2
[1] FALSE

Clustering(1185) Variable = DHX15 MUTATION ANALYSIS
D1185V1, survival
                 sevent
clus2               0   1
  DHX15 MUTATED     7   3
  DHX15 WILD-TYPE 223 136
  DHX15 MUTATED DHX15 WILD-TYPE 
             10             359 
  DHX15 MUTATED DHX15 WILD-TYPE 
              3             136 
$`DHX15 MUTATED`
TCGA-BR-6452 TCGA-BR-8680 TCGA-BR-A4QM TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5723 
       34.68        31.96         5.13        15.95         1.02       105.07 
TCGA-CG-5725 TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4H8 
       15.02        22.32         0.10        14.07 

$`DHX15 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        21.44        16.14        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-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-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
        0.99        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-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-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 

  DHX15 MUTATED DHX15 WILD-TYPE 
            0.1             0.0 
  DHX15 MUTATED DHX15 WILD-TYPE 
         105.07          122.30 
  DHX15 MUTATED DHX15 WILD-TYPE 
         15.485          14.170 
[1] "0.1 - 105.1 (15.5)" "0.0 - 122.3 (14.2)"
[1] "hr=" "1.4"
D1185V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  DHX15 MUTATED         0        0        2        2         1         1
  DHX15 WILD-TYPE       2       15       38       28        36        51
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DHX15 MUTATED           0          1          0          1        2
  DHX15 WILD-TYPE         3         69         53         31       36
D1185V3, multiclass
            clus
vv           DHX15 MUTATED DHX15 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               2              38
  STAGE II               2              28
  STAGE IIA              1              36
  STAGE IIB              1              51
  STAGE III              0               3
  STAGE IIIA             1              69
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               2              36
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DHX15 MUTATED     1   3   3   3
  DHX15 WILD-TYPE  21  89 170  94
D1185V4, multiclass
    clus
vv   DHX15 MUTATED DHX15 WILD-TYPE
  T1             1              21
  T2             3              89
  T3             3             170
  T4             3              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
  DHX15 MUTATED     3   4   4   0
  DHX15 WILD-TYPE 115 100  73  77
D1185V5, multiclass
    clus
vv   DHX15 MUTATED DHX15 WILD-TYPE
  N0             3             115
  N1             4             100
  N2             4              73
  N3             0              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"
D1185V6, binary
                 cls
clus                0   1
  DHX15 MUTATED     9   2
  DHX15 WILD-TYPE 337  27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX15 MUTATED      9    2
  DHX15 WILD-TYPE  337   27
   clus
vv  DHX15 MUTATED DHX15 WILD-TYPE
  0             9             337
  1             2              27
[1] 2 2
[1] FALSE
D1185V7, binary
                 cls
clus                0   1
  DHX15 MUTATED     3   8
  DHX15 WILD-TYPE 142 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX15 MUTATED      3    8
  DHX15 WILD-TYPE  142  240
        clus
vv       DHX15 MUTATED DHX15 WILD-TYPE
  FEMALE             3             142
  MALE               8             240
[1] 2 2
[1] FALSE
D1185V8, binary
                 cls
clus                0   1
  DHX15 MUTATED     9   0
  DHX15 WILD-TYPE 283  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX15 MUTATED      9    0
  DHX15 WILD-TYPE  283   59
     clus
vv    DHX15 MUTATED DHX15 WILD-TYPE
  NO              9             283
  YES             0              59
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  DHX15 MUTATED                                          0
  DHX15 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  DHX15 MUTATED                                       1
  DHX15 WILD-TYPE                                    69
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DHX15 MUTATED                                                        7
  DHX15 WILD-TYPE                                                    151
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  DHX15 MUTATED                                                   0
  DHX15 WILD-TYPE                                                21
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  DHX15 MUTATED                                                                   0
  DHX15 WILD-TYPE                                                                68
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  DHX15 MUTATED                                                    0
  DHX15 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  DHX15 MUTATED                                                  3
  DHX15 WILD-TYPE                                               58
D1185V9, multiclass
                                                                   clus
vv                                                                  DHX15 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              3
                                                                   clus
vv                                                                  DHX15 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        151
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DHX15 MUTATED     9   0   1   1
  DHX15 WILD-TYPE 302  14  14  23
D1185V10, multiclass
    clus
vv   DHX15 MUTATED DHX15 WILD-TYPE
  R0             9             302
  R1             0              14
  R2             1              14
  RX             1              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1185V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  DHX15 MUTATED       4                         0
  DHX15 WILD-TYPE    83                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DHX15 MUTATED                                           0     3
  DHX15 WILD-TYPE                                         1   240
D1185V12, multiclass
                                           clus
vv                                          DHX15 MUTATED DHX15 WILD-TYPE
  ASIAN                                                 4              83
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 3             240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1185V13, binary
                 cls
clus                0   1
  DHX15 MUTATED     0   7
  DHX15 WILD-TYPE   4 303
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX15 MUTATED      0    7
  DHX15 WILD-TYPE    4  303
                        clus
vv                       DHX15 MUTATED DHX15 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             303
[1] 2 2
[1] FALSE

Clustering(1186) Variable = LRRC4 MUTATION ANALYSIS
D1186V1, survival
                 sevent
clus2               0   1
  LRRC4 MUTATED    11   7
  LRRC4 WILD-TYPE 219 132
  LRRC4 MUTATED LRRC4 WILD-TYPE 
             18             351 
  LRRC4 MUTATED LRRC4 WILD-TYPE 
              7             132 
$`LRRC4 MUTATED`
TCGA-BR-4184 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8360 TCGA-BR-8372 
        6.97        14.43        29.59        32.25         6.18        31.27 
TCGA-BR-A44U TCGA-BR-A4CS TCGA-BR-A4QL TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 
       13.87         1.48        16.14        12.59        12.33        12.30 
TCGA-CD-8531 TCGA-CG-4306 TCGA-CG-5719 TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-A4GU 
       12.59         1.02         1.02        30.51         5.92         6.58 

$`LRRC4 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-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-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       10.68        34.13         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-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.53         7.17        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-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-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-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-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 

  LRRC4 MUTATED LRRC4 WILD-TYPE 
           1.02            0.00 
  LRRC4 MUTATED LRRC4 WILD-TYPE 
          32.25          122.30 
  LRRC4 MUTATED LRRC4 WILD-TYPE 
          12.46           14.76 
[1] "1.0 - 32.2 (12.5)"  "0.0 - 122.3 (14.8)"
[1] "hr=" "1.3"
D1186V2, 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       2       15       40       30        36        48
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC4 MUTATED           1          4          2          4        3
  LRRC4 WILD-TYPE         2         66         51         28       35
D1186V3, multiclass
            clus
vv           LRRC4 MUTATED LRRC4 WILD-TYPE
  STAGE I                0               2
  STAGE IA               0              15
  STAGE IB               0              40
  STAGE II               0              30
  STAGE IIA              1              36
  STAGE IIB              4              48
  STAGE III              1               2
  STAGE IIIA             4              66
  STAGE IIIB             2              51
  STAGE IIIC             4              28
  STAGE IV               3              35
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LRRC4 MUTATED     1   0   8  11
  LRRC4 WILD-TYPE  21  92 165  86
D1186V4, multiclass
    clus
vv   LRRC4 MUTATED LRRC4 WILD-TYPE
  T1             1              21
  T2             0              92
  T3             8             165
  T4            11              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
  LRRC4 MUTATED     7   6   1   6
  LRRC4 WILD-TYPE 111  98  76  71
D1186V5, multiclass
    clus
vv   LRRC4 MUTATED LRRC4 WILD-TYPE
  N0             7             111
  N1             6              98
  N2             1              76
  N3             6              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"
D1186V6, binary
                 cls
clus                0   1
  LRRC4 MUTATED    17   3
  LRRC4 WILD-TYPE 329  26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC4 MUTATED     17    3
  LRRC4 WILD-TYPE  329   26
   clus
vv  LRRC4 MUTATED LRRC4 WILD-TYPE
  0            17             329
  1             3              26
[1] 2 2
[1] FALSE
D1186V7, binary
                 cls
clus                0   1
  LRRC4 MUTATED    10  11
  LRRC4 WILD-TYPE 135 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC4 MUTATED     10   11
  LRRC4 WILD-TYPE  135  237
        clus
vv       LRRC4 MUTATED LRRC4 WILD-TYPE
  FEMALE            10             135
  MALE              11             237
[1] 2 2
[1] FALSE
D1186V8, binary
                 cls
clus                0   1
  LRRC4 MUTATED    12   5
  LRRC4 WILD-TYPE 280  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC4 MUTATED     12    5
  LRRC4 WILD-TYPE  280   54
     clus
vv    LRRC4 MUTATED LRRC4 WILD-TYPE
  NO             12             280
  YES             5              54
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  LRRC4 MUTATED                                          0
  LRRC4 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  LRRC4 MUTATED                                       2
  LRRC4 WILD-TYPE                                    68
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LRRC4 MUTATED                                                       11
  LRRC4 WILD-TYPE                                                    147
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  LRRC4 MUTATED                                                   3
  LRRC4 WILD-TYPE                                                18
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  LRRC4 MUTATED                                                                   4
  LRRC4 WILD-TYPE                                                                64
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  LRRC4 MUTATED                                                    0
  LRRC4 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  LRRC4 MUTATED                                                  1
  LRRC4 WILD-TYPE                                               60
D1186V9, multiclass
                                                                   clus
vv                                                                  LRRC4 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              1
                                                                   clus
vv                                                                  LRRC4 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        147
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              18
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              64
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LRRC4 MUTATED    16   1   1   3
  LRRC4 WILD-TYPE 295  13  14  21
D1186V10, multiclass
    clus
vv   LRRC4 MUTATED LRRC4 WILD-TYPE
  R0            16             295
  R1             1              13
  R2             1              14
  RX             3              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1186V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  LRRC4 MUTATED       6                         0
  LRRC4 WILD-TYPE    81                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  LRRC4 MUTATED                                           0    12
  LRRC4 WILD-TYPE                                         1   231
D1186V12, multiclass
                                           clus
vv                                          LRRC4 MUTATED LRRC4 WILD-TYPE
  ASIAN                                                 6              81
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                12             231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1186V13, binary
                 cls
clus                0   1
  LRRC4 MUTATED     0  18
  LRRC4 WILD-TYPE   4 292
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC4 MUTATED      0   18
  LRRC4 WILD-TYPE    4  292
                        clus
vv                       LRRC4 MUTATED LRRC4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            18             292
[1] 2 2
[1] FALSE

Clustering(1187) Variable = FIGNL1 MUTATION ANALYSIS
D1187V1, survival
                  sevent
clus2                0   1
  FIGNL1 MUTATED     6   2
  FIGNL1 WILD-TYPE 224 137
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               8              361 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               2              137 
$`FIGNL1 MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-6802 TCGA-BR-8361 TCGA-BR-8487 TCGA-BR-8682 
       26.70         6.97        30.90        31.10         1.12        32.58 
TCGA-CD-A4MG TCGA-HU-8602 
        6.58        22.32 

$`FIGNL1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-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-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-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 

  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
            1.12             0.00 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
           32.58           122.30 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
           24.51            14.17 
[1] "1.1 - 32.6 (24.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1.7"
D1187V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FIGNL1 MUTATED         0        0        0        0         2         3
  FIGNL1 WILD-TYPE       2       15       40       30        35        49
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FIGNL1 MUTATED           0          3          0          1        0
  FIGNL1 WILD-TYPE         3         67         53         31       38
D1187V3, multiclass
            clus
vv           FIGNL1 MUTATED FIGNL1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                0               40
  STAGE II                0               30
  STAGE IIA               2               35
  STAGE IIB               3               49
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              0               53
  STAGE IIIC              1               31
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FIGNL1 MUTATED     0   0   4   5
  FIGNL1 WILD-TYPE  22  92 169  92
D1187V4, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  T1              0               22
  T2              0               92
  T3              4              169
  T4              5               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
  FIGNL1 MUTATED     6   1   2   0
  FIGNL1 WILD-TYPE 112 103  75  77
D1187V5, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  N0              6              112
  N1              1              103
  N2              2               75
  N3              0               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"
D1187V6, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED     8   0
  FIGNL1 WILD-TYPE 338  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED      8    0
  FIGNL1 WILD-TYPE  338   29
   clus
vv  FIGNL1 MUTATED FIGNL1 WILD-TYPE
  0              8              338
  1              0               29
[1] 2 2
[1] FALSE
D1187V7, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED     5   4
  FIGNL1 WILD-TYPE 140 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED      5    4
  FIGNL1 WILD-TYPE  140  244
        clus
vv       FIGNL1 MUTATED FIGNL1 WILD-TYPE
  FEMALE              5              140
  MALE                4              244
[1] 2 2
[1] FALSE
D1187V8, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED     8   0
  FIGNL1 WILD-TYPE 284  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED      8    0
  FIGNL1 WILD-TYPE  284   59
     clus
vv    FIGNL1 MUTATED FIGNL1 WILD-TYPE
  NO               8              284
  YES              0               59
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FIGNL1 MUTATED                                          0
  FIGNL1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FIGNL1 MUTATED                                       3
  FIGNL1 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FIGNL1 MUTATED                                                        5
  FIGNL1 WILD-TYPE                                                    153
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FIGNL1 MUTATED                                                   1
  FIGNL1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FIGNL1 MUTATED                                                                   0
  FIGNL1 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FIGNL1 MUTATED                                                    0
  FIGNL1 WILD-TYPE                                                  5
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FIGNL1 MUTATED                                                  0
  FIGNL1 WILD-TYPE                                               61
D1187V9, multiclass
                                                                   clus
vv                                                                  FIGNL1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               0
                                                                   clus
vv                                                                  FIGNL1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FIGNL1 MUTATED     6   0   0   2
  FIGNL1 WILD-TYPE 305  14  15  22
D1187V10, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  R0              6              305
  R1              0               14
  R2              0               15
  RX              2               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1187V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  FIGNL1 MUTATED       3                         0
  FIGNL1 WILD-TYPE    84                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FIGNL1 MUTATED                                           0     6
  FIGNL1 WILD-TYPE                                         1   237
D1187V12, multiclass
                                           clus
vv                                          FIGNL1 MUTATED FIGNL1 WILD-TYPE
  ASIAN                                                  3               84
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  6              237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1187V13, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED     0   9
  FIGNL1 WILD-TYPE   4 301
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED      0    9
  FIGNL1 WILD-TYPE    4  301
                        clus
vv                       FIGNL1 MUTATED FIGNL1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              301
[1] 2 2
[1] FALSE

Clustering(1188) Variable = CD6 MUTATION ANALYSIS
D1188V1, survival
               sevent
clus2             0   1
  CD6 MUTATED     5   2
  CD6 WILD-TYPE 225 137
  CD6 MUTATED CD6 WILD-TYPE 
            7           362 
  CD6 MUTATED CD6 WILD-TYPE 
            2           137 
$`CD6 MUTATED`
TCGA-BR-6452 TCGA-BR-8486 TCGA-BR-A4J2 TCGA-FP-A4BF TCGA-HU-A4GX TCGA-VQ-A8P2 
       34.68        20.22        14.17         5.52        20.25        38.14 
TCGA-VQ-AA64 
       18.41 

$`CD6 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
       25.18         9.21         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-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98         0.72         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-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-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-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 

  CD6 MUTATED CD6 WILD-TYPE 
         5.52          0.00 
  CD6 MUTATED CD6 WILD-TYPE 
        38.14        122.30 
  CD6 MUTATED CD6 WILD-TYPE 
        20.22         14.07 
[1] "5.5 - 38.1 (20.2)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "1.6"
D1188V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  CD6 MUTATED         1        1        0        0         1         2
  CD6 WILD-TYPE       1       14       40       30        36        50
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CD6 MUTATED           0          3          1          1        0
  CD6 WILD-TYPE         3         67         52         31       38
D1188V3, multiclass
            clus
vv           CD6 MUTATED CD6 WILD-TYPE
  STAGE I              1             1
  STAGE IA             1            14
  STAGE IB             0            40
  STAGE II             0            30
  STAGE IIA            1            36
  STAGE IIB            2            50
  STAGE III            0             3
  STAGE IIIA           3            67
  STAGE IIIB           1            52
  STAGE IIIC           1            31
  STAGE IV             0            38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CD6 MUTATED     2   0   3   5
  CD6 WILD-TYPE  20  92 170  92
D1188V4, multiclass
    clus
vv   CD6 MUTATED CD6 WILD-TYPE
  T1           2            20
  T2           0            92
  T3           3           170
  T4           5            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
  CD6 MUTATED     5   2   3   0
  CD6 WILD-TYPE 113 102  74  77
D1188V5, multiclass
    clus
vv   CD6 MUTATED CD6 WILD-TYPE
  N0           5           113
  N1           2           102
  N2           3            74
  N3           0            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"
D1188V6, binary
               cls
clus              0   1
  CD6 MUTATED     9   0
  CD6 WILD-TYPE 337  29
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD6 MUTATED      9    0
  CD6 WILD-TYPE  337   29
   clus
vv  CD6 MUTATED CD6 WILD-TYPE
  0           9           337
  1           0            29
[1] 2 2
[1] FALSE
D1188V7, binary
               cls
clus              0   1
  CD6 MUTATED     4   6
  CD6 WILD-TYPE 141 242
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD6 MUTATED      4    6
  CD6 WILD-TYPE  141  242
        clus
vv       CD6 MUTATED CD6 WILD-TYPE
  FEMALE           4           141
  MALE             6           242
[1] 2 2
[1] FALSE
D1188V8, binary
               cls
clus              0   1
  CD6 MUTATED     7   2
  CD6 WILD-TYPE 285  57
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD6 MUTATED      7    2
  CD6 WILD-TYPE  285   57
     clus
vv    CD6 MUTATED CD6 WILD-TYPE
  NO            7           285
  YES           2            57
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  CD6 MUTATED                                          1
  CD6 WILD-TYPE                                        7
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  CD6 MUTATED                                       2
  CD6 WILD-TYPE                                    68
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD6 MUTATED                                                        4
  CD6 WILD-TYPE                                                    154
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  CD6 MUTATED                                                   1
  CD6 WILD-TYPE                                                20
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  CD6 MUTATED                                                                   2
  CD6 WILD-TYPE                                                                66
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  CD6 MUTATED                                                    0
  CD6 WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  CD6 MUTATED                                                  0
  CD6 WILD-TYPE                                               61
D1188V9, multiclass
                                                                   clus
vv                                                                  CD6 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           2
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            0
                                                                   clus
vv                                                                  CD6 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            66
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  CD6 MUTATED     8   1   0   1
  CD6 WILD-TYPE 303  13  15  23
D1188V10, multiclass
    clus
vv   CD6 MUTATED CD6 WILD-TYPE
  R0           8           303
  R1           1            13
  R2           0            15
  RX           1            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1188V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  CD6 MUTATED       2                         1
  CD6 WILD-TYPE    85                         8
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  CD6 MUTATED                                           0     7
  CD6 WILD-TYPE                                         1   236
D1188V12, multiclass
                                           clus
vv                                          CD6 MUTATED CD6 WILD-TYPE
  ASIAN                                               2            85
  BLACK OR AFRICAN AMERICAN                           1             8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               7           236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1188V13, binary
               cls
clus              0   1
  CD6 MUTATED     0   8
  CD6 WILD-TYPE   4 302
[1] "tbl2"
               cls
clus            [,1] [,2]
  CD6 MUTATED      0    8
  CD6 WILD-TYPE    4  302
                        clus
vv                       CD6 MUTATED CD6 WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           8           302
[1] 2 2
[1] FALSE

Clustering(1189) Variable = POGZ MUTATION ANALYSIS
D1189V1, survival
                sevent
clus2              0   1
  POGZ MUTATED    14   9
  POGZ WILD-TYPE 216 130
  POGZ MUTATED POGZ WILD-TYPE 
            23            346 
  POGZ MUTATED POGZ WILD-TYPE 
             9            130 
$`POGZ MUTATED`
TCGA-BR-4184 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-7197 TCGA-BR-8077 
        6.97        34.68        32.78        18.05         9.21         0.69 
TCGA-BR-8361 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-A4QL 
       31.10        26.33         4.31         1.12        27.12        16.14 
TCGA-CD-5801 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-5726 TCGA-D7-A6EY TCGA-F1-6874 
       13.18        12.43         6.58        28.96        11.44        14.47 
TCGA-HJ-7597 TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-MX-A5UJ TCGA-VQ-A8P2 
       26.47         6.58        14.07        19.73        38.14 

$`POGZ WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-6707 
       19.33        39.12        26.10         9.17        25.61        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-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-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-8363 TCGA-BR-8364 TCGA-BR-8365 
        2.20         7.40         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        0.95        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-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-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-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-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-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-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 

  POGZ MUTATED POGZ WILD-TYPE 
          0.69           0.00 
  POGZ MUTATED POGZ WILD-TYPE 
         38.14         122.30 
  POGZ MUTATED POGZ WILD-TYPE 
         14.47          14.22 
[1] "0.7 - 38.1 (14.5)"  "0.0 - 122.3 (14.2)"
[1] "hr=" "1"  
D1189V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  POGZ MUTATED         0        1        4        2         4         1
  POGZ WILD-TYPE       2       14       36       28        33        51
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POGZ MUTATED           0          6          5          1        0
  POGZ WILD-TYPE         3         64         48         31       38
D1189V3, multiclass
            clus
vv           POGZ MUTATED POGZ WILD-TYPE
  STAGE I               0              2
  STAGE IA              1             14
  STAGE IB              4             36
  STAGE II              2             28
  STAGE IIA             4             33
  STAGE IIB             1             51
  STAGE III             0              3
  STAGE IIIA            6             64
  STAGE IIIB            5             48
  STAGE IIIC            1             31
  STAGE IV              0             38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  POGZ MUTATED     2   3  14   5
  POGZ WILD-TYPE  20  89 159  92
D1189V4, multiclass
    clus
vv   POGZ MUTATED POGZ WILD-TYPE
  T1            2             20
  T2            3             89
  T3           14            159
  T4            5             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
  POGZ MUTATED    11   8   2   3
  POGZ WILD-TYPE 107  96  75  74
D1189V5, multiclass
    clus
vv   POGZ MUTATED POGZ WILD-TYPE
  N0           11            107
  N1            8             96
  N2            2             75
  N3            3             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"
D1189V6, binary
                cls
clus               0   1
  POGZ MUTATED    22   0
  POGZ WILD-TYPE 324  29
[1] "tbl2"
                cls
clus             [,1] [,2]
  POGZ MUTATED     22    0
  POGZ WILD-TYPE  324   29
   clus
vv  POGZ MUTATED POGZ WILD-TYPE
  0           22            324
  1            0             29
[1] 2 2
[1] FALSE
D1189V7, binary
                cls
clus               0   1
  POGZ MUTATED    11  13
  POGZ WILD-TYPE 134 235
[1] "tbl2"
                cls
clus             [,1] [,2]
  POGZ MUTATED     11   13
  POGZ WILD-TYPE  134  235
        clus
vv       POGZ MUTATED POGZ WILD-TYPE
  FEMALE           11            134
  MALE             13            235
[1] 2 2
[1] FALSE
D1189V8, binary
                cls
clus               0   1
  POGZ MUTATED    20   1
  POGZ WILD-TYPE 272  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  POGZ MUTATED     20    1
  POGZ WILD-TYPE  272   58
     clus
vv    POGZ MUTATED POGZ WILD-TYPE
  NO            20            272
  YES            1             58
[1] 2 2
[1] FALSE
                vv
clus             STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  POGZ MUTATED                                          1
  POGZ WILD-TYPE                                        7
                vv
clus             STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  POGZ MUTATED                                       2
  POGZ WILD-TYPE                                    68
                vv
clus             STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  POGZ MUTATED                                                       14
  POGZ WILD-TYPE                                                    144
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  POGZ MUTATED                                                   1
  POGZ WILD-TYPE                                                20
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  POGZ MUTATED                                                                   3
  POGZ WILD-TYPE                                                                65
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  POGZ MUTATED                                                    0
  POGZ WILD-TYPE                                                  5
                vv
clus             STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  POGZ MUTATED                                                  3
  POGZ WILD-TYPE                                               58
D1189V9, multiclass
                                                                   clus
vv                                                                  POGZ MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                     1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      14
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             3
                                                                   clus
vv                                                                  POGZ WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         68
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                       144
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              58
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  POGZ MUTATED    21   0   0   2
  POGZ WILD-TYPE 290  14  15  22
D1189V10, multiclass
    clus
vv   POGZ MUTATED POGZ WILD-TYPE
  R0           21            290
  R1            0             14
  R2            0             15
  RX            2             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1189V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN
  POGZ MUTATED       5                         0
  POGZ WILD-TYPE    82                         9
                vv
clus             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  POGZ MUTATED                                           0    18
  POGZ WILD-TYPE                                         1   225
D1189V12, multiclass
                                           clus
vv                                          POGZ MUTATED POGZ WILD-TYPE
  ASIAN                                                5             82
  BLACK OR AFRICAN AMERICAN                            0              9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER            0              1
  WHITE                                               18            225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1189V13, binary
                cls
clus               0   1
  POGZ MUTATED     0  22
  POGZ WILD-TYPE   4 288
[1] "tbl2"
                cls
clus             [,1] [,2]
  POGZ MUTATED      0   22
  POGZ WILD-TYPE    4  288
                        clus
vv                       POGZ MUTATED POGZ WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           22            288
[1] 2 2
[1] FALSE

Clustering(1190) Variable = RBM16 MUTATION ANALYSIS
D1190V1, survival
                 sevent
clus2               0   1
  RBM16 MUTATED     8   2
  RBM16 WILD-TYPE 222 137
  RBM16 MUTATED RBM16 WILD-TYPE 
             10             359 
  RBM16 MUTATED RBM16 WILD-TYPE 
              2             137 
$`RBM16 MUTATED`
TCGA-BR-6452 TCGA-BR-7704 TCGA-BR-8487 TCGA-CD-8536 TCGA-CD-A487 TCGA-CG-5726 
       34.68        35.24         1.12        12.43        12.30        28.96 
TCGA-HU-A4GX TCGA-R5-A7ZI TCGA-RD-A8N5 TCGA-VQ-A8P2 
       20.25        74.53        57.44        38.14 

$`RBM16 WILD-TYPE`
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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-A486 
       12.59        11.64        15.39        12.07        12.82         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-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-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-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-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 

  RBM16 MUTATED RBM16 WILD-TYPE 
           1.12            0.00 
  RBM16 MUTATED RBM16 WILD-TYPE 
          74.53          122.30 
  RBM16 MUTATED RBM16 WILD-TYPE 
          31.82           14.07 
[1] "1.1 - 74.5 (31.8)"  "0.0 - 122.3 (14.1)"
[1] "hr=" "2.9"
D1190V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  RBM16 MUTATED         0        1        0        2         2         2
  RBM16 WILD-TYPE       2       14       40       28        35        50
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RBM16 MUTATED           0          3          0          1        1
  RBM16 WILD-TYPE         3         67         53         31       37
D1190V3, multiclass
            clus
vv           RBM16 MUTATED RBM16 WILD-TYPE
  STAGE I                0               2
  STAGE IA               1              14
  STAGE IB               0              40
  STAGE II               2              28
  STAGE IIA              2              35
  STAGE IIB              2              50
  STAGE III              0               3
  STAGE IIIA             3              67
  STAGE IIIB             0              53
  STAGE IIIC             1              31
  STAGE IV               1              37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM16 MUTATED     1   0   6   5
  RBM16 WILD-TYPE  21  92 167  92
D1190V4, multiclass
    clus
vv   RBM16 MUTATED RBM16 WILD-TYPE
  T1             1              21
  T2             0              92
  T3             6             167
  T4             5              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
  RBM16 MUTATED     7   5   1   0
  RBM16 WILD-TYPE 111  99  76  77
D1190V5, multiclass
    clus
vv   RBM16 MUTATED RBM16 WILD-TYPE
  N0             7             111
  N1             5              99
  N2             1              76
  N3             0              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"
D1190V6, binary
                 cls
clus                0   1
  RBM16 MUTATED    12   1
  RBM16 WILD-TYPE 334  28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED     12    1
  RBM16 WILD-TYPE  334   28
   clus
vv  RBM16 MUTATED RBM16 WILD-TYPE
  0            12             334
  1             1              28
[1] 2 2
[1] FALSE
D1190V7, binary
                 cls
clus                0   1
  RBM16 MUTATED     7   6
  RBM16 WILD-TYPE 138 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED      7    6
  RBM16 WILD-TYPE  138  242
        clus
vv       RBM16 MUTATED RBM16 WILD-TYPE
  FEMALE             7             138
  MALE               6             242
[1] 2 2
[1] FALSE
D1190V8, binary
                 cls
clus                0   1
  RBM16 MUTATED     8   2
  RBM16 WILD-TYPE 284  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED      8    2
  RBM16 WILD-TYPE  284   57
     clus
vv    RBM16 MUTATED RBM16 WILD-TYPE
  NO              8             284
  YES             2              57
[1] 2 2
[1] FALSE
                 vv
clus              STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  RBM16 MUTATED                                          0
  RBM16 WILD-TYPE                                        8
                 vv
clus              STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  RBM16 MUTATED                                       3
  RBM16 WILD-TYPE                                    67
                 vv
clus              STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RBM16 MUTATED                                                        5
  RBM16 WILD-TYPE                                                    153
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  RBM16 MUTATED                                                   2
  RBM16 WILD-TYPE                                                19
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  RBM16 MUTATED                                                                   3
  RBM16 WILD-TYPE                                                                65
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  RBM16 MUTATED                                                    0
  RBM16 WILD-TYPE                                                  5
                 vv
clus              STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  RBM16 MUTATED                                                  0
  RBM16 WILD-TYPE                                               61
D1190V9, multiclass
                                                                   clus
vv                                                                  RBM16 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                         3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                             2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)             3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                              0
                                                                   clus
vv                                                                  RBM16 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                        8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                        153
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              19
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                              5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               61
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RBM16 MUTATED    11   0   0   2
  RBM16 WILD-TYPE 300  14  15  22
D1190V10, multiclass
    clus
vv   RBM16 MUTATED RBM16 WILD-TYPE
  R0            11             300
  R1             0              14
  R2             0              15
  RX             2              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1190V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN
  RBM16 MUTATED       3                         0
  RBM16 WILD-TYPE    84                         9
                 vv
clus              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  RBM16 MUTATED                                           0     9
  RBM16 WILD-TYPE                                         1   234
D1190V12, multiclass
                                           clus
vv                                          RBM16 MUTATED RBM16 WILD-TYPE
  ASIAN                                                 3              84
  BLACK OR AFRICAN AMERICAN                             0               9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER             0               1
  WHITE                                                 9             234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1190V13, binary
                 cls
clus                0   1
  RBM16 MUTATED     1  10
  RBM16 WILD-TYPE   3 300
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED      1   10
  RBM16 WILD-TYPE    3  300
                        clus
vv                       RBM16 MUTATED RBM16 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            10             300
[1] 2 2
[1] FALSE

Clustering(1191) Variable = SPOCK1 MUTATION ANALYSIS
D1191V1, survival
                  sevent
clus2                0   1
  SPOCK1 MUTATED     8   4
  SPOCK1 WILD-TYPE 222 135
  SPOCK1 MUTATED SPOCK1 WILD-TYPE 
              12              357 
  SPOCK1 MUTATED SPOCK1 WILD-TYPE 
               4              135 
$`SPOCK1 MUTATED`
TCGA-B7-5816 TCGA-B7-A5TI TCGA-BR-8382 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CG-5723 
       26.70        19.56        25.05         6.58        11.77       105.07 
TCGA-D7-6527 TCGA-D7-A4YU TCGA-HU-A4GD TCGA-HU-A4GT TCGA-VQ-A8P2 TCGA-VQ-A91V 
       10.26        16.44        22.75         6.51        38.14        42.64 

$`SPOCK1 WILD-TYPE`
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-B7-5818 TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       20.15         9.86        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-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-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-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       13.35        17.19        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-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       22.68        24.20         3.25        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-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
       20.81         1.71        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 

  SPOCK1 MUTATED SPOCK1 WILD-TYPE 
            6.51             0.00 
  SPOCK1 MUTATED SPOCK1 WILD-TYPE 
          105.07           122.30 
  SPOCK1 MUTATED SPOCK1 WILD-TYPE 
          21.155           14.070 
[1] "6.5 - 105.1 (21.2)" "0.0 - 122.3 (14.1)"
[1] "hr=" "1.5"
D1191V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  SPOCK1 MUTATED         0        0        1        2         2         2
  SPOCK1 WILD-TYPE       2       15       39       28        35        50
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPOCK1 MUTATED           0          3          1          2        0
  SPOCK1 WILD-TYPE         3         67         52         30       38
D1191V3, multiclass
            clus
vv           SPOCK1 MUTATED SPOCK1 WILD-TYPE
  STAGE I                 0                2
  STAGE IA                0               15
  STAGE IB                1               39
  STAGE II                2               28
  STAGE IIA               2               35
  STAGE IIB               2               50
  STAGE III               0                3
  STAGE IIIA              3               67
  STAGE IIIB              1               52
  STAGE IIIC              2               30
  STAGE IV                0               38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SPOCK1 MUTATED     0   3   6   4
  SPOCK1 WILD-TYPE  22  89 167  93
D1191V4, multiclass
    clus
vv   SPOCK1 MUTATED SPOCK1 WILD-TYPE
  T1              0               22
  T2              3               89
  T3              6              167
  T4              4               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
  SPOCK1 MUTATED     4   5   1   3
  SPOCK1 WILD-TYPE 114  99  76  74
D1191V5, multiclass
    clus
vv   SPOCK1 MUTATED SPOCK1 WILD-TYPE
  N0              4              114
  N1              5               99
  N2              1               76
  N3              3               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"
D1191V6, binary
                  cls
clus                 0   1
  SPOCK1 MUTATED    13   0
  SPOCK1 WILD-TYPE 333  29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPOCK1 MUTATED     13    0
  SPOCK1 WILD-TYPE  333   29
   clus
vv  SPOCK1 MUTATED SPOCK1 WILD-TYPE
  0             13              333
  1              0               29
[1] 2 2
[1] FALSE
D1191V7, binary
                  cls
clus                 0   1
  SPOCK1 MUTATED     4   9
  SPOCK1 WILD-TYPE 141 239
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPOCK1 MUTATED      4    9
  SPOCK1 WILD-TYPE  141  239
        clus
vv       SPOCK1 MUTATED SPOCK1 WILD-TYPE
  FEMALE              4              141
  MALE                9              239
[1] 2 2
[1] FALSE
D1191V8, binary
                  cls
clus                 0   1
  SPOCK1 MUTATED    10   3
  SPOCK1 WILD-TYPE 282  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPOCK1 MUTATED     10    3
  SPOCK1 WILD-TYPE  282   56
     clus
vv    SPOCK1 MUTATED SPOCK1 WILD-TYPE
  NO              10              282
  YES              3               56
[1] 2 2
[1] FALSE
                  vv
clus               STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SPOCK1 MUTATED                                          0
  SPOCK1 WILD-TYPE                                        8
                  vv
clus               STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SPOCK1 MUTATED                                       3
  SPOCK1 WILD-TYPE                                    67
                  vv
clus               STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPOCK1 MUTATED                                                        4
  SPOCK1 WILD-TYPE                                                    154
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SPOCK1 MUTATED                                                   1
  SPOCK1 WILD-TYPE                                                20
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SPOCK1 MUTATED                                                                   0
  SPOCK1 WILD-TYPE                                                                68
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SPOCK1 MUTATED                                                    1
  SPOCK1 WILD-TYPE                                                  4
                  vv
clus               STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SPOCK1 MUTATED                                                  4
  SPOCK1 WILD-TYPE                                               57
D1191V9, multiclass
                                                                   clus
vv                                                                  SPOCK1 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                       0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                          3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         4
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                              1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)              0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                             1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                               4
                                                                   clus
vv                                                                  SPOCK1 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                           67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                         154
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                               20
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)               68
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                57
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SPOCK1 MUTATED    10   0   0   0
  SPOCK1 WILD-TYPE 301  14  15  24
D1191V10, multiclass
    clus
vv   SPOCK1 MUTATED SPOCK1 WILD-TYPE
  R0             10              301
  R1              0               14
  R2              0               15
  RX              0               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1191V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN
  SPOCK1 MUTATED       4                         0
  SPOCK1 WILD-TYPE    83                         9
                  vv
clus               NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SPOCK1 MUTATED                                           0     7
  SPOCK1 WILD-TYPE                                         1   236
D1191V12, multiclass
                                           clus
vv                                          SPOCK1 MUTATED SPOCK1 WILD-TYPE
  ASIAN                                                  4               83
  BLACK OR AFRICAN AMERICAN                              0                9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER              0                1
  WHITE                                                  7              236
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1191V13, binary
                  cls
clus                 0   1
  SPOCK1 MUTATED     0  10
  SPOCK1 WILD-TYPE   4 300
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPOCK1 MUTATED      0   10
  SPOCK1 WILD-TYPE    4  300
                        clus
vv                       SPOCK1 MUTATED SPOCK1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              300
[1] 2 2
[1] FALSE

Clustering(1192) Variable = FAH MUTATION ANALYSIS
D1192V1, survival
               sevent
clus2             0   1
  FAH MUTATED     5   1
  FAH WILD-TYPE 225 138
  FAH MUTATED FAH WILD-TYPE 
            6           363 
  FAH MUTATED FAH WILD-TYPE 
            1           138 
$`FAH MUTATED`
TCGA-B7-5816 TCGA-BR-4184 TCGA-CD-8526 TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 
       26.70         6.97        12.53         6.58        20.25        12.95 

$`FAH WILD-TYPE`
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-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK 
       20.15         9.86        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-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-D7-5579 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-A4GY TCGA-HU-A4H0 
       29.98         8.98         0.10         6.51         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-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 

  FAH MUTATED FAH WILD-TYPE 
         6.58          0.00 
  FAH MUTATED FAH WILD-TYPE 
         26.7         122.3 
  FAH MUTATED FAH WILD-TYPE 
        12.74         14.43 
[1] "6.6 - 26.7 (12.7)"  "0.0 - 122.3 (14.4)"
[1] "hr=" "1.9"
D1192V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  FAH MUTATED         0        0        0        0         0         2
  FAH WILD-TYPE       2       15       40       30        37        50
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAH MUTATED           0          2          1          1        0
  FAH WILD-TYPE         3         68         52         31       38
D1192V3, multiclass
            clus
vv           FAH MUTATED FAH WILD-TYPE
  STAGE I              0             2
  STAGE IA             0            15
  STAGE IB             0            40
  STAGE II             0            30
  STAGE IIA            0            37
  STAGE IIB            2            50
  STAGE III            0             3
  STAGE IIIA           2            68
  STAGE IIIB           1            52
  STAGE IIIC           1            31
  STAGE IV             0            38
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  FAH MUTATED     1   0   4   2
  FAH WILD-TYPE  21  92 169  95
D1192V4, multiclass
    clus
vv   FAH MUTATED FAH WILD-TYPE
  T1           1            21
  T2           0            92
  T3           4           169
  T4           2            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
  FAH MUTATED     1   3   1   1
  FAH WILD-TYPE 117 101  76  76
D1192V5, multiclass
    clus
vv   FAH MUTATED FAH WILD-TYPE
  N0           1           117
  N1           3           101
  N2           1            76
  N3           1            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"
D1192V6, binary
               cls
clus              0   1
  FAH MUTATED     6   0
  FAH WILD-TYPE 340  29
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAH MUTATED      6    0
  FAH WILD-TYPE  340   29
   clus
vv  FAH MUTATED FAH WILD-TYPE
  0           6           340
  1           0            29
[1] 2 2
[1] FALSE
D1192V7, binary
               cls
clus              0   1
  FAH MUTATED     5   2
  FAH WILD-TYPE 140 246
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAH MUTATED      5    2
  FAH WILD-TYPE  140  246
        clus
vv       FAH MUTATED FAH WILD-TYPE
  FEMALE           5           140
  MALE             2           246
[1] 2 2
[1] FALSE
D1192V8, binary
               cls
clus              0   1
  FAH MUTATED     6   0
  FAH WILD-TYPE 286  59
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAH MUTATED      6    0
  FAH WILD-TYPE  286   59
     clus
vv    FAH MUTATED FAH WILD-TYPE
  NO            6           286
  YES           0            59
[1] 2 2
[1] FALSE
               vv
clus            STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  FAH MUTATED                                          0
  FAH WILD-TYPE                                        8
               vv
clus            STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  FAH MUTATED                                       3
  FAH WILD-TYPE                                    67
               vv
clus            STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAH MUTATED                                                        2
  FAH WILD-TYPE                                                    156
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  FAH MUTATED                                                   0
  FAH WILD-TYPE                                                21
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  FAH MUTATED                                                                   1
  FAH WILD-TYPE                                                                67
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  FAH MUTATED                                                    0
  FAH WILD-TYPE                                                  5
               vv
clus            STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  FAH MUTATED                                                  1
  FAH WILD-TYPE                                               60
D1192V9, multiclass
                                                                   clus
vv                                                                  FAH MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                    0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                       3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                           0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)           1
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                          0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                            1
                                                                   clus
vv                                                                  FAH WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                      8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                        67
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                      156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                            21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)            67
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                            5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                             60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  FAH MUTATED     5   0   0   2
  FAH WILD-TYPE 306  14  15  22
D1192V10, multiclass
    clus
vv   FAH MUTATED FAH WILD-TYPE
  R0           5           306
  R1           0            14
  R2           0            15
  RX           2            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1192V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN
  FAH MUTATED       4                         0
  FAH WILD-TYPE    83                         9
               vv
clus            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  FAH MUTATED                                           0     3
  FAH WILD-TYPE                                         1   240
D1192V12, multiclass
                                           clus
vv                                          FAH MUTATED FAH WILD-TYPE
  ASIAN                                               4            83
  BLACK OR AFRICAN AMERICAN                           0             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0             1
  WHITE                                               3           240
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1192V13, binary
               cls
clus              0   1
  FAH MUTATED     0   7
  FAH WILD-TYPE   4 303
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAH MUTATED      0    7
  FAH WILD-TYPE    4  303
                        clus
vv                       FAH MUTATED FAH WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           7           303
[1] 2 2
[1] FALSE

Clustering(1193) Variable = SERPINB8 MUTATION ANALYSIS
D1193V1, survival
                    sevent
clus2                  0   1
  SERPINB8 MUTATED     6   1
  SERPINB8 WILD-TYPE 224 138
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
                 7                362 
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
                 1                138 
$`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-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-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       20.15         9.86        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-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-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-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       28.96         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-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-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-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 

  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
             14.07               0.00 
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
            105.07             122.30 
  SERPINB8 MUTATED SERPINB8 WILD-TYPE 
            36.160             14.055 
[1] "14.1 - 105.1 (36.2)" "0.0 - 122.3 (14.1)" 
[1] "hr=" "5.6"
D1193V2, 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       2       14       36       29        37        52
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB8 MUTATED           0          0          0          1        1
  SERPINB8 WILD-TYPE         3         70         53         31       37
D1193V3, multiclass
            clus
vv           SERPINB8 MUTATED SERPINB8 WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 14
  STAGE IB                  4                 36
  STAGE II                  1                 29
  STAGE IIA                 0                 37
  STAGE IIB                 0                 52
  STAGE III                 0                  3
  STAGE IIIA                0                 70
  STAGE IIIB                0                 53
  STAGE IIIC                1                 31
  STAGE IV                  1                 37
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SERPINB8 MUTATED     2   5   0   1
  SERPINB8 WILD-TYPE  20  87 173  96
D1193V4, multiclass
    clus
vv   SERPINB8 MUTATED SERPINB8 WILD-TYPE
  T1                2                 20
  T2                5                 87
  T3                0                173
  T4                1                 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
  SERPINB8 MUTATED     4   2   0   2
  SERPINB8 WILD-TYPE 114 102  77  75
D1193V5, multiclass
    clus
vv   SERPINB8 MUTATED SERPINB8 WILD-TYPE
  N0                4                114
  N1                2                102
  N2                0                 77
  N3                2                 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"
D1193V6, binary
                    cls
clus                   0   1
  SERPINB8 MUTATED     8   0
  SERPINB8 WILD-TYPE 338  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB8 MUTATED      8    0
  SERPINB8 WILD-TYPE  338   29
   clus
vv  SERPINB8 MUTATED SERPINB8 WILD-TYPE
  0                8                338
  1                0                 29
[1] 2 2
[1] FALSE
D1193V7, binary
                    cls
clus                   0   1
  SERPINB8 MUTATED     3   5
  SERPINB8 WILD-TYPE 142 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB8 MUTATED      3    5
  SERPINB8 WILD-TYPE  142  243
        clus
vv       SERPINB8 MUTATED SERPINB8 WILD-TYPE
  FEMALE                3                142
  MALE                  5                243
[1] 2 2
[1] FALSE
D1193V8, binary
                    cls
clus                   0   1
  SERPINB8 MUTATED     5   0
  SERPINB8 WILD-TYPE 287  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB8 MUTATED      5    0
  SERPINB8 WILD-TYPE  287   59
     clus
vv    SERPINB8 MUTATED SERPINB8 WILD-TYPE
  NO                 5                287
  YES                0                 59
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  SERPINB8 MUTATED                                          0
  SERPINB8 WILD-TYPE                                        8
                    vv
clus                 STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  SERPINB8 MUTATED                                       1
  SERPINB8 WILD-TYPE                                    69
                    vv
clus                 STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SERPINB8 MUTATED                                                        2
  SERPINB8 WILD-TYPE                                                    156
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  SERPINB8 MUTATED                                                   0
  SERPINB8 WILD-TYPE                                                21
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  SERPINB8 MUTATED                                                                   3
  SERPINB8 WILD-TYPE                                                                65
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  SERPINB8 MUTATED                                                    1
  SERPINB8 WILD-TYPE                                                  4
                    vv
clus                 STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  SERPINB8 MUTATED                                                  1
  SERPINB8 WILD-TYPE                                               60
D1193V9, multiclass
                                                                   clus
vv                                                                  SERPINB8 MUTATED
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                         0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                            1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           2
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                               1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                 1
                                                                   clus
vv                                                                  SERPINB8 WILD-TYPE
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                           8
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                             69
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                           156
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                                 21
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                 65
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                                 4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                                  60
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SERPINB8 MUTATED     8   0   0   0
  SERPINB8 WILD-TYPE 303  14  15  24
D1193V10, multiclass
    clus
vv   SERPINB8 MUTATED SERPINB8 WILD-TYPE
  R0                8                303
  R1                0                 14
  R2                0                 15
  RX                0                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1193V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  SERPINB8 MUTATED       2                         0
  SERPINB8 WILD-TYPE    85                         9
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  SERPINB8 MUTATED                                           0     2
  SERPINB8 WILD-TYPE                                         1   241
D1193V12, multiclass
                                           clus
vv                                          SERPINB8 MUTATED SERPINB8 WILD-TYPE
  ASIAN                                                    2                 85
  BLACK OR AFRICAN AMERICAN                                0                  9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    2                241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1193V13, binary
                    cls
clus                   0   1
  SERPINB8 MUTATED     0   4
  SERPINB8 WILD-TYPE   4 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB8 MUTATED      0    4
  SERPINB8 WILD-TYPE    4  306
                        clus
vv                       SERPINB8 MUTATED SERPINB8 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                4                306
[1] 2 2
[1] FALSE
